Precigen (PGEN) 10-K 1 Mar 17 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($) $ in Billions	12 Months Ended
	Dec. 31, 2016	Feb. 15, 2017	Jun. 30, 2016
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY
Trading Symbol	XON
Entity Registrant Name	INTREXON CORP
Entity Central Index Key	1,356,090
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	Yes
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		118,730,518
Entity Public Float			$ 1.4

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets
Cash and cash equivalents	$ 62,607	$ 135,782
Restricted cash	6,987	0
Short-term investments	174,602	102,528
Receivables
Trade, net	21,637	25,101
Related parties	16,793	23,597
Notes, net	1,500	601
Other	2,555	2,995
Inventory	21,139	26,563
Prepaid expenses and other	7,361	6,634
Total current assets	315,181	323,801
Long-term investments	5,993	105,447
Equity securities	23,522	83,653
Investment in preferred stock	129,545	0
Property, plant and equipment, net	64,672	42,739
Intangible assets, net	225,615	247,535
Goodwill	157,175	165,169
Investments in affiliates	23,655	9,977
Other assets	3,710	3,725
Total assets	949,068	982,046
Current liabilities
Accounts payable	8,478	4,967
Accrued compensation and benefits	6,540	19,050
Other accrued liabilities	15,776	7,949
Deferred revenue	53,364	35,366
Lines of credit	820	561
Current portion of long term debt	386	930
Current portion of deferred consideration	8,801	6,931
Related party payables	440	150
Total current liabilities	94,605	75,904
Long term debt, net of current portion	7,562	7,598
Deferred consideration, net of current portion	0	8,698
Deferred revenue, net of current portion	256,778	162,363
Deferred tax liabilities	17,007	21,802
Other long term liabilities	3,868	795
Total liabilities	379,820	277,160
Commitments and contingencies (Note 17)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of December 31, 2016 and 2015; and 118,688,770 shares and 116,658,886 shares issued and outstanding as of December 31, 2016 and 2015, respectively	0	0
Additional paid-in capital	1,325,780	1,249,559
Accumulated deficit	(729,341)	(542,729)
Accumulated other comprehensive loss	(36,202)	(12,752)
Total Intrexon shareholders' equity	560,237	694,078
Noncontrolling interests	9,011	10,808
Total equity	569,248	704,886
Total liabilities and total equity	$ 949,068	$ 982,046

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - shares	Dec. 31, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	118,688,770	116,658,886
Common stock, shares outstanding	118,688,770	116,658,886

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Revenues
Collaboration and licensing revenues, including $93,792, $77,354, and $41,030 from related parties in 2016, 2015, and 2014, respectively	$ 109,871	$ 87,821	$ 45,212
Product revenues	36,958	41,879	11,481
Service revenues	43,049	42,923	14,761
Other revenues	1,048	982	476
Total revenues	190,926	173,605	71,930
Operating Expenses
Cost of products	37,709	40,746	11,035
Cost of services	23,930	23,183	8,225
Research and development	112,135	147,483	58,983
Selling, general and administrative	142,318	109,057	63,649
Total operating expenses	316,092	320,469	141,892
Operating loss	(125,166)	(146,864)	(69,962)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock	(58,894)	66,876	(10,469)
Interest expense	(861)	(1,244)	(666)
Interest and dividend income	10,190	1,884	806
Other income (expense), net	1,700	1,314	(168)
Total other income (expense), net	(47,865)	68,830	(10,497)
Equity in net loss of affiliates	(21,120)	(8,944)	(5,260)
Loss before income taxes	(194,151)	(86,978)	(85,719)
Income tax benefit (expense)	3,877	(1,016)	103
Net loss	(190,274)	(87,994)	(85,616)
Net loss attributable to the noncontrolling interests	3,662	3,501	3,794
Net loss attributable to Intrexon	$ (186,612)	$ (84,493)	$ (81,822)
Net loss attributable to Intrexon per share, basic and diluted	$ (1.58)	$ (0.76)	$ (0.83)
Weighted average shares outstanding, basic and diluted	117,983,836	111,066,352	99,170,653

Consolidated Statements of Ope5

Consolidated Statements of Operations Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Related Party Transaction [Line Items]
Collaboration and licensing revenues	$ 109,871	$ 87,821	$ 45,212
Related Parties, Aggregated
Related Party Transaction [Line Items]
Collaboration and licensing revenues	$ 93,792	$ 77,354	$ 41,030

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Statement of Comprehensive Income [Abstract]
Net loss	$ (190,274)	$ (87,994)	$ (85,616)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	430	(561)	21
Loss on foreign currency translation adjustments	(23,901)	(12,108)	(33)
Comprehensive loss	(213,745)	(100,663)	(85,628)
Comprehensive loss attributable to the noncontrolling interests	3,683	3,422	3,750
Comprehensive loss attributable to Intrexon	$ (210,062)	$ (97,241)	$ (81,878)

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
Beginning balance at Dec. 31, 2013	$ 381,343		$ 743,084	$ 52	$ (376,414)	$ 366,722	$ 14,621
Beginning balance, shares at Dec. 31, 2013		97,053,712
Changes in Stockholders' Equity
Stock-based compensation expense	21,849		21,692			21,692	157
Exercises of stock options and warrants, shares		374,471
Exercises of stock options and warrants	1,489		1,477			1,477	12
Contribution of services by shareholder	1,991		1,991			1,991
Shares issued as compensation for services	486		486			486
Shares issued as compensation for services, shares		16,908
Shares issued in public or private offerings	25,000		25,000			25,000
Shares issued in public or private offerings, shares		972,004
Shares issued in acquisitions	51,682		51,682			51,682
Shares issued in acquisitions, shares		2,140,837
Shares issued in asset acquisition	0
Shares issued as payment for contingent consideration	0
Adjustments for noncontrolling interests	11,077		(2,411)			(2,411)	13,488
Noncash dividend	0
Net loss	(85,616)				(81,822)	(81,822)	(3,794)
Other comprehensive income (loss)	(12)			(56)		(56)	44
Ending balance at Dec. 31, 2014	409,289		843,001	(4)	(458,236)	384,761	24,528
Ending balance, shares at Dec. 31, 2014		100,557,932
Changes in Stockholders' Equity
Stock-based compensation expense	38,688		38,507			38,507	181
Exercises of stock options and warrants, shares		1,148,463
Exercises of stock options and warrants	14,462		14,462			14,462	0
Shares issued as compensation for services	2,169		2,169			2,169
Shares issued as compensation for services, shares		70,925
Shares issued in public or private offerings	328,234		328,234			328,234
Shares issued in public or private offerings, shares		9,922,256
Shares issued as consideration for license agreement	59,579		59,579			59,579
Shares issued as consideration for licensing agreement, shares		2,100,085
Shares issued in acquisitions	126,863		126,863			126,863
Shares issued in acquisitions, shares		2,552,151
Shares issued in asset acquisition	0
Shares issued as payment for contingent consideration	0
Acquisition of noncontrolling interest	(1,566)		9,412			9,412	(10,978)
Acquisition of noncontrolling interest, shares		307,074
Adjustments for noncontrolling interests	250		(249)			(249)	499
Noncash dividend	(172,419)		(172,419)			(172,419)
Net loss	(87,994)				(84,493)	(84,493)	(3,501)
Other comprehensive income (loss)	(12,669)			(12,748)		(12,748)	79
Ending balance at Dec. 31, 2015	$ 704,886		1,249,559	(12,752)	(542,729)	694,078	10,808
Ending balance, shares at Dec. 31, 2015	116,658,886	116,658,886
Changes in Stockholders' Equity
Stock-based compensation expense	$ 42,181		42,108			42,108	73
Exercises of stock options and warrants, shares		1,400,146
Exercises of stock options and warrants	19,165		19,165			19,165	0
Shares issued as compensation for services	10,777		10,777			10,777
Shares issued as compensation for services, shares		434,061
Shares issued in acquisitions	0
Shares issued in asset acquisition	4,401		4,401			4,401
Shares issued in asset acquisition, shares		136,340
Shares issued as payment for contingent consideration	1,583		1,583			1,583
Shares issued as payment for contingent consideration, shares		59,337
Adjustments for noncontrolling interests	0		(1,813)			(1,813)	1,813
Noncash dividend	0
Net loss	(190,274)				(186,612)	(186,612)	(3,662)
Other comprehensive income (loss)	(23,471)			(23,450)		(23,450)	(21)
Ending balance at Dec. 31, 2016	$ 569,248		$ 1,325,780	$ (36,202)	$ (729,341)	$ 560,237	$ 9,011
Ending balance, shares at Dec. 31, 2016	118,688,770	118,688,770

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Cash flows from operating activities
Net loss	$ (190,274)	$ (87,994)	$ (85,616)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization	24,572	17,743	10,415
Loss on disposal of property, plant and equipment	666	633	208
Unrealized and realized (appreciation) depreciation on equity securities and preferred stock	58,894	(66,876)	10,469
Noncash dividend income	(7,421)	0	0
Amortization of discount/premium on investments	1,070	642	1,357
Equity in net loss of affiliates	21,120	8,944	5,260
Stock-based compensation expense	42,202	38,667	21,849
Contribution of services by shareholder	0	0	1,991
Shares issued as payment for services	10,777	2,169	486
Shares issued as consideration for license agreement	0	59,579	0
Provision for bad debts	1,963	1,757	565
Deferred income taxes	(3,467)	1,117	0
Other noncash items	1,662	460	723
Changes in operating assets and liabilities:
Restricted cash	(6,987)	0	0
Receivables:
Trade	2,588	(12,138)	4,332
Related parties	6,804	(11,042)	(6,117)
Notes	(42)	0	(1)
Other	271	5,286	15
Inventory	3,807	(774)	(7,313)
Prepaid expenses and other	(932)	(2,729)	(465)
Other assets	2,189	(2,119)	80
Accounts payable	3,618	(3,263)	1,266
Accrued compensation and benefits	(12,402)	10,491	1,587
Other accrued liabilities	9,002	1,593	(586)
Deferred revenue	(25,481)	74,434	20,934
Deferred consideration	(630)	(943)	0
Related party payables	310	(64)	(1,137)
Other long term liabilities	146	96	(160)
Net cash provided by (used in) operating activities	(55,975)	35,669	(19,858)
Cash flows from investing activities
Purchases of investments	(75,246)	(181,572)	(60,478)
Sales of investments	0	0	9,100
Maturities of investments	101,987	88,000	122,992
Purchases of equity securities and warrants	(2,308)	(17,080)	(19,496)
Proceeds from sales of equity securities	280	0	0
Acquisitions of businesses, net of cash received	0	(123,928)	(67,577)
Acquisition of noncontrolling interest	0	(1,566)	0
Investments in affiliates	(11,542)	(13,442)	(2,875)
Cash paid in asset acquisition	(7,244)	0	0
Purchases of property, plant and equipment	(31,629)	(12,749)	(6,371)
Proceeds from sale of property, plant and equipment	274	626	176
Issuances of notes receivable	(2,964)	(600)	(1,500)
Proceeds from notes receivable	0	1,500	0
Net cash used in investing activities	(28,392)	(260,811)	(26,029)
Cash flows from financing activities
Proceeds from issuance of shares in a private placement	0	0	25,000
Proceeds from issuance of shares in public offerings, net of issuance costs	0	328,234	0
Advances from lines of credit	5,075	15,232	4,676
Repayments of advances from lines of credit	(4,816)	(16,944)	(6,494)
Proceeds from long term debt	547	81	268
Payments of long term debt	(1,201)	(1,564)	(679)
Payments of deferred consideration	(6,705)	(6,252)	0
Proceeds from stock option exercises	19,165	14,462	1,489
Payment of stock issuance costs	0	0	(256)
Net cash provided by financing activities	12,065	333,249	24,004
Effect of exchange rate changes on cash and cash equivalents	(873)	209	(160)
Net increase (decrease) in cash and cash equivalents	(73,175)	108,316	(22,043)
Cash and cash equivalents
Beginning of period	135,782	27,466	49,509
End of period	62,607	135,782	27,466
Supplemental disclosure of cash flow information
Cash paid during the period for interest	964	1,195	158
Cash paid during the period for income taxes	10	1,165	0
Significant noncash financing and investing activities
Stock received as consideration for collaboration agreements	18,766	9,149	14,246
Preferred stock received as consideration for collaboration amendments	120,000	0	0
Stock issued in business combinations	0	126,863	51,682
Stock issued to acquire noncontrolling interest	0	9,412	0
Shares issued in asset acquisition	4,401	0	0
Contingent consideration assumed in asset acquisition	3,660	0	0
Shares issued as payment for contingent consideration	1,583	0	0
Noncash dividend to shareholders	0	172,419	0
Deferred consideration payable related to acquisition	0	1,992	20,115
Purchases of equipment included in accounts payable and other accrued liabilities	652	782	790
Transfer of inventory to breeding stock	$ 1,191	$ 0	$ 0

Organization and Basis of Prese

Organization and Basis of Presentation	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization and Basis of Presentation	Organization and Basis of Presentation Intrexon Corporation ("Intrexon"), a Virginia corporation, forms collaborations to create biologically based products and processes using synthetic biology. Intrexon's primary domestic operations are in California, Florida, Maryland, and Virginia, and its primary international operations are in Belgium and Hungary. There have been no commercialized products derived from Intrexon's collaborations to date. Trans Ova Genetics, L.C. ("Trans Ova"), a provider of bovine reproductive technologies and other genetic processes to cattle breeders and producers, is a wholly owned subsidiary of Intrexon with primary operations in Iowa, Maryland, Missouri, Oklahoma and Texas. Oxitec Limited ("Oxitec"), a pioneering company in biological insect control solutions, is a wholly owned subsidiary of Intrexon with primary operations in England and Brazil. Intrexon Produce Holdings, Inc. ("IPHI") is a wholly owned subsidiary of Intrexon. Okanagan Specialty Fruits, Inc. ("Okanagan"), a company which developed and received regulatory approval for the world's first non-browning apple without the use of any flavor-altering chemical or antioxidant additives, is a wholly owned subsidiary of IPHI with primary operations in Canada. Fruit Orchard Holdings, Inc. ("FOHI") is a wholly owned subsidiary of IPHI with primary operations in Washington. ViaGen, L.C. ("ViaGen"), a provider of genetic preservation and cloning technologies, and Exemplar Genetics, LLC ("Exemplar"), a provider of genetically engineered swine for medical and genetic research, are wholly owned subsidiaries with primary operations in Texas and Iowa, respectively. As of December 31, 2016 , Intrexon owned approximately 70% of AquaBounty Technologies, Inc. ("AquaBounty"), a company focused on improving productivity in commercial aquaculture, which includes the conversion of the principal balance of an outstanding promissory note receivable and related accrued interest held by Intrexon totaling $10,396 . See Note 22 for additional discussion regarding Intrexon's investment in AquaBounty. As of December 31, 2016 , Intrexon owned approximately 51% of Biological & Popular Culture, Inc. ("BioPop"), a company developing artwork, children's toys and novelty goods that are derived from living organisms or enabled by synthetic biology. Intrexon Corporation and its consolidated subsidiaries are hereinafter referred to as the "Company." These consolidated financial statements are presented in United States dollars and are prepared under accounting principles generally accepted in the United States of America ("U.S. GAAP").

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Principles of Consolidation The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated. Revenue Recognition The Company generates collaboration and licensing revenue through the execution of agreements with collaborators (known as exclusive channel collaborations, "ECC" or "ECCs") and licensing agreements whereby the collaborators or the licensee obtain exclusive access to the Company's proprietary technologies for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Generally, the terms of these agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration or licensing agreement. The Company's collaboration and licensing agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborator or licensee on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement. Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence ("VSOE") of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price ("BESP") for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators or licensees, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations, which is reevaluated each reporting period. The terms of the Company's agreements may provide for milestone payments upon achievement of certain defined events. The Company applies the Milestone Method for recognizing milestone payments. Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria: (1) The consideration is commensurate with either the entity's performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity's performance to achieve the milestone; (2) The consideration relates solely to past performance; and (3) The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments. Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration and licensing agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned. From time to time, the Company and certain collaborators may cancel their agreements, relieving the Company of any further performance obligations under the agreement. When no further performance obligations are required of the Company under an agreement, the Company recognizes any remaining deferred revenue. The Company generates product and service revenues primarily through sales of products and services which are created from technologies developed or owned by the Company. The Company's current offerings include sales of advanced reproductive technologies, including the Company's bovine embryo transfer and in vitro fertilization processes and from genetic preservation and sexed semen processes and applications of such processes to other livestock, as well as sales of livestock and embryos produced using these processes and used in production. Revenue is recognized when (i) persuasive evidence of an arrangement exists, (ii) services have been rendered or delivery has occurred such that risk of loss has passed to the customer, (iii) the price is fixed or determinable, and (iv) collection from the customer is reasonably assured. Research and Development The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, including stock-based compensation expense, and the costs of consultants, certain in-licensed technology rights, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses. The Company has research and development arrangements with third parties that include upfront and milestone payments. As of December 31, 2016 and 2015 , the Company had research and development commitments with third parties that had not yet been incurred totaling $10,631 and $4,138 , respectively. The commitments are generally cancellable by the Company at any time upon written notice. Cash and Cash Equivalents All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer. As of December 31, 2016 and 2015 , the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $43,808 and $112,776 , respectively. Restricted Cash Restricted cash represents funds deposited with the U.S. Treasury, as required by a court decision resulting from litigation against Trans Ova (Note 17 ). Short-term and Long-term Investments As of December 31, 2016 , short-term and long-term investments include U.S. government debt securities and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management's reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company's written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor's, Moody's and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer. Equity Securities The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator's security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter. Investment in Preferred Stock The Company holds preferred stock received from one of its collaborators, ZIOPHARM Oncology, Inc. ("ZIOPHARM"), which may be converted to common stock upon the occurrence of certain events in the future (Note 7 ). The Company elected the fair value option to account for its investment in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. This investment is subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of ZIOPHARM's common stock, and changes in general economic and financial conditions of ZIOPHARM. The investment is classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell the investment nor expect it to be converted into shares of common stock within one year. Until such time as the Company converts the preferred stock into common stock, the Company is entitled to a monthly dividend payable in additional shares of preferred stock and records dividend income based on the fair value of the preferred shares received. Fair Value of Financial Instruments Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows: Level 1: Quoted prices in active markets for identical assets and liabilities; Level 2: Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and Level 3: Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available. Concentrations of Risk Due to the Company's mix of fixed and variable rate securities holdings, the Company's investment portfolio is susceptible to changes in interest rates. As of December 31, 2016 , gross unrealized losses on the Company's short-term and long-term investments were not material. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions, or distribute its equity securities to shareholders as a stock dividend. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses. Financial instruments which potentially subject the Company to concentrations of credit risk consist primarily of trade receivables. The Company controls credit risk through credit approvals, credit limits and monitoring procedures. The Company performs ongoing credit evaluations of its customers but generally does not require collateral to support accounts receivable. Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest"), a related party, (Note 18 ) using the equity method of accounting based upon relative ownership interest. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets. The Company accounts for its investment in Oragenics, Inc. ("Oragenics"), one of its collaborators, using the fair value option. The fair value of the Company's investment in Oragenics was $7,244 and $16,601 as of December 31, 2016 and 2015 , respectively, and is included as equity securities in the accompanying consolidated balance sheets. The Company's ownership percentage of Oragenics was 29.5% and 30.7% as of December 31, 2016 and 2015 , respectively. Unrealized appreciation (depreciation) in the fair value of these securities was $(10,523) , $4,863 , and $(14,969) for the years ended December 31, 2016 , 2015 , and 2014 , respectively. The Company determined it had significant influence over ZIOPHARM until the Company distributed its investment in ZIOPHARM to shareholders in the form of a special stock dividend (Note 14 ). Upon disposition, the Company realized a gain of $81,401 during the year ended December 31, 2015. Unrealized appreciation in the fair value of the Company's equity securities held in ZIOPHARM was $11,965 for the year ended December 31, 2014. In 2015 and 2014, the Company determined that ZIOPHARM met the criteria of SEC Regulation S-X Article 3-09 for inclusion of separate financial statements of an equity method investment. Summarized financial data as of December 31, 2016 and 2015 , and for the years ended December 31, 2016 , 2015 , and 2014 , for the Company's equity method investments for which separate financial statements are not included, pursuant to SEC Regulation S-X Article 3-09, are shown in the following tables. December 31, 2016 2015 Current assets $ 77,761 $ 28,123 Non-current assets 11,040 1,539 Total assets 88,801 29,662 Current liabilities 11,588 6,274 Net assets $ 77,213 $ 23,388 Year Ended December 31, 2016 2015 2014 Revenues, net $ 417 $ 1,176 $ 940 Operating expenses 62,373 32,513 17,289 Operating loss (61,956 ) (31,337 ) (16,349 ) Other, net 1,535 (64 ) 35 Net loss $ (60,421 ) $ (31,401 ) $ (16,314 ) Variable Interest Entities The Company identifies entities that (i) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (ii) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities ("VIE" or "VIEs"). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are VIEs. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (i) the power to direct activities that most significantly impact the VIE's economic performance and (ii) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE. As of December 31, 2016 and 2015 , the Company determined that certain of its collaborators and joint ventures as well as Harvest were VIEs. The Company was not the primary beneficiary for these entities since it did not have the power to direct the activities that most significantly impact the economic performance of the VIEs. The Company's aggregate investment balances of these VIEs as of December 31, 2016 and 2015 , were $159,115 and $3,598 , respectively, which represents the Company's maximum risk of loss related to the identified VIEs. Trade Receivables Trade receivables consist of credit extended to the Company's customers in the normal course of business and are reported net of an allowance for doubtful accounts. The Company reviews its customer accounts on a periodic basis and records bad debt expense for specific amounts the Company evaluates as uncollectible. Past due status is determined based upon contractual terms. Amounts are written off at the point when collection attempts have been exhausted. Management estimates uncollectible amounts considering such factors as current economic conditions and historic and anticipated customer performance. This estimate can fluctuate due to changes in economic, industry or specific customer conditions which may require adjustment to the allowance recorded by the Company. Management has included amounts believed to be uncollectible in the allowance for doubtful accounts. The following table shows the activity in the allowance for doubtful receivable accounts for the years ended December 31, 2016 and 2015 : 2016 2015 Beginning balance $ 2,081 $ 565 Charged to operating expenses 1,963 1,757 Write offs of accounts receivable (341 ) (241 ) Ending balance $ 3,703 $ 2,081 Inventory The Company's inventory primarily includes adult female cows which are used in certain production processes and are recorded at acquisition cost using the first-in, first-out method or at market, whichever is lower. Work-in-process inventory includes allocations of production costs and facility costs for products currently in production and is recorded at the lower of cost or market. Significant declines in the price of cows could result in unfavorable adjustments to inventory balances. Property, Plant and Equipment Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows: Years Land improvements 4–20 Buildings and building improvements 3–25 Furniture and fixtures 1–10 Equipment 1–10 Breeding stock 1–4 Computer hardware and software 1–7 Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to twenty years . Goodwill Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized. Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required. If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit's goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed. The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review. Intangible Assets Intangible assets subject to amortization consist of patents, developed technologies and know-how; customer relationships; trademarks; and a covenant not to compete acquired as a result of mergers or acquisitions. These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development technologies acquired in mergers or acquisitions and were recorded at fair value at the dates of the respective acquisitions. The Company amortizes long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their estimated useful lives, ranging from two to twenty-one years for the patents, developed technologies and know-how; customer relationships; trademarks; and the covenant not to compete. Impairment of Long-Lived Assets Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable. Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval. Foreign Currency Translation The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period. Income Taxes Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized. The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in selling, general and administrative expenses. Share-Based Payments Intrexon uses the Black-Scholes option pricing model to estimate the grant-date fair value of all stock options. The Black-Scholes option pricing model requires the use of assumptions for estimated expected volatility, estimated expected term of stock options, risk-free rate, estimated expected dividend yield, and the fair value of the underlying common stock at the date of grant. Since Intrexon does not have sufficient history to estimate the expected volatility of its common stock price, expected volatility is based on a blended approach which utilizes the volatility of Intrexon's common stock and the volatility of peer public entities that are similar in size and industry. Intrexon estimates the expected term of all options based on previous history of exercises. The risk-free rate is based on the U.S. Treasury yield curve in effect at the time of grant for the expected term of the option. The expected dividend yield is 0% as Intrexon does not expect to declare cash dividends in the near future. The fair value of the underlying common stock is determined based on the quoted market price on the New York Stock Exchange. Intrexon estimates forfeitures based on its historical analysis of actual stock option forfeitures. Actual forfeitures are recorded when incurred and estimated forfeitures are reviewed and adjusted at least annually. The assumptions used in the Black-Scholes option pricing model for the years ended December 31, 2016 , 2015 and 2014 are set forth in the table below: 2016 2015 2014 Valuation assumptions Expected dividend yield 0% 0% 0% Expected volatility 59%—60% 59%—62% 62%—64% Expected term (years) 6.25 6.25 6.25 Risk-free interest rate 1.23%—2.17% 1.56%—1.95% 1.82%—2.14% Net Loss per Share Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented. Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment. As of December 31, 2016 and 2015 , the Company had $13,265 and $3,877 , respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $11,969 , $5,918 , and $2,166 for the years ended December 31, 2016 , 2015 and 2014 , respectively. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates. Recently Issued Accounting Pronouncements In January 2017, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2017-04, Intangibles-Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment (" ASU 2017-04"). The provisions of ASU 2017-04 simplify how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2017, the FASB issued ASU 2017-01, Business Combinations (Topic 805) - Clarifying the Definition of a Business ("ASU 2017-01"). The provisions of ASU 2017-01 clarify the definition of a business to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230) - Restricted Cash (A Consensus of the FASB Emerging Issues Task Force) ("ASU 2016-18"). The provisions of ASU 2016-18 require amounts generally described as restricted cash and restricted cash equivalents to be included with cash and cash equivalents when reconciling the total beginning and ending balances for the periods presented on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods b

Mergers and Acquisitions

Mergers and Acquisitions	12 Months Ended
	Dec. 31, 2016
Business Combinations [Abstract]
Mergers and Acquisitions	Mergers and Acquisitions Oxitec Acquisition In September 2015, pursuant to a Stock Purchase Agreement (the "Oxitec Purchase Agreement"), the Company acquired 100% of the issued outstanding share capital of Oxitec. The aggregated consideration paid consisted of (i) 1,359,343 shares of the Company's common stock (the "Stock Consideration") and (ii) $ 90,199 in cash (the "Cash Consideration"), inclusive of net cash and working capital adjustments as defined in the Oxitec Purchase Agreement totaling $9,449 . Stock Consideration totaling 480,422 shares and Cash Consideration totaling $1,991 were withheld as escrow at closing and are issuable and payable, respectively, eighteen months after closing, subject to reduction for satisfaction of any claims for indemnification made by the Company under the Oxitec Purchase Agreement. Cash Consideration withheld is included in deferred consideration as of December 31, 2016 . The results of Oxitec's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $ 146,394 . The acquisition date fair value of the Stock Consideration and Cash Consideration is presented below: Cash $ 90,199 Common shares 56,195 $ 146,394 The fair value of the shares of the Company common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,780 Trade receivables 125 Other receivables 7,395 Prepaid expenses and other 121 Property, plant, and equipment 1,198 Intangible assets 96,854 Total assets acquired 109,473 Accounts payable 1,187 Accrued compensation and benefits 246 Other accrued liabilities 210 Deferred revenue 120 Deferred tax liabilities 12,584 Total liabilities assumed 14,347 Net assets acquired 95,126 Goodwill 51,268 Total consideration $ 146,394 The acquired intangible assets primarily include in-process research and development, the fair value of which was determined using the multi-period excess earning method, which is a variation of the income approach that converts future cash flows to single discounted present value amounts. In November 2016, the Company re-evaluated certain of the acquired in-process research and development technology and determined it was placed in service as developed technology and began amortizing the original amount capitalized using a useful life of eighteen years . Goodwill, which is not deductible for tax purposes, represents the assembled workforce and the potential for future Oxitec products and technologies. The Company incurred $ 1,675 of acquisition related costs, which is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the year ended December 31, 2015. Okanagan Acquisition In April 2015, pursuant to a Stock Purchase Agreement (the "Okanagan Purchase Agreement"), the Company acquired 100% of the outstanding shares of Okanagan. Pursuant to the Okanagan Purchase Agreement, the former shareholders of Okanagan received an aggregate of 707,853 shares of the Company's common stock and $10,000 cash in exchange for all shares in Okanagan. The results of Okanagan's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 36,500 Total assets acquired 36,655 Accounts payable 181 Deferred revenue 181 Deferred tax liabilities 8,847 Total liabilities assumed 9,209 Net assets acquired 27,446 Goodwill 13,487 Total consideration $ 40,933 The acquired intangible assets primarily include developed technology, patents and know-how and the fair values of the acquired assets were determined using the with-and-without method, which is a variation of the income approach that utilizes estimated cash flows with all assets in place at the valuation date and estimated cash flows with all assets in place except the intangible assets at the valuation date. The intangible assets are being amortized over a useful life of fourteen years . Goodwill, which is not deductible for tax purposes, represents potential future applications of Okanagan's technology to other fruits, including additional apple varietals, and anticipated buyer-specific synergies arising from the combination of the Company's and Okanagan's technologies. The Company incurred $ 341 of acquisition-related costs, of which $267 and $74 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the years ended December 31, 2015 and 2014, respectively. ActoGeniX Acquisition In February 2015, the Company acquired 100% of the membership interests of ActoGeniX NV ("ActoGeniX"), a European biopharmaceutical company, pursuant to a Stock Purchase Agreement (the "ActoGeniX Purchase Agreement"). ActoGeniX's platform technology complements the Company's suite of proprietary technologies available for current and future collaborators. Pursuant to the ActoGeniX Purchase Agreement, the former members of ActoGeniX received an aggregate of 965,377 shares of the Company's common stock and $ 32,739 in cash in exchange for all membership interests of ActoGeniX. The results of ActoGeniX's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $ 72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,180 Other receivables 305 Prepaid expenses and other 31 Property, plant and equipment 209 Intangible assets 68,100 Other non-current assets 23 Total assets acquired 71,848 Accounts payable 230 Accrued compensation and benefits 196 Other accrued liabilities 253 Deferred revenue 732 Deferred tax liabilities 612 Total liabilities assumed 2,023 Net assets acquired 69,825 Goodwill 2,649 Total consideration $ 72,474 The acquired intangible assets primarily include in-process research and development, the fair value of which was determined using the multi-period excess earnings and with-and-without methods, which are both variations of the income approach that convert future cash flows to single discounted present value amounts. In August 2015, the Company re-evaluated the acquired in-process research and development technology and determined that it was placed in service as developed technology and began amortizing the original amount capitalized using a useful life of eighteen years . Goodwill, which is not deductible for tax purposes, represents the assembled workforce and anticipated buyer-specific synergies arising from the combination of the Company's and ActoGeniX's technologies. The Company incurred $ 418 of acquisition-related costs, of which $ 381 and $37 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the years ended December 31, 2015 and 2014, respectively. Trans Ova Acquisition In August 2014, the Company acquired 100% of the membership interests of Trans Ova, a provider of bovine reproductive technologies, pursuant to an Amended and Restated Membership Interest Purchase Agreement (the "Purchase Agreement"). The Company and Trans Ova intend to build upon Trans Ova's current platform with new capabilities with a goal of achieving higher levels of delivered value to dairy and beef cattle producers. Pursuant to the Purchase Agreement, the former members of Trans Ova received an aggregate of 1,444,388 shares of the Company's common stock and $63,625 in cash, and are entitled to receive deferred cash consideration valued at $20,115 in exchange for all membership interests of Trans Ova. The first two installments of the deferred cash consideration were paid in August 2015 and 2016, respectively, and the remaining payment is due in August 2017. The Purchase Agreement also provides for payment to the former members of Trans Ova a portion of certain cash proceeds in the event there is an award under certain litigation matters pending as of the transaction date to which Trans Ova is a party. The results of Trans Ova's operations subsequent to the acquisition date have been included in the consolidated financial statements, including revenues of $78,143 , $83,912 , and $26,352 , and net income (loss) of $(9,679) , $(1,531) , and $2 for the years ended December 31, 2016, 2015, and 2014, respectively. The fair value of the total consideration transferred, including the noncontrolling interest in a majority-owned subsidiary of Trans Ova, was $127,875 . The acquisition date fair value of each class of consideration transferred and noncontrolling interest is presented below: Cash $ 63,625 Common shares 32,802 Deferred cash consideration 20,115 Total consideration transferred 116,542 Fair value of noncontrolling interest 11,333 Total $ 127,875 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below: Cash $ 960 Trade receivables 18,693 Related party receivables 1,219 Inventory 18,476 Prepaid expenses and other 590 Property, plant and equipment 21,164 Intangible assets 23,700 Other non-current assets 147 Total assets acquired 84,949 Accounts payable 3,317 Accrued compensation and benefits 913 Other accrued liabilities 271 Deferred revenue 4,458 Lines of credit 4,091 Related party payables 1,246 Long term debt 9,090 Total liabilities assumed 23,386 Net assets acquired 61,563 Goodwill 66,312 Total consideration and fair value of noncontrolling interest $ 127,875 The fair value of acquired inventory was determined using the cost approach, which establishes value based on the cost of reproducing or replacing the asset. The fair value of acquired property, plant and equipment was determined using the cost approach and the market approach. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The acquired intangible assets include various developed technologies and know-how, customer relationships, and trademarks, and the fair values of these assets were determined using the relief-from-royalty, multi-period excess earnings, and with-and-without methods, which are all variations of the income approach that convert future cash flows to single discounted present value amounts. The acquired intangible assets are being amortized over useful lives ranging from three to nine years . Goodwill, which is deductible for tax purposes, represents the assembled workforce, potential future expansion of Trans Ova business lines and anticipated buyer-specific synergies arising from the combination of the Company's and Trans Ova's technologies. As a result of a 2012 transaction between Trans Ova and its wholly owned subsidiary, ViaGen, the Company may be obligated to make certain future contingent payments to the former equity holders of ViaGen, up to a total of $3,000 if certain revenue targets, as defined in the share purchase agreement, are met. The Company does not expect these revenue targets to be met and accordingly has assigned no value to this liability. The Company incurred $713 of acquisition-related costs, which is included in selling, general, and administrative expenses in the accompanying consolidated statement of operations for the year ended December 31, 2014. In February 2015, the Company acquired, through an exchange offer, the remaining outstanding membership interests of Trans Ova's majority-owned subsidiary, Exemplar, for $1,566 in cash and 307,074 shares of the Company's common stock. Medistem Acquisition In March 2014, the Company acquired 100% of the outstanding common stock and securities convertible into common stock of Medistem, Inc. ("Medistem"), an entity engaged in the development of Endometrial Regenerative Cells ("ERCs"), for a combination of cash and the Company's common stock. The acquisition allows the Company to employ its synthetic biology platforms to engineer a diverse array of cell-based therapeutic candidates using Medistem's multipotent ERCs. Pursuant to the terms of the merger agreement, Medistem equity holders received 714,144 shares of the Company's common stock and $4,920 in cash in exchange for the outstanding Medistem common stock and securities convertible into common stock. Additionally, Medistem had issued the Company two promissory notes in the amount of $707 , including accrued interest, both of which were settled upon closing of the merger. Certain members of Medistem's management surrendered a total of 17,695 shares of their merger consideration to reimburse the Company for required payroll tax withholdings. The results of Medistem's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $24,995 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 4,920 Common shares 19,368 Settlement of promissory notes 707 $ 24,995 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 8 Intangible assets 4,824 Total assets acquired 4,832 Accounts payable 644 Accrued compensation and benefits 67 Other accrued liabilities 50 Total liabilities assumed 761 Net assets acquired 4,071 Goodwill 20,924 Total consideration $ 24,995 The acquired intangible assets consist of in-process research and development, the fair value of which was determined using the cost approach. In November 2016, the Company re-evaluated the acquired in-process research and development technology and determined it was placed in service as developed technology and began amortizing the original amount capitalized using a useful life of ten years . Goodwill, which is not deductible for tax purposes, consists of buyer-specific synergies between the Company's and Medistem's technologies. The Company incurred $680 of acquisition related costs, of which $310 is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the year ended December 31, 2014. Unaudited Condensed Pro Forma Financial Information The results of operations of the 2015 acquisitions discussed above are included in the consolidated statements of operations beginning on the day after their respective acquisition dates. The following unaudited condensed pro forma financial information for the years ended December 31, 2015 and 2014 , is presented as if the 2015 acquisitions had been consummated on January 1, 2014 : Year Ended December 31, 2015 2014 Pro Forma Revenues $ 174,558 $ 73,240 Loss before income taxes (99,751 ) (105,085 ) Net loss (99,594 ) (104,577 ) Net loss attributable to the noncontrolling interests 3,501 3,794 Net loss attributable to Intrexon (96,093 ) (100,783 ) The results of operations of the 2014 acquisitions discussed above are included in the consolidated statements of operations beginning on the day after their respective acquisition dates. The following unaudited condensed pro forma financial information for the year ended December 31, 2014 is presented as if the 2014 acquisitions had been consummated on January 1, 2013 : Year Ended December 31, 2014 Pro Forma Revenues $ 119,721 Loss before income taxes (82,041 ) Net loss (81,938 ) Net loss attributable to the noncontrolling interests 4,159 Net loss attributable to Intrexon (77,779 )

Investments in Joint Ventures

Investments in Joint Ventures	12 Months Ended
	Dec. 31, 2016
Equity Method Investments and Joint Ventures [Abstract]
Investments in Joint Ventures	Investments in Joint Ventures S & I Ophthalmic In September 2013, the Company entered into a Limited Liability Company Agreement ("Sun LLC Agreement") with Caraco Pharmaceutical Laboratories, Ltd. ("Sun Pharmaceutical Subsidiary"), an indirect subsidiary of Sun Pharmaceutical Industries Ltd. ("Sun Pharmaceutical"), an international specialty pharmaceutical company focused on chronic diseases, to form S & I Ophthalmic, LLC ("S & I Ophthalmic"). The Sun LLC Agreement governs the affairs and the conduct of business of S & I Ophthalmic. S & I Ophthalmic leverages experience and technology from both the Company and Sun Pharmaceutical. Both the Company and Sun Pharmaceutical Subsidiary made an initial capital contribution of $5,000 in October 2013 for a 50% membership interest in S & I Ophthalmic. S & I Ophthalmic is governed by a board of managers ("S & I Ophthalmic Board") which has four members, two each from the Company and Sun Pharmaceutical Subsidiary. In cases in which the S & I Ophthalmic Board determines that additional capital contributions are necessary in order for S & I Ophthalmic to conduct business and comply with its obligations, each of the Company and Sun Pharmaceutical Subsidiary has committed to making additional capital contributions to S & I Ophthalmic subject to certain limits defined in the agreement. Each has the right, but not the obligation, to make additional capital contributions above the defined limits when and if solicited by the S & I Ophthalmic Board. In 2015, both the Company and Sun Pharmaceutical Subsidiary made subsequent capital contributions of $5,000 . Beginning on the seventh anniversary of the effective date of the Sun LLC Agreement, and upon the second anniversary thereafter, the Company, as well as Sun Pharmaceutical Subsidiary, may make a cash offer to purchase all of the other party's interest in S & I Ophthalmic. Upon receipt of such an offer, the other party must either agree to tender its interests at the offered price or submit a counteroffer at a price higher than the original offer. Such offer and counteroffer may continue until one party agrees to the other's price. The Company's investment in S & I Ophthalmic was $3,236 and $6,379 as of December 31, 2016 and 2015 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. OvaXon In December 2013, the Company and OvaScience, Inc. ("OvaScience"), a life sciences company focused on the discovery, development and commercialization of new treatments for infertility, entered into a Limited Liability Company Agreement ("OvaXon LLC Agreement") to form OvaXon, LLC ("OvaXon"), a joint venture to create new applications for improving human and animal health. Both the Company and OvaScience made an initial capital contribution of $1,500 in January 2014 for a 50% membership interest in OvaXon. OvaXon is governed by the OvaXon board of managers ("OvaXon Board") which has four members, two each from the Company and OvaScience. In cases in which the OvaXon Board determines that additional capital contributions are necessary in order for OvaXon to conduct business and comply with its obligations, each of the Company and OvaScience has the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement. The Company's investment in OvaXon was $65 and $(144) as of December 31, 2016 and 2015 , respectively, and is included in investments in affiliates and other accrued liabilities, respectively, in the accompanying consolidated balance sheets. Intrexon Energy Partners In March 2014, the Company and certain investors (the "IEP Investors"), including an affiliate of Third Security, LLC ("Third Security"), entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners, LLC ("Intrexon Energy Partners"), a joint venture formed to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. The Company also entered into an ECC with Intrexon Energy Partners providing exclusive rights to the Company's technology for the use in bioconversion, as a result of which the Company received a technology access fee of $25,000 while retaining a 50% membership interest in Intrexon Energy Partners. The IEP Investors made initial capital contributions, totaling $25,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners totaling 50% . In addition, Intrexon has committed to make capital contributions of up to $25,000 , and the IEP Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners, have committed to make additional capital contributions of up to $25,000 , at the request of Intrexon Energy Partners' board of managers (the "Intrexon Energy Partners Board") and subject to certain limitations. As of December 31, 2016 , the Company's remaining commitment was $10,240 . Intrexon Energy Partners is governed by the Intrexon Energy Partners Board which has five members. Two members of the Intrexon Energy Partners Board are designated by the Company and three members are designated by a majority of the IEP Investors. The Company and the IEP Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners Board. The Company's investment in Intrexon Energy Partners was $(477) and $(1,270) as of December 31, 2016 and 2015 , respectively, and is included in other accrued liabilities in the accompanying consolidated balance sheets. Intrexon Energy Partners II In December 2015, the Company and certain investors (the "IEPII Investors"), including Harvest, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners II, LLC ("Intrexon Energy Partners II"), a joint venture formed to utilize the Company's natural gas bioconversion platform for the production of 1,4-butanediol, an industrial chemical used to manufacture spandex, polyurethane, plastics, and polyester. The Company also entered into an ECC with Intrexon Energy Partners II which provides exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $18,000 while retaining a 50% membership interest in Intrexon Energy Partners II. The IEPII Investors made initial capital contributions, totaling $18,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners II totaling 50% . In December 2015, the owners of Intrexon Energy Partners II made a capital contribution of $4,000 , half of which was paid by the Company. Intrexon has committed to make additional capital contributions of up to $10,000 , and the IEPII Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners II, have committed to make additional capital contributions of up to $10,000 , at the request of Intrexon Energy Partners II's board of managers (the "Intrexon Energy Partners II Board") and subject to certain limitations. Intrexon Energy Partners II is governed by the Intrexon Energy Partners II Board which has five members. One member of the Intrexon Energy Partners II Board is designated by the Company and four members are designated by a majority of the IEPII Investors. The Company and the IEPII Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners II Board. The Company's investment in Intrexon Energy Partners II was $1,414 and $2,000 as of December 31, 2016 and 2015 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. EnviroFlight In February 2016, the Company entered into a series of transactions involving EnviroFlight, LLC ("Old EnviroFlight"), Darling Ingredients Inc. ("Darling") and a newly formed venture between the Company and Darling ("New EnviroFlight"). The Company determined that the series of integrated transactions to acquire substantially all of the assets of Old EnviroFlight for cash, common stock, and contingent consideration should be accounted for as a single transaction, which constituted a business, and considered New EnviroFlight to be the accounting acquirer pursuant to Accounting Standards Codification ("ASC") 805, Business Combinations . Consideration paid to Old EnviroFlight was $4,244 in cash, 136,340 shares of the Company's common stock valued at $4,401 and contingent consideration estimated at $3,660 . Contemporaneously, all the assets acquired from Old EnviroFlight, with the exception of certain developed technology, and $3,000 of cash were contributed to New EnviroFlight in exchange for a non-controlling, 50% membership interest in New EnviroFlight. The Company's contributions to New EnviroFlight included an exclusive license to the developed technology that was retained by the Company. Darling received the remaining 50% membership interest in New EnviroFlight as consideration for terminating rights previously held in the developed technology with Old EnviroFlight. New EnviroFlight was formed to generate high-nutrition, low environmental impact animal and fish feed, as well as fertilizer products. The Company and Darling as members have each agreed to make additional capital contributions of up to $5,000 to fund ongoing operations of New EnviroFlight. All of the employees of Old EnviroFlight became employees of New EnviroFlight. The Company determined that its investment in New EnviroFlight should be accounted for using the equity method of accounting. The Company recorded an estimated fair value of $5,425 for its investment in New EnviroFlight and $9,880 for the retained developed technology intangible asset. The developed technology is being amortized over a period of twenty-one years . The contingent consideration liability payable to the members of Old EnviroFlight is considered a freestanding financial instrument in accordance with ASC 480, Distinguishing Liabilities and Equity , and is recorded at fair value each reporting period. The value of this liability was estimated at $2,081 as of December 31, 2016 . New EnviroFlight met a regulatory milestone, as defined in the asset purchase agreement, and the members of Old EnviroFlight received a portion of the contingent consideration consisting of 59,337 shares of the Company's common stock valued at $1,583 in October 2016. The members of Old EnviroFlight may receive up to $4,000 of additional shares of the Company's common stock if certain commercial milestones are met prior to February 2019. The Company's investment in New EnviroFlight was $4,189 as of December 31, 2016 and is included in investments in affiliates in the accompanying consolidated balance sheet. Intrexon T1D Partners In March 2016, the Company and certain investors (the "T1D Investors"), including affiliates of Third Security, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon T1D Partners, LLC ("Intrexon T1D Partners"), a joint venture formed to utilize the Company's proprietary ActoBiotics platform to develop and commercialize products to treat type 1 diabetes. The Company also entered into an ECC with Intrexon T1D Partners which provides the exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $10,000 while retaining a 50% membership interest in Intrexon T1D Partners. The T1D Investors made initial capital contributions, totaling $10,000 in the aggregate, in exchange for pro rata membership interests in Intrexon T1D Partners totaling 50% . Intrexon has committed to make capital contributions of up to $5,000 , and the T1D Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon T1D Partners, have committed to make additional capital contributions of up to $5,000 , at the request of Intrexon T1D Partners' board of managers (the "Intrexon T1D Partners Board") and subject to certain limitations. As of December 31, 2016 , the Company's remaining commitment was $3,650 . Intrexon T1D Partners is governed by the Intrexon T1D Partners Board, which has five members. Two members of the Intrexon T1D Partners Board are designated by the Company and three members are designated by a majority of the T1D Investors. The Company and the T1D Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the Intrexon T1D Partners Board. The Company's investment in Intrexon T1D Partners was $806 as of December 31, 2016 and is included in investments in affiliates in the accompanying consolidated balance sheet.

Collaboration and Licensing Rev

Collaboration and Licensing Revenue	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaboration and Licensing Revenue	Collaboration and Licensing Revenue The Company's collaborations and licensing agreements provide for multiple deliverables to be delivered by the Company and typically include a license to the Company's technology platforms, participation in collaboration committees, performance of certain research and development services and may include obligations for certain manufacturing services. The Company typically groups these deliverables into two units of accounting based on the nature of the deliverables and the separation criteria. The first deliverable ("Unit of Accounting 1") includes the license to the Company's technology platform, the Company's participation on the collaboration committees and any research and development services associated with its technology platforms. The deliverables for Unit of Accounting 1 are combined because they cannot be individually separated. If applicable, the second deliverable ("Unit of Accounting 2") includes manufacturing services to be provided for any Company materials in an approved product. These services have standalone value and are contingent due to uncertainties on whether an approved product will ever be developed thereby requiring manufacture by the Company at that time. All upfront consideration is allocated to Unit of Accounting 1. Unit of Accounting 2 is determined to be a contingent deliverable at the inception of the collaboration due to the uncertainties surrounding whether an approved product will ever be developed and require manufacturing by the Company. The upfront consideration allocated to Unit of Accounting 1 is recognized over the expected life of the Company's technology platform using a straight-line approach which approximates the period the Company expects to complete its performance obligations. The Company recognizes the reimbursement payments received for research and development services in the period when the services are performed and collection is reasonably assured. At the inception of each collaboration, the Company determines whether any milestone payments are substantive and can be recognized when earned. The milestone payments are typically not considered substantive. Royalties related to product sales will be recognized when earned since payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations. The Company determines whether collaborations and licensing agreements are individually significant for disclosure based on a number of factors, including total revenue recorded by the Company pursuant to collaboration and licensing agreements, collaborators or licensees either consolidated or accounted for using the equity method, or other qualitative factors. Collaboration and licensing revenues generated from consolidated subsidiaries are eliminated in consolidation. The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant collaboration or licensing agreement for the years ended December 31, 2016 , 2015 and 2014 . Year Ended December 31, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 11,529 $ 22,307 $ 33,836 Oragenics, Inc. 1,047 1,705 2,752 Fibrocell Science, Inc. 2,419 3,523 5,942 Genopaver, LLC 273 5,844 6,117 S & I Ophthalmic, LLC — 6,141 6,141 OvaXon, LLC — 2,934 2,934 Intrexon Energy Partners, LLC 2,500 15,052 17,552 Persea Bio, LLC 500 778 1,278 Ares Trading S.A. 6,389 3,803 10,192 Thrive Agrobiotics, Inc. 185 1,529 1,714 Intrexon Energy Partners II, LLC 2,000 1,169 3,169 Exotech Bio, Inc. 417 375 792 Relieve Genetics, Inc. 361 878 1,239 Intrexon T1D Partners, LLC 821 1,087 1,908 AD Skincare, Inc. 241 454 695 Genten Therapeutics, Inc. 122 264 386 CRS Bio, Inc. 57 91 148 Other 5,572 7,504 13,076 Total $ 34,433 $ 75,438 $ 109,871 Year Ended December 31, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 2,855 $ 16,451 $ 19,306 Oragenics, Inc. 5,679 856 6,535 Fibrocell Science, Inc. 6,046 6,133 12,179 Genopaver, LLC 273 3,556 3,829 S & I Ophthalmic, LLC — 4,115 4,115 OvaXon, LLC — 2,540 2,540 Intrexon Energy Partners, LLC 2,500 10,947 13,447 Persea Bio, LLC 500 741 1,241 Ares Trading S.A. 3,933 795 4,728 Thrive Agrobiotics, Inc. 46 220 266 Intrexon Energy Partners II, LLC 167 — 167 Other 10,514 8,954 19,468 Total $ 32,513 $ 55,308 $ 87,821 Year Ended December 31, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 2,577 $ 12,044 $ 14,621 Oragenics, Inc. 1,045 598 1,643 Fibrocell Science, Inc. 1,794 4,398 6,192 Genopaver, LLC 273 1,510 1,783 S & I Ophthalmic, LLC — 2,832 2,832 OvaXon, LLC — 2,799 2,799 Intrexon Energy Partners, LLC 1,875 4,227 6,102 Other 2,061 7,179 9,240 Total $ 9,625 $ 35,587 $ 45,212 The following is a summary of the terms of the Company's significant collaborations and licensing agreements. ZIOPHARM Collaborations In January 2011, the Company entered into an ECC with ZIOPHARM, a related party. Pursuant to the ECC, ZIOPHARM received a license to the Company's technology platform within the field of oncology as defined more specifically in the agreement. Upon execution of the ECC, the Company received 3,636,926 shares of ZIOPHARM's common stock valued at $17,457 as upfront consideration. In addition to the deliverables discussed above, the Company transferred two clinical product candidates to ZIOPHARM that resulted in a separate unit of accounting for which $1,115 of the upfront consideration was allocated and recognized as collaboration revenue in 2011. The remaining $16,342 of upfront consideration was allocated to Unit of Accounting 1 discussed above. The Company was entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 7.495% of ZIOPHARM's outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by ZIOPHARM using the Company's technology ("ZIOPHARM Milestone"). In October 2012, the ZIOPHARM Milestone was achieved and the Company received 3,636,926 shares of ZIOPHARM's common stock valued at $18,330 as milestone consideration. Since the ZIOPHARM Milestone was not substantive, the Company allocated the ZIOPHARM Milestone to the applicable units of accounting and is recognizing it in a manner similar to these units of accounting. The Company receives reimbursement payments for research and development services provided and manufacturing services for Company materials provided to ZIOPHARM during the ECC. Subject to certain expense allocations, ZIOPHARM will pay the Company a percentage of the quarterly net profits derived from the sale of products developed from the ECC, as defined and amended in the agreement. ZIOPHARM is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of product candidates. The term of the ECC commenced in January 2011 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by ZIOPHARM upon 90 days written notice to the Company. In March 2015, in conjunction with the Merck Agreement, the Company and ZIOPHARM amended their existing ECC. The amendment modifies the scope of the ECC in connection with the Merck Agreement and provides that the Company will pay to ZIOPHARM 50% of all payments received for upfront fees, milestones and royalties under the Merck Agreement. In September 2015, the Company entered into its second ECC with ZIOPHARM ("ZIOPHARM ECC 2"). Pursuant to the ECC, ZIOPHARM received a license to the Company's technology platform to develop and commercialize novel biotherapeutics for the treatment of patients with graft-versus-host disease, or GvHD. Upon execution of ZIOPHARM ECC 2, the Company received a technology access fee of $10,000 . The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to ZIOPHARM during the ECC. ZIOPHARM will pay the Company a percentage of quarterly net profits derived from the sale of products developed from ZIOPHARM ECC 2, as defined and amended in the agreement. ZIOPHARM is responsible for funding the further development of ZIOPHARM ECC 2 products towards the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ZIOPHARM ECC 2 commenced in September 2015 and may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by ZIOPHARM upon 90 days written notice to the Company. In June 2016, the Company amended each of its two existing collaboration agreements with ZIOPHARM and as a result the rate of the royalty which the Company is entitled to receive on certain products commercialized pursuant to the agreements was reduced from 50% to 20% . As consideration for execution of the amendments, ZIOPHARM issued the Company 100,000 shares of ZIOPHARM's Series 1 Preferred Stock valued at $120,000 . The Company allocated the consideration received to each ECC based on the cumulative value of upfront and milestone payments previously received pursuant to that ECC. Because the Company has remaining performance obligations under each of the ZIOPHARM ECCs, the Company recorded the initial fair value received as deferred revenue and recognizes this amount straight-line over the remaining performance period for each ZIOPHARM ECC. No other financially significant terms of the ZIOPHARM ECCs were changed as a result of the amendments. See Note 7 for additional discussion of the terms of the preferred stock and the accounting treatment. Oragenics Collaborations In June 2012, the Company entered into an ECC with Oragenics, a publicly traded company focused on becoming the world leader in novel antibiotics against infectious diseases and a related party. Pursuant to the ECC, at the transaction effective date, Oragenics received a license to the Company's technology platform within the field of lantibiotics for the treatment of infectious diseases in humans and companion animals as defined more specifically in the agreement. Upon execution of the ECC, the Company received a technology access fee of 4,392,425 shares of Oragenics' common stock valued at $6,588 as upfront consideration. The Company is entitled to receive additional shares of common stock, or at Oragenics' option, receive a cash payment based upon the fair market value of the shares, upon the separate achievement of certain regulatory milestones of the first product candidate developed from the ECC ("Oragenics ECC 1 Milestones"). The Oragenics ECC 1 Milestones include: (i) 1% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the filing of the first Investigative New Drug Application with the U.S. Food and Drug Administration ("U.S. FDA") for a product candidate created, produced or developed using the Company's technology ("Oragenics ECC 1 Product"); (ii) 1.5% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase II clinical trial of an Oragenics ECC 1 Product; (iii) 2% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase III clinical trial of an Oragenics ECC 1 Product; (iv) 2.5% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the first New Drug Application or Biologics License Application with the U.S. FDA for an Oragenics ECC 1 Product, or alternatively the first equivalent regulatory filing with a foreign agency; and (v) 3% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the granting of the first regulatory approval of an Oragenics ECC 1 Product. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during the ECC. Oragenics will pay the Company 25% of the quarterly profits derived from the sale of products developed from the ECC, as defined in the agreement. Oragenics is responsible for funding the further development of lantibiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced in June 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company. In September 2013, the Company entered into its second ECC with Oragenics ("Oragenics ECC 2"). Pursuant to Oragenics ECC 2, at the transaction effective date, Oragenics received a license to the Company's technology platform to develop and commercialize probiotics, specifically the direct administration to humans of genetically modified probiotics for the treatment of diseases of the oral cavity, throat, sinus and esophagus as defined more specifically in the agreement. Upon execution of Oragenics ECC 2, the Company received a technology access fee of 1,348,000 shares of Oragenics' common stock valued at $3,503 and a $1,956 convertible promissory note maturing on or before December 31, 2013 as upfront consideration. Prior to the maturity date, Oragenics had the right to convert the promissory note into shares of Oragenics' common stock subject to its shareholders' approval. The conversion price was equal to the closing price of Oragenics' common stock on the last trading day immediately prior to the date of conversion. In December 2013, Oragenics converted the promissory note into 698,241 shares of Oragenics' common stock. In September 2015, Oragenics and the Company mutually agreed to terminate Oragenics ECC 2 and accordingly, the Company recognized the remaining balance of the deferred revenue associated with the upfront payment. In June 2015, the Company entered into its third ECC with Oragenics ("Oragenics ECC 3"). Pursuant to Oragenics ECC 3, at the transaction effective date, Oragenics received a license to the Company's technology platform within the field of biotherapeutics for use in certain treatments of oral mucositis and other diseases and conditions of the oral cavity, throat, and esophagus. Upon execution of Oragenics ECC 3, the Company received a technology access fee of a $5,000 convertible promissory note maturing on or before December 31, 2015 as upfront consideration. Prior to the maturity date, Oragenics had the right to convert the promissory note into shares of Oragenics' common stock, subject to its shareholders' approval. In December 2015, Oragenics converted the promissory note into 3,381,004 shares of Oragenics' common stock. The Company is also entitled to up to $22,000 of potential payments for development and commercial milestones for each Oragenics product developed from Oragenics ECC 3 and up to $10,000 of potential one-time payments for certain regulatory milestones under Oragenics ECC 3. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during Oragenics ECC 3. Oragenics will pay the Company royalties as a percentage in the low-teens of net sales derived from the sale of products developed from Oragenics ECC 3, as defined in the agreement. Oragenics is responsible for funding the further development of Oragenics ECC 3 products towards the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of Oragenics ECC 3 commenced in June 2015 and may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company. Fibrocell Science Collaborations In October 2012, the Company entered into an ECC ("Fibrocell ECC 1") with Fibrocell Science, Inc. ("Fibrocell"), a publicly traded cell and gene therapy company focused on diseases affecting the skin and connective tissue and a related party. Pursuant to the ECC, at the transaction effective date, Fibrocell received a license to the Company's technology platform to develop and commercialize genetically modified and non-genetically modified autologous fibroblasts and autologous dermal cells in the United States of America. Upon execution of the ECC, the Company received a technology access fee of 1,317,520 shares of Fibrocell's common stock valued at $7,576 as upfront consideration. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Fibrocell during the ECC. On a quarterly basis, Fibrocell will pay the Company royalties of 7% of net sales up to $25,000 and 14% of net sales above $25,000 on each product developed from the ECC, as defined in the agreement. If Fibrocell uses the Company's technology platform to improve the production of a current or new Fibrocell product not developed from the ECC, Fibrocell will pay the Company quarterly royalties equal to 33% of the cost of goods sold savings generated by the improvement, as defined in the agreement. Fibrocell is responsible for conducting preclinical and clinical development of product candidates associated with Fibrocell ECC 1, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced in October 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Fibrocell upon 90 days written notice to the Company. In June 2013, the Company and Fibrocell entered into an amendment to the Fibrocell ECC 1. The amendment expanded the field of use defined in the ECC agreement. Under the terms of the amendment to the Fibrocell ECC 1, the Company received 1,243,781 shares of Fibrocell's common stock valued at $7,612 as a supplemental technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting and is recognizing it consistent with the unit of accounting. In January 2014, the Company and Fibrocell entered into a second amendment to the Fibrocell ECC 1. The second amendment further expanded the field of use defined in the ECC agreement. Under the terms of the second amendment to the Fibrocell ECC 1, the Company received 1,024,590 shares of Fibrocell's common stock valued at $5,225 as a supplemental technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting. In September 2015, Fibrocell and the Company mutually agreed to terminate the second amendment to the ECC and accordingly, the Company recognized the remaining balance of deferred revenue associated with the related upfront payment. In December 2015, the Company entered into a second ECC with Fibrocell ("Fibrocell ECC 2"). Pursuant to the ECC, at the transaction effective date, Fibrocell received a license to the Company's technology platform to develop and commercialize genetically-modified fibroblasts to treat chronic inflammatory and degenerative diseases of the joint, including arthritis and related conditions. Upon execution of the ECC, the Company received a technology access fee of $10,000 . The Company is also entitled to (i) up to $30,000 of potential one-time payments for certain development and regulatory milestones for the first product developed under Fibrocell ECC 2, (ii) up to $30,000 of potential payments for certain regulatory milestones for each additional product developed under Fibrocell ECC 2, and (iii) up to $22,500 of potential payments for certain sales milestones for each product developed under Fibrocell ECC 2. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Fibrocell during the ECC. Fibrocell will pay the Company royalties as a percentage in the low double-digits of net sales derived from the sale of products developed from Fibrocell ECC 2, as defined in the agreement. Fibrocell is responsible for conducting preclinical and clinical development of product candidates associated with Fibrocell ECC 2, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced in December 2015 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Fibrocell upon 90 days written notice to the Company. Genopaver Collaboration In March 2013, the Company entered into an ECC with Genopaver, LLC ("Genopaver"), an affiliate of Third Security and a related party. Genopaver was formed for the purpose of entering into the ECC and developing and commercializing products in the field of the fermentative production of alkaloids through genetically modified cell-lines and substrate feeds for use as active pharmaceutical ingredients or as commercially sold intermediates in the manufacture of active pharmaceutical ingredients. Upon execution of the ECC, the Company received a technology access fee of $3,000 as upfront consideration. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Genopaver will pay the Company royalties as a percentage in the lower-double digits on the quarterly gross profits of product sales from products developed under the ECC, as defined in the agreement. Genopaver is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in March 2013 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Genopaver upon 90 days written notice to the Company. AquaBounty Collaboration In February 2013, the Company entered into an ECC with AquaBounty, a majority-owned consolidated subsidiary. The Company will be reimbursed for research and development services as provided for in the ECC agreement. In the event of product sales from a product developed from the ECC, the Company will receive 16.66% of quarterly gross profits for each product, as defined in the agreement. All revenues and expenses related to this ECC are eliminated in consolidation. S & I Ophthalmic Collaboration In September 2013, the Company entered into an ECC with S & I Ophthalmic, a joint venture between the Company and Sun Pharmaceutical Subsidiary, an indirect subsidiary of Sun Pharmaceutical, an international specialty pharmaceutical company focused on chronic diseases, and a related party. The ECC grants S & I Ophthalmic an exclusive license to the Company's technology platform to develop and commercialize therapies in humans for the treatment of ocular diseases defined more specifically in the agreement. The Company will be reimbursed for research and development services pursuant to the agreement and manufacturing services for Company materials provided to S & I Ophthalmic during the ECC. Subject to certain expense allocations, S & I Ophthalmic will pay the Company royalties with percentages ranging from mid-single digits and above of the net sales derived from the sale of products developed under the ECC, as defined in the agreement. The term of the ECC commenced in September 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by S & I Ophthalmic upon 90 days written notice to the Company. BioPop Collaboration In October 2013, the Company entered into an ECC with BioPop, a majority-owned consolidated subsidiary. The ECC grants BioPop an exclusive license to the Company's technology platform to develop and commercialize artwork, children's toys and novelty goods that are derived from living organisms or are enabled by synthetic biology. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The Company is entitled to royalties in the mid-single digits as a percentage of the net product sales of a product developed under the ECC, as defined in the agreement. All revenues and expenses related to this ECC are eliminated in consolidation. OvaXon Collaboration In December 2013, the Company entered into an ECC with OvaXon, a joint venture between the Company and OvaScience, a life sciences company focused on infertility treatments, and a related party. The ECC grants OvaXon an exclusive license to the Company's technology platform to create new applications for improving human and animal health. OvaScience also licensed certain technology to OvaXon pursuant to a separate license agreement. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The term of the ECC commenced in December 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by OvaXon upon 90 days written notice to the Company. Intrexon Energy Partners Collaboration In March 2014, the Company entered into an ECC with Intrexon Energy Partners, a joint venture between the Company and certain investors and a related party. The ECC grants Intrexon Energy Partners an exclusive license to the Company's technology platform to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. Upon execution of the ECC, the Company received a technology access fee of $25,000 as upfront consideration. The Company will be reimbursed for research and development services as provided for in the ECC agreement. The term of the ECC commenced in March 2014 and continues until March 2034 unless terminated prior to that date by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Intrexon Energy Partners upon 90 days written notice to the Company. Persea Bio Collaboration In December 2014, the Company entered into an ECC with Persea Bio, LLC ("Persea Bio"), an affiliate of Third Security and a related party. Persea Bio was formed for the purpose of entering into the ECC and developing and commercializing a food program, as defined in the agreement. Upon effectiveness of the ECC, the Company received a technology access fee of $5,000 as upfront consideration. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Persea Bio will pay the Company royalties as a percentage in the lower-double digits on the quarterly gross profits of product sales from products derived from the ECC, as defined in the agreement. Persea Bio is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in December 2014 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Persea Bio upon 90 days written notice to the Company. Merck Licensing Agreement In March 2015, the Company signed a worldwide License and Collaboration Agreement ("Merck Agreement") with Ares Trading S.A. ("Ares Trading"), a subsidiary of the biopharmaceutical business of Merck KGaA, and ZIOPHARM through which the parties established a collaboration for the research and development and commercialization of certain products for the prophylactic, therapeutic, palliative or diagnostic use for cancer in humans. Pursuant to the Merck Agreement, the Company received a technology access fee of $115,000 as upfront consideration, of which $57,500 was paid to ZIOPHARM in accordance with the terms of the agreement. Upon the selection of the first two targets by Ares Trading, the Company is entitled to receive $10,000 payable in equal quarterly installments over two years, of which $3,750 is included in trade receivables on the accompanying consolidated balance sheet as of December 31, 2016 . The Company is entitled to receive a further $5,000 for each additional target selected by Ares Trading. The Company is also entitled to up to $413,000 of potential payments for substantive and non-substantive development and commercial milestones for each product, and royalties ranging from the lower-single digits to the low-teens of the net sales derived from the sale of products developed under the Merck Agreement. The Company may also receive up to $50,000 of further cash fees upon certain technical milestones as provided for in the agreement. The term of the Merck Agreement commenced in May 2015 and may be terminated by either party in the event of a material breach as defined in the agreement and may be terminated voluntarily by Ares Trading upon 90 days written notice to the Company. The Company will pay to ZIOPHARM 50% of all payments received for upfront fees, milestones, and royalties under the Merck Agreement. Thrive Agrobiotics Collaboration In September 2015, the Company entered into an ECC with Thrive Agrobiotics, Inc. ("Thrive Agrobiotics"), an affiliate of Harvest and a related party. Thrive Agrobiotics was formed for the purpose of entering into the ECC and developing and commercializing products to improve the overall growth and feed efficiency in piglets. Upon execution of the ECC, the Company received a technology access fee in the form of equity in Thrive Agrobiotics valued at $1,667 as upfront consideration. The Company is also entitled to up to $5,500 of potential payments for development and commercial milestones for each product developed under the ECC. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Thrive Agrobiotics will pay the Company royalties as a percentage in the lower-double digits on the quarterly gross profits of product sales from products developed under the ECC, as defined in the agreement. Thrive Agrobiotics is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in September 2015 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Thrive Agrobiotics upon 90 days written notice to the Company. Intrexon Energy Partners II Collaboration In December 2015, the Company entered into an ECC with Intrexon Energy Partners II, a joint venture between the Company and certain investors and a related party. Pursuant to the ECC, Intrexon Energy Partners II received an exclusive license to the Company's technology platform to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of 1,4-butanediol (BDO), a key chemical intermediate that is used to manufacture spandex, polyurethane, plastics, and polyester. Upon execution of the ECC, the Company received a technology access fee of $18,000 and is entitled to reimbursement of research and development services as provided for in the ECC agreement. The term of the ECC commenced in December 2015 and continues until December 2035; termination prior to that date may be initiated (i) by either party in the event of certain material breaches defined in the agreement or (ii) may

Short-term and Long-term Invest

Short-term and Long-term Investments	12 Months Ended
	Dec. 31, 2016
Investments, Debt and Equity Securities [Abstract]
Short-term and Long-term Investments	Short-term and Long-term Investments The Company's investments are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 180,412 $ 5 $ (94 ) $ 180,323 Certificates of deposit 272 — — 272 Total $ 180,684 $ 5 $ (94 ) $ 180,595 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 208,223 $ 21 $ (540 ) $ 207,704 Certificates of deposit 271 — — 271 Total $ 208,494 $ 21 $ (540 ) $ 207,975 For more information on the Company's method for determining the fair value of its assets, see Note 2 – "Fair Value of Financial Instruments". The estimated fair value of available-for-sale investments classified by their contractual maturities as of December 31, 2016 was: Due within one year $ 174,602 After one year through two years 5,993 Total $ 180,595 Changes in market interest rates and bond yields cause certain investments to fall below their cost basis, resulting in unrealized losses on investments. The unrealized losses of the Company's investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and have been in a loss position for less than 12 months. As of December 31, 2016 and 2015 , the Company did not consider any of its investments to be other-than-temporarily impaired. When evaluating its investments for other-than-temporary impairment, the Company reviews factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, the Company's ability and intent to hold the security and whether it is more likely than not that it will be required to sell the investment before recovery of its cost basis.

Investment in Preferred Stock

Investment in Preferred Stock	12 Months Ended
	Dec. 31, 2016
Investment in Preferred Stock [Abstract]
Investment In Preferred Stock	Investment in Preferred Stock In June 2016, the Company received 100,000 shares of ZIOPHARM's Series 1 Preferred Stock (the "Preferred Shares"), with a per share stated value of $1,200 , as consideration for amending their two previously existing ECC agreements (Note 5 ). A summary of the terms of the Preferred Shares follows. Conversion. The Preferred Shares shall automatically convert into shares of ZIOPHARM common stock upon the date the first approval in the United States of (i) a ZIOPHARM product, as defined in and developed under one of the ECC agreements, or (ii) a product, as defined and developed under the License and Collaboration Agreement with Ares Trading and ZIOPHARM, is publicly announced (the "Conversion Event Date"). The Preferred Shares shall convert into a number of shares of ZIOPHARM common stock equal to the stated value of such Preferred Share, divided by the greater of: (i) the volume weighted average closing price of ZIOPHARM's common stock over the twenty trading days ending on the Conversion Event Date or (ii) $1.00 . The number of converted shares is subject to certain limitations defined in the amended and restated Certificate of Designation, Preferences, and Rights of Series 1 Preferred Stock (the "A&R Certificate of Designation"). Dividend Rights. The Company shall receive a monthly dividend, payable in additional Preferred Shares, equal to $12.00 per Preferred Share held per month divided by the stated value of the Preferred Shares, which is referred to as the PIK Dividend. For any Preferred Shares that are not converted on the Conversion Event Date, the rate of PIK Dividend on these unconverted Preferred Shares will automatically increase from $12.00 to $24.00 per Preferred Share per month. Voting Rights . The Preferred Shares do not have any voting rights except for certain protective voting rights defined in the A&R Certificate of Designation. Liquidation Rights. In the event of any voluntary or involuntary liquidation, dissolution or winding up of ZIOPHARM or a deemed liquidation event, as defined in the A&R Certificate of Designation, including a change of control or the sale, lease transfer or exclusive license of all or substantially all of ZIOPHARM's assets, the holders of the Preferred Shares shall be entitled to receive a portion of all funds to be distributed in proportion to the holders' proportionate share of ZIOPHARM's common stock on an as-converted to common stock basis (the "Series 1 Liquidation Amount"). For purposes of calculating the Series 1 Liquidation Amount, if such liquidation event occurs prior to the Conversion Event Date, each Preferred Share shall be deemed to be convertible into the number of shares of ZIOPHARM's common stock equal to (i) the stated value of each Preferred Share, divided by (ii) the volume weighted average price of ZIOPHARM's common stock for the twenty day period ending on the date of the public announcement of the liquidation event. In addition, ZIOPHARM may elect to redeem the Preferred Shares in connection with or following a deemed liquidation event at a price per share equal to the Series 1 Liquidation Amount. The Company elected the fair value option to account for its investment in ZIOPHARM preferred stock (the "investment in preferred stock"). The investment in preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Preferred Shares are not traded on a public exchange. The fair value of the investment in preferred stock was estimated using a probability-weighted expected return ("PWERM") model. The key inputs used in the PWERM model were (i) estimating the future returns for conversion of the Preferred Shares for both product approval and a change in control of ZIOPHARM (the "conversion events") using market data of the change in value for guideline companies as a result of these conversion events; (ii) estimating the expected date and likelihood of each conversion event; and (iii) discounting these estimated future returns using a discount rate for the Preferred Shares considering industry debt issuances originated by public funds and venture capital rates of return. A significant change in unobservable inputs discussed above could result in a significant impact to the fair value of the Company's investment in preferred stock. During the year ended December 31, 2016 , the Company received 6,184 shares of additional Preferred Shares and recognized $7,421 of dividend income in the accompanying consolidated statement of operations. The changes in the Level 3 investment during the year ended December 31, 2016 were as follows: 2016 Beginning balance $ — Receipt of Preferred Shares as consideration for amendments to collaboration agreements 120,000 Additional Preferred Shares received as dividend income 7,421 Unrealized appreciation in the fair value of the investment in preferred stock 2,124 Ending balance $ 129,545

Fair Value Measurements

Fair Value Measurements	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The carrying amount of cash and cash equivalents, restricted cash, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments. The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, as of December 31, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) December 31, Assets U.S. government debt securities $ — $ 180,323 $ — $ 180,323 Equity securities 15,544 7,978 — 23,522 Preferred stock — — 129,545 129,545 Other — 1,917 — 1,917 Total $ 15,544 $ 190,218 $ 129,545 $ 335,307 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, as of December 31, 2015 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) December 31, Assets U.S. government debt securities $ — $ 207,704 $ — $ 207,704 Equity securities 65,850 17,803 — 83,653 Other — 405 — 405 Total $ 65,850 $ 225,912 $ — $ 291,762 The method used to estimate the fair value of the Level 1 assets in the tables above is based on observable market data as these equity securities are publicly-traded. The method used to estimate the fair value of the Level 2 short-term and long-term investments in the tables above is based on professional pricing sources for identical or comparable instruments, rather than direct observations of quoted prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability. The method used to estimate the fair value of the Level 3 asset is discussed in Note 7 . There were no transfers between levels of the fair value hierarchy during the year ended December 31, 2016 . The carrying values of the Company's long term debt approximates fair value due to the length of time to maturity and/or the existence of interest rates that approximate prevailing market rates. Significant financial liabilities measured on a recurring basis were $2,081 as of December 31, 2016 . The Company accounted for the contingent consideration liability to the members of Old EnviroFlight by recording its fair value as a liability on the date of the asset acquisition (Note 4 ) whereby the regulatory and commercial milestones were valued using a probability-weighted discounted cash flow model using discount rates reflecting the time value of money and additional risk inherent in meeting the milestones. These fair value measurements were based on significant inputs not observable in the market and thus represented a Level 3 measurement. A significant change in unobservable inputs discussed above could result in a significant impact to the fair value of the Company's contingent consideration liability. The contingent consideration liability is remeasured to fair value at each reporting date until the contingency is resolved, and those changes in fair value are recognized in earnings. The changes in the fair value of the Level 3 liability during the year ended December 31, 2016 were as follows: 2016 Beginning balance $ — Fair value of contingent consideration assumed in asset acquisition 3,660 Payment of contingent consideration (Note 4) (1,583 ) Change in fair value of contingent consideration recognized in selling, general and administrative expenses 4 Ending balance $ 2,081 Financial liabilities measured on a recurring basis were not significant as of December 31, 2015 .

Inventory

Inventory	12 Months Ended
	Dec. 31, 2016
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: December 31, 2016 2015 Supplies, embryos and other production materials $ 1,835 $ 1,402 Work in process 5,466 6,290 Livestock 11,752 16,907 Feed 2,086 1,964 Total inventory $ 21,139 $ 26,563

Property, Plant and Equipment,

Property, Plant and Equipment, Net	12 Months Ended
	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Property, Plant and Equipment, Net	Property, Plant and Equipment, Net Property, plant and equipment consist of the following: December 31, 2016 2015 Land and land improvements $ 11,324 $ 9,119 Buildings and building improvements 8,123 7,520 Furniture and fixtures 2,176 1,283 Equipment 44,392 36,016 Leasehold improvements 15,105 6,888 Breeding stock 3,893 — Computer hardware and software 6,844 5,960 Construction and other assets in progress 6,865 2,193 98,722 68,979 Less: Accumulated depreciation and amortization (34,050 ) (26,240 ) Property, plant and equipment, net $ 64,672 $ 42,739 Depreciation expense was $9,387 , $7,872 and $6,178 for the years ended December 31, 2016 , 2015 and 2014 , respectively.

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, Net	12 Months Ended
	Dec. 31, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets, Net	Goodwill and Intangible Assets, Net The changes in the carrying amount of goodwill for the years ended December 31, 2016 and 2015 , are as follows: 2016 2015 Beginning balance $ 165,169 $ 101,059 Acquisitions — 67,403 Foreign currency translation adjustments (7,994 ) (3,293 ) Ending balance $ 157,175 $ 165,169 No goodwill or accumulated impairment losses existed as of December 31, 2016 and 2015 . Intangible assets consist of the following as of December 31, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how 15.9 $ 236,401 $ (29,748 ) $ 206,653 Customer relationships 6.5 10,700 (4,672 ) 6,028 Trademarks 9.3 6,800 (1,792 ) 5,008 Covenant not to compete 2.0 370 (339 ) 31 In-process research and development 7,895 — 7,895 Total $ 262,166 $ (36,551 ) $ 225,615 Intangible assets consist of the following as of December 31, 2015 : Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how $ 157,411 $ (17,775 ) $ 139,636 Customer relationships 10,700 (2,739 ) 7,961 Trademarks 6,800 (1,018 ) 5,782 Covenant not to compete 384 (160 ) 224 In-process research and development 93,932 — 93,932 Total $ 269,227 $ (21,692 ) $ 247,535 The balance of in-process research and development as of December 31, 2016 includes certain in-process research and development technology acquired in the Company's Oxitec acquisition and amortization will begin once certain regulatory approvals have been obtained for the in-process programs. See Note 3 for additional discussion of in-process research and development technologies placed in service during 2016 . Amortization expense was $15,185 , $9,871 and $4,237 for the years ended December 31, 2016 , 2015 and 2014 , respectively. Total amortization expense is estimated to be $18,002 for 2017 , $17,391 for 2018 , $17,068 for 2019 , $16,648 for 2020 , $16,431 for 2021 , and $132,180 for the cumulative period thereafter.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Lines of Credit and Long Term Debt	Lines of Credit and Long Term Debt Lines of Credit Trans Ova has a $6,000 revolving line of credit with First National Bank of Omaha which matures on May 1, 2017. The line of credit bears interest at the greater of 2.95% above the London Interbank Offered Rate or 3.00% and the actual rate was 3.57% as of December 31, 2016 . As of December 31, 2016 , there was an outstanding balance of $322 . The amount available under the line of credit is based on eligible accounts receivable and inventory up to the maximum principal amount. The line of credit is collateralized by certain of Trans Ova's assets and contains certain restricted covenants that include maintaining minimum tangible net worth, maximum allowable annual capital expenditures and working capital. Trans Ova was in compliance with these covenants as of December 31, 2016 . Exemplar has a $700 revolving line of credit with American State Bank which matures on October 30, 2017. The line of credit bears interest at 4.50% per annum. As of December 31, 2016 , there was an outstanding balance of $498 . Long Term Debt Long term debt consists of the following: December 31, 2016 2015 Notes payable $ 5,453 $ 6,477 Royalty-based financing 1,896 1,807 Other 599 244 Long term debt 7,948 8,528 Less current portion 386 930 Long term debt, less current portion $ 7,562 $ 7,598 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $5,246 as of December 31, 2016 . Trans Ova pays monthly installments of $39 , which includes interest at 3.95% . The note payable is collateralized by certain of Trans Ova's real estate and non-real estate assets. Exemplar has notes payable with outstanding principal balances totaling $207 as of December 31, 2016 . Exemplar pays monthly installments ranging from $1 to $4 with interest rates ranging from 0% to 3% . These notes mature from September 2018 to May 2020 and are collateralized by certain of Exemplar's real estate or letters of credit of certain of its members. In August 2016, AquaBounty obtained a loan from Finance PEI ("FPEI"), a Canadian government-owned corporation. As of December 31, 2016 , there was an outstanding balance of $527 . AquaBounty pays monthly installments of $4 , which includes interest of 4% , with a balloon payment due in July 2021. The loan is collateralized by certain of AquaBounty's assets. AquaBounty has a royalty-based financing grant from the Atlantic Canada Opportunities Agency ("ACOA"), a Canadian government agency, to provide funding of a research and development project. The total amount available under the award was $2,136 , which AquaBounty claimed over a five year period. All amounts claimed by AquaBounty must be repaid in the form of a 10% royalty on any products commercialized out of this research and development project until fully paid. Because the timing of commercialization is subject to additional regulatory considerations, the timing of repayment is uncertain. As of the acquisition date in March 2013, AquaBounty had claimed $1,952 of the available funds and this amount was recorded at its acquisition date fair value of $1,107 . The Company accretes the difference of $845 between the face value of amounts drawn and the acquisition date fair value over the expected period of repayment. Since the acquisition date, AquaBounty has claimed the remaining balance available under the grant, resulting in total long term debt of $1,896 as of December 31, 2016 . Future maturities of long term debt are as follows: 2017 $ 386 2018 408 2019 365 2020 336 2021 765 Thereafter 3,792 Total $ 6,052 The AquaBounty royalty-based financing grant is not included in the table above due to the uncertainty of the timing of repayment.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The components of loss before income taxes are presented below: Year Ended December 31, 2016 2015 2014 Domestic $ (157,067 ) $ (69,287 ) $ (83,256 ) Foreign (37,084 ) (17,691 ) (2,463 ) Loss before income taxes $ (194,151 ) $ (86,978 ) $ (85,719 ) The components of income tax expense (benefit) are presented below: Year Ended December 31, 2016 2015 2014 U.S. federal income taxes: Current $ (17 ) $ 22 $ — Deferred 1,396 1,732 — Foreign income taxes: Current (393 ) (123 ) (103 ) Deferred (5,177 ) (1,003 ) — State income taxes: Deferred 314 388 — Income tax expense (benefit) $ (3,877 ) $ 1,016 $ (103 ) Income tax expense (benefit) for the years ended December 31, 2016 , 2015 and 2014 differed from amounts computed by applying the applicable U.S. federal corporate income tax rate of 34% to loss before income taxes as a result of the following: 2016 2015 2014 Computed statutory income tax benefit $ (66,011 ) $ (29,573 ) $ (29,144 ) State and provincial income tax benefit, net of federal income taxes (7,905 ) (3,157 ) (3,544 ) Nondeductible stock based compensation 3,321 3,182 1,386 Nondeductible officer compensation — 2,433 — Contribution of services by shareholder — — 677 Research and development tax incentives (6,350 ) (348 ) 258 Acquisition and internal restructuring transaction costs 571 883 — Enacted change in tax rates — (961 ) — U.S.-foreign rate differential 3,463 620 — Other, net 1,485 (98 ) 1,503 (71,426 ) (27,019 ) (28,864 ) Change in valuation allowance for deferred tax assets 67,549 28,035 28,761 Total income tax expense (benefit) $ (3,877 ) $ 1,016 $ (103 ) The tax effects of temporary differences that comprise the deferred tax assets and liabilities as of December 31, 2016 and 2015 , are as follows: 2016 2015 Deferred tax assets Allowance for doubtful accounts $ 1,676 $ 1,056 Inventory 447 967 Equity securities and investments in affiliates 31,729 10,413 Accrued liabilities and long-term debt 4,168 4,585 Stock-based compensation 8,460 7,223 Deferred revenue 68,056 31,637 Research and development tax credits 10,396 9,113 Net operating and capital loss carryforwards 144,502 135,633 Total deferred tax assets 269,434 200,627 Less: Valuation allowance 256,165 190,174 Net deferred tax assets 13,269 10,453 Deferred tax liabilities Property, plant and equipment 406 160 Intangible assets 29,870 32,095 Total deferred tax liabilities 30,276 32,255 Net deferred tax liabilities $ (17,007 ) $ (21,802 ) Activity within the valuation allowance for deferred tax assets during the years ended December 31, 2016 , 2015 and 2014 was as follows: 2016 2015 2014 Valuation allowance at beginning of year $ 190,174 $ 161,660 $ 131,985 Increase (decrease) in valuation allowance as a result of Mergers and acquisitions, net (1,416 ) 1,228 914 Current year operations 67,549 28,035 28,761 Foreign currency translation adjustment (142 ) (749 ) — Valuation allowance at end of year $ 256,165 $ 190,174 $ 161,660 In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected future taxable income and tax planning strategies in making this assessment. Due to the Company and its subsidiaries' histories of net losses incurred from inception, any corresponding net domestic and certain foreign deferred tax assets have been fully reserved as the Company and its subsidiaries cannot sufficiently be assured that these deferred tax assets will be realized. The components of the deferred tax assets and liabilities as of the date of the mergers and acquisitions by the Company prior to consideration of the valuation allowance are substantially similar to the components of deferred tax assets presented herein. The Company's past issuances of stock and mergers and acquisitions have resulted in ownership changes as defined in Section 382 of the Internal Revenue Code of 1986, as amended ("Section 382"). As a result, utilization of portions of the net operating losses may be subject to annual limitations. As of December 31, 2016 , approximately $15,100 of the Company's domestic net operating losses generated prior to 2008 are limited by Section 382 to annual usage limits of approximately $1,500 . As of December 31, 2016 , approximately $18,600 of the Company's domestic net operating losses were inherited via acquisition and are limited based on the value of the target at the time of the transaction. As of December 31, 2016 , the Company has loss carryforwards for U.S. federal income tax purposes of approximately $252,971 available to offset future taxable income and federal and state research and development tax credits of $7,514 , prior to consideration of annual limitations that may be imposed under Section 382. These carryforwards will begin to expire in 2022 . Of these loss carryforwards, $44,929 relate to benefits from stock compensation deductions that will be recorded as a component of paid-in capital when realized. The Company's direct foreign subsidiaries have foreign loss carryforwards of approximately $119,155 , most of which do not expire. The Company does not record deferred taxes on the undistributed earnings of its direct foreign subsidiaries because it does not expect the temporary differences related to those unremitted earnings to reverse in the foreseeable future. As of December 31, 2016 , the Company's direct foreign subsidiaries had accumulated deficits of approximately $27,885 . Future distributions of accumulated earnings of the Company's direct foreign subsidiaries may be subject to U.S. income and foreign withholding taxes. The Company does not file a consolidated income tax return with AquaBounty or BioPop. As of December 31, 2016 , AquaBounty has loss carryforwards for federal and foreign income tax purposes of approximately $22,215 and $12,925 , respectively, and foreign tax credits of approximately $2,428 available to offset future taxable income, prior to consideration of annual limitations that may be imposed under Section 382 or analogous foreign provisions. These carryforwards will begin to expire in 2018 . As a result of the Company's ownership in AquaBounty passing 50% in 2013, an annual Section 382 of approximately $900 per year will apply to domestic losses and credits carried forward by AquaBounty from prior years, which are also subject to prior Section 382 limitations. As of December 31, 2016 , BioPop had loss carryforwards of approximately $1,402 for federal income tax purposes available to offset future taxable income. The Company and its subsidiaries do not have material unrecognized tax benefits as of December 31, 2016 . The Company does not anticipate significant changes in the amount of unrecognized tax benefits in the next 12 months. The Company's tax returns for years 2004 and forward are subject to examination by federal or state tax authorities due to the carryforward of unutilized net operating losses and research and development tax credits.

Shareholders' Equity

Shareholders' Equity	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Shareholders' Equity	Shareholders' Equity Issuances of Common Stock In August 2015, the Company closed a public offering of 5,609,756 shares of its common stock, the aggregate proceeds of which were $218,193 , net of underwriting discounts of $11,500 and offering expenses paid by the Company of approximately $306 , all of which were capitalized. In January 2015, the Company closed a public offering of 4,312,500 shares of its common stock, including 555,556 shares of common stock purchased by affiliates of Third Security. The aggregate proceeds of the offering were $110,041 , net of underwriting discounts and commissions of $6,086 and offering expenses paid by the Company of approximately $311 , all of which were capitalized. In March 2014 and concurrent with the formation of Intrexon Energy Partners, the Company entered into securities purchase agreements with each of the IEP Investors in Intrexon Energy Partners for the private placement of 972,004 shares of the Company's common stock for gross proceeds of $25,000 . Each IEP Investor purchased an amount proportionate to its investment in Intrexon Energy Partners, including 243,001 shares, or $6,250 , purchased by an affiliate of Third Security. Dividend to Shareholders In June 2015, the Company distributed to its shareholders 17,830,305 shares of ZIOPHARM common stock, representing all of the equity interests of ZIOPHARM held by the Company at the time of the distribution and resulting in a realized gain of $81,401 . The distribution constituted a dividend to shareholders of record as of June 4, 2015. In connection with the distribution, pursuant to the terms of the Company's equity incentive plans, the conversion terms of all outstanding options for shares of the Company's common stock as of June 4, 2015 were adjusted to reflect the value of the distribution with respect to shares of the Company's common stock by decreasing the exercise prices and increasing the number of shares. This adjustment resulted in 312,795 additional shares at a weighted average exercise price of $25.40 . Components of Accumulated Other Comprehensive Loss The components of accumulated other comprehensive loss are as follows: December 31, 2016 2015 Unrealized loss on investments $ (89 ) $ (519 ) Loss on foreign currency translation adjustments (36,113 ) (12,233 ) Total accumulated other comprehensive loss $ (36,202 ) $ (12,752 )

Share-Based Payments

Share-Based Payments	12 Months Ended
	Dec. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Share-Based Payments	Share-Based Payments The Company records the fair value of stock options issued to employees and non-employees as of the grant date as stock-based compensation expense. Stock-based compensation expense for employees and non-employees is recognized over the requisite service period, which is typically the vesting period. Stock-based compensation costs included in the consolidated statements of operations are presented below: Year Ended December 31, 2016 2015 2014 Cost of products $ 81 $ 95 $ 14 Cost of services 274 354 142 Research and development 9,251 8,614 4,817 Selling, general and administrative 32,596 29,604 16,876 Total $ 42,202 $ 38,667 $ 21,849 Intrexon Stock Option Plans In April 2008, Intrexon adopted the 2008 Equity Incentive Plan (the "2008 Plan") for employees and nonemployees pursuant to which Intrexon's board of directors granted share based awards, including stock options, to officers, key employees and nonemployees. Upon the effectiveness of the 2013 Omnibus Incentive Plan (the "2013 Plan"), no new awards may be granted under the 2008 Plan. As of December 31, 2016 , there were 562,951 stock options outstanding under the 2008 Plan. Intrexon adopted the 2013 Plan for employees and nonemployees pursuant to which Intrexon's board of directors may grant share based awards, including stock options and shares of common stock, to employees, officers, consultants, advisors, and nonemployee directors. The 2013 Plan became effective upon the closing of the of the Company's initial public offering in August 2013, and as of December 31, 2016 , there were 16,000,000 shares authorized for issuance under the 2013 Plan, of which 10,077,432 stock options were outstanding and 4,291,530 shares were available for grant. As of December 31, 2016 , an additional 1,000,000 options were issued and outstanding outside the 2008 Plan and 2013 Plan. These options were awarded as an inducement grant to an executive officer in accordance with New York Stock Exchange Rule 303A.08 and are generally subject to the same terms and conditions as awards granted under the 2013 Plan. Stock options may be granted with an exercise price equal to or greater than the stock's fair market value at the date of grant. Stock options may be granted with an exercise price less than the stock's fair market value at the date of grant if the stock options are replacement options in accordance with certain U.S. Treasury regulations. Virtually all stock options have ten -year terms and vest four years from the date of grant. Stock option activity under Intrexon's award plans was as follows for the periods presented: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2013 2,840,648 $ 8.27 7.75 Granted 7,655,050 27.51 Exercised (315,964 ) (4.80 ) Forfeited (1,855,578 ) (24.00 ) Expired (612 ) (7.12 ) Balances at December 31, 2014 8,323,544 22.59 8.64 Granted 5,051,500 45.82 Adjustment due to dividend (Note 14) 312,795 25.40 Exercised (1,029,291 ) (15.16 ) Forfeited (1,610,335 ) (26.75 ) Expired (4,685 ) (28.29 ) Balances at December 31, 2015 11,043,528 32.66 8.49 Granted 4,644,860 29.39 Exercised (1,210,840 ) (15.83 ) Forfeited (2,760,809 ) (40.34 ) Expired (76,356 ) (37.81 ) Balances at December 31, 2016 11,640,383 31.25 8.21 Exercisable at December 31, 2016 3,418,035 28.09 6.88 Vested and Expected to Vest at December 31, 2016(1) 10,019,307 31.04 8.08 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures. Total unrecognized compensation costs related to unvested awards as of December 31, 2016 , 2015 and 2014 were $94,038 , $113,655 and $62,281 , respectively, and are expected to be recognized over a weighted-average period of approximately three years . The weighted average grant date fair value of options granted during 2016 , 2015 and 2014 was $16.28 , $25.96 and $16.40 , respectively. The aggregate intrinsic value of options exercised during 2016 , 2015 and 2014 was $22,704 , $24,675 and $6,350 , respectively. The aggregate intrinsic value of options is calculated as the difference between the exercise price of the underlying options and the fair value of Intrexon's common stock for those shares where the exercise price was lower than the fair value of Intrexon's common stock on the date of exercise. The following table summarizes additional information about stock options outstanding as of December 31, 2016 : Options Outstanding Options Exercisable Range of Exercise Prices Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value $ 2.65 — $ 9.34 562,951 $ 6.23 4.13 $ 10,172 525,755 $ 6.01 3.97 $ 9,615 $ 15.21 — $ 27.19 2,785,705 23.47 8.54 4,797 684,704 21.07 7.29 2,237 $ 27.21 — $ 29.68 3,147,242 29.30 7.53 — 1,400,707 29.35 7.31 — $ 29.70 — $ 42.22 3,590,423 32.89 9.09 — 345,274 37.06 6.85 — $ 43.99 — $ 65.34 1,554,062 54.40 8.43 — 461,595 53.06 8.33 — 11,640,383 $ 31.25 8.21 $ 14,969 3,418,035 $ 28.09 6.88 $ 11,852 The following table summarizes additional information about stock options outstanding as of December 31, 2015 : Options Outstanding Options Exercisable Range of Exercise Prices Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value $ 0.38 — $ 9.34 1,261,192 $ 6.40 5.40 $ 29,956 1,147,978 $ 6.19 5.25 $ 27,507 $ 15.21 — $ 28.93 2,682,516 24.25 8.43 15,831 602,023 24.43 8.36 3,445 $ 29.14 — $ 29.68 2,895,885 29.63 8.44 1,508 635,743 29.68 7.99 299 $ 30.10 — $ 56.77 3,118,935 44.48 9.46 — 108,682 45.87 8.02 — $ 57.95 — $ 65.34 1,085,000 58.07 9.55 — — — — — 11,043,528 $ 32.66 8.49 $ 47,295 2,494,426 $ 18.31 6.82 $ 31,251 Intrexon currently uses authorized and unissued shares to satisfy share award exercises. In October 2015, the compensation committee and the independent members of Intrexon's board of directors approved a compensation arrangement whereby the Company's Chief Executive Officer ("CEO") would receive a monthly salary. Previously, the CEO did not receive compensation for his services as an employee of the Company other than through his participation in the Company's Annual Executive Incentive Plan which became effective January 1, 2015. Pursuant to the compensation agreement, the CEO receives a base salary of $200 per month payable in fully vested shares of Intrexon common stock with such shares subject to a three -year lock-up on resale. The monthly number of shares of common stock is calculated based on the closing price on the last trading day of each month and the shares are issued pursuant to the terms of a Restricted Stock Unit Agreement ("RSU Agreement") which was executed between Intrexon and the CEO pursuant to the terms of the 2013 Plan. The RSU Agreement became effective in November 2015 and had an initial term of twelve months . In October 2016, the independent members of Intrexon's board of directors, with the recommendation of the compensation committee of the board of directors, approved a new RSU Agreement for the CEO providing for a term of two months, expiring on December 31, 2016, at the same monthly salary payable in fully vested shares of common stock and on the same terms as the original RSU Agreement. The fair value of the shares issued as compensation for services is included in selling, general, and administrative expenses in the Company's consolidated statements of operations for the years ended December 31, 2016 and 2015 , and totaled $1,861 and $314 , respectively. In December 2016, the independent members of Intrexon's board of directors, with the recommendation of the compensation committee of the board of directors, approved a new RSU Agreement for the CEO providing for a term of three months expiring on March 30, 2017 and on the same terms as the original RSU Agreement. Prior to 2015, the CEO did not receive compensation for his services as CEO, and as a result, the Company recorded $1,991 in compensation expense for the year ended December 31, 2014 based on the estimated salary and benefits appropriate for the role. AquaBounty Stock Option Plans As of December 31, 2016 , there were 185,591 options outstanding, of which 181,766 were exercisable, under the AquaBounty 2006 Equity Incentive Plan ("AquaBounty 2006 Plan") at a weighted average exercise price of $7.89 per share. As of December 31, 2015 , there were 179,426 options outstanding under this plan at a weighted average exercise price of $7.83 per share. The AquaBounty stock option data reflect a 1-for-30 reverse stock split of AquaBounty's common stock effective January 5, 2017. In March 2016, AquaBounty's board of directors adopted the AquaBounty 2016 Equity Incentive Plan ("AquaBounty 2016 Plan") to replace the AquaBounty 2006 Plan. The AquaBounty 2016 Plan provides for the issuance of incentive stock options, non-qualified stock options and awards of restricted and direct stock purchases to directors, officers, employees and consultants of AquaBounty. The AquaBounty 2016 Plan was approved by AquaBounty's shareholders at its annual meeting in April 2016. Upon the effectiveness of the AquaBounty 2016 Plan, no new awards may be granted under the AquaBounty 2006 Plan. As of December 31, 2016 , there were no options outstanding under the AquaBounty 2016 Plan.

License Agreement

License Agreement	12 Months Ended
	Dec. 31, 2016
License Agreement [Abstract]
License Agreement	License Agreement In January 2015, the Company and ZIOPHARM jointly entered into a license agreement with the University of Texas System Board of Regents on behalf of the University of Texas MD Anderson Cancer Center ("MD Anderson") whereby the Company received an exclusive license to certain research and development technologies owned and licensed by MD Anderson, including technologies relating to novel chimeric antigen receptor (CAR) T-cell therapies, as well as co-licenses and non-exclusive licenses to certain other related technologies. ZIOPHARM received access to these technologies pursuant to the terms of the Company's ECC with ZIOPHARM. The Company issued 2,100,085 shares of its common stock valued at $59,579 to MD Anderson as consideration, which is included in research and development expenses in the accompanying consolidated statement of operations for the year ended December 31, 2015. Subject to certain exceptions, the license agreement expires on the last to occur of (i) the expiration of all patents licensed thereunder, or (ii) the twentieth anniversary of the date of the license agreement. In connection with the license agreement, the Company, ZIOPHARM, and MD Anderson entered into a research and development agreement which governs certain operational activities between the parties and pursuant to which ZIOPHARM provides funding for certain research and development activities of MD Anderson for a period of three years , in an amount between $15,000 and $20,000 per year. The Company and ZIOPHARM reimburse MD Anderson for out of pocket expenses for maintaining patents covering the licensed technologies.

Commitments and Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases The Company leases certain facilities and equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. As of December 31, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2017 $ 5,503 2018 5,774 2019 5,515 2020 5,566 2021 4,936 Thereafter 20,179 Total $ 47,473 Rent expense, including other facility expenses, was $8,593 , $8,610 and $8,511 in 2016 , 2015 and 2014 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $1,051 , $1,486 and $908 for the years ended December 31, 2016 , 2015 and 2014 , respectively. Future rental income is expected to be $114 for 2017 , $80 for 2018 , and $67 for 2019 . Contingencies In March 2012, Trans Ova was named as a defendant in a licensing and patent infringement suit brought by XY, LLC ("XY") alleging that certain of Trans Ova's activities breach a licensing agreement and infringe on patents that XY allegedly owns. Trans Ova filed a number of counterclaims in the case. In Colorado District Court, the matter proceeded to a jury trial in January 2016. The jury determined that XY and Trans Ova had each breached the licensing agreement and that Trans Ova had infringed the intellectual property of XY. In April 2016, the court issued its order, entering a jury award of damages to Trans Ova in the amount of $528 and a jury award of damages to XY in the amount of $6,066 , each with prejudgment interest. The order provides for the continuation of Trans Ova's license to XY's technology, subject to an ongoing royalty for Trans Ova. Since the inception of the license, Trans Ova has remitted payments to XY pursuant to the terms of the original license agreement and has recorded these payments in cost of services in the consolidated statements of operations for the respective periods. For the period from inception of the agreement through the court's order, aggregate royalty and license payments were $3,170 , of which $2,759 had not yet been deposited by XY. For the year ended December 31, 2016, the Company recorded litigation expense of $4,228 , which is included in selling, general and administrative expenses on the accompanying consolidated statement of operations and represents the excess of the net damages awarded to XY, including prejudgment interest, over the liability previously recorded by Trans Ova for uncashed checks previously remitted to XY. In August 2016, Trans Ova deposited the net damages amount, including prejudgment interest, into the court's treasury, to be held until the appeals process is complete and final judgment amounts are determined. As of December 31, 2016 , this amount is included in restricted cash on the accompanying consolidated balance sheet. In December 2016, Trans Ova elected to void the outstanding checks and these amounts have been reclassified to other accrued liabilities on the accompanying consolidated balance sheet as of December 31, 2016 . In 2017, Trans Ova and XY will each file an appeal seeking to overturn respective adverse rulings. As a result of an appeal decision, the damages awarded to either party could decrease, increase, or be eliminated. The appeal decision may remand to the Colorado District Court all, or a portion, of the appellate issues. Trans Ova and the Company could elect to enter into a settlement agreement in order to avoid the further costs and uncertainties of litigation, to modify the license to XY's technologies, or to recover monetary damages related to Trans Ova's antitrust counterclaims. In May 2016, two putative shareholder class action lawsuits, captioned Hoffman v. Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al. , were filed in the U.S. District Court for the Northern District of California on behalf of purchasers of Intrexon's common stock between May 12, 2015 and April 20, 2016 (the "Class Period"). In July 2016, the court consolidated the lawsuits and appointed a lead plaintiff. The consolidated amended complaint names as defendants Intrexon and certain of Intrexon's current and former officers (the "Defendants"). It alleges, among other things, that the Defendants made materially false and/or misleading statements during the Class Period with respect to the Company's business, operations, and prospects in violation of Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended. The plaintiffs' claims are based in part upon allegations in a report published in April 2016 on the Seeking Alpha financial blog. The plaintiffs seek compensatory damages, interest and an award of reasonable attorneys' fees and costs. The Defendants moved to dismiss the case. On February 24, 2017, the court granted the Company's motion to dismiss the lawsuit on the grounds that plaintiff failed to state a claim, while granting plaintiff leave to amend. Any such amended complaint must be filed by the plaintiff within 30 days . The Company intends to continue to defend the lawsuit vigorously; however, there can be no assurance regarding the ultimate outcome of this case. In July 2016, a putative shareholder derivative action captioned Basile v. Kirk et al. was filed in the Circuit Court of Fairfax County, Virginia, against certain of the Company's directors, the Company's CEO, and Third Security, and naming the Company as a nominal defendant. The complaint alleges causes of action for breaches of fiduciary duty and unjust enrichment relating to the entry by the Company into the Services Agreement with Third Security. The plaintiff seeks, among other things, damages in an unspecified amount, disgorgement of improper benefits, appropriate equitable relief, and an award of attorney fees and other costs and expenses. The complaint is substantially similar to two separate demands made by shareholders concerning the Services Agreement and Mr. Kirk's compensation. The board of directors of the Company appointed a Special Litigation Committee ("SLC") consisting of independent directors to investigate the claims and allegations made in the derivative action and in the two shareholder demands and to decide on behalf of the Company whether the claims and allegations should be pursued. The Basile case was stayed pending the report of the SLC. In November 2016, the SLC completed its review and evaluation and unanimously determined that the claims were without merit because the compensation arrangements were the result of an informed and disinterested decision-making process and were fair to the Company, and that prosecution of the asserted claims was not in the best interest of Intrexon or its shareholders. Based upon the determination of the SLC, on February 24, 2017, the Company moved to dismiss the court action pursuant to Virgina statute. There can be no assurance, however, regarding the ultimate outcome of the case. In addition to the shareholder demands above, in June and July 2016, two shareholders made separate demands under Virginia law demanding that the Company file suit against certain of its current officers and directors for alleged breaches of fiduciary duty and other claims. The demands were based upon and asserted the allegations previously published in April 2016 in the Seeking Alpha financial blog. In July 2016, the Company's board of directors authorized the SLC to expand its review to include all such allegations. In February 2017, the SLC completed its review and evaluation and unanimously determined that there was no basis for any of the allegations, that the Company's officers and directors did not breach their fiduciary duties or any other applicable law, and that prosecution of the asserted claims was not in the best interest of Intrexon or its shareholders. The Division of Enforcement, U.S. Securities and Exchange Commission is conducting an investigation which the Company believes concerns certain issues raised by the foregoing matters. The Company has met with the SEC staff and is voluntarily cooperating with their investigation. The Company's board of directors has authorized the SLC to monitor the Company's interaction with the SEC staff. The Company may become subject to other claims and assessments from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of December 31, 2016 and 2015 , the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company's business, financial condition, results of operations, or cash flows.

Related Party Transactions

Related Party Transactions	12 Months Ended
	Dec. 31, 2016
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company's CEO and Chairman of the board of directors is also the Senior Managing Director and CEO of Third Security and owns 100% of the equity interests of Third Security. In November 2015, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved the execution of a Services Agreement ("Services Agreement") with Third Security pursuant to which Third Security provides the Company with certain professional, legal, financial, administrative, and other support services necessary to support the Company and its CEO. As consideration for providing these services, Third Security is entitled to a fee of $800 per month to be paid in the form of fully-vested shares of the Company's common stock. The number of shares of common stock is calculated based on the closing price of the Company's common stock on the 15th day of each month. The payments made by the Company under the Services Agreement constitute, in the aggregate, an award under the 2013 Plan and are subject to the terms of the 2013 Plan (Note 15 ). The Services Agreement had a term of one year , can be terminated by the Company at any time, and may be extended only by agreement of the parties, including approval of a majority of the independent members of Intrexon's board of directors. In October 2016, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved an extension of the Services Agreement for a term of two months, expiring on December 31, 2016. For the years ended December 31, 2016 and 2015 , the Company issued 337,163 shares and 48,678 shares, respectively, with values of $8,571 and $1,375 , respectively, to Third Security as payment for services pursuant to the Services Agreement. In December 2016, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved an extension of the Services Agreement through December 2017. In addition to the foregoing Services Agreement, the Company reimburses Third Security for certain out-of-pocket expenses incurred on the Company's behalf, and the total expenses incurred by the Company under this arrangement was $309 , $428 , and $291 for the years ended December 31, 2016 , 2015 and 2014 , respectively. See also Note 15 regarding compensation arrangements between the Company and its CEO. Transactions with ECC Parties In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties. In September 2016, Fibrocell, one of the Company's collaborators, sold promissory notes convertible into shares of Fibrocell common stock ("convertible note") and warrants to purchase shares of Fibrocell common stock to certain institutional and accredited investors, including the Company and affiliates of Third Security. The Company paid $2,604 for a convertible note and warrants. As of December 31, 2016 , the value of the convertible note and warrants totaled $1,642 and is included in other assets on the accompanying consolidated balance sheet. In July 2015, the Company purchased 375,868 shares of common stock of Fibrocell at $5.80 per share. In June 2016, the Company purchased 2,261,419 shares of Oragenics common stock at $0.52 per share. In March 2015, the Company purchased 278,788 shares of common stock of AmpliPhi Biosciences Corporation ("AmpliPhi") and 69,696 warrants for $2,300 . Of the total purchase price, $1,979 was allocated to the value of the shares of common stock and $321 was allocated to the value of the warrants. In December 2016, the Company sold all of its investment in AmpliPhi common stock, resulting in a realized loss of $4,098 , which is included in unrealized and realized depreciation in fair value of equity securities on the consolidated statement of operations for the year ended December 31, 2016. Between February 2011 and February 2015, the Company purchased $43,582 of ZIOPHARM common stock. See Note 14 for additional discussion related to the Company's investment in ZIOPHARM. The Company entered into an ECC with Histogenics Corporation ("Histogenics") in September 2014 and received a $10,000 convertible promissory note as upfront consideration. The note originally matured in September 2015 and accrued interest at 6.0% per annum. Upon the closing of Histogenics' IPO in December 2014, the note, with accrued interest, was converted to Histogenics common stock. Additionally, the Company purchased 1,772,364 shares of Histogenics common stock at $11.00 per share in the IPO. Other Related Parties In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development opportunities that the Company offers to Harvest. These are investment proposals that are suitable for pursuit by a start-up venture, characterized by the agreement as "start-up opportunities." For such start-up opportunities, the Company provides Harvest with exclusive rights of first-look and first negotiation. For any opportunities it decides to pursue, Harvest establishes new collaboration entities which enter into an ECC with the Company in a designated field. The terms of such ECCs are negotiated between the Company and Harvest. In addition, the agreement provides the Company the right to present to Harvest the opportunity to invest in other ventures, including investment opportunities with respect to the Company's existing collaborations. Any such opportunities are presented at the Company's discretion on a non-exclusive basis. The agreement with Harvest does not limit the Company's ability to execute other collaborations and joint ventures with third parties. As consideration for providing exclusive rights of first-look and first negotiation for start-up opportunities, the Company receives a portion of the management fee collected by the fund sponsor of Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $2,483 and $1,349 for the years ended December 31, 2016 and 2015 , respectively.

Net Loss per Share

Net Loss per Share	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Net Loss per Share	Net Loss per Share The following table presents the computation of basic and diluted net loss per share: 2016 2015 2014 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (186,612 ) $ (84,493 ) $ (81,822 ) Denominator: Weighted average shares outstanding, basic and diluted 117,983,836 111,066,352 99,170,653 Net loss attributable to Intrexon per share, basic and diluted $ (1.58 ) $ (0.76 ) $ (0.83 ) The following potentially dilutive securities as of December 31, 2016 , 2015 , and 2014 , have been excluded from the above computations of diluted weighted average shares outstanding for the years then ended as they would have been anti-dilutive: December 31, 2016 2015 2014 Options 11,640,383 11,043,528 8,323,544 Warrants — 194,719 352,483 Total 11,640,383 11,238,247 8,676,027

Quarterly Financial Information

Quarterly Financial Information (Unaudited)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Quarterly Financial Information (Unaudited)	Quarterly Financial Information (Unaudited) The following information has been derived from unaudited consolidated statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information. Three Months Ended March 31, June 30, September 30, December 31, Total revenues $ 43,438 $ 52,501 $ 48,985 $ 46,002 Operating loss (40,533 ) (23,222 ) (28,821 ) (32,590 ) Net loss (65,320 ) (50,031 ) (30,011 ) (44,912 ) Net loss attributable to Intrexon (64,429 ) (49,064 ) (28,982 ) (44,137 ) Net loss attributable to Intrexon per share, basic and diluted $ (0.55 ) $ (0.42 ) $ (0.24 ) $ (0.37 ) Three Months Ended March 31, June 30, September 30, December 31, Total revenues $ 33,849 $ 44,891 $ 53,367 $ 41,498 Operating loss (87,123 ) (17,430 ) (7,916 ) (34,395 ) Net income (loss) 25,804 (41,494 ) (39,029 ) (33,275 ) Net income (loss) attributable to Intrexon 27,097 (40,663 ) (38,213 ) (32,714 ) Net income (loss) attributable to Intrexon per share, basic $ 0.26 $ (0.37 ) $ (0.34 ) $ (0.28 ) Net income (loss) attributable to Intrexon per share, diluted 0.25 (0.37 ) (0.34 ) (0.28 )

Defined Contribution Plans

Defined Contribution Plans	12 Months Ended
	Dec. 31, 2016
Compensation and Retirement Disclosure [Abstract]
Defined Contribution Plans	Defined Contribution Plans The Company sponsors defined contribution plans covering employees who meet certain eligibility requirements. The Company makes contributions to the plans in accordance with terms specified in the plan agreement. The Company's contributions to the plans were $1,857 , $1,157 and $776 in 2016 , 2015 and 2014 , respectively.

Subsequent Events

Subsequent Events	12 Months Ended
	Dec. 31, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In January 2017, the Company entered into a definitive agreement to acquire GenVec, Inc. ("GenVec"), a clinical-stage company and pioneer in the development of AdenoVerse™ gene delivery technology. Upon closing of the transaction, GenVec stockholders will receive 0.297 of a share of the Company's common stock in exchange for each share of GenVec common stock. This exchange ratio represents $7.00 per share of GenVec's common stock divided by the Company's five -day volume weighted average price as of January 23, 2017. GenVec stockholders may also receive contingent consideration equal to 50% of any milestone or royalty payments received under one of GenVec's collaboration agreements, provided such payments are received within three years after the closing of the transaction. Consummation of the transaction, anticipated in the second quarter of 2017, is subject to customary closing conditions, including GenVec stockholder approval. In January 2017, in conjunction with the listing of AquaBounty common stock on the NASDAQ Stock Market, the Company invested $25,000 in AquaBounty in exchange for 2,421,073 shares of AquaBounty common stock. Subsequent to the equity purchase, the Company distributed 1,776,557 shares of AquaBounty common stock as a dividend to shareholders of record as of January 9, 2017. Immediately following the distribution, the Company's ownership interest in AquaBounty was 58% .

Summary of Significant Accoun31

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Principles of Consolidation	Principles of Consolidation The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.
Revenue Recognition	Revenue Recognition The Company generates collaboration and licensing revenue through the execution of agreements with collaborators (known as exclusive channel collaborations, "ECC" or "ECCs") and licensing agreements whereby the collaborators or the licensee obtain exclusive access to the Company's proprietary technologies for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Generally, the terms of these agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration or licensing agreement. The Company's collaboration and licensing agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborator or licensee on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement. Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence ("VSOE") of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price ("BESP") for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators or licensees, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations, which is reevaluated each reporting period. The terms of the Company's agreements may provide for milestone payments upon achievement of certain defined events. The Company applies the Milestone Method for recognizing milestone payments. Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria: (1) The consideration is commensurate with either the entity's performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity's performance to achieve the milestone; (2) The consideration relates solely to past performance; and (3) The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments. Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration and licensing agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned. From time to time, the Company and certain collaborators may cancel their agreements, relieving the Company of any further performance obligations under the agreement. When no further performance obligations are required of the Company under an agreement, the Company recognizes any remaining deferred revenue. The Company generates product and service revenues primarily through sales of products and services which are created from technologies developed or owned by the Company. The Company's current offerings include sales of advanced reproductive technologies, including the Company's bovine embryo transfer and in vitro fertilization processes and from genetic preservation and sexed semen processes and applications of such processes to other livestock, as well as sales of livestock and embryos produced using these processes and used in production. Revenue is recognized when (i) persuasive evidence of an arrangement exists, (ii) services have been rendered or delivery has occurred such that risk of loss has passed to the customer, (iii) the price is fixed or determinable, and (iv) collection from the customer is reasonably assured.
Research and Development	Research and Development The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, including stock-based compensation expense, and the costs of consultants, certain in-licensed technology rights, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses.
Cash and Cash Equivalents	Cash and Cash Equivalents All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer.
Restricted Cash	Restricted Cash Restricted cash represents funds deposited with the U.S. Treasury, as required by a court decision resulting from litigation against Trans Ova (Note 17 ).
Short-term and Long-term Investments	Short-term and Long-term Investments As of December 31, 2016 , short-term and long-term investments include U.S. government debt securities and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management's reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company's written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor's, Moody's and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.
Equity Securities	Equity Securities The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator's security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.
Investment in Preferred Stock	Investment in Preferred Stock The Company holds preferred stock received from one of its collaborators, ZIOPHARM Oncology, Inc. ("ZIOPHARM"), which may be converted to common stock upon the occurrence of certain events in the future (Note 7 ). The Company elected the fair value option to account for its investment in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. This investment is subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of ZIOPHARM's common stock, and changes in general economic and financial conditions of ZIOPHARM. The investment is classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell the investment nor expect it to be converted into shares of common stock within one year. Until such time as the Company converts the preferred stock into common stock, the Company is entitled to a monthly dividend payable in additional shares of preferred stock and records dividend income based on the fair value of the preferred shares received.
Fair Value of Financial Instruments	Fair Value of Financial Instruments Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows: Level 1: Quoted prices in active markets for identical assets and liabilities; Level 2: Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and Level 3: Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.
Concentrations of Risk	Concentrations of Risk Due to the Company's mix of fixed and variable rate securities holdings, the Company's investment portfolio is susceptible to changes in interest rates. As of December 31, 2016 , gross unrealized losses on the Company's short-term and long-term investments were not material. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions, or distribute its equity securities to shareholders as a stock dividend. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses. Financial instruments which potentially subject the Company to concentrations of credit risk consist primarily of trade receivables. The Company controls credit risk through credit approvals, credit limits and monitoring procedures. The Company performs ongoing credit evaluations of its customers but generally does not require collateral to support accounts receivable.
Equity Method Investments	Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest"), a related party, (Note 18 ) using the equity method of accounting based upon relative ownership interest. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets. The Company accounts for its investment in Oragenics, Inc. ("Oragenics"), one of its collaborators, using the fair value option.
Variable Interest Entities	Variable Interest Entities The Company identifies entities that (i) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (ii) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities ("VIE" or "VIEs"). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are VIEs. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (i) the power to direct activities that most significantly impact the VIE's economic performance and (ii) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE.
Trade Receivables	Trade Receivables Trade receivables consist of credit extended to the Company's customers in the normal course of business and are reported net of an allowance for doubtful accounts. The Company reviews its customer accounts on a periodic basis and records bad debt expense for specific amounts the Company evaluates as uncollectible. Past due status is determined based upon contractual terms. Amounts are written off at the point when collection attempts have been exhausted. Management estimates uncollectible amounts considering such factors as current economic conditions and historic and anticipated customer performance. This estimate can fluctuate due to changes in economic, industry or specific customer conditions which may require adjustment to the allowance recorded by the Company. Management has included amounts believed to be uncollectible in the allowance for doubtful accounts.
Inventory	Inventory The Company's inventory primarily includes adult female cows which are used in certain production processes and are recorded at acquisition cost using the first-in, first-out method or at market, whichever is lower. Work-in-process inventory includes allocations of production costs and facility costs for products currently in production and is recorded at the lower of cost or market. Significant declines in the price of cows could result in unfavorable adjustments to inventory balances.
Property, Plant and Equipment	Property, Plant and Equipment Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows: Years Land improvements 4–20 Buildings and building improvements 3–25 Furniture and fixtures 1–10 Equipment 1–10 Breeding stock 1–4 Computer hardware and software 1–7 Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to twenty years
Goodwill	Goodwill Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized. Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required. If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit's goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed. The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.
Intangible Assets	Intangible Assets Intangible assets subject to amortization consist of patents, developed technologies and know-how; customer relationships; trademarks; and a covenant not to compete acquired as a result of mergers or acquisitions. These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development technologies acquired in mergers or acquisitions and were recorded at fair value at the dates of the respective acquisitions. The Company amortizes long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their estimated useful lives, ranging from two to twenty-one years for the patents, developed technologies and know-how; customer relationships; trademarks; and the covenant not to compete.
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable. Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval.
Foreign Currency Translation	Foreign Currency Translation The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.
Income Taxes	Income Taxes Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized. The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in selling, general and administrative expenses.
Share-Based Payments	Share-Based Payments Intrexon uses the Black-Scholes option pricing model to estimate the grant-date fair value of all stock options. The Black-Scholes option pricing model requires the use of assumptions for estimated expected volatility, estimated expected term of stock options, risk-free rate, estimated expected dividend yield, and the fair value of the underlying common stock at the date of grant. Since Intrexon does not have sufficient history to estimate the expected volatility of its common stock price, expected volatility is based on a blended approach which utilizes the volatility of Intrexon's common stock and the volatility of peer public entities that are similar in size and industry. Intrexon estimates the expected term of all options based on previous history of exercises. The risk-free rate is based on the U.S. Treasury yield curve in effect at the time of grant for the expected term of the option. The expected dividend yield is 0% as Intrexon does not expect to declare cash dividends in the near future. The fair value of the underlying common stock is determined based on the quoted market price on the New York Stock Exchange. Intrexon estimates forfeitures based on its historical analysis of actual stock option forfeitures. Actual forfeitures are recorded when incurred and estimated forfeitures are reviewed and adjusted at least annually. The assumptions used in the Black-Scholes option pricing model for the years ended December 31, 2016 , 2015 and 2014 are set forth in the table below: 2016 2015 2014 Valuation assumptions Expected dividend yield 0% 0% 0% Expected volatility 59%—60% 59%—62% 62%—64% Expected term (years) 6.25 6.25 6.25 Risk-free interest rate 1.23%—2.17% 1.56%—1.95% 1.82%—2.14%
Net Loss per Share	Net Loss per Share Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented.
Segment Information	Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In January 2017, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2017-04, Intangibles-Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment (" ASU 2017-04"). The provisions of ASU 2017-04 simplify how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2017, the FASB issued ASU 2017-01, Business Combinations (Topic 805) - Clarifying the Definition of a Business ("ASU 2017-01"). The provisions of ASU 2017-01 clarify the definition of a business to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230) - Restricted Cash (A Consensus of the FASB Emerging Issues Task Force) ("ASU 2016-18"). The provisions of ASU 2016-18 require amounts generally described as restricted cash and restricted cash equivalents to be included with cash and cash equivalents when reconciling the total beginning and ending balances for the periods presented on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In October 2016, the FASB issued ASU 2016-17, Consolidation (Topic 810) - Interests Held through Related Parties That Are under Common Control ("ASU 2016-17"). The provisions of ASU 2016-17 amend the consolidation guidance on how a reporting entity that is the single decision maker of a VIE should treat indirect interests in the entity held through related parties that are under common control with the reporting entity when determining whether it is the primary beneficiary of that VIE. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company does not believe the implementation of this standard will result in a material impact to its consolidated financial statements. In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash Flows , and other Topics. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In March 2016, the FASB issued ASU 2016-09, Stock Compensation (Topic 718) - Improvements to Employee Share-Based Payment Accounting ("ASU 2016-09"). The provisions of ASU 2016-09 simplify various aspects of the accounting for employee share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. Upon adoption in the first quarter of 2017, the Company expects to elect to recognize forfeitures as they occur and anticipates making an opening adjustment to additional paid-in capital and accumulated deficit for previously unrecognized stock-based compensation costs due to estimating forfeitures on unvested shares. The adoption is on a prospective basis and therefore has no impact on prior periods. In March 2016, the FASB issued ASU 2016-07, Investments-Equity Method and Joint Ventures (Topic 323) - Simplifying the Transition to the Equity Method of Accounting ("ASU 2016-07"). The provisions of ASU 2016-07 eliminate the requirement that when an investment qualifies for use of the equity method as a result of an increase in the level of ownership interest or degree of influence, an adjustment must be made to the investment, results of operations, and retained earnings retroactively on a step-by-step basis as if the equity method had been in effect during all previous periods that the investment had been held. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company does not believe the implementation of this standard will result in a material impact to its consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, Topic 840, Leases . The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2015, the FASB issued ASU 2015-17, Income Taxes (Topic 740) - Balance Sheet Classification of Deferred Taxes ("ASU 2015-17"). The provisions of ASU 2015-17 simplify the presentation of deferred income taxes by requiring an entity to classify deferred tax liabilities and assets as noncurrent on a classified balance sheet. The Company elected to early adopt this guidance during the first quarter of 2016 and applied it prospectively, and there was no significant impact on the Company's consolidated financial statements. In July 2015, the FASB issued ASU 2015-11, Inventory (Topic 330) - Simplifying the Measurement of Inventory ("ASU 2015-11"). The provisions of ASU 2015-11 provide guidance for simplifying the calculation for subsequent measurement of inventory measured using the first-in-first-out or average cost methods. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, and is effective for the Company for the year ending December 31, 2017. The Company does not believe the implementation of this standard will result in a material impact to its consolidated financial statements. In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers ("ASU 2014-09"). The FASB issued ASU 2014-09 to clarify the principles for recognizing revenue and to develop a common revenue standard for U.S. GAAP. The standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes the most current revenue recognition guidance. This guidance was originally effective for annual periods and interim periods within those annual periods beginning after December 15, 2016 and early adoption was not permitted. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606) - Deferral of the Effective Date ("ASU 2015-14"), which deferred the effective date of the guidance in ASU 2014-09 by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016, and is effective for the Company for the year ending December 31, 2018. In 2016, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, licensing, narrow-scope improvements, practical expedients, and to expedite improvements to 2014-09 by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations ("ASU 2016-08"), ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing ("ASU 2016-10"), ASU 2016-12, Revenue from Contracts with Customers (Topic 606) - Narrow-Scope Improvements and Practical Expedients ("ASU 2016-12"), and ASU 2016-20, Technical Corrections and Improvements to Topic 606, Revenue from Contacts with Customers ("ASU 2016-20"). The Company does not intend to early adopt this standard. The Company is currently evaluating its collaborations and licensing agreements to determine the impact, if any, that the implementation of this standard will have on the Company's consolidated financial statements as it relates to the recognition of upfront and milestone payments that have been deferred under the current revenue guidance, reimbursements for costs incurred by the Company for research and development services provided pursuant to collaborations, and royalties on sales of products arising from collaborations.

Summary of Significant Accoun32

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Summarized Financial Information of Equity Method Investments	Summarized financial data as of December 31, 2016 and 2015 , and for the years ended December 31, 2016 , 2015 , and 2014 , for the Company's equity method investments for which separate financial statements are not included, pursuant to SEC Regulation S-X Article 3-09, are shown in the following tables. December 31, 2016 2015 Current assets $ 77,761 $ 28,123 Non-current assets 11,040 1,539 Total assets 88,801 29,662 Current liabilities 11,588 6,274 Net assets $ 77,213 $ 23,388 Year Ended December 31, 2016 2015 2014 Revenues, net $ 417 $ 1,176 $ 940 Operating expenses 62,373 32,513 17,289 Operating loss (61,956 ) (31,337 ) (16,349 ) Other, net 1,535 (64 ) 35 Net loss $ (60,421 ) $ (31,401 ) $ (16,314 )
Rollforward of Allowance for Doubtful Receivable Accounts	The following table shows the activity in the allowance for doubtful receivable accounts for the years ended December 31, 2016 and 2015 : 2016 2015 Beginning balance $ 2,081 $ 565 Charged to operating expenses 1,963 1,757 Write offs of accounts receivable (341 ) (241 ) Ending balance $ 3,703 $ 2,081
Estimated Useful Lives of Property, Plant and Equipment	The estimated useful lives of these assets are as follows: Years Land improvements 4–20 Buildings and building improvements 3–25 Furniture and fixtures 1–10 Equipment 1–10 Breeding stock 1–4 Computer hardware and software 1–7 Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to twenty years .
Summary of Assumptions Used in Option Pricing Model	The assumptions used in the Black-Scholes option pricing model for the years ended December 31, 2016 , 2015 and 2014 are set forth in the table below: 2016 2015 2014 Valuation assumptions Expected dividend yield 0% 0% 0% Expected volatility 59%—60% 59%—62% 62%—64% Expected term (years) 6.25 6.25 6.25 Risk-free interest rate 1.23%—2.17% 1.56%—1.95% 1.82%—2.14%

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	12 Months Ended
	Dec. 31, 2016
Oxitec Limited
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $ 146,394 . The acquisition date fair value of the Stock Consideration and Cash Consideration is presented below: Cash $ 90,199 Common shares 56,195 $ 146,394
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,780 Trade receivables 125 Other receivables 7,395 Prepaid expenses and other 121 Property, plant, and equipment 1,198 Intangible assets 96,854 Total assets acquired 109,473 Accounts payable 1,187 Accrued compensation and benefits 246 Other accrued liabilities 210 Deferred revenue 120 Deferred tax liabilities 12,584 Total liabilities assumed 14,347 Net assets acquired 95,126 Goodwill 51,268 Total consideration $ 146,394
Okanagan Specialty Fruits Inc.
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 36,500 Total assets acquired 36,655 Accounts payable 181 Deferred revenue 181 Deferred tax liabilities 8,847 Total liabilities assumed 9,209 Net assets acquired 27,446 Goodwill 13,487 Total consideration $ 40,933
ActoGeniX NV
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $ 72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,180 Other receivables 305 Prepaid expenses and other 31 Property, plant and equipment 209 Intangible assets 68,100 Other non-current assets 23 Total assets acquired 71,848 Accounts payable 230 Accrued compensation and benefits 196 Other accrued liabilities 253 Deferred revenue 732 Deferred tax liabilities 612 Total liabilities assumed 2,023 Net assets acquired 69,825 Goodwill 2,649 Total consideration $ 72,474
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred, including the noncontrolling interest in a majority-owned subsidiary of Trans Ova, was $127,875 . The acquisition date fair value of each class of consideration transferred and noncontrolling interest is presented below: Cash $ 63,625 Common shares 32,802 Deferred cash consideration 20,115 Total consideration transferred 116,542 Fair value of noncontrolling interest 11,333 Total $ 127,875
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below: Cash $ 960 Trade receivables 18,693 Related party receivables 1,219 Inventory 18,476 Prepaid expenses and other 590 Property, plant and equipment 21,164 Intangible assets 23,700 Other non-current assets 147 Total assets acquired 84,949 Accounts payable 3,317 Accrued compensation and benefits 913 Other accrued liabilities 271 Deferred revenue 4,458 Lines of credit 4,091 Related party payables 1,246 Long term debt 9,090 Total liabilities assumed 23,386 Net assets acquired 61,563 Goodwill 66,312 Total consideration and fair value of noncontrolling interest $ 127,875
Medistem, Inc.
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $24,995 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 4,920 Common shares 19,368 Settlement of promissory notes 707 $ 24,995
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 8 Intangible assets 4,824 Total assets acquired 4,832 Accounts payable 644 Accrued compensation and benefits 67 Other accrued liabilities 50 Total liabilities assumed 761 Net assets acquired 4,071 Goodwill 20,924 Total consideration $ 24,995
2015 Business Acquisitions
Business Acquisition [Line Items]
Condensed Pro forma Financial Information	The following unaudited condensed pro forma financial information for the years ended December 31, 2015 and 2014 , is presented as if the 2015 acquisitions had been consummated on January 1, 2014 : Year Ended December 31, 2015 2014 Pro Forma Revenues $ 174,558 $ 73,240 Loss before income taxes (99,751 ) (105,085 ) Net loss (99,594 ) (104,577 ) Net loss attributable to the noncontrolling interests 3,501 3,794 Net loss attributable to Intrexon (96,093 ) (100,783 )
2014 Business Acquisitions
Business Acquisition [Line Items]
Condensed Pro forma Financial Information	The following unaudited condensed pro forma financial information for the year ended December 31, 2014 is presented as if the 2014 acquisitions had been consummated on January 1, 2013 : Year Ended December 31, 2014 Pro Forma Revenues $ 119,721 Loss before income taxes (82,041 ) Net loss (81,938 ) Net loss attributable to the noncontrolling interests 4,159 Net loss attributable to Intrexon (77,779 )

Collaboration and Licensing R34

Collaboration and Licensing Revenue (Tables)	12 Months Ended
	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summarized Collaboration and Licensing Revenues	The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant collaboration or licensing agreement for the years ended December 31, 2016 , 2015 and 2014 . Year Ended December 31, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 11,529 $ 22,307 $ 33,836 Oragenics, Inc. 1,047 1,705 2,752 Fibrocell Science, Inc. 2,419 3,523 5,942 Genopaver, LLC 273 5,844 6,117 S & I Ophthalmic, LLC — 6,141 6,141 OvaXon, LLC — 2,934 2,934 Intrexon Energy Partners, LLC 2,500 15,052 17,552 Persea Bio, LLC 500 778 1,278 Ares Trading S.A. 6,389 3,803 10,192 Thrive Agrobiotics, Inc. 185 1,529 1,714 Intrexon Energy Partners II, LLC 2,000 1,169 3,169 Exotech Bio, Inc. 417 375 792 Relieve Genetics, Inc. 361 878 1,239 Intrexon T1D Partners, LLC 821 1,087 1,908 AD Skincare, Inc. 241 454 695 Genten Therapeutics, Inc. 122 264 386 CRS Bio, Inc. 57 91 148 Other 5,572 7,504 13,076 Total $ 34,433 $ 75,438 $ 109,871 Year Ended December 31, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 2,855 $ 16,451 $ 19,306 Oragenics, Inc. 5,679 856 6,535 Fibrocell Science, Inc. 6,046 6,133 12,179 Genopaver, LLC 273 3,556 3,829 S & I Ophthalmic, LLC — 4,115 4,115 OvaXon, LLC — 2,540 2,540 Intrexon Energy Partners, LLC 2,500 10,947 13,447 Persea Bio, LLC 500 741 1,241 Ares Trading S.A. 3,933 795 4,728 Thrive Agrobiotics, Inc. 46 220 266 Intrexon Energy Partners II, LLC 167 — 167 Other 10,514 8,954 19,468 Total $ 32,513 $ 55,308 $ 87,821 Year Ended December 31, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 2,577 $ 12,044 $ 14,621 Oragenics, Inc. 1,045 598 1,643 Fibrocell Science, Inc. 1,794 4,398 6,192 Genopaver, LLC 273 1,510 1,783 S & I Ophthalmic, LLC — 2,832 2,832 OvaXon, LLC — 2,799 2,799 Intrexon Energy Partners, LLC 1,875 4,227 6,102 Other 2,061 7,179 9,240 Total $ 9,625 $ 35,587 $ 45,212
Summary of Deferred Revenue	Deferred revenue consists of the following: December 31, 2016 2015 Upfront and milestone payments $ 297,867 $ 181,331 Prepaid research and development services 6,015 10,938 Prepaid product and service revenues 5,554 4,759 Other 706 701 Total $ 310,142 $ 197,729 Current portion of deferred revenue $ 53,364 $ 35,366 Long-term portion of deferred revenue 256,778 162,363 Total $ 310,142 $ 197,729
Summary of Deferred Revenue by Collaborator	The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant collaboration and licensing agreement. December 31, 2016 2015 ZIOPHARM Oncology, Inc. $ 138,809 $ 30,338 Oragenics, Inc. 7,766 8,813 Fibrocell Science, Inc. 19,026 21,445 Genopaver, LLC 1,977 2,250 Intrexon Energy Partners, LLC 18,125 20,625 Persea Bio, LLC 4,000 4,500 Ares Trading S.A. 47,178 53,567 Thrive Agrobiotics, Inc. 1,436 1,621 Intrexon Energy Partners II, LLC 15,833 17,833 Exotech Bio, Inc. 4,583 — Relieve Genetics, Inc. 3,972 — Intrexon T1D Partners, LLC 8,653 — AD Skincare, Inc. 4,092 — Genten Therapeutics, Inc. 4,176 — CRS Bio, Inc. 1,949 — Other 16,292 20,339 Total $ 297,867 $ 181,331

Short-term and Long-term Inve35

Short-term and Long-term Investments (Tables)	12 Months Ended
	Dec. 31, 2016
Investments, Debt and Equity Securities [Abstract]
Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Investments	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 180,412 $ 5 $ (94 ) $ 180,323 Certificates of deposit 272 — — 272 Total $ 180,684 $ 5 $ (94 ) $ 180,595 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 208,223 $ 21 $ (540 ) $ 207,704 Certificates of deposit 271 — — 271 Total $ 208,494 $ 21 $ (540 ) $ 207,975
Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities	The estimated fair value of available-for-sale investments classified by their contractual maturities as of December 31, 2016 was: Due within one year $ 174,602 After one year through two years 5,993 Total $ 180,595

Investment in Preferred Stock (

Investment in Preferred Stock (Tables)	12 Months Ended
	Dec. 31, 2016
Investment in Preferred Stock [Abstract]
Schedule of Changes in Level 3 Investments	The changes in the Level 3 investment during the year ended December 31, 2016 were as follows: 2016 Beginning balance $ — Receipt of Preferred Shares as consideration for amendments to collaboration agreements 120,000 Additional Preferred Shares received as dividend income 7,421 Unrealized appreciation in the fair value of the investment in preferred stock 2,124 Ending balance $ 129,545

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, as of December 31, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) December 31, Assets U.S. government debt securities $ — $ 180,323 $ — $ 180,323 Equity securities 15,544 7,978 — 23,522 Preferred stock — — 129,545 129,545 Other — 1,917 — 1,917 Total $ 15,544 $ 190,218 $ 129,545 $ 335,307 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, as of December 31, 2015 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) December 31, Assets U.S. government debt securities $ — $ 207,704 $ — $ 207,704 Equity securities 65,850 17,803 — 83,653 Other — 405 — 405 Total $ 65,850 $ 225,912 $ — $ 291,762
Schedule of Changes in Level 3 Liabilities	The changes in the fair value of the Level 3 liability during the year ended December 31, 2016 were as follows: 2016 Beginning balance $ — Fair value of contingent consideration assumed in asset acquisition 3,660 Payment of contingent consideration (Note 4) (1,583 ) Change in fair value of contingent consideration recognized in selling, general and administrative expenses 4 Ending balance $ 2,081

Inventory (Tables)

Inventory (Tables)	12 Months Ended
	Dec. 31, 2016
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: December 31, 2016 2015 Supplies, embryos and other production materials $ 1,835 $ 1,402 Work in process 5,466 6,290 Livestock 11,752 16,907 Feed 2,086 1,964 Total inventory $ 21,139 $ 26,563

Property, Plant and Equipment39

Property, Plant and Equipment, Net (Tables)	12 Months Ended
	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: December 31, 2016 2015 Land and land improvements $ 11,324 $ 9,119 Buildings and building improvements 8,123 7,520 Furniture and fixtures 2,176 1,283 Equipment 44,392 36,016 Leasehold improvements 15,105 6,888 Breeding stock 3,893 — Computer hardware and software 6,844 5,960 Construction and other assets in progress 6,865 2,193 98,722 68,979 Less: Accumulated depreciation and amortization (34,050 ) (26,240 ) Property, plant and equipment, net $ 64,672 $ 42,739

Goodwill and Intangible Asset40

Goodwill and Intangible Assets, Net (Tables)	12 Months Ended
	Dec. 31, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Schedule of Changes in Carrying Amount of Goodwill	The changes in the carrying amount of goodwill for the years ended December 31, 2016 and 2015 , are as follows: 2016 2015 Beginning balance $ 165,169 $ 101,059 Acquisitions — 67,403 Foreign currency translation adjustments (7,994 ) (3,293 ) Ending balance $ 157,175 $ 165,169
Schedule of Intangible Assets	Intangible assets consist of the following as of December 31, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how 15.9 $ 236,401 $ (29,748 ) $ 206,653 Customer relationships 6.5 10,700 (4,672 ) 6,028 Trademarks 9.3 6,800 (1,792 ) 5,008 Covenant not to compete 2.0 370 (339 ) 31 In-process research and development 7,895 — 7,895 Total $ 262,166 $ (36,551 ) $ 225,615 Intangible assets consist of the following as of December 31, 2015 : Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how $ 157,411 $ (17,775 ) $ 139,636 Customer relationships 10,700 (2,739 ) 7,961 Trademarks 6,800 (1,018 ) 5,782 Covenant not to compete 384 (160 ) 224 In-process research and development 93,932 — 93,932 Total $ 269,227 $ (21,692 ) $ 247,535

Lines of Credit and Long Term41

Lines of Credit and Long Term Debt (Tables)	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Schedule of Long Term Debt Instruments	Long term debt consists of the following: December 31, 2016 2015 Notes payable $ 5,453 $ 6,477 Royalty-based financing 1,896 1,807 Other 599 244 Long term debt 7,948 8,528 Less current portion 386 930 Long term debt, less current portion $ 7,562 $ 7,598
Schedule of Maturities of Long Term Debt	Future maturities of long term debt are as follows: 2017 $ 386 2018 408 2019 365 2020 336 2021 765 Thereafter 3,792 Total $ 6,052

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Components of Loss Before Income Taxes	The components of loss before income taxes are presented below: Year Ended December 31, 2016 2015 2014 Domestic $ (157,067 ) $ (69,287 ) $ (83,256 ) Foreign (37,084 ) (17,691 ) (2,463 ) Loss before income taxes $ (194,151 ) $ (86,978 ) $ (85,719 )
Components of Income Tax Expense (Benefit)	The components of income tax expense (benefit) are presented below: Year Ended December 31, 2016 2015 2014 U.S. federal income taxes: Current $ (17 ) $ 22 $ — Deferred 1,396 1,732 — Foreign income taxes: Current (393 ) (123 ) (103 ) Deferred (5,177 ) (1,003 ) — State income taxes: Deferred 314 388 — Income tax expense (benefit) $ (3,877 ) $ 1,016 $ (103 )
Schedule of Effective Income Tax Rate Reconciliation	Income tax expense (benefit) for the years ended December 31, 2016 , 2015 and 2014 differed from amounts computed by applying the applicable U.S. federal corporate income tax rate of 34% to loss before income taxes as a result of the following: 2016 2015 2014 Computed statutory income tax benefit $ (66,011 ) $ (29,573 ) $ (29,144 ) State and provincial income tax benefit, net of federal income taxes (7,905 ) (3,157 ) (3,544 ) Nondeductible stock based compensation 3,321 3,182 1,386 Nondeductible officer compensation — 2,433 — Contribution of services by shareholder — — 677 Research and development tax incentives (6,350 ) (348 ) 258 Acquisition and internal restructuring transaction costs 571 883 — Enacted change in tax rates — (961 ) — U.S.-foreign rate differential 3,463 620 — Other, net 1,485 (98 ) 1,503 (71,426 ) (27,019 ) (28,864 ) Change in valuation allowance for deferred tax assets 67,549 28,035 28,761 Total income tax expense (benefit) $ (3,877 ) $ 1,016 $ (103 )
Schedule of Deferred Tax Assets and Liabilities	The tax effects of temporary differences that comprise the deferred tax assets and liabilities as of December 31, 2016 and 2015 , are as follows: 2016 2015 Deferred tax assets Allowance for doubtful accounts $ 1,676 $ 1,056 Inventory 447 967 Equity securities and investments in affiliates 31,729 10,413 Accrued liabilities and long-term debt 4,168 4,585 Stock-based compensation 8,460 7,223 Deferred revenue 68,056 31,637 Research and development tax credits 10,396 9,113 Net operating and capital loss carryforwards 144,502 135,633 Total deferred tax assets 269,434 200,627 Less: Valuation allowance 256,165 190,174 Net deferred tax assets 13,269 10,453 Deferred tax liabilities Property, plant and equipment 406 160 Intangible assets 29,870 32,095 Total deferred tax liabilities 30,276 32,255 Net deferred tax liabilities $ (17,007 ) $ (21,802 )
Summary of Valuation Allowance	Activity within the valuation allowance for deferred tax assets during the years ended December 31, 2016 , 2015 and 2014 was as follows: 2016 2015 2014 Valuation allowance at beginning of year $ 190,174 $ 161,660 $ 131,985 Increase (decrease) in valuation allowance as a result of Mergers and acquisitions, net (1,416 ) 1,228 914 Current year operations 67,549 28,035 28,761 Foreign currency translation adjustment (142 ) (749 ) — Valuation allowance at end of year $ 256,165 $ 190,174 $ 161,660

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Schedule of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss are as follows: December 31, 2016 2015 Unrealized loss on investments $ (89 ) $ (519 ) Loss on foreign currency translation adjustments (36,113 ) (12,233 ) Total accumulated other comprehensive loss $ (36,202 ) $ (12,752 )

Share-Based Payments (Tables)

Share-Based Payments (Tables)	12 Months Ended
	Dec. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Stock-based Compensation Expense	Stock-based compensation costs included in the consolidated statements of operations are presented below: Year Ended December 31, 2016 2015 2014 Cost of products $ 81 $ 95 $ 14 Cost of services 274 354 142 Research and development 9,251 8,614 4,817 Selling, general and administrative 32,596 29,604 16,876 Total $ 42,202 $ 38,667 $ 21,849
Schedule of Stock Option Activity	Stock option activity under Intrexon's award plans was as follows for the periods presented: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2013 2,840,648 $ 8.27 7.75 Granted 7,655,050 27.51 Exercised (315,964 ) (4.80 ) Forfeited (1,855,578 ) (24.00 ) Expired (612 ) (7.12 ) Balances at December 31, 2014 8,323,544 22.59 8.64 Granted 5,051,500 45.82 Adjustment due to dividend (Note 14) 312,795 25.40 Exercised (1,029,291 ) (15.16 ) Forfeited (1,610,335 ) (26.75 ) Expired (4,685 ) (28.29 ) Balances at December 31, 2015 11,043,528 32.66 8.49 Granted 4,644,860 29.39 Exercised (1,210,840 ) (15.83 ) Forfeited (2,760,809 ) (40.34 ) Expired (76,356 ) (37.81 ) Balances at December 31, 2016 11,640,383 31.25 8.21 Exercisable at December 31, 2016 3,418,035 28.09 6.88 Vested and Expected to Vest at December 31, 2016(1) 10,019,307 31.04 8.08 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures.
Summary of Information About Stock Options Outstanding	The following table summarizes additional information about stock options outstanding as of December 31, 2016 : Options Outstanding Options Exercisable Range of Exercise Prices Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value $ 2.65 — $ 9.34 562,951 $ 6.23 4.13 $ 10,172 525,755 $ 6.01 3.97 $ 9,615 $ 15.21 — $ 27.19 2,785,705 23.47 8.54 4,797 684,704 21.07 7.29 2,237 $ 27.21 — $ 29.68 3,147,242 29.30 7.53 — 1,400,707 29.35 7.31 — $ 29.70 — $ 42.22 3,590,423 32.89 9.09 — 345,274 37.06 6.85 — $ 43.99 — $ 65.34 1,554,062 54.40 8.43 — 461,595 53.06 8.33 — 11,640,383 $ 31.25 8.21 $ 14,969 3,418,035 $ 28.09 6.88 $ 11,852 The following table summarizes additional information about stock options outstanding as of December 31, 2015 : Options Outstanding Options Exercisable Range of Exercise Prices Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value Number of Options Weighted Average Exercise Price Weighted Average Remaining Life (Years) Aggregate Intrinsic Value $ 0.38 — $ 9.34 1,261,192 $ 6.40 5.40 $ 29,956 1,147,978 $ 6.19 5.25 $ 27,507 $ 15.21 — $ 28.93 2,682,516 24.25 8.43 15,831 602,023 24.43 8.36 3,445 $ 29.14 — $ 29.68 2,895,885 29.63 8.44 1,508 635,743 29.68 7.99 299 $ 30.10 — $ 56.77 3,118,935 44.48 9.46 — 108,682 45.87 8.02 — $ 57.95 — $ 65.34 1,085,000 58.07 9.55 — — — — — 11,043,528 $ 32.66 8.49 $ 47,295 2,494,426 $ 18.31 6.82 $ 31,251

Commitments and Contingencies (

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	As of December 31, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2017 $ 5,503 2018 5,774 2019 5,515 2020 5,566 2021 4,936 Thereafter 20,179 Total $ 47,473

Net Loss per Share (Tables)

Net Loss per Share (Tables)	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Computation of Basic and Diluted Net Loss per Share	The following table presents the computation of basic and diluted net loss per share: 2016 2015 2014 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (186,612 ) $ (84,493 ) $ (81,822 ) Denominator: Weighted average shares outstanding, basic and diluted 117,983,836 111,066,352 99,170,653 Net loss attributable to Intrexon per share, basic and diluted $ (1.58 ) $ (0.76 ) $ (0.83 )
Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share	The following potentially dilutive securities as of December 31, 2016 , 2015 , and 2014 , have been excluded from the above computations of diluted weighted average shares outstanding for the years then ended as they would have been anti-dilutive: December 31, 2016 2015 2014 Options 11,640,383 11,043,528 8,323,544 Warrants — 194,719 352,483 Total 11,640,383 11,238,247 8,676,027

Quarterly Financial Informati47

Quarterly Financial Information (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Schedule of Quarterly Financial Information (Unaudited)	The following information has been derived from unaudited consolidated statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information. Three Months Ended March 31, June 30, September 30, December 31, Total revenues $ 43,438 $ 52,501 $ 48,985 $ 46,002 Operating loss (40,533 ) (23,222 ) (28,821 ) (32,590 ) Net loss (65,320 ) (50,031 ) (30,011 ) (44,912 ) Net loss attributable to Intrexon (64,429 ) (49,064 ) (28,982 ) (44,137 ) Net loss attributable to Intrexon per share, basic and diluted $ (0.55 ) $ (0.42 ) $ (0.24 ) $ (0.37 ) Three Months Ended March 31, June 30, September 30, December 31, Total revenues $ 33,849 $ 44,891 $ 53,367 $ 41,498 Operating loss (87,123 ) (17,430 ) (7,916 ) (34,395 ) Net income (loss) 25,804 (41,494 ) (39,029 ) (33,275 ) Net income (loss) attributable to Intrexon 27,097 (40,663 ) (38,213 ) (32,714 ) Net income (loss) attributable to Intrexon per share, basic $ 0.26 $ (0.37 ) $ (0.34 ) $ (0.28 ) Net income (loss) attributable to Intrexon per share, diluted 0.25 (0.37 ) (0.34 ) (0.28 )

Organization and Basis of Pre48

Organization and Basis of Presentation - Additional Information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2016USD ($)
AquaBounty Technologies, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Parent ownership interest	70.00%
Biological & Popular Culture, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Parent ownership interest	51.00%
AquaBounty Technologies, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Conversion of the principal balance of an outstanding promissory note receivable and related accrued interest	$ 10,396

Summary of Significant Accoun49

Summary of Significant Accounting Policies - Additional Information (Details) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016USD ($)	Sep. 30, 2016USD ($)	Jun. 30, 2016USD ($)	Mar. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Sep. 30, 2015USD ($)	Jun. 30, 2015USD ($)	Mar. 31, 2015USD ($)	Dec. 31, 2016USD ($)segment	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Organization And Significant Accounting Policies [Line Items]
Research and development commitments with third parties not incurred	$ 10,631				$ 4,138				$ 10,631	$ 4,138
Maturity period of highly liquid investment									3 months
Cash equivalent investments in highly liquid money market accounts	43,808				112,776				$ 43,808	112,776
Fair value of financial assets measured at fair value on a recurring basis	335,307				291,762				335,307	291,762
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock									(58,894)	66,876	$ (10,469)
Maximum risk of loss related to the identified VIEs	159,115				3,598				$ 159,115	3,598
Number of segments | segment									1
Property, plant and equipment, net	64,672				42,739				$ 64,672	42,739
Revenues	$ 46,002	$ 48,985	$ 52,501	$ 43,438	$ 41,498	$ 53,367	$ 44,891	$ 33,849	$ 190,926	$ 173,605	71,930
Oragenics, Inc.
Organization And Significant Accounting Policies [Line Items]
Company's ownership percentage	29.50%				30.70%				29.50%	30.70%
ZIOPHARM Oncology, Inc.
Organization And Significant Accounting Policies [Line Items]
Realized investment gain										$ 81,401
Equity securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 23,522				$ 83,653				$ 23,522	83,653
Equity securities | Oragenics, Inc.
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	7,244				16,601				7,244	16,601
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock									(10,523)	4,863	(14,969)
Equity securities | ZIOPHARM Oncology, Inc.
Organization And Significant Accounting Policies [Line Items]
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock											11,965
Foreign Countries
Organization And Significant Accounting Policies [Line Items]
Property, plant and equipment, net	$ 13,265				$ 3,877				13,265	3,877
Revenues									$ 11,969	$ 5,918	$ 2,166
Minimum
Organization And Significant Accounting Policies [Line Items]
Expected useful life of intangible asset									2 years
Maximum
Organization And Significant Accounting Policies [Line Items]
Expected useful life of intangible asset									21 years
Intrexon Stock Option Plans
Organization And Significant Accounting Policies [Line Items]
Expected dividend yield									0.00%	0.00%	0.00%

Summary of Significant Accoun50

Summary of Significant Accounting Policies - Summarized Financial Data of Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Equity Method Investment, Summarized Financial Information, Gross Profit (Loss) [Abstract]
Operating expenses									$ 316,092	$ 320,469	$ 141,892
Operating loss	$ (32,590)	$ (28,821)	$ (23,222)	$ (40,533)	$ (34,395)	$ (7,916)	$ (17,430)	$ (87,123)	(125,166)	(146,864)	(69,962)
Other, net									(47,865)	68,830	(10,497)
Equity Method Investments
Equity Method Investment, Summarized Financial Information, Assets [Abstract]
Current assets	77,761				28,123				77,761	28,123
Non-current assets	11,040				1,539				11,040	1,539
Total assets	88,801				29,662				88,801	29,662
Equity Method Investment, Summarized Financial Information, Liabilities [Abstract]
Current liabilities	11,588				6,274				11,588	6,274
Net assets	$ 77,213				$ 23,388				77,213	23,388
Equity Method Investment, Summarized Financial Information, Gross Profit (Loss) [Abstract]
Revenues, net									417	1,176	940
Operating expenses									62,373	32,513	17,289
Operating loss									(61,956)	(31,337)	(16,349)
Other, net									1,535	(64)	35
Net loss									$ (60,421)	$ (31,401)	$ (16,314)

Summary of Significant Accoun51

Summary of Significant Accounting Policies - Rollforward of Allowance for Doubtful Accounts (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Allowance for Doubtful Accounts
Beginning balance	$ 2,081	$ 565
Charged to operating expenses	1,963	1,757	$ 565
Write offs of accounts receivable	(341)	(241)
Ending balance	$ 3,703	$ 2,081	$ 565

Summary of Significant Accoun52

Summary of Significant Accounting Policies - Estimated Useful Lives of Property, Plant and Equipment (Details)	12 Months Ended
	Dec. 31, 2016
Minimum | Land improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	4 years
Minimum | Building and building improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	3 years
Minimum | Furniture and fixtures
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Equipment
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Breeding stock
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Computer hardware and software
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Leasehold improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Maximum | Land improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	20 years
Maximum | Building and building improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	25 years
Maximum | Furniture and fixtures
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	10 years
Maximum | Equipment
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	10 years
Maximum | Breeding stock
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	4 years
Maximum | Computer hardware and software
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years
Maximum | Leasehold improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	20 years

Summary of Significant Accoun53

Summary of Significant Accounting Policies - Summary of Assumptions Used in Option Pricing Model (Details) - Intrexon Stock Option Plans	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected dividend yield	0.00%	0.00%	0.00%
Expected volatility, minimum	59.00%	59.00%	62.00%
Expected volatility, maximum	60.00%	62.00%	64.00%
Expected term (years)	6 years 3 months	6 years 3 months	6 years 3 months
Risk-free interest rate, minimum	1.23%	1.56%	1.82%
Risk-free interest rate, maximum	2.17%	1.95%	2.14%

Mergers and Acquisitions - Oxit

Mergers and Acquisitions - Oxitec - Fair Value of Consideration Transferred (Details) - Oxitec Limited $ in Thousands	1 Months Ended
	Sep. 30, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 90,199
Common shares	56,195
Total consideration transferred	$ 146,394

Mergers and Acquisitions - Ox55

Mergers and Acquisitions - Oxitec - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Goodwill	$ 157,175	$ 165,169		$ 101,059
Oxitec Limited
Business Acquisition [Line Items]
Cash			$ 3,780
Trade receivables			125
Other receivables			7,395
Prepaid expenses and other			121
Property, plant and equipment			1,198
Intangible assets			96,854
Total assets acquired			109,473
Accounts payable			1,187
Accrued compensation and benefits			246
Other accrued liabilities			210
Deferred revenue			120
Deferred tax liabilities			12,584
Total liabilities assumed			14,347
Net assets acquired			95,126
Goodwill			51,268
Total consideration and fair value of noncontrolling interest			$ 146,394

Mergers and Acquisitions - Ox56

Mergers and Acquisitions - Oxitec - Additional Information (Details) - Oxitec Limited - USD ($) $ in Thousands	1 Months Ended		12 Months Ended
	Nov. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Business combination, consideration paid, shares issued		1,359,343
Cash		$ 90,199
Business combination, consideration transferred, cash and working capital adjustments		$ 9,449
Business combination, equity interest issued or issuable, number of shares withheld as escrow		480,422
Business combination, cash consideration withheld as escrow		$ 1,991
Business combination, consideration withheld as escrow, transfer period after closing		18 months
Expected useful life of intangible asset	18 years
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost			$ 1,675

Mergers and Acquisitions - Okan

Mergers and Acquisitions - Okanagan - Fair Value of Consideration Transferred (Details) - Okanagan Specialty Fruits Inc. $ in Thousands	1 Months Ended
	Apr. 30, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 10,000
Common shares	30,933
Total consideration transferred	$ 40,933

Mergers and Acquisitions - Ok58

Mergers and Acquisitions - Okanagan - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Apr. 30, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Goodwill	$ 157,175	$ 165,169		$ 101,059
Okanagan Specialty Fruits Inc.
Business Acquisition [Line Items]
Cash			$ 58
Trade receivables			16
Other receivables			49
Property, plant and equipment			32
Intangible assets			36,500
Total assets acquired			36,655
Accounts payable			181
Deferred revenue			181
Deferred tax liabilities			8,847
Total liabilities assumed			9,209
Net assets acquired			27,446
Goodwill			13,487
Total consideration and fair value of noncontrolling interest			$ 40,933

Mergers and Acquisitions - Ok59

Mergers and Acquisitions - Okanagan - Additional Information (Details) - Okanagan Specialty Fruits Inc. - USD ($) $ in Thousands	1 Months Ended	12 Months Ended
	Apr. 30, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Business combination, consideration paid, shares issued	707,853
Cash	$ 10,000
Expected useful life of intangible asset	14 years
Business combination, acquisition related cost		$ 341
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost			$ 267	$ 74

Mergers and Acquisitions - Acto

Mergers and Acquisitions - ActoGeniX - Fair Value of Consideration Transferred (Details) - ActoGeniX NV $ in Thousands	1 Months Ended
	Feb. 28, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 32,739
Common shares	39,735
Total consideration transferred	$ 72,474

Mergers and Acquisitions - Ac61

Mergers and Acquisitions - ActoGeniX - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Feb. 28, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Goodwill	$ 157,175	$ 165,169		$ 101,059
ActoGeniX NV
Business Acquisition [Line Items]
Cash			$ 3,180
Other receivables			305
Prepaid expenses and other			31
Property, plant and equipment			209
Intangible assets			68,100
Other non-current assets			23
Total assets acquired			71,848
Accounts payable			230
Accrued compensation and benefits			196
Other accrued liabilities			253
Deferred revenue			732
Deferred tax liabilities			612
Total liabilities assumed			2,023
Net assets acquired			69,825
Goodwill			2,649
Total consideration and fair value of noncontrolling interest			$ 72,474

Mergers and Acquisitions - Ac62

Mergers and Acquisitions - ActoGeniX - Additional Information (Details) - ActoGeniX NV - USD ($) $ in Thousands	1 Months Ended		12 Months Ended
	Aug. 31, 2015	Feb. 28, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Business combination, consideration paid, shares issued		965,377
Cash		$ 32,739
Expected useful life of intangible asset	18 years
Business combination, acquisition related cost			$ 418
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost				$ 381	$ 37

Mergers and Acquisitions - Tran

Mergers and Acquisitions - Trans Ova - Fair Value of Consideration Transferred (Details) - USD ($) $ in Thousands	1 Months Ended	12 Months Ended
	Aug. 31, 2014	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Deferred cash consideration		$ 0	$ 1,992	$ 20,115
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Cash	$ 63,625
Common shares	32,802
Deferred cash consideration	20,115
Total consideration transferred	116,542
Fair value of noncontrolling interest	11,333
Total	$ 127,875

Mergers and Acquisitions - Tr64

Mergers and Acquisitions - Trans Ova - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Aug. 31, 2014
Business Acquisition [Line Items]
Goodwill	$ 157,175	$ 165,169	$ 101,059
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Cash				$ 960
Trade receivables				18,693
Related party receivables				1,219
Inventory				18,476
Prepaid expenses and other				590
Property, plant and equipment				21,164
Intangible assets				23,700
Other non-current assets				147
Total assets acquired				84,949
Accounts payable				3,317
Accrued compensation and benefits				913
Other accrued liabilities				271
Deferred revenue				4,458
Lines of credit				4,091
Related party payables				1,246
Long term debt				9,090
Total liabilities assumed				23,386
Net assets acquired				61,563
Goodwill				66,312
Total consideration and fair value of noncontrolling interest				$ 127,875

Mergers and Acquisitions - Tr65

Mergers and Acquisitions - Trans Ova - Additional Information (Details) - USD ($)	1 Months Ended		3 Months Ended								12 Months Ended
	Feb. 28, 2015	Aug. 31, 2014	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Deferred cash consideration											$ 0	$ 1,992,000	$ 20,115,000
Revenues			$ 46,002,000	$ 48,985,000	$ 52,501,000	$ 43,438,000	$ 41,498,000	$ 53,367,000	$ 44,891,000	$ 33,849,000	190,926,000	173,605,000	71,930,000
Net income (loss)			(44,912,000)	$ (30,011,000)	$ (50,031,000)	$ (65,320,000)	$ (33,275,000)	$ (39,029,000)	$ (41,494,000)	$ 25,804,000	(190,274,000)	(87,994,000)	(85,616,000)
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Business combination, consideration paid, shares issued		1,444,388
Cash		$ 63,625,000
Deferred cash consideration		$ 20,115,000
Revenues											78,143,000	83,912,000	26,352,000
Net income (loss)											(9,679,000)	$ (1,531,000)	2,000
Future contingent payments based on revenue targets			3,000,000								3,000,000
Current contingent consideration liability			$ 0								$ 0
Exemplar Genetics, LLC
Business Acquisition [Line Items]
Cash paid to acquire minority interest	$ 1,566,000
Shares issued to acquire minority interest	307,074
Minimum
Business Acquisition [Line Items]
Expected useful life of intangible asset											2 years
Minimum | Trans Ova Genetics, LC
Business Acquisition [Line Items]
Expected useful life of intangible asset		3 years
Maximum
Business Acquisition [Line Items]
Expected useful life of intangible asset											21 years
Maximum | Trans Ova Genetics, LC
Business Acquisition [Line Items]
Expected useful life of intangible asset		9 years
Selling, general and administrative | Trans Ova Genetics, LC
Business Acquisition [Line Items]
Business combination, acquisition related cost													$ 713,000

Mergers and Acquisitions - Medi

Mergers and Acquisitions - Medistem - Fair Value of Consideration Transferred (Details) - Medistem, Inc. $ in Thousands	1 Months Ended
	Mar. 31, 2014USD ($)
Business Acquisition [Line Items]
Cash	$ 4,920
Common shares	19,368
Total consideration transferred	24,995
Settlement of promissory notes
Business Acquisition [Line Items]
Total consideration transferred	$ 707

Mergers and Acquisitions - Me67

Mergers and Acquisitions - Medistem - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Mar. 31, 2014
Business Acquisition [Line Items]
Goodwill	$ 157,175	$ 165,169	$ 101,059
Medistem, Inc.
Business Acquisition [Line Items]
Cash				$ 8
Intangible assets				4,824
Total assets acquired				4,832
Accounts payable				644
Accrued compensation and benefits				67
Other accrued liabilities				50
Total liabilities assumed				761
Net assets acquired				4,071
Goodwill				20,924
Total consideration and fair value of noncontrolling interest				$ 24,995

Mergers and Acquisitions - Me68

Mergers and Acquisitions - Medistem - Additional Information (Details) - Medistem, Inc. $ in Thousands	1 Months Ended		12 Months Ended
	Nov. 30, 2016	Mar. 31, 2014USD ($)noteshares	Dec. 31, 2016USD ($)	Dec. 31, 2014USD ($)
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Business combination, consideration paid, shares issued | shares		714,144
Cash		$ 4,920
Number of promissory notes settled | note		2
Total consideration transferred		$ 24,995
Shares surrendered to pay withholding taxes shares | shares		17,695
Expected useful life of intangible asset	10 years
Business combination, acquisition related cost			$ 680
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost				$ 310
Promissory Notes
Business Acquisition [Line Items]
Total consideration transferred		$ 707

Mergers and Acquisitions - 2015

Mergers and Acquisitions - 2015 Acquisitions - Pro Forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Loss before income taxes									$ (194,151)	$ (86,978)	$ (85,719)
Net loss	$ (44,912)	$ (30,011)	$ (50,031)	$ (65,320)	$ (33,275)	$ (39,029)	$ (41,494)	$ 25,804	(190,274)	(87,994)	(85,616)
Net loss attributable to the noncontrolling interests									$ 3,662	3,501	3,794
2015 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues										174,558	73,240
Loss before income taxes										(99,751)	(105,085)
Net loss										(99,594)	(104,577)
Net loss attributable to the noncontrolling interests										3,501	3,794
Net loss attributable to Intrexon										$ (96,093)	$ (100,783)

Mergers and Acquisitions - 2014

Mergers and Acquisitions - 2014 Acquisitions - Pro Forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Business Acquisition [Line Items]
Loss before income taxes									$ (194,151)	$ (86,978)	$ (85,719)
Net loss	$ (44,912)	$ (30,011)	$ (50,031)	$ (65,320)	$ (33,275)	$ (39,029)	$ (41,494)	$ 25,804	(190,274)	(87,994)	(85,616)
Net loss attributable to the noncontrolling interests									$ 3,662	$ 3,501	3,794
Pro Forma | 2014 Business Acquisitions
Business Acquisition [Line Items]
Revenues											119,721
Loss before income taxes											(82,041)
Net loss											(81,938)
Net loss attributable to the noncontrolling interests											4,159
Net loss attributable to Intrexon											$ (77,779)

Investments in Joint Ventures -

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details)	1 Months Ended	12 Months Ended
	Oct. 31, 2013USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2016USD ($)board_seat
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 9,977,000	$ 23,655,000
S & I Ophthalmic, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contribution	$ 5,000,000	5,000,000
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat			4
Investor | S & I Ophthalmic, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contribution	$ 5,000,000	5,000,000
Membership interest	50.00%
Investments in affiliates | S & I Ophthalmic, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 6,379,000	$ 3,236,000

Investments in Joint Ventures72

Investments in Joint Ventures - OvaXon - Additional Information (Details)	1 Months Ended
	Jan. 31, 2014USD ($)	Dec. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 23,655,000	$ 9,977,000
OvaXon, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contribution	$ 1,500,000
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat		4
OvaXon, LLC | Investor
Schedule Of Investments In Joint Venture [Line Items]
Capital contribution	$ 1,500,000
Membership interest	50.00%
Investments in affiliates | OvaXon, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 65,000
Other accrued liabilities | OvaXon, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment			$ (144,000)

Investments in Joint Ventures73

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Dec. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 23,655,000	$ 9,977,000
Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contributions committed	$ 25,000,000
Additional capital contributions committed, remaining commitment		$ 10,240,000
Total number of seats on the joint venture's governing board | board_seat		5
Investor | Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contribution	$ 25,000,000
Maximum additional capital contributions committed	25,000,000
Upfront and Milestone Payments | Upfront | Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Collaborative agreement, consideration received, value	$ 25,000,000
Other accrued liabilities | Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ (477,000)	$ (1,270,000)

Investments in Joint Ventures74

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015USD ($)	Dec. 31, 2016USD ($)board_seat
Schedule Of Investments In Joint Venture [Line Items]
Investment	$ 9,977,000	$ 23,655,000
Intrexon Energy Partners II, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contributions committed	$ 10,000,000
Total number of seats on the joint venture's governing board | board_seat		5
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments | Upfront
Schedule Of Investments In Joint Venture [Line Items]
Collaborative agreement, consideration received, value	$ 18,000,000
Investor | Intrexon Energy Partners II, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contribution	$ 18,000,000
Maximum additional capital contributions committed	10,000,000
All Investors | Intrexon Energy Partners II, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contribution	4,000,000
Investments in affiliates | Intrexon Energy Partners II, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment	$ 2,000,000	$ 1,414,000

Investments in Joint Ventures75

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($)	1 Months Ended		12 Months Ended
	Oct. 31, 2016	Feb. 29, 2016	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Schedule Of Investments In Joint Venture [Line Items]
Cash paid in asset acquisition			$ 7,244,000	$ 0	$ 0
Shares issued in asset acquisition			4,401,000	0	0
Contingent consideration assumed in asset acquisition			3,660,000	0	0
Shares issued as payment for contingent consideration			1,583,000	0	$ 0
Investment			23,655,000	$ 9,977,000
EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Cash paid in asset acquisition		$ 4,244,000
Shares issued in asset acquisition, shares		136,340
Shares issued in asset acquisition		$ 4,401,000
Contingent consideration assumed in asset acquisition		3,660,000
Capital contribution		$ 3,000,000
Membership interest		50.00%
Maximum additional capital contributions committed		$ 5,000,000
Estimated fair value of investment		5,425,000
Shares issued as payment for contingent consideration, shares	59,337
Shares issued as payment for contingent consideration	$ 1,583,000
Contingent consideration for commercial milestones payable in common stock, maximum		$ 4,000,000
Investor | EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest		50.00%
Maximum additional capital contributions committed		$ 5,000,000
Patents, developed technologies and know-how | EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Estimated fair value of developed technology acquired		$ 9,880,000
Expected useful life of intangible asset		21 years
Significant Unobservable Inputs (Level 3)
Schedule Of Investments In Joint Venture [Line Items]
Contingent consideration assumed in asset acquisition			3,660,000
Fair value of financial liabilities measured at fair value on a recurring basis			2,081,000
Shares issued as payment for contingent consideration			1,583,000
Significant Unobservable Inputs (Level 3) | EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis			2,081,000
Investments in affiliates | EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment			$ 4,189,000

Investments in Joint Ventures76

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2016USD ($)	Dec. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 23,655,000	$ 9,977,000
Intrexon T1D Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contributions committed	$ 5,000,000
Additional capital contributions committed, remaining commitment		$ 3,650,000
Total number of seats on the joint venture's governing board | board_seat		5
Upfront | Intrexon T1D Partners, LLC | Upfront and Milestone Payments
Schedule Of Investments In Joint Venture [Line Items]
Collaborative agreement, consideration received, value	$ 10,000,000
Investor | Intrexon T1D Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contribution	$ 10,000,000
Maximum additional capital contributions committed	$ 5,000,000
Investments in affiliates | Intrexon T1D Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 806,000

Collaboration and Licensing R77

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 109,871	$ 87,821	$ 45,212
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	33,836	19,306	14,621
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,752	6,535	1,643
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,942	12,179	6,192
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,117	3,829	1,783
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,141	4,115	2,832
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,934	2,540	2,799
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	17,552	13,447	6,102
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,278	1,241
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	10,192	4,728
Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,714	266
Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,169	167
Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	792
Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,239
Intrexon T1D Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,908
AD Skincare, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	695
Genten Therapeutics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	386
CRS Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	148
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	13,076	19,468	9,240
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	34,433	32,513	9,625
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	11,529	2,855	2,577
Upfront and Milestone Payments | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,047	5,679	1,045
Upfront and Milestone Payments | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,419	6,046	1,794
Upfront and Milestone Payments | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	273	273	273
Upfront and Milestone Payments | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0	0
Upfront and Milestone Payments | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0	0
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,500	2,500	1,875
Upfront and Milestone Payments | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	500	500
Upfront and Milestone Payments | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,389	3,933
Upfront and Milestone Payments | Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	185	46
Upfront and Milestone Payments | Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,000	167
Upfront and Milestone Payments | Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	417
Upfront and Milestone Payments | Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	361
Upfront and Milestone Payments | Intrexon T1D Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	821
Upfront and Milestone Payments | AD Skincare, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	241
Upfront and Milestone Payments | Genten Therapeutics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	122
Upfront and Milestone Payments | CRS Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	57
Upfront and Milestone Payments | Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,572	10,514	2,061
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	75,438	55,308	35,587
Research and Development Services | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	22,307	16,451	12,044
Research and Development Services | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,705	856	598
Research and Development Services | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,523	6,133	4,398
Research and Development Services | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,844	3,556	1,510
Research and Development Services | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,141	4,115	2,832
Research and Development Services | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,934	2,540	2,799
Research and Development Services | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	15,052	10,947	4,227
Research and Development Services | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	778	741
Research and Development Services | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,803	795
Research and Development Services | Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,529	220
Research and Development Services | Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,169	0
Research and Development Services | Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	375
Research and Development Services | Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	878
Research and Development Services | Intrexon T1D Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,087
Research and Development Services | AD Skincare, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	454
Research and Development Services | Genten Therapeutics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	264
Research and Development Services | CRS Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	91
Research and Development Services | Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 7,504	$ 8,954	$ 7,179

Collaboration and Licensing R78

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Current portion of deferred revenue	$ 53,364	$ 35,366
Long-term portion of deferred revenue	256,778	162,363
Deferred revenue	310,142	197,729
Upfront and milestone payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	297,867	181,331
Prepaid research and development services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	6,015	10,938
Prepaid product and service revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	5,554	4,759
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 706	$ 701

Collaboration and Licensing R79

Collaboration and Licensing Revenue - Summary of Deferred Revenue by Collaborator (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	$ 310,142	$ 197,729
Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	297,867	181,331
ZIOPHARM Oncology, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	138,809	30,338
Oragenics, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	7,766	8,813
Fibrocell Science, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	19,026	21,445
Genopaver, LLC | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	1,977	2,250
Intrexon Energy Partners, LLC | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	18,125	20,625
Persea Bio, LLC | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	4,000	4,500
Ares Trading S.A. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	47,178	53,567
Thrive Agrobiotics, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	1,436	1,621
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	15,833	17,833
Exotech Bio, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	4,583	0
Relieve Genetics, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	3,972	0
Intrexon T1D Partners, LLC | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	8,653	0
AD Skincare, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	4,092	0
Genten Therapeutics, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	4,176	0
CRS Bio, Inc. | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	1,949	0
Other | Upfront and Milestone Payments
Summary of Deferred Revenue by Collaborator [Line Items]
Deferred revenue	$ 16,292	$ 20,339

Collaboration and Licensing R80

Collaboration and Licensing Revenue - Additional Information (Details)

1 Months Ended

5 Months Ended

12 Months Ended

Sep. 30, 2016USD ($)

Jun. 30, 2016USD ($)shares

Mar. 31, 2016USD ($)

Dec. 31, 2015USD ($)shares

Sep. 30, 2015USD ($)

Jun. 30, 2015USD ($)

May 31, 2015USD ($)target

Dec. 31, 2014USD ($)

Mar. 31, 2014USD ($)

Jan. 31, 2014USD ($)shares

Dec. 31, 2013shares

Sep. 30, 2013USD ($)shares

Jun. 30, 2013USD ($)shares

Mar. 31, 2013USD ($)

Feb. 28, 2013

Oct. 31, 2012USD ($)shares

Jun. 30, 2012USD ($)shares

Jan. 31, 2011USD ($)shares

May 31, 2016

Dec. 31, 2016USD ($)

Dec. 31, 2015USD ($)

Dec. 31, 2014USD ($)

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

$ 109,871,000

$ 87,821,000

$ 45,212,000

Deferred revenue

$ 197,729,000

310,142,000

197,729,000

Trade, net

25,101,000

21,637,000

25,101,000

Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

34,433,000

32,513,000

9,625,000

Deferred revenue

181,331,000

297,867,000

181,331,000

Prepaid research and development services

Collaboration Agreements [Line Items]

Deferred revenue

10,938,000

6,015,000

10,938,000

ZIOPHARM ECC 1

Collaboration Agreements [Line Items]

Percentage of shares outstanding at the date of achievement of future milestone

7.495%

Required notice period for voluntary termination of collaborative agreement

90 days

ZIOPHARM ECC 1 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

3,636,926

Collaborative agreement, consideration received, value

$ 17,457,000

ZIOPHARM ECC 1 | Milestone One | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

3,636,926

Collaborative agreement, consideration received, value

$ 18,330,000

ZIOPHARM ECC 1 Separate Unit Of Accounting | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

1,115,000

ZIOPHARM ECC 1 Unit of Accounting 1 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Deferred revenue

$ 16,342,000

ZIOPHARM Oncology, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

33,836,000

19,306,000

14,621,000

Royalty rate as a percentage of net profit

20.00%

50.00%

ZIOPHARM Oncology, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

11,529,000

2,855,000

2,577,000

Deferred revenue

30,338,000

138,809,000

30,338,000

ZIOPHARM Oncology, Inc. | Other Contractual Payments | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 120,000,000

Collaborative arrangement consideration received, number of preferred shares (in shares) | shares

100,000

Ares Trading S.A.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

10,192,000

4,728,000

Required notice period for voluntary termination of collaborative agreement

90 days

Trade, net

3,750,000

Collaborative agreement, additional target fee

$ 5,000,000

Ares Trading S.A. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

6,389,000

3,933,000

Deferred revenue

$ 53,567,000

47,178,000

53,567,000

Ares Trading S.A. | Prepaid research and development services

Collaboration Agreements [Line Items]

Deferred revenue

$ 10,000,000

Collaborative agreement, consideration receivable, minimum targets required | target

2

Collaborative agreement, consideration receivable, collection period

2 years

Ares Trading S.A. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 115,000,000

ZIOPHARM ECC 2

Collaboration Agreements [Line Items]

Required notice period for voluntary termination of collaborative agreement

90 days

ZIOPHARM ECC 2 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 10,000,000

Oragenics ECC 1

Collaboration Agreements [Line Items]

Percentage of shares outstanding at the date of achievement of future milestone

1.00%

Required notice period for voluntary termination of collaborative agreement

90 days

Royalty rate as a percentage of net profit

25.00%

Percentage of shares outstanding at the date of achievement of future milestone 2

1.50%

Percentage of shares outstanding at the date of achievement of future milestone 3

2.00%

Percentage of shares outstanding at the date of achievement of future milestone 4

2.50%

Percentage of shares outstanding at the date of achievement of future milestone 5

3.00%

Oragenics ECC 1 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

4,392,425

Collaborative agreement, consideration received, value

$ 6,588,000

Oragenics ECC 2 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

1,348,000

Collaborative agreement, consideration received, value

$ 3,503,000

Collaborative agreement, consideration received, value of convertible promissory note

$ 1,956,000

Conversion of promissory note into common stock (in shares) | shares

698,241

Oragenics ECC 3

Collaboration Agreements [Line Items]

Required notice period for voluntary termination of collaborative agreement

90 days

Oragenics ECC 3 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value of convertible promissory note

$ 5,000,000

Conversion of promissory note into common stock (in shares) | shares

3,381,004

Fibrocell ECC 1

Collaboration Agreements [Line Items]

Required notice period for voluntary termination of collaborative agreement

90 days

Royalty rate as a percentage of net sales, tier 1

7.00%

Level of net sales at which royalty rate changes to tier 2

$ 25,000,000

Royalty rate as a percentage of net sales, tier 2

14.00%

Royalty rate of savings from improvement

33.00%

Fibrocell ECC 1 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

1,317,520

Collaborative agreement, consideration received, value

$ 7,576,000

Fibrocell ECC 1 | Supplemental Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received (in shares) | shares

1,024,590

1,243,781

Collaborative agreement, consideration received, value

$ 5,225,000

$ 7,612,000

Fibrocell ECC 2

Collaboration Agreements [Line Items]

Required notice period for voluntary termination of collaborative agreement

90 days

Maximum milestone payments required upon successful achievement, first product

$ 30,000,000

Maximum milestone payments required upon successful achievement, per each additional product

30,000,000

Maximum milestone payments required for certain sales milestones, per product

22,500,000

Fibrocell ECC 2 | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

10,000,000

Genopaver, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

6,117,000

3,829,000

1,783,000

Required notice period for voluntary termination of collaborative agreement

90 days

Genopaver, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

273,000

273,000

273,000

Deferred revenue

2,250,000

1,977,000

2,250,000

Genopaver, LLC | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 3,000,000

AquaBounty Technologies, Inc.

Collaboration Agreements [Line Items]

Royalty rate as a percentage of gross profit

16.66%

S & I Ophthalmic, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

6,141,000

4,115,000

2,832,000

Required notice period for voluntary termination of collaborative agreement

90 days

S & I Ophthalmic, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

0

0

0

OvaXon, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

2,934,000

2,540,000

2,799,000

Required notice period for voluntary termination of collaborative agreement

90 days

OvaXon, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

0

0

0

Intrexon Energy Partners, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

17,552,000

13,447,000

6,102,000

Required notice period for voluntary termination of collaborative agreement

90 days

Intrexon Energy Partners, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

2,500,000

2,500,000

$ 1,875,000

Deferred revenue

20,625,000

18,125,000

20,625,000

Intrexon Energy Partners, LLC | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 25,000,000

Persea Bio, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

1,278,000

1,241,000

Required notice period for voluntary termination of collaborative agreement

90 days

Persea Bio, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

500,000

500,000

Deferred revenue

4,500,000

4,000,000

4,500,000

Persea Bio, LLC | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 5,000,000

Thrive Agrobiotics, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

1,714,000

266,000

Required notice period for voluntary termination of collaborative agreement

90 days

Thrive Agrobiotics, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

185,000

46,000

Deferred revenue

$ 1,621,000

1,436,000

1,621,000

Thrive Agrobiotics, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 1,667,000

Intrexon Energy Partners II, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

3,169,000

167,000

Required notice period for voluntary termination of collaborative agreement

90 days

Intrexon Energy Partners II, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

2,000,000

167,000

Deferred revenue

$ 17,833,000

15,833,000

17,833,000

Intrexon Energy Partners II, LLC | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

18,000,000

Exotech Bio, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

792,000

Required notice period for voluntary termination of collaborative agreement

90 days

Exotech Bio, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

417,000

Deferred revenue

0

4,583,000

0

Exotech Bio, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 5,000,000

Relieve Genetics, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

1,239,000

Required notice period for voluntary termination of collaborative agreement

90 days

Relieve Genetics, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

361,000

Deferred revenue

0

3,972,000

0

Relieve Genetics, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 4,333,000

Intrexon T1D Partners, LLC

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

1,908,000

Required notice period for voluntary termination of collaborative agreement

90 days

Intrexon T1D Partners, LLC | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

821,000

Deferred revenue

0

8,653,000

0

Intrexon T1D Partners, LLC | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 10,000,000

AD Skincare, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

695,000

Required notice period for voluntary termination of collaborative agreement

90 days

AD Skincare, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

241,000

Deferred revenue

0

4,092,000

0

AD Skincare, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 4,333,000

Genten Therapeutics, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

386,000

Required notice period for voluntary termination of collaborative agreement

90 days

Genten Therapeutics, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

122,000

Deferred revenue

0

4,176,000

0

Genten Therapeutics, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 3,000,000

Collaborative agreement, consideration received, cash

$ 1,500,000

CRS Bio, Inc.

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

148,000

Required notice period for voluntary termination of collaborative agreement

90 days

CRS Bio, Inc. | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaboration and licensing revenues

57,000

Deferred revenue

$ 0

$ 1,949,000

$ 0

CRS Bio, Inc. | Upfront | Upfront and Milestone Payments

Collaboration Agreements [Line Items]

Collaborative agreement, consideration received, value

$ 2,100,000

ZIOPHARM Oncology, Inc. | Ares Trading S.A.

Collaboration Agreements [Line Items]

Collaboration agreement, percent of collaboration payments

50.00%

Payments to related parties

57,500,000

Maximum | Ares Trading S.A.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

413,000,000

Milestone payments required upon successful achievement, one-time

$ 50,000,000

Maximum | Oragenics ECC 3

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

22,000,000

Milestone payments required upon successful achievement, one-time

$ 10,000,000

Maximum | Thrive Agrobiotics, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

$ 5,500,000

Maximum | Exotech Bio, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

52,500,000

Maximum | Relieve Genetics, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

$ 52,500,000

Maximum | AD Skincare, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

2,000,000

Milestone payments required upon successful achievement, one-time

$ 17,000,000

Maximum | Genten Therapeutics, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

82,000,000

Maximum | CRS Bio, Inc.

Collaboration Agreements [Line Items]

Milestone payments required upon successful achievement, per product

$ 75,000,000

Short-term and Long-term Inve81

Short-term and Long-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Short-term and Long-term Investments (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 180,684	$ 208,494
Gross Unrealized Gains	5	21
Gross Unrealized Losses	(94)	(540)
Aggregate Fair Value	180,595	207,975
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	180,412	208,223
Gross Unrealized Gains	5	21
Gross Unrealized Losses	(94)	(540)
Aggregate Fair Value	180,323	207,704
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	272	271
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Aggregate Fair Value	$ 272	$ 271

Short-term and Long-term Inve82

Short-term and Long-term Investments - Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Investments, Debt and Equity Securities [Abstract]
Due within one year	$ 174,602
After one year through two years	5,993
Total	$ 180,595	$ 207,975

Investment in Preferred Stock -

Investment in Preferred Stock - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Jun. 30, 2016	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Schedule of Investments [Line Items]
Noncash dividend income on preferred shares		$ 7,421	$ 0	$ 0
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, stated value (in usd per share)	$ 1,200
Threshold consecutive trading days, conversion in shares		20 days
Preferred shares, dividend rate (in usd per share)		$ 12
Preferred shares, dividend rate, for unconverted shares after conversion event (in usd per share)		24
Minimum | ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, conversion calculation, divisor (in usd per share)		$ 1
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Dividend income, number of preferred shares received (in shares)		6,184
Other Contractual Payments | Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Collaborative arrangement consideration received, number of preferred shares (in shares)	100,000

Investment in Preferred Stock84

Investment in Preferred Stock - Schedule of Changes in Level 3 Investments (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Receipt of Preferred Shares as consideration for amendments to collaboration agreements	$ 120,000	$ 0	$ 0
Additional Preferred Shares received as dividend income	7,421	0	$ 0
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Beginning balance	0
Receipt of Preferred Shares as consideration for amendments to collaboration agreements	120,000
Additional Preferred Shares received as dividend income	7,421
Unrealized appreciation in the fair value of the investment in preferred stock	2,124
Ending balance	$ 129,545	$ 0

Fair Value Measurements - Summa

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Assets
Fair value of assets	$ 335,307	$ 291,762
US government debt securities
Assets
Fair value of assets	180,323	207,704
Equity securities
Assets
Fair value of assets	23,522	83,653
Preferred stock
Assets
Fair value of assets	129,545
Other
Assets
Fair value of assets	1,917	405
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of assets	15,544	65,850
Quoted Prices in Active Markets (Level 1) | US government debt securities
Assets
Fair value of assets	0	0
Quoted Prices in Active Markets (Level 1) | Equity securities
Assets
Fair value of assets	15,544	65,850
Quoted Prices in Active Markets (Level 1) | Preferred stock
Assets
Fair value of assets	0
Quoted Prices in Active Markets (Level 1) | Other
Assets
Fair value of assets	0	0
Significant Other Observable Inputs (Level 2)
Assets
Fair value of assets	190,218	225,912
Significant Other Observable Inputs (Level 2) | US government debt securities
Assets
Fair value of assets	180,323	207,704
Significant Other Observable Inputs (Level 2) | Equity securities
Assets
Fair value of assets	7,978	17,803
Significant Other Observable Inputs (Level 2) | Preferred stock
Assets
Fair value of assets	0
Significant Other Observable Inputs (Level 2) | Other
Assets
Fair value of assets	1,917	405
Significant Unobservable Inputs (Level 3)
Assets
Fair value of assets	129,545	0
Significant Unobservable Inputs (Level 3) | US government debt securities
Assets
Fair value of assets	0	0
Significant Unobservable Inputs (Level 3) | Equity securities
Assets
Fair value of assets	0	0
Significant Unobservable Inputs (Level 3) | Preferred stock
Assets
Fair value of assets	129,545
Significant Unobservable Inputs (Level 3) | Other
Assets
Fair value of assets	$ 0	$ 0

Fair Value Measurements - Addit

Fair Value Measurements - Additional Information (Details) $ in Thousands	Dec. 31, 2016USD ($)
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of liabilities	$ 2,081

Fair Value Measurements - Sched

Fair Value Measurements - Schedule of Changes in Level 3 Liabilities (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Contingent consideration assumed in asset acquisition	$ 3,660	$ 0	$ 0
Payment of contingent consideration	(1,583)	0	$ 0
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Beginning balance	0
Contingent consideration assumed in asset acquisition	3,660
Payment of contingent consideration	(1,583)
Change in fair value of contingent consideration	4
Ending Balance	$ 2,081	$ 0

Inventory - Schedule of Invento

Inventory - Schedule of Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Inventory [Line Items]
Inventory	$ 21,139	$ 26,563
Supplies, embryos and other production materials
Inventory [Line Items]
Inventory	1,835	1,402
Work in process
Inventory [Line Items]
Inventory	5,466	6,290
Livestock
Inventory [Line Items]
Inventory	11,752	16,907
Feed
Inventory [Line Items]
Inventory	$ 2,086	$ 1,964

Property, Plant and Equipment89

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 11,324	$ 9,119
Buildings and building improvements	8,123	7,520
Furniture and fixtures	2,176	1,283
Equipment	44,392	36,016
Leasehold improvements	15,105	6,888
Breeding stock	3,893	0
Computer hardware and software	6,844	5,960
Construction and other assets in progress	6,865	2,193
Property, plant and equipment, gross	98,722	68,979
Less: Accumulated depreciation and amortization	(34,050)	(26,240)
Property, plant and equipment, net	$ 64,672	$ 42,739

Property, Plant and Equipment90

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 9,387	$ 7,872	$ 6,178

Goodwill and Intangible Asset91

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Goodwill and Intangible Assets Disclosure [Abstract]
Accumulated impairment losses	$ 0	$ 0
Amortization expense	15,185,000	$ 9,871,000	$ 4,237,000
Total estimated amortization expense, 2017	18,002,000
Total estimated amortization expense, 2018	17,391,000
Total estimated amortization expense, 2019	17,068,000
Total estimated amortization expense, 2020	16,648,000
Total estimated amortization expense, 2021	16,431,000
Total estimated amortization expense, thereafter	$ 132,180,000

Goodwill and Intangible Asset92

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Goodwill
Beginning Balance	$ 165,169	$ 101,059
Acquisitions	0	67,403
Foreign currency translation adjustments	(7,994)	(3,293)
Ending Balance	$ 157,175	$ 165,169

Goodwill and Intangible Asset93

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 262,166	$ 269,227
Accumulated Amortization	(36,551)	(21,692)
Net	225,615	247,535
Patents, developed technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	236,401	157,411
Accumulated Amortization	(29,748)	(17,775)
Net	206,653	139,636
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(4,672)	(2,739)
Net	6,028	7,961
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(1,792)	(1,018)
Net	5,008	5,782
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	370	384
Accumulated Amortization	(339)	(160)
Net	31	224
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	7,895	93,932
Net	$ 7,895	$ 93,932
Weighted Average | Patents, developed technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	15 years 10 months 24 days
Weighted Average | Customer relationships
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	6 years 6 months
Weighted Average | Trademarks
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	9 years 3 months 18 days
Weighted Average | Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	2 years

Lines of Credit and Long Term94

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Revolving Credit Facility	12 Months Ended
	Dec. 31, 2016USD ($)
Trans Ova Genetics, LC | First National Bank of Omaha
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 6,000,000
Line of credit facility, interest rate at period end	3.57%
Line of credit outstanding	$ 322,000
Trans Ova Genetics, LC | First National Bank of Omaha | London Interbank Offered Rate (LIBOR)
Line of Credit Facility [Line Items]
Debt instrument, basis spread on variable rate	2.95%
Exemplar Genetics, LLC | American State Bank
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 700,000
Debt instrument, interest rate, stated percentage	4.50%
Line of credit outstanding	$ 498,000
Minimum | Trans Ova Genetics, LC | First National Bank of Omaha
Line of Credit Facility [Line Items]
Debt instrument, interest rate, stated percentage	3.00%

Lines of Credit and Long Term95

Lines of Credit and Long Term Debt - Components of Long Term Debt (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Long term debt	$ 7,948	$ 8,528
Less current portion	386	930
Long term debt, less current portion	7,562	7,598
Notes payable
Debt Instrument [Line Items]
Long term debt	5,453	6,477
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	1,896	1,807
Other
Debt Instrument [Line Items]
Long term debt	$ 599	$ 244

Lines of Credit and Long Term96

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Dec. 31, 2016USD ($)
Debt Disclosure [Abstract]
2,017	$ 386
2,018	408
2,019	365
2,020	336
2,021	765
Thereafter	3,792
Total	$ 6,052

Lines of Credit and Long Term97

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Mar. 31, 2013
Debt Instrument [Line Items]
Long term debt	$ 7,948,000	$ 8,528,000
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Long term debt	5,246,000
Debt instrument, periodic payment	$ 39,000
Debt instrument, interest rate, stated percentage	3.95%
Notes payable
Debt Instrument [Line Items]
Long term debt	$ 5,453,000	6,477,000
Notes payable | Exemplar Genetics, LLC
Debt Instrument [Line Items]
Long term debt	207,000
Notes payable | Exemplar Genetics, LLC | Minimum
Debt Instrument [Line Items]
Debt instrument, periodic payment	$ 1,000
Debt instrument, interest rate, stated percentage	0.00%
Notes payable | Exemplar Genetics, LLC | Maximum
Debt Instrument [Line Items]
Debt instrument, periodic payment	$ 4,000
Debt instrument, interest rate, stated percentage	3.00%
Other
Debt Instrument [Line Items]
Long term debt	$ 599,000	244,000
Other | AquaBounty Technologies, Inc. | Finance PEI
Debt Instrument [Line Items]
Long term debt	527,000
Debt instrument, periodic payment	$ 4,000
Debt instrument, interest rate, stated percentage	4.00%
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	$ 1,896,000	$ 1,807,000
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long term debt	1,896,000
Amount available under the grant for research and development	$ 2,136,000
Claims period	5 years
Royalty on products	10.00%
Amount claimed			$ 1,952,000
Long term debt			1,107,000
Accreted difference between face value of amount drawn and acquisition date fair value			$ 845,000

Income Taxes - Components of Lo

Income Taxes - Components of Loss Before Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax [Line Items]
Loss before income taxes	$ (194,151)	$ (86,978)	$ (85,719)
Domestic
Income Tax [Line Items]
Loss before income taxes	(157,067)	(69,287)	(83,256)
Foreign
Income Tax [Line Items]
Loss before income taxes	$ (37,084)	$ (17,691)	$ (2,463)

Income Taxes - Components of In

Income Taxes - Components of Income Tax Expense (Benefit) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
U.S. federal income taxes:
Current	$ (17)	$ 22	$ 0
Deferred	1,396	1,732	0
Foreign income taxes:
Current	(393)	(123)	(103)
Deferred	(5,177)	(1,003)	0
State income taxes:
Deferred	314	388	0
Total income tax expense (benefit)	$ (3,877)	$ 1,016	$ (103)

Income Taxes - Schedule of Effe

Income Taxes - Schedule of Effective Income Tax Rate Reconciliation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Computed statutory income tax benefit	$ (66,011)	$ (29,573)	$ (29,144)
State and provincial income tax benefit, net of federal income taxes	(7,905)	(3,157)	(3,544)
Nondeductible stock based compensation	3,321	3,182	1,386
Nondeductible officer compensation	0	2,433	0
Contribution of services by shareholder	0	0	677
Research and development tax incentives	(6,350)	(348)	258
Acquisition and internal restructuring transaction costs	571	883	0
Enacted change in tax rates	0	(961)	0
U.S.-foreign rate differential	3,463	620	0
Other, net	1,485	(98)	1,503
Income tax reconciliation income tax benefit before valuation allowance, total	(71,426)	(27,019)	(28,864)
Change in valuation allowance for deferred tax assets	67,549	28,035	28,761
Total income tax expense (benefit)	$ (3,877)	$ 1,016	$ (103)

Income Taxes - Schedule of Defe

Income Taxes - Schedule of Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Deferred tax assets
Allowance for doubtful accounts	$ 1,676	$ 1,056
Inventory	447	967
Equity securities and investments in affiliates	31,729	10,413
Accrued liabilities and long-term debt	4,168	4,585
Stock-based compensation	8,460	7,223
Deferred revenue	68,056	31,637
Research and development tax credits	10,396	9,113
Net operating and capital loss carryforwards	144,502	135,633
Total deferred tax assets	269,434	200,627
Less: Valuation allowance	256,165	190,174	$ 161,660	$ 131,985
Net deferred tax assets	13,269	10,453
Deferred tax liabilities
Property, plant and equipment	406	160
Intangible assets	29,870	32,095
Total deferred tax liabilities	30,276	32,255
Net deferred tax liabilities	$ (17,007)	$ (21,802)

Income Taxes - Summary of Valua

Income Taxes - Summary of Valuation Allowance (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Valuation Allowance
Valuation allowance at beginning of year	$ 190,174	$ 161,660	$ 131,985
Increase (decrease) in valuation allowance as a result of mergers and acquisitions, net	(1,416)	1,228	914
Increase in valuation allowance as a result of current year operations	67,549	28,035	28,761
Decrease in valuation allowance as a result of foreign currency translation adjustment	(142)	(749)	0
Valuation allowance at end of year	$ 256,165	$ 190,174	$ 161,660

Income Taxes - Additional Infor

Income Taxes - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Operating Loss Carryforwards [Line Items]
Federal corporate income tax rate	34.00%	34.00%	34.00%
Federal and state research and development tax credits	$ 10,396	$ 9,113
Retained earnings (accumulated deficit)	(729,341)	$ (542,729)
AquaBounty Technologies, Inc.
Operating Loss Carryforwards [Line Items]
Annual usage limit of operating loss carryforwards	$ 900
Expiration date of Federal income tax loss carryforwards	2,018
Ownership percentage in AquaBounty (more than)				50.00%
Foreign Subsidiaries
Operating Loss Carryforwards [Line Items]
Retained earnings (accumulated deficit)	$ (27,885)
Domestic
Operating Loss Carryforwards [Line Items]
Operating losses subject to annual limits	15,100
Annual usage limit of operating loss carryforwards	1,500
Net operating losses inherited via acquisition	18,600
Operating loss carryforwards	252,971
Federal and state research and development tax credits	$ 7,514
Expiration date of Federal income tax loss carryforwards	2,022
Domestic | AquaBounty Technologies, Inc.
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	$ 22,215
Domestic | Biological & Popular Culture, Inc.
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	1,402
Domestic | Share Based Compensation
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	44,929
Foreign
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	119,155
Foreign | AquaBounty Technologies, Inc.
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	12,925
Tax credit	$ 2,428

Shareholders' Equity - Componen

Shareholders' Equity - Components of Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ 560,237	$ 694,078
Unrealized loss on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(89)	(519)
Loss on foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(36,113)	(12,233)
Total accumulated other comprehensive loss
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ (36,202)	$ (12,752)

Shareholders' Equity - Addition

Shareholders' Equity - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended				12 Months Ended
	Aug. 31, 2015	Jun. 30, 2015	Jan. 31, 2015	Mar. 31, 2014	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Class of Stock [Line Items]
Shares issued in public or private offerings, shares	5,609,756		4,312,500	972,004
Value of shares issued in public or private offerings	$ 218,193		$ 110,041			$ 328,234	$ 25,000
Underwriting discounts and commissions	11,500		6,086
Capitalized offering expenses	$ 306		$ 311
Proceeds from issuance of shares in a private placement				$ 25,000	$ 0	0	$ 25,000
Affiliates Of Third Security
Class of Stock [Line Items]
Shares issued in public or private offerings, shares			555,556	243,001
Value of shares issued in public or private offerings				$ 6,250
ZIOPHARM Oncology, Inc.
Class of Stock [Line Items]
Noncash dividend, shares		17,830,305
Realized investment gain						$ 81,401
Intrexon Stock Option Plans
Class of Stock [Line Items]
Adjustment due to dividend (in shares)						312,795
Adjustment due to dividend (in usd per share)						$ 25.40

Share-Based Payments - Schedule

Share-Based Payments - Schedule of Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation cost	$ 42,202	$ 38,667	$ 21,849
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation cost	81	95	14
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation cost	274	354	142
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation cost	9,251	8,614	4,817
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation cost	$ 32,596	$ 29,604	$ 16,876

Share-Based Payments - Intrexon

Share-Based Payments - Intrexon Stock Option Plans - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares		12 Months Ended
		Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Number of Shares
Balances at beginning of period (in shares)		11,043,528	8,323,544	2,840,648
Granted (in shares)		4,644,860	5,051,500	7,655,050
Adjustment due to dividend (in shares)			312,795
Exercised (in shares)		(1,210,840)	(1,029,291)	(315,964)
Forfeited (in shares)		(2,760,809)	(1,610,335)	(1,855,578)
Expired (in shares)		(76,356)	(4,685)	(612)
Balances at period end (in shares)		11,640,383	11,043,528	8,323,544	2,840,648
Weighted Average Exercise Price (usd per share)
Balances at beginning of period (in usd per share)		$ 32.66	$ 22.59	$ 8.27
Granted (in usd per share)		29.39	45.82	27.51
Adjustment due to dividend (in usd per share)			25.40
Exercised (in usd per share)		(15.83)	(15.16)	(4.80)
Forfeited (in usd per share)		(40.34)	(26.75)	(24)
Expired (in usd per share)		(37.81)	(28.29)	(7.12)
Balances at period end (in usd per share)		$ 31.25	32.66	$ 22.59	$ 8.27
Additional Disclosures
Exercisable at period end (in shares)		3,418,035
Vested and expected to vest at period end (in shares)	[1]	10,019,307
Options exercisable, weighted average exercise price (in usd per share)		$ 28.09	$ 18.31
Vested and expected to vest, weighted average exercise price (in usd per share)	[1]	$ 31.04
Balances at period end, weighted average remaining contractual period		8 years 2 months 15 days	8 years 5 months 27 days	8 years 7 months 21 days	7 years 9 months
Exercisable at period end, weighted average remaining contractual period		6 years 10 months 17 days
Vested and expected to vest at period end, weighted average remaining contractual period	[1]	8 years 1 month
[1]	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Share-Based Payments - Intre108

Share-Based Payments - Intrexon Stock Option Plans - Summary of Information About Stock Options Outstanding (Details) - Intrexon Stock Option Plans - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Options outstanding, number of options (in shares)	11,640,383	11,043,528
Options outstanding, weighted average exercise price (in usd per share)	$ 31.25	$ 32.66	$ 22.59	$ 8.27
Options outstanding, weighted average remaining life (in years)	8 years 2 months 15 days	8 years 5 months 27 days
Options outstanding, aggregate intrinsic value	$ 14,969	$ 47,295
Options exercisable, number of options (in shares)	3,418,035	2,494,426
Options exercisable, weighted average exercise price (in usd per share)	$ 28.09	$ 18.31
Options exercisable, weighted average remaining life (in years)	6 years 10 months 17 days	6 years 9 months 26 days
Options exercisable, aggregate intrinsic value	$ 11,852	$ 31,251
Price range 1
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Stock options, exercise price range, lower limit (in usd per share)	$ 2.65	$ 0.38
Stock options, exercise price range, upper limit (in usd per share)	$ 9.34	$ 9.34
Options outstanding, number of options (in shares)	562,951	1,261,192
Options outstanding, weighted average exercise price (in usd per share)	$ 6.23	$ 6.40
Options outstanding, weighted average remaining life (in years)	4 years 1 month 18 days	5 years 4 months 24 days
Options outstanding, aggregate intrinsic value	$ 10,172	$ 29,956
Options exercisable, number of options (in shares)	525,755	1,147,978
Options exercisable, weighted average exercise price (in usd per share)	$ 6.01	$ 6.19
Options exercisable, weighted average remaining life (in years)	3 years 11 months 20 days	5 years 3 months
Options exercisable, aggregate intrinsic value	$ 9,615	$ 27,507
Price range 2
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Stock options, exercise price range, lower limit (in usd per share)	$ 15.21	$ 15.21
Stock options, exercise price range, upper limit (in usd per share)	$ 27.19	$ 28.93
Options outstanding, number of options (in shares)	2,785,705	2,682,516
Options outstanding, weighted average exercise price (in usd per share)	$ 23.47	$ 24.25
Options outstanding, weighted average remaining life (in years)	8 years 5 months 45 days	8 years 5 months 5 days
Options outstanding, aggregate intrinsic value	$ 4,797	$ 15,831
Options exercisable, number of options (in shares)	684,704	602,023
Options exercisable, weighted average exercise price (in usd per share)	$ 21.07	$ 24.43
Options exercisable, weighted average remaining life (in years)	7 years 3 months 15 days	8 years 4 months 10 days
Options exercisable, aggregate intrinsic value	$ 2,237	$ 3,445
Price range 3
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Stock options, exercise price range, lower limit (in usd per share)	$ 27.21	$ 29.14
Stock options, exercise price range, upper limit (in usd per share)	$ 29.68	$ 29.68
Options outstanding, number of options (in shares)	3,147,242	2,895,885
Options outstanding, weighted average exercise price (in usd per share)	$ 29.30	$ 29.63
Options outstanding, weighted average remaining life (in years)	7 years 5 months 42 days	8 years 5 months 9 days
Options outstanding, aggregate intrinsic value	$ 0	$ 1,508
Options exercisable, number of options (in shares)	1,400,707	635,743
Options exercisable, weighted average exercise price (in usd per share)	$ 29.35	$ 29.68
Options exercisable, weighted average remaining life (in years)	7 years 3 months 22 days	7 years 11 months 27 days
Options exercisable, aggregate intrinsic value	$ 0	$ 299
Price range 4
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Stock options, exercise price range, lower limit (in usd per share)	$ 29.70	$ 30.10
Stock options, exercise price range, upper limit (in usd per share)	$ 42.22	$ 56.77
Options outstanding, number of options (in shares)	3,590,423	3,118,935
Options outstanding, weighted average exercise price (in usd per share)	$ 32.89	$ 44.48
Options outstanding, weighted average remaining life (in years)	9 years 33 days	9 years 5 months 16 days
Options outstanding, aggregate intrinsic value	$ 0	$ 0
Options exercisable, number of options (in shares)	345,274	108,682
Options exercisable, weighted average exercise price (in usd per share)	$ 37.06	$ 45.87
Options exercisable, weighted average remaining life (in years)	6 years 10 months 6 days	8 years 7 days
Options exercisable, aggregate intrinsic value	$ 0	$ 0
Price range 5
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Stock options, exercise price range, lower limit (in usd per share)	$ 43.99	$ 57.95
Stock options, exercise price range, upper limit (in usd per share)	$ 65.34	$ 65.34
Options outstanding, number of options (in shares)	1,554,062	1,085,000
Options outstanding, weighted average exercise price (in usd per share)	$ 54.40	$ 58.07
Options outstanding, weighted average remaining life (in years)	8 years 4 months 35 days	9 years 6 months 18 days
Options outstanding, aggregate intrinsic value	$ 0	$ 0
Options exercisable, number of options (in shares)	461,595	0
Options exercisable, weighted average exercise price (in usd per share)	$ 53.06	$ 0
Options exercisable, weighted average remaining life (in years)	8 years 3 months 30 days	0 years
Options exercisable, aggregate intrinsic value	$ 0	$ 0

Share-Based Payments - Addition

Share-Based Payments - Additional Information (Details) $ / shares in Units, $ in Thousands	Jan. 05, 2017	Dec. 31, 2016USD ($)$ / sharesshares	Oct. 31, 2016	Nov. 30, 2015	Dec. 31, 2016USD ($)$ / sharesshares	Dec. 31, 2015USD ($)$ / sharesshares	Dec. 31, 2014USD ($)$ / sharesshares	Apr. 30, 2016shares	Dec. 31, 2013$ / sharesshares	Aug. 31, 2013shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services | $					$ 10,777	$ 2,169	$ 486
Contribution of services by shareholder | $					$ 0	$ 0	$ 1,991
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)										0
Options outstanding (in shares)		562,951			562,951
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)		4,291,530			4,291,530
Options outstanding (in shares)		10,077,432			10,077,432
Number of authorized awards (in shares)		16,000,000			16,000,000
Intrexon Stock Option Plan - Other Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		1,000,000			1,000,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		11,640,383			11,640,383	11,043,528	8,323,544		2,840,648
Term at issuance of option					10 years
Vesting period of option					4 years
Unrecognized compensation costs related to unvested awards | $		$ 94,038			$ 94,038	$ 113,655	$ 62,281
Recognized over weighted-average period					3 years	3 years	3 years
Weighted average grant date fair value of options granted (in usd per share) | $ / shares					$ 16.28	$ 25.96	$ 16.40
Aggregate intrinsic value of options exercised | $					$ 22,704	$ 24,675	$ 6,350
Options outstanding, weighted average exercise price (in usd per share) | $ / shares		$ 31.25			$ 31.25	$ 32.66	$ 22.59		$ 8.27
Options exercisable (in shares)		3,418,035			3,418,035
AquaBounty Stock Option Plan - 2006 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)								0
Options outstanding (in shares)		185,591			185,591	179,426
Options outstanding, weighted average exercise price (in usd per share) | $ / shares		$ 7.89			$ 7.89	$ 7.83
Options exercisable (in shares)		181,766			181,766
AquaBounty Stock Option Plan - 2016 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		0			0
Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Monthly base salary | $					$ 200
Lock-up period					3 years
Term of compensation arrangement		3 months	2 months	12 months
Contribution of services by shareholder | $							$ 1,991
Selling, general and administrative | Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services | $					$ 1,861	$ 314
AquaBounty Technologies, Inc. | Subsequent Event
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Reverse stock split ratio	1-for-30
Reverse stock split, conversion ratio	0.0333

License Agreement - Additional

License Agreement - Additional Information (Details)	1 Months Ended
	Jan. 31, 2015USD ($)shares
Other Commitments [Line Items]
Shares issued as consideration for licensing agreement, shares | shares	2,100,085
Research and development
Other Commitments [Line Items]
Payment of license fees	$ 59,579,000
ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, term	3 years
Minimum | ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, amount	$ 15,000,000
Maximum | ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, amount	$ 20,000,000

Commitments and Contingencies -

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Details) $ in Thousands	Dec. 31, 2016USD ($)
Commitments and Contingencies Disclosure [Abstract]
2,017	$ 5,503
2,018	5,774
2,019	5,515
2,020	5,566
2,021	4,936
Thereafter	20,179
Future minimum lease payments under operating leases, total	$ 47,473

Commitments and Contingencie112

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Leases [Abstract]
Rent expense, including other facility expenses	$ 8,593	$ 8,610	$ 8,511
Rental income under sublease agreement	1,051	$ 1,486	$ 908
Expected future rental income under sublease agreement, 2017	114
Expected future rental income under sublease agreement, 2018	80
Expected future rental income under sublease agreement, 2019	$ 67

Commitments and Contingencie113

Commitments and Contingencies - Contingencies - Additional Information (Details) $ in Thousands	Feb. 24, 2017	Jul. 31, 2016claim	May 31, 2016claim	Apr. 30, 2016USD ($)	Jul. 31, 2016claim	Sep. 30, 2016USD ($)	Apr. 30, 2016USD ($)
Licensing and patent infringement suit
Loss Contingencies [Line Items]
Damages awarded to (against) TransOva				$ 528
Cumulative payments for royalties							$ 3,170
Royalty payments not yet deposited						$ 2,759
Hoffman v Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al.
Loss Contingencies [Line Items]
Number of lawsuits | claim			2
Shareholder demand regarding Third Security Services Agreement and CEO Compensation
Loss Contingencies [Line Items]
Number of similar lawsuits | claim		2
Shareholder demand regarding allegations made by Seeking Alpha financial blog
Loss Contingencies [Line Items]
Number of lawsuits | claim					2
XY, LLC | Licensing and patent infringement suit
Loss Contingencies [Line Items]
Damages awarded to (against) TransOva				$ (6,066)
Selling, general and administrative | Licensing and patent infringement suit
Loss Contingencies [Line Items]
Litigation settlement expense						$ 4,228
Subsequent Event | Hoffman v Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al.
Loss Contingencies [Line Items]
Period of time for plaintiff to file amended claim for dismissed lawsuit	30 days

Related Party Transactions - Ad

Related Party Transactions - Additional Information (Details) - USD ($)

1 Months Ended

12 Months Ended

49 Months Ended

Dec. 31, 2016

Oct. 31, 2016

Sep. 30, 2016

Jun. 30, 2016

Nov. 30, 2015

Jul. 31, 2015

Mar. 31, 2015

Dec. 31, 2014

Sep. 30, 2014

Dec. 31, 2016

Dec. 31, 2015

Dec. 31, 2014

Feb. 28, 2015

Related Party Transaction [Line Items]

Shares issued as compensation for services

$ 10,777,000

$ 2,169,000

$ 486,000

Fair value of assets

$ 335,307,000

335,307,000

291,762,000

Other nonoperating income

1,700,000

1,314,000

(168,000)

Purchases of equity securities and warrants

2,308,000

17,080,000

19,496,000

Third Security, LLC

Related Party Transaction [Line Items]

Expense for services

$ 309,000

$ 428,000

$ 291,000

Services agreement, term

2 months

1 year

Shares issued as compensation for services, shares

337,163

48,678

Shares issued as compensation for services

$ 8,571,000

$ 1,375,000

ZIOPHARM Oncology, Inc.

Related Party Transaction [Line Items]

Common stock purchased from collaborative partners, value

$ 43,582,000

Oragenics, Inc.

Related Party Transaction [Line Items]

Common stock purchased from collaborative partners, shares

2,261,419

Price per share of common shares (in usd per share)

$ 0.52

Fibrocell Science, Inc.

Related Party Transaction [Line Items]

Payments to acquire convertible notes and warrants

$ 2,604,000

Common stock purchased from collaborative partners, shares

375,868

Price per share of common shares (in usd per share)

$ 5.80

AmpliPhi Biosciences Corporation

Related Party Transaction [Line Items]

Common stock purchased from collaborative partners, shares

278,788

Warrants purchased from collaborative partners, shares

69,696

Purchases of equity securities and warrants

$ 2,300,000

Histogenics Corporation

Related Party Transaction [Line Items]

Common stock purchased from collaborative partners, shares

1,772,364

Price per share of common shares (in usd per share)

$ 11

Note receivable interest rate

6.00%

Histogenics Corporation | Upfront and milestone payments | Upfront

Related Party Transaction [Line Items]

Collaborative agreement, consideration received, value of convertible promissory note

$ 10,000,000

Harvest Intrexon Enterprise Fund I, LP

Related Party Transaction [Line Items]

Other nonoperating income

2,483,000

$ 1,349,000

Common Stock | Third Security, LLC

Related Party Transaction [Line Items]

Expense for services

$ 800,000

Warrants | AmpliPhi Biosciences Corporation

Related Party Transaction [Line Items]

Purchases of equity securities and warrants

321,000

Common Stock | AmpliPhi Biosciences Corporation

Related Party Transaction [Line Items]

Purchases of equity securities and warrants

$ 1,979,000

Other assets | Convertible note and warrants | Fibrocell Science, Inc.

Related Party Transaction [Line Items]

Fair value of assets

$ 1,642,000

$ 1,642,000

Third Security, LLC | Chief Executive Officer

Related Party Transaction [Line Items]

Ownership interest

100.00%

100.00%

AmpliPhi Biosciences Corporation

Related Party Transaction [Line Items]

Realized investment gain (loss)

$ (4,098,000)

Net Loss per Share - Computatio

Net Loss per Share - Computation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Numerator:
Net loss attributable to Intrexon	$ (44,137)	$ (28,982)	$ (49,064)	$ (64,429)	$ (32,714)	$ (38,213)	$ (40,663)	$ 27,097	$ (186,612)	$ (84,493)	$ (81,822)
Denominator:
Weighted average shares outstanding, basic and diluted									117,983,836	111,066,352	99,170,653
Net loss attributable to Intrexon per share, basic and diluted	$ (0.37)	$ (0.24)	$ (0.42)	$ (0.55)					$ (1.58)	$ (0.76)	$ (0.83)

Net Loss per Share - Potentiall

Net Loss per Share - Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share (Details) - shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	11,640,383	11,238,247	8,676,027
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	11,640,383	11,043,528	8,323,544
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	0	194,719	352,483

Quarterly Financial Informat117

Quarterly Financial Information (Unaudited) - Schedule of Quarterly Financial Information (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 46,002	$ 48,985	$ 52,501	$ 43,438	$ 41,498	$ 53,367	$ 44,891	$ 33,849	$ 190,926	$ 173,605	$ 71,930
Operating loss	(32,590)	(28,821)	(23,222)	(40,533)	(34,395)	(7,916)	(17,430)	(87,123)	(125,166)	(146,864)	(69,962)
Net income (loss)	(44,912)	(30,011)	(50,031)	(65,320)	(33,275)	(39,029)	(41,494)	25,804	(190,274)	(87,994)	(85,616)
Net income (loss) attributable to Intrexon	$ (44,137)	$ (28,982)	$ (49,064)	$ (64,429)	$ (32,714)	$ (38,213)	$ (40,663)	$ 27,097	$ (186,612)	$ (84,493)	$ (81,822)
Net income (loss) attributable to Intrexon per share, basic					$ (0.28)	$ (0.34)	$ (0.37)	$ 0.26
Net income (loss) attributable to Intrexon per share, diluted					$ (0.28)	$ (0.34)	$ (0.37)	$ 0.25
Net loss attributable to Intrexon per share, basic and diluted	$ (0.37)	$ (0.24)	$ (0.42)	$ (0.55)					$ (1.58)	$ (0.76)	$ (0.83)

Defined Contribution Plans - Ad

Defined Contribution Plans - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Compensation and Retirement Disclosure [Abstract]
Defined contribution plans, cost recognized	$ 1,857	$ 1,157	$ 776

Subsequent Events - Additional

Subsequent Events - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended
	Jan. 31, 2017	Dec. 31, 2016
AquaBounty Technologies, Inc. | Subsequent Event
Subsequent Event [Line Items]
Additional equity interest purchased by parent	$ 25,000
Additional equity interest purchased by parent (in shares)	2,421,073
AquaBounty Technologies, Inc. | Subsequent Event
Subsequent Event [Line Items]
Noncash dividend, shares	1,776,557
GenVec, Inc. | Subsequent Event
Subsequent Event [Line Items]
Number of shares of common stock to be issued per share of acquiree's common stock	0.297
Calculated value of share of acquiree's common stock (in usd per share)	$ 7
Period used to calculate volume weighted average price	5 days
Percent of collaboration payments	50.00%
Period during which a portion of collaboration payments received will be paid to former stockholders of acquiree	3 years
AquaBounty Technologies, Inc.
Subsequent Event [Line Items]
Parent ownership interest		70.00%
AquaBounty Technologies, Inc. | Subsequent Event
Subsequent Event [Line Items]
Parent ownership interest	58.00%