Acceleron Pharma (XLRN) 10-Q 3 Nov 16 2016 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2016	Oct. 31, 2016
Document and Entity Information
Entity Registrant Name	ACCELERON PHARMA INC
Entity Central Index Key	1,280,600
Document Type	10-Q
Document Period End Date	Sep. 30, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		37,746,503
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q3

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 31,016	$ 27,783
Collaboration receivables (all amounts are with related party)	3,019	3,628
Prepaid expenses and other current assets	3,676	2,458
Short-term investments	107,279	77,064
Total current assets	144,990	110,933
Property and equipment, net	4,215	3,106
Restricted cash	946	796
Other assets	6	368
Long-term investments	112,728	31,134
Total assets	262,885	146,337
Current liabilities:
Accounts payable	2,071	875
Accrued expenses	12,814	12,400
Deferred revenue	541	555
Deferred rent	766	661
Total current liabilities	16,192	14,491
Deferred revenue, net of current portion	3,839	4,239
Deferred rent, net of current portion	1,146	1,157
Warrants to purchase common stock	12,161	17,187
Total liabilities	33,338	37,074
Commitments and contingencies
Stockholders’ equity:
Undesignated preferred stock, $0.001 par value: 25,000,000 shares authorized and no shares issued or outstanding	0	0
Common stock, $0.001 par value: 175,000,000 shares authorized; 37,700,693 and 33,313,355 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	38	34
Additional paid-in capital	574,834	416,926
Accumulated deficit	(345,203)	(307,477)
Accumulated other comprehensive loss	(122)	(220)
Total stockholders’ equity	229,547	109,263
Total liabilities and stockholders’ equity	$ 262,885	$ 146,337

Condensed Consolidated Balance3

Condensed Consolidated Balance Sheets (Unaudited) (Parenthetical) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	25,000,000	25,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	175,000,000	175,000,000
Common stock, shares issued	37,700,693	33,313,355
Common stock, shares outstanding	37,700,693	33,313,355

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Collaboration revenue:
License and milestone	$ 135	$ 205	$ 15,415	$ 1,008
Cost-sharing, net	2,870	3,950	8,987	13,286
Total revenue (all amounts are with related party)	3,005	4,155	24,402	14,294
Costs and expenses:
Research and development	17,102	13,335	49,492	42,261
General and administrative	6,411	5,433	19,029	14,796
Total costs and expenses	23,513	18,768	68,521	57,057
Loss from operations	(20,508)	(14,613)	(44,119)	(42,763)
Other (expense) income, net:
Other (expense) income, net	(794)	2,616	5,026	5,595
Interest income	512	139	1,348	356
Total other (expense) income, net	(282)	2,755	6,374	5,951
Loss before income taxes	(20,790)	(11,858)	(37,745)	(36,812)
Income tax benefit	20	0	20	0
Net loss applicable to common stockholders	$ (20,770)	$ (11,858)	$ (37,725)	$ (36,812)
Net loss per share applicable to common stockholders-basic and diluted (in dollars per share)	$ (0.55)	$ (0.36)	$ (1.01)	$ (1.12)
Weighted-average number of common shares used in computing net loss per share applicable to common stockholders-basic and diluted (in shares)	37,616	33,097	37,268	32,869
Other comprehensive loss:
Net loss applicable to common stockholders	$ (20,770)	$ (11,858)	$ (37,725)	$ (36,812)
Unrealized holding (losses) gains on short-term and long-term investments during the period, net of tax of $0.1 million and $0.1 million, for the three and nine months ended September 30, 2016, respectively, and zero and zero for the three and nine months ended September 30, 2015, respectively	(374)	41	98	(21)
Comprehensive loss	$ (21,144)	$ (11,817)	$ (37,627)	$ (36,833)

Condensed Consolidated Stateme5

Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Income Statement [Abstract]
Unrealized holding gain (loss) on securities, tax	$ 53	$ 0	$ 53	$ 0

Condensed Consolidated Stateme6

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Operating Activities
Net loss	$ (37,725)	$ (36,812)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	1,158	871
Stock-based compensation	13,387	8,295
Change in fair value of warrants	(5,026)	(5,595)
Other non-cash items	(262)	(531)
Changes in assets and liabilities:
Prepaid expenses and other assets	(1,211)	(99)
Collaboration receivables	609	(583)
Accounts payable	1,196	1,923
Accrued expenses	389	2,037
Restricted cash	(150)	106
Deferred revenue	(414)	(1,008)
Deferred rent	94	(354)
Net cash used in operating activities	(27,955)	(31,750)
Investing Activities
Purchase of investments	(132,565)	(134,328)
Proceeds from maturities of investments	21,120	30,138
Purchases of property and equipment	(2,246)	(659)
Net cash used in investing activities	(113,691)	(104,849)
Financing Activities
Proceeds from issuance of common stock from public offering, net issuance costs	140,697	0
Proceeds from exercise of stock options and warrants to purchase common stock	3,524	2,987
Proceeds from issuances of common stock related to employee stock purchase plan	658	590
Net cash provided by financing activities	144,879	3,577
Net increase (decrease) in cash and cash equivalents	3,233	(133,022)
Cash and cash equivalents at beginning of period	27,783	176,460
Cash and cash equivalents at end of period	31,016	43,438
Supplemental Disclosure of Non-Cash Investing and Financing Activities:
Reclassification of warrant liability to additional paid-in capital	0	465
Purchase of property and equipment included in accounts payable and accrued expenses	$ 25	$ 82

Nature of Business

Nature of Business	9 Months Ended
	Sep. 30, 2016
Nature of Business
Nature of Business	Nature of Business Acceleron Pharma Inc. (Acceleron or the Company) is a Cambridge, Massachusetts-based clinical stage biopharmaceutical company focused on the discovery, development and commercialization of highly innovative therapeutics to treat serious and rare diseases. The Company’s research focuses on key natural regulators of cellular growth and repair, particularly the Transforming Growth Factor-Beta (TGF-beta) protein superfamily. By combining its discovery and development expertise, including its proprietary knowledge of the TGF-beta superfamily, and its internal protein engineering and manufacturing capabilities, the Company has built a highly productive discovery and development platform that has generated innovative therapeutic candidates with novel mechanisms of action. The Company has four internally discovered therapeutic candidates that are currently in clinical trials. The Company is subject to risks common to companies in the biotechnology industry, including, but not limited to, risk that the Company never achieves profitability, the need for substantial additional financing, risk of relying on third parties, risks of clinical trial failures, dependence on key personnel, protection of proprietary technology and compliance with government regulations.

Basis of Presentation

Basis of Presentation	9 Months Ended
	Sep. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	Basis of Presentation The accompanying interim condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (GAAP). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (ASC) and Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB). The accompanying interim condensed consolidated financial statements are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements as of and for the year ended December 31, 2015 , and, in the opinion of management, reflect all adjustments, consisting of normal recurring adjustments, necessary for the fair presentation of the Company’s financial position as of September 30, 2016 , and the results of its operations and its cash flows for the three and nine months ended September 30, 2016 and 2015 . The results for the three and nine months ended September 30, 2016 are not necessarily indicative of the results to be expected for the year ending December 31, 2016 , any other interim periods, or any future year or period. These interim financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2015 , and the notes thereto, together with Management’s Discussion and Analysis of Financial Condition and Results of Operations, contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 . On January 11, 2016, the Company completed its underwritten public offering of 3,750,000 shares of common stock at a public offering price of $40.00 per share. The aggregate net proceeds received by the Company, after underwriting discounts and commissions and other offering expenses, were $140.3 million . The accompanying interim condensed consolidated financial statements reflect the application of certain significant accounting policies as described below and elsewhere in these notes to the financial statements. As of September 30, 2016 , the Company’s significant accounting policies and estimates, which are detailed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 , have not changed.

Use of Estimates

Use of Estimates	9 Months Ended
	Sep. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with 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 expensed during the reporting period. Management considers many factors in selecting appropriate financial accounting policies and controls, and in developing the estimates and assumptions that are used in the preparation of these consolidated financial statements. Management must apply significant judgment in this process. In addition, other factors may affect estimates, including: expected business and operational changes, sensitivity and volatility associated with the assumptions used in developing estimates, and whether historical trends are expected to be representative of future trends. The estimation process often may yield a range of potentially reasonable estimates of the ultimate future outcomes and management must select an amount that falls within that range of reasonable estimates. This process may result in actual results differing materially from those estimated amounts used in the preparation of the consolidated financial statements if these results differ from historical experience, or other assumptions do not turn out to be substantially accurate, even if such assumptions are reasonable when made. In preparing these consolidated financial statements, management used significant estimates in the following areas, among others: revenue recognition, stock-based compensation expense, the determination of the fair value of stock-based awards, the fair value of liability-classified warrants, accrued expenses, and the recoverability of the Company’s net deferred tax assets and related valuation allowance.

Segment Information

Segment Information	9 Months Ended
	Sep. 30, 2016
Segment Reporting [Abstract]
Segment Information	Segment Information Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision maker, or decision making group, in making decisions on how to allocate resources and assess performance. The Company’s chief operating decision maker is the chief executive officer. The Company and the chief executive officer view the Company’s operations and manage its business as one operating segment, which is the discovery, development and commercialization of highly innovative therapeutics to treat serious and rare diseases. The Company does use contract research organizations and research institutions located outside the United States. Some of these expenses are subject to collaboration reimbursement which is presented as a component of cost sharing, net in the consolidated statements of operations and comprehensive loss.

Cash Equivalents and Short-term

Cash Equivalents and Short-term and Long-term Investments	9 Months Ended
	Sep. 30, 2016
Cash and Cash Equivalents [Abstract]
Cash Equivalents and Short-term and Long-term Investments	Cash Equivalents and Short-term and Long-term Investments The Company considers all highly liquid investments purchased with original maturities of 90 days or less at acquisition to be cash equivalents. Cash and cash equivalents include cash held in banks and amounts held primarily in interest-bearing money market accounts. Cash equivalents are carried at cost, which approximates their fair market value. The Company determines the appropriate classification of marketable securities at the time of purchase and reevaluates such designation at each balance sheet date. The Company has classified all of its marketable securities at September 30, 2016 as “available-for-sale” pursuant to ASC 320, Investments – Debt and Equity Securities. The Company records available-for-sale securities at fair value, with the unrealized gains and losses included in accumulated other comprehensive income (loss) in stockholders’ equity. There were no realized gains or losses on marketable securities for the three and nine months ended September 30, 2016 and 2015 . Investments not classified as cash equivalents are presented as either short-term or long-term investments based on both their maturities as well as the time period the Company intends to hold such securities. The Company reviews marketable securities for other-than-temporary impairment whenever the fair value of a marketable security is less than the amortized cost and evidence indicates that a marketable security’s carrying amount is not recoverable within a reasonable period of time. Other-than-temporary impairments of investments are recognized in the consolidated statements of operations if the Company has experienced a credit loss, has the intent to sell the marketable security, or if it is more likely than not that the Company will be required to sell the marketable security before recovery of the amortized cost basis. Evidence considered in this assessment includes reasons for the impairment, compliance with the Company’s investment policy, the severity and the duration of the impairment and changes in value subsequent to the end of the period. The following is a summary of cash, cash equivalents and investments as of September 30, 2016 and December 31, 2015 (in thousands): September 30, 2016 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value Cash and cash equivalents due in 90 days or less $ 31,016 $ — $ — $ 31,016 Available-for-sale securities: Corporate obligations due in one year or less 42,643 1 (23 ) 42,621 Corporate obligations due in more than one year 48,203 31 (66 ) 48,168 U.S. Treasury securities due in one year or less 22,985 10 — 22,995 U.S. Treasury securities due in more than one year 14,048 14 (1 ) 14,061 Certificates of deposit due in one year or less 20,385 — — 20,385 Certificates of deposit due in more than one year 10,280 — (1 ) 10,279 Mortgage and other asset backed securities due in one year or less 21,278 4 (4 ) 21,278 Mortgage and other asset backed securities due in more than one year 40,253 1 (34 ) 40,220 Total available-for-sale securities 220,075 61 (129 ) 220,007 Total cash, cash equivalents and available-for-sale securities $ 251,091 $ 61 $ (129 ) $ 251,023 December 31, 2015 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value Cash and cash equivalents due in 90 days or less $ 27,783 $ — $ — $ 27,783 Available-for-sale securities: Corporate obligations due in one year or less 53,243 — (81 ) $ 53,162 Corporate obligations due in more than one year 14,112 — (72 ) 14,040 U.S. Treasury securities due in one year or less 6,016 — (4 ) 6,012 U.S. Treasury securities due in more than one year 4,995 — (15 ) 4,980 Certificates of deposit due in one year or less 11,890 — — 11,890 Certificates of deposit due in more than one year 4,886 — — 4,886 Mortgage and other asset backed securities due in one year or less 6,010 — (10 ) 6,000 Mortgage and other asset backed securities due in more than one year 7,266 — (38 ) 7,228 Total available-for-sale securities 108,418 — (220 ) 108,198 Total cash, cash equivalents and available-for-sale securities $ 136,201 $ — $ (220 ) $ 135,981 The Company adjusts the cost of available-for-sale debt securities for amortization of premiums and accretion of discounts to maturity. The Company includes such amortization and accretion in interest income. The cost of securities sold is based on the specific identification method. The Company includes in interest income interest and dividends on securities classified as available-for-sale. The aggregate fair value of securities held by the Company in an unrealized loss position for less than twelve months as of September 30, 2016 and December 31, 2015 was $106.7 million and $89.7 million , respectively. The aggregate fair value of securities held by the Company in an unrealized loss position for more than twelve months as of September 30, 2016 was $5.5 million . The aggregate unrealized loss for those securities in an unrealized loss position for more than twelve months is $5,000 .

Restricted Cash

Restricted Cash	9 Months Ended
	Sep. 30, 2016
Receivables [Abstract]
Restricted Cash	Restricted Cash As of September 30, 2016 the Company maintained letters of credit totaling $0.9 million held in the form of certificates of deposit and money market funds as collateral for the Company’s facility lease obligations and its credit cards. As of December 31, 2015 , the Company maintained letters of credit totaling $0.8 million held in the form of certificates of deposit.

Concentrations of Credit Risk a

Concentrations of Credit Risk and Off-Balance Sheet Risk	9 Months Ended
	Sep. 30, 2016
Risks and Uncertainties [Abstract]
Concentrations of Credit Risk and Off-Balance Sheet Risk	Concentrations of Credit Risk and Off-Balance Sheet Risk The Company has no off-balance sheet risk, such as foreign exchange contracts, option contracts, or other foreign hedging arrangements. Financial instruments that potentially subject the Company to concentrations of credit risk primarily consist of cash, cash equivalents, restricted cash, short-term and long-term investments and collaboration receivables. The Company maintains its cash and cash equivalent balances and short-term and long-term investments with financial institutions that management believes are creditworthy. Short-term and long-term investments consist of investment grade corporate obligations, treasury notes, asset backed securities, and certificates of deposit. The Company’s investment policy includes guidelines on the quality of the institutions and financial instruments and defines allowable investments that the Company believes minimizes the exposure to concentrations of credit risk. The Company routinely assesses the creditworthiness of its customers and collaboration partners. The Company has not experienced any material losses related to receivables from individual customers and collaboration partners, or groups of customers. The Company does not require collateral. Due to these factors, no additional credit risk beyond amounts provided for collection losses is believed by management to be probable in the Company’s collaboration receivables.

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The following tables set forth the Company’s financial instruments carried at fair value using the lowest level of input applicable to each financial instrument as of September 30, 2016 and December 31, 2015 (in thousands): September 30, 2016 Quoted Prices in Active Markets for Identical Items (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Total Assets: Money market funds $ 26,611 $ — $ — $ 26,611 Corporate obligations — 90,789 — 90,789 U.S. Treasury securities — 37,057 — 37,057 Certificates of deposit — 31,154 — 31,154 Mortgage and other asset backed securities — 61,498 — 61,498 Restricted cash 946 — — 946 Total assets $ 27,557 $ 220,498 $ — $ 248,055 Liabilities: Warrants to purchase common stock $ — $ — $ 12,161 $ 12,161 Total liabilities $ — $ — $ 12,161 12,161 December 31, 2015 Quoted Prices in Active Markets for Identical Items (Level 1) Significant other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Total Assets: Money market funds $ 24,811 $ — $ — $ 24,811 Corporate obligations — 67,706 — 67,706 U.S. Treasury securities — 10,991 — 10,991 Certificates of deposit — 16,776 — 16,776 Mortgage and other asset backed securities — 13,228 — 13,228 Restricted cash 796 — — 796 Total assets $ 25,607 $ 108,701 $ — $ 134,308 Liabilities: Warrants to purchase common stock $ — $ — $ 17,187 $ 17,187 Total liabilities $ — $ — $ 17,187 $ 17,187 The money market funds noted above are included in cash and cash equivalents in the accompanying condensed consolidated balance sheets. The Company recognizes transfers between levels of the fair value hierarchy as of the end of the reporting period. There were no transfers within the hierarchy during the nine months ended September 30, 2016 or the year ended December 31, 2015 . Items measured at fair value on a recurring basis include warrants to purchase common stock (Note 13). During the periods presented, the Company has not changed the manner in which it values assets and liabilities that are measured at fair value using Level 3 inputs. The following table sets forth a summary of changes in the fair value of the Company’s common stock warrant liability, which has been classified within Level 3 of the fair value hierarchy, wherein fair value is estimated using significant unobservable inputs (in thousands): Nine Months Ended September 30, 2016 2015 Beginning balance $ 17,187 $ 14,124 Change in fair value (5,026 ) (5,595 ) Exercises — (465 ) Ending balance $ 12,161 $ 8,064 The fair value of the warrants to purchase common stock on the date of issuance and on each re-measurement date for those warrants classified as liabilities was estimated using either the Monte Carlo simulation framework, which incorporates future financing events over the remaining life of the warrants to purchase common stock, or for certain re-measurement dates, when the warrants are deeply in the money, the Black-Scholes option pricing model. At each reporting period the Company evaluates the best valuation methodology, and at September 30, 2016 , the Black-Scholes option pricing model was used. Due to the nature of these inputs, the valuation of the warrants is considered a Level 3 measurement. The Company measures eligible assets and liabilities at fair value, with changes in value recognized in earnings. Fair value treatment may be elected either upon initial recognition of an eligible asset or liability or, for an existing asset or liability, if an event triggers a new basis of accounting. The Company did not elect to re-measure any of its existing financial assets or liabilities, and did not elect the fair value option for any financial assets and liabilities transacted in the nine months ended September 30, 2016 or the year ended December 31, 2015 .

Net Loss Per Share

Net Loss Per Share	9 Months Ended
	Sep. 30, 2016
Earnings Per Share [Abstract]
Net Loss Per Share	Net Loss Per Share The following common stock equivalents were excluded from the calculation of diluted net loss per share for the periods indicated because their inclusion would have had an anti-dilutive effect (in thousands): Three Months Ended Nine Months Ended 2016 2015 2016 2015 Outstanding stock options 3,193 3,328 3,193 3,328 Common stock warrants 397 398 397 398 Shares issuable under employee stock purchase plan 18 19 18 19 Restricted stock units 670 524 670 524 4,278 4,269 4,278 4,269

Comprehensive Income (Loss)

Comprehensive Income (Loss)	9 Months Ended
	Sep. 30, 2016
Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract]
Comprehensive Income (Loss)	Comprehensive Income (Loss) Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions, other events, and circumstances from non-owner sources. Accumulated other comprehensive income (loss) is presented separately on the consolidated balance sheets and consists of cumulative unrealized gains and losses from short-term and long-term investments and the tax expense associated with the gains as of September 30, 2016 .

Subsequent Events

Subsequent Events	9 Months Ended
	Sep. 30, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events The Company considers events or transactions that occur after the balance sheet date but prior to the issuance of the financial statements to provide additional evidence relative to certain estimates or to identify matters that require additional disclosure. The Company has evaluated all subsequent events and determined that there are no material recognized or unrecognized subsequent events requiring disclosure.

Recently Adopted Accounting Pro

Recently Adopted Accounting Pronouncements	9 Months Ended
	Sep. 30, 2016
New Accounting Pronouncements and Changes in Accounting Principles [Abstract]
Recently Adopted Accounting Pronouncements	Recently Adopted Accounting Pronouncements From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption. In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606) , which supersedes all existing revenue recognition requirements, including most industry-specific guidance. The new standard requires a company to recognize revenue when it transfers goods or services to customers in an amount that reflects the consideration that the company expects to receive for those goods or services. The new standard will be effective for the Company on January 1, 2018. The Company is currently evaluating the method of adoption and the potential impact that Topic 606 may have on its financial position and results of operations. In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40) . The ASU requires all entities to evaluate for the existence of conditions or events that raise substantial doubt about the entity’s ability to continue as a going concern within one year after the issuance date of the financial statements. The accounting standard is effective for interim and annual periods ending after December 15, 2016, and will not have a material impact on the consolidated financial statements, but may impact the Company’s footnote disclosures. In February 2015, the FASB issued ASU 2015-02, Consolidation (Topic 810), Amendments to the Consolidation Analysis , which updated accounting guidance on consolidation requirements. This update changes the guidance with respect to the analysis that a reporting entity must perform to determine whether it should consolidate certain types of legal entities. This guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2015, with early adoption permitted. The Company adopted this standard on January 1, 2016 and the adoption did not have a material impact on the Company’s consolidated financial statements. In November 2015, the FASB issued ASU No. 2015-17, Income Taxes (Topic 740), Balance Sheet Classification of Deferred Taxes. The new standard requires that deferred tax assets and liabilities be classified as non-current in a classified statement of financial position. The new standard will be effective for the Company on January 1, 2017. The Company is currently evaluating the method of adoption and the potential impact that Topic 740 may have on its financial position and results of operations. In February 2016 the FASB issued ASU 2016-02, Leases (Topic 842), Amendments to the FASB Accounting Standards Codification, which replaces the existing guidance for leases. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, for lease arrangements exceeding a twelve month term, these arrangements must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation will be recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization/interest expense for financing leases. The balance sheet amount recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. In addition, ASU 2016-02 requires the use of the modified retrospective method, which will require adjustment to all comparative periods presented in the consolidated financial statements. This guidance is effective for annual and interim periods beginning after December 15, 2018 and requires retrospective application. The Company is currently assessing the impact that adopting ASU 2016-02 will have on its consolidated financial statements and related disclosures. In March 2016 the FASB issued ASU 2016-09, Compensation - Stock Compensation (Topic 718), Improvements to Employee Share-Based Payment Accounting . ASU 2016-09 identifies areas for simplification involving several aspects of accounting for share based payments, including income tax consequences, classification of awards as either equity, or liabilities, an option to make a policy election to recognize gross share based compensation expense with actual forfeitures recognized as they occur as well as certain classification changes on the statement of cash flows. This guidance is effective for annual and interim reporting periods beginning after December 15, 2016, with early adoption permitted. The Company is currently assessing the impact that adopting ASU 2016-09 will have on its consolidated financial statements and related disclosures.

Warrants

Warrants	9 Months Ended
	Sep. 30, 2016
Warrants and Rights Note Disclosure [Abstract]
Warrants	Warrants Below is a summary of the number of shares issuable upon exercise of outstanding warrants and the terms and accounting treatment for the outstanding warrants (in thousands, except per share data): Warrants as of Weighted- Average Exercise Balance Sheet Classification September 30, 2016 December 31, 2015 Price Per Share Expiration September 30, 2016 December 31, 2015 Warrants to purchase common stock 393 393 $ 5.88 June 10, 2020 - July 9, 2020 Liability Liability Warrants to purchase common stock 4 5 4.00 - 7.40 March 28, 2017 - December 31, 2017 Equity(1) (2) Equity(2) All warrants 397 398 $ 5.88 (1) In March 2016, the warrant holders exercised warrants to purchase 1,317 shares of Common Stock on a net basis, resulting in the issuance of 1,109 shares of Common Stock. (2) Warrants to purchase common stock were issued in connection with various debt financing transactions that were consummated in periods prior to December 31, 2012. See discussion below for further details. In connection with the Series E redeemable convertible preferred stock (Series E Preferred Stock) financing transactions that took place in June 2010 and July 2010, the Company issued warrants to purchase up to 871,580 shares of common stock. Each warrant was immediately exercisable and expires ten years from the original date of issuance. The warrants to purchase shares of the Company’s common stock have an exercise price equal to the estimated fair value of the underlying instrument as of the initial date such warrants were issued. Each warrant is exercisable on either a physical settlement or net share settlement basis from the date of issuance. The warrant agreement contains a provision requiring an adjustment to the number of shares in the event the Company issues common stock, or securities convertible into or exercisable for common stock, at a price per share lower than the warrant exercise price. The Company concluded the anti-dilution feature required the warrants to be classified as liabilities under ASC Topic 815, Derivatives and Hedging—Contracts in Entity’s Own Equity (ASC 815). The warrants are measured at fair value, with changes in fair value recognized as a gain or loss to other income (expense) in the statements of operations and comprehensive income (loss) for each reporting period thereafter. The fair value of the common stock warrants were recorded as a discount to the preferred stock issued of $3.0 million , and the preferred stock was being accreted to the redemption value. At the end of each reporting period or through the life of the instrument, the Company re-measured the fair value of the outstanding warrants, using current assumptions, resulting in an increase in fair value of $0.8 million and a decrease of $2.6 million for the three months ended September 30, 2016 and 2015 , respectively, and a decrease in fair value of $5.0 million and $5.6 million for the nine months ended September 30, 2016 and 2015 , respectively, which was recorded in other (expense) income in the accompanying consolidated statements of operations and comprehensive loss. The Company will continue to re-measure the fair value of the liability associated with the warrants to purchase common stock at the end of each reporting period until the earlier of the exercise or the expiration of the applicable warrants. All remaining outstanding warrants were fully vested and exercisable as of September 30, 2016 and December 31, 2015 .

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Legal Proceedings The Company, from time to time, may be party to litigation arising in the ordinary course of its business. The Company was not subject to any material legal proceedings during the three months ended September 30, 2016 , and, to the best of its knowledge, no material legal proceedings are currently pending or threatened. Other The Company is also party to various agreements, principally relating to licensed technology, that require future payments relating to milestones not met at September 30, 2016 and December 31, 2015 , or royalties on future sales of specified products. No royalty payments under these agreements are expected to be payable in the immediate future. See Note 15 for discussion of these arrangements. The Company enters into standard indemnification agreements in the ordinary course of business. Pursuant to the agreements, the Company indemnifies, holds harmless, and agrees to reimburse the indemnified party for losses suffered or incurred by the indemnified party, generally the Company’s business partners or customers, in connection with any U.S. patent or any copyright or other intellectual property infringement claim by any third party with respect to the Company’s products. The term of these indemnification agreements is generally perpetual any time after execution of the agreement. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited. The Company has never incurred costs to defend lawsuits or settle claims related to these indemnification agreements.

Significant Agreements

Significant Agreements	9 Months Ended
	Sep. 30, 2016
Significant Agreements [Abstract]
Significant Agreements	Significant Agreements Celgene Overview On February 20, 2008 the Company entered into a collaboration, license, and option agreement with Celgene Corporation (Celgene) relating to sotatercept (the Sotatercept Agreement). On August 2, 2011, the Company entered into a second collaboration, license and option agreement with Celgene for luspatercept (the Luspatercept Agreement), and also amended certain terms of the Sotatercept Agreement. These agreements provide Celgene exclusive licenses for sotatercept and luspatercept in all indications, as well as exclusive rights to obtain a license to certain future compounds. Celgene is an integrated global biopharmaceutical company engaged primarily in the discovery, development and commercialization of innovative therapies for the treatment of cancer and inflammatory diseases through next-generation solutions in protein homeostasis, immuno-oncology, epigenetics, immunology and neuro-inflammation. There have been no material changes to the key terms of the Sotatercept and Luspatercept Agreements since December 31, 2015 . For further information on the terms of the agreements as well as the historical accounting analysis, please see the notes to the consolidated financial statements included in the Company’s Form 10-K for the year ended December 31, 2015 . Sotatercept Agreement Under the terms of the Sotatercept Agreement, the Company and Celgene collaborate worldwide for the joint development and commercialization of sotatercept. The Company also granted Celgene an option to license three discovery stage compounds. Under the terms of the agreement, the Company and Celgene will jointly develop, manufacture and commercialize sotatercept. The Company retained responsibility for research and development through the end of Phase 2a clinical trials, as well as manufacturing the clinical supplies for these trials. These activities were substantially completed in 2011. Celgene is conducting the ongoing Phase 2 trials and will be responsible for any Phase 3 clinical trials, as well as additional Phase 2 clinical trials, and will be responsible for overseeing the manufacture of Phase 3 and commercial supplies by third party contract manufacturing organizations. Through September 30, 2016 , the Company has received $43.5 million in research and development funding and milestone payments for sotatercept under the original and modified agreements. The next likely clinical milestone payment would be $10.0 million and result from Celgene’s start of a Phase 3 study in chronic kidney disease. Luspatercept Agreement Under the terms of the Luspatercept Agreement, the Company and Celgene collaborate worldwide for the joint development and commercialization of luspatercept. The Company also granted Celgene an option for future products for which Acceleron files an Investigational New Drug application for the treatment of anemia. The Company has not yet identified additional compounds for the treatment of anemia. Accordingly, there is no assurance that the Company will generate future value from additional programs. The Company retains responsibility for research and development through the end of Phase 1 and initial Phase 2 clinical trials, as well as manufacturing the clinical supplies for these studies. Celgene will conduct subsequent Phase 2 and Phase 3 clinical studies. Acceleron will manufacture luspatercept for the Phase 1 and Phase 2 clinical trials and Celgene will be responsible for overseeing the manufacture of Phase 3 and commercial supplies by third party contract manufacturing organizations. Through September 30, 2016 , the Company has received $84.5 million in research and development funding and milestone payments for luspatercept. The next likely milestone payment would be $25.0 million and result from U.S. Food and Drug Administration or European Medical Association acceptance of a Biologics Licensing Application or equivalent for luspatercept in either myelodysplastic syndromes or beta-thalassemia. Both Agreements The Company and Celgene shared development costs under the Sotatercept and Luspatercept Agreements through December 31, 2012. As of January 1, 2013, Celgene has been responsible for paying 100% of worldwide development costs under both agreements. Celgene will be responsible for all commercialization costs worldwide. The Company has the right to co-promote sotatercept, luspatercept and future products under both agreements in North America. Celgene’s option to buy down royalty rates for sotatercept and luspatercept expired unexercised and, therefore, the Company will receive tiered royalties in the low-to-mid twenty percent range on net sales of sotatercept and luspatercept. The royalty schedules for sotatercept and luspatercept are the same. Accounting Analysis During the three months ended September 30, 2016 and 2015 , the Company recognized $0.1 million and $0.2 million , respectively, and during the nine months ended September 30, 2016 and 2015 , $0.4 million and $1.0 million , respectively, of the total deferred revenue as license and milestone revenue in the accompanying consolidated statements of operations and comprehensive loss. As noted above, under the terms of the Luspatercept Agreement the Company retained responsibility for certain research and development activities through the completion of Phase 1 and initial Phase 2 clinical trials, as well as manufacturing the clinical supplies for these studies. Celgene is responsible for the conduct of subsequent Phase 2 and Phase 3 clinical studies. In November 2013, the Company agreed to conduct additional activities for the benefit of the luspatercept program including certain clinical and non-clinical services such as multiple toxicology studies and associated assay development and sample testing, clinical extension studies, and market development work. These activities are reimbursed under the same terms and rates of the existing Agreements. The Company evaluated the additional services to be provided and determined that as the Company is under no obligation to conduct these additional activities, these services do not represent a deliverable under or modification to the Luspatercept Agreement, but rather, represent a separate services arrangement which should be accounted for as the services are delivered. Pursuant to the terms of the agreement, Celgene and the Company shared development costs, with Celgene responsible for substantially more than half of the costs for sotatercept and luspatercept until December 31, 2012 and 100% of the costs from January 1, 2013 and thereafter. Payments from Celgene with respect to research and development costs incurred by the Company are recorded as cost-sharing revenue. Payments by the Company to Celgene for research and development costs incurred by Celgene are recorded as a reduction to cost-sharing revenue. The Company recorded net cost-sharing revenue of $2.9 million and $3.9 million during the three months ended September 30, 2016 and 2015 , respectively, and $9.0 million and $13.3 million during the nine months ended September 30, 2016 and 2015 , respectively. Other Agreements Other In 2004, the Company entered into a license agreement with a non-profit institution for an exclusive, sublicensable, worldwide, royalty-bearing license to certain patents developed by the institution (Primary Licensed Products). In addition, the Company was granted a non-exclusive, non-sub-licensable license for Secondary Licensed Products. As compensation for the licenses, the Company issued 62,500 shares of its common stock to the institution, the fair value of which was $25,000 , and was expensed during 2004 to research and development expense. The Company also agreed to pay specified development milestone payments totaling up to $2.0 million for sotatercept and $0.7 million for luspatercept. In addition, the Company is obligated to pay milestone fees based on the Company’s research and development progress, and U.S. sublicensing revenue ranging from 10% - 25% , as well as a royalty ranging from 1.0% - 3.5% of net sales on any products under the licenses. During the three months ended September 30, 2016 and 2015 , the Company expensed zero and zero , respectively, and during the nine months ended September 30, 2016 and 2015 , respectively, the Company expensed $1.0 million and $0.1 million of milestones and fees defined under the agreement. In 2004, the Company entered into another license agreement with certain individuals for an exclusive, sublicensable, worldwide, royalty-bearing license to certain patents developed by the individuals. The Company agreed to pay specified development and sales milestone payments aggregating up to $1.0 million relating to the development and commercialization of dalantercept. In addition, the Company is required to pay royalties in the low single-digits on worldwide net product sales of dalantercept, with royalty obligations continuing at a 50% reduced rate for a period of time after patent expiration. If the Company sublicenses its patent rights, it will owe a percentage of sublicensing revenue, excluding payments based on the level of sales, profits or other levels of commercialization. During the three and nine months ended September 30, 2016 and 2015 , the Company did no t reach any milestones defined under the agreement and, therefore, no amounts have been paid or expensed. During 2012, the Company executed a license agreement with a research institution for an exclusive, sublicensable, worldwide, royalty-bearing license. The Company is obligated to pay development milestones and commercial milestone fees relating to dalantercept totaling up to $1.0 million . The Company will also pay $25,000 annually upon first commercial sale as well as royalties of 1.5% of net sales on any products developed under the patents. During the three and nine months ended September 30, 2016 and 2015 , the Company did no t reach any milestones defined under the agreement and, therefore, no amounts have been paid or expensed. In May 2014, the Company executed a collaboration agreement with a research technology company. The Company paid an upfront research fee of $0.3 million upon execution of the agreement. The Company also received an option to obtain a commercial license to the molecules developed during the collaboration. During the three months ended September 30, 2016 and 2015 , the Company expensed $0.4 million and $0.2 million , respectively, and during the nine months ended September 30, 2016 and 2015 , the Company expensed $0.9 million and $1.0 million , respectively, of milestones and fees, which is recorded as research and development expense.

Stock-Based Compensation

Stock-Based Compensation	9 Months Ended
	Sep. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Compensation	Stock-Based Compensation The Company recognized stock-based compensation expense related to stock options, restricted stock units and the 2013 Employee Stock Purchase Plan (2013 ESPP) totaling $4.6 million , $3.1 million , $13.4 million and $8.3 million during the three months ended September 30, 2016 and 2015 and the nine months ended September 30, 2016 and 2015, respectively. Total compensation cost recognized for all stock-based compensation awards in the consolidated statements of operations and comprehensive loss is as follows (in thousands): Three Months Ended Nine Months Ended 2016 2015 2016 2015 Research and development $ 1,942 $ 1,201 $ 5,617 $ 3,302 General and administrative 2,646 1,863 7,770 4,993 $ 4,588 $ 3,064 $ 13,387 $ 8,295 Stock Options The fair value of each stock option issued to employees was estimated at the date of grant using the Black-Scholes option pricing model with the following weighted-average assumptions: Three Months Ended Nine Months Ended 2016 2015 2016 2015 Expected volatility 65.4 % 66.0 % 64.5 % 67.1 % Expected term (in years) 6.0 6.0 5.9 6.0 Risk-free interest rate 1.2 % 1.7 % 1.4 % 1.7 % Expected dividend yield — % — % — % — % The following table summarizes the stock option activity under the Company’s 2003 Stock Option and Restricted Stock Plan and 2013 Equity Incentive Plan during the nine months ended September 30, 2016 (in thousands): Number of Grants Weighted- Average Exercise Price Per Share Weighted- Average Contractual Life (in years) Aggregate Intrinsic Value(1) Outstanding at December 31, 2015 3,191 $ 18.85 6.31 Granted 639 $ 28.69 Exercised (606 ) $ 5.82 Canceled or forfeited (31 ) $ 36.28 Outstanding at September 30, 2016 3,193 $ 23.12 6.69 $ 46,294 Exercisable at September 30, 2016 1,932 $ 16.72 5.37 $ 39,724 Vested and expected to vest at September 30, 2016 (2) 3,147 $ 22.97 6.65 $ 46,058 (1) The aggregate intrinsic value is calculated as the difference between the exercise price of the underlying options and the estimated fair value of the common stock for the options that were in the money at September 30, 2016 . (2) This represents the number of vested options at September 30, 2016 , plus the number of unvested options expected to vest at September 30, 2016 , based on the unvested options outstanding at September 30, 2016 , adjusted for the estimated forfeiture rate. During the nine months ended September 30, 2016 , the Company granted stock options to purchase an aggregate of 639,070 shares of its common stock, with a weighted-average grant date fair value of options granted of $28.69 . During the nine months ended September 30, 2016 , current and former employees of the Company exercised a total of 605,558 options, resulting in total proceeds of $3.5 million . The aggregate intrinsic value of options exercised during the nine months ended September 30, 2016 was $16.7 million . As of September 30, 2016 , there was $21.5 million of unrecognized compensation expense related to unvested stock options that is expected to be recognized over a weighted-average period of 2.43 years . Restricted Stock Units The following table summarizes the restricted stock unit (RSU) activity under the 2013 Equity Incentive Plan during the nine months ended September 30, 2016 (in thousands): Number Weighted- Unvested balance at December 31, 2015 521 $ 31.57 Granted 158 30.17 Vested — — Forfeited (9 ) 34.01 Unvested balance at September 30, 2016 670 $ 31.22 During the nine months ended September 30, 2016 , the Company issued 133,980 RSUs to employees. These RSUs are subject to time-based vesting. As of September 30, 2016 , there was approximately $4.7 million of unrecognized compensation cost related to the time-based RSUs, which the Company expects to recognize over a remaining weighted-average period of 2.23 years . 181,710 restricted stock units remained unvested and outstanding at September 30, 2016 . During the nine months ended September 30, 2016 , the Company issued 23,977 performance-based RSUs in addition to the 464,000 issued in 2015. The vesting of these performance-based RSUs is accelerated upon the occurrence of certain milestone events, but otherwise these RSUs vest in September 2019. As a result, when probable, compensation cost is recognized over the estimated period of achievement. If achievement is not considered probable the expense is recognized over the vesting period. As of September 30, 2016 , there was approximately $9.5 million of unrecognized compensation cost related to the performance-based RSUs, which the Company expects to recognize over a remaining weighted-average period of 2.08 years . All 487,977 of these performance-based RSUs remained outstanding at September 30, 2016 . Employee Stock Purchase Plan During the three months ended September 30, 2016 and 2015 , the Company recorded $0.1 million and $0.1 million , respectively, and during the nine months ended September 30, 2016 and 2015 , the Company recorded $0.2 million and $0.2 million , respectively, of stock-based compensation expense related to the 2013 ESPP.

Income Taxes

Income Taxes	9 Months Ended
	Sep. 30, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes For the three and nine months ended September 30, 2016 , the Company recognized an income tax benefit of $20,000 and $20,000 and tax expense in other comprehensive income of $53,000 and $53,000 related to the unrealized gain on available for sale securities. As of September 30, 2016, the Company recorded an accrued tax provision of $17,000 related to this tax benefit included within accrued expenses and other current liabilities in the condensed consolidated balance sheet, which is expected to be generated from continued operations. The Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets. Based on the Company’s history of operating losses, the Company has concluded that it is more likely than not that the benefit of its deferred tax assets will not be realized. Accordingly, the Company has provided a full valuation allowance for deferred tax assets as of September 30, 2016 and December 31, 2015 . The Company files income tax returns in the United States, and various state and foreign jurisdictions. The federal, state and foreign income tax returns are generally subject to tax examinations for the tax years ended December 31, 2012 through December 31, 2015 . To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the Internal Revenue Service, state or foreign tax authorities to the extent utilized in a future period. The Company accounts for uncertain tax positions in accordance with the provisions of ASC 740. When uncertain tax positions exist, the Company recognizes the tax benefit of tax positions to the extent that the benefit will more likely than not be realized. The determination as to whether the tax benefit will more likely than not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. As of September 30, 2016 and December 31, 2015 , the Company did not have any significant uncertain tax positions.

Related Party Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2016
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Celgene Corporation In connection with prior arrangements, Celgene owned 12.9% and 12.3% of the Company’s fully diluted equity as of September 30, 2016 and December 31, 2015 , respectively. Refer to Note 15 for additional information regarding this collaboration arrangement. During the three and nine months ended September 30, 2016 and 2015 , all revenue recognized by the Company was recognized under the Celgene collaboration arrangement and, as of September 30, 2016 , the Company had $4.4 million of deferred revenue related to the Celgene collaboration arrangement.

Basis of Presentation (Policies

Basis of Presentation (Policies)	9 Months Ended
	Sep. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	The accompanying interim condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (GAAP). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (ASC) and Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB). The accompanying interim condensed consolidated financial statements are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements as of and for the year ended December 31, 2015 , and, in the opinion of management, reflect all adjustments, consisting of normal recurring adjustments, necessary for the fair presentation of the Company’s financial position as of September 30, 2016 , and the results of its operations and its cash flows for the three and nine months ended September 30, 2016 and 2015 . The results for the three and nine months ended September 30, 2016 are not necessarily indicative of the results to be expected for the year ending December 31, 2016 , any other interim periods, or any future year or period. These interim financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2015 , and the notes thereto, together with Management’s Discussion and Analysis of Financial Condition and Results of Operations, contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 . On January 11, 2016, the Company completed its underwritten public offering of 3,750,000 shares of common stock at a public offering price of $40.00 per share. The aggregate net proceeds received by the Company, after underwriting discounts and commissions and other offering expenses, were $140.3 million . The accompanying interim condensed consolidated financial statements reflect the application of certain significant accounting policies as described below and elsewhere in these notes to the financial statements. As of September 30, 2016 , the Company’s significant accounting policies and estimates, which are detailed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 , have not changed.
Use of Estimates	The preparation of financial statements in conformity with 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 expensed during the reporting period. Management considers many factors in selecting appropriate financial accounting policies and controls, and in developing the estimates and assumptions that are used in the preparation of these consolidated financial statements. Management must apply significant judgment in this process. In addition, other factors may affect estimates, including: expected business and operational changes, sensitivity and volatility associated with the assumptions used in developing estimates, and whether historical trends are expected to be representative of future trends. The estimation process often may yield a range of potentially reasonable estimates of the ultimate future outcomes and management must select an amount that falls within that range of reasonable estimates. This process may result in actual results differing materially from those estimated amounts used in the preparation of the consolidated financial statements if these results differ from historical experience, or other assumptions do not turn out to be substantially accurate, even if such assumptions are reasonable when made. In preparing these consolidated financial statements, management used significant estimates in the following areas, among others: revenue recognition, stock-based compensation expense, the determination of the fair value of stock-based awards, the fair value of liability-classified warrants, accrued expenses, and the recoverability of the Company’s net deferred tax assets and related valuation allowance.
Recently Adopted Accounting Pronouncements	From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption. In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606) , which supersedes all existing revenue recognition requirements, including most industry-specific guidance. The new standard requires a company to recognize revenue when it transfers goods or services to customers in an amount that reflects the consideration that the company expects to receive for those goods or services. The new standard will be effective for the Company on January 1, 2018. The Company is currently evaluating the method of adoption and the potential impact that Topic 606 may have on its financial position and results of operations. In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40) . The ASU requires all entities to evaluate for the existence of conditions or events that raise substantial doubt about the entity’s ability to continue as a going concern within one year after the issuance date of the financial statements. The accounting standard is effective for interim and annual periods ending after December 15, 2016, and will not have a material impact on the consolidated financial statements, but may impact the Company’s footnote disclosures. In February 2015, the FASB issued ASU 2015-02, Consolidation (Topic 810), Amendments to the Consolidation Analysis , which updated accounting guidance on consolidation requirements. This update changes the guidance with respect to the analysis that a reporting entity must perform to determine whether it should consolidate certain types of legal entities. This guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2015, with early adoption permitted. The Company adopted this standard on January 1, 2016 and the adoption did not have a material impact on the Company’s consolidated financial statements. In November 2015, the FASB issued ASU No. 2015-17, Income Taxes (Topic 740), Balance Sheet Classification of Deferred Taxes. The new standard requires that deferred tax assets and liabilities be classified as non-current in a classified statement of financial position. The new standard will be effective for the Company on January 1, 2017. The Company is currently evaluating the method of adoption and the potential impact that Topic 740 may have on its financial position and results of operations. In February 2016 the FASB issued ASU 2016-02, Leases (Topic 842), Amendments to the FASB Accounting Standards Codification, which replaces the existing guidance for leases. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, for lease arrangements exceeding a twelve month term, these arrangements must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation will be recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization/interest expense for financing leases. The balance sheet amount recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. In addition, ASU 2016-02 requires the use of the modified retrospective method, which will require adjustment to all comparative periods presented in the consolidated financial statements. This guidance is effective for annual and interim periods beginning after December 15, 2018 and requires retrospective application. The Company is currently assessing the impact that adopting ASU 2016-02 will have on its consolidated financial statements and related disclosures. In March 2016 the FASB issued ASU 2016-09, Compensation - Stock Compensation (Topic 718), Improvements to Employee Share-Based Payment Accounting . ASU 2016-09 identifies areas for simplification involving several aspects of accounting for share based payments, including income tax consequences, classification of awards as either equity, or liabilities, an option to make a policy election to recognize gross share based compensation expense with actual forfeitures recognized as they occur as well as certain classification changes on the statement of cash flows. This guidance is effective for annual and interim reporting periods beginning after December 15, 2016, with early adoption permitted. The Company is currently assessing the impact that adopting ASU 2016-09 will have on its consolidated financial statements and related disclosures.

Cash Equivalents and Short-te26

Cash Equivalents and Short-term and Long-term Investments (Tables)	9 Months Ended
	Sep. 30, 2016
Cash and Cash Equivalents [Abstract]
Available-for-sale Securities	The following is a summary of cash, cash equivalents and investments as of September 30, 2016 and December 31, 2015 (in thousands): September 30, 2016 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value Cash and cash equivalents due in 90 days or less $ 31,016 $ — $ — $ 31,016 Available-for-sale securities: Corporate obligations due in one year or less 42,643 1 (23 ) 42,621 Corporate obligations due in more than one year 48,203 31 (66 ) 48,168 U.S. Treasury securities due in one year or less 22,985 10 — 22,995 U.S. Treasury securities due in more than one year 14,048 14 (1 ) 14,061 Certificates of deposit due in one year or less 20,385 — — 20,385 Certificates of deposit due in more than one year 10,280 — (1 ) 10,279 Mortgage and other asset backed securities due in one year or less 21,278 4 (4 ) 21,278 Mortgage and other asset backed securities due in more than one year 40,253 1 (34 ) 40,220 Total available-for-sale securities 220,075 61 (129 ) 220,007 Total cash, cash equivalents and available-for-sale securities $ 251,091 $ 61 $ (129 ) $ 251,023 December 31, 2015 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value Cash and cash equivalents due in 90 days or less $ 27,783 $ — $ — $ 27,783 Available-for-sale securities: Corporate obligations due in one year or less 53,243 — (81 ) $ 53,162 Corporate obligations due in more than one year 14,112 — (72 ) 14,040 U.S. Treasury securities due in one year or less 6,016 — (4 ) 6,012 U.S. Treasury securities due in more than one year 4,995 — (15 ) 4,980 Certificates of deposit due in one year or less 11,890 — — 11,890 Certificates of deposit due in more than one year 4,886 — — 4,886 Mortgage and other asset backed securities due in one year or less 6,010 — (10 ) 6,000 Mortgage and other asset backed securities due in more than one year 7,266 — (38 ) 7,228 Total available-for-sale securities 108,418 — (220 ) 108,198 Total cash, cash equivalents and available-for-sale securities $ 136,201 $ — $ (220 ) $ 135,981

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2016
Fair Value Disclosures [Abstract]
Schedule of financial instruments carried at fair value	The following tables set forth the Company’s financial instruments carried at fair value using the lowest level of input applicable to each financial instrument as of September 30, 2016 and December 31, 2015 (in thousands): September 30, 2016 Quoted Prices in Active Markets for Identical Items (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Total Assets: Money market funds $ 26,611 $ — $ — $ 26,611 Corporate obligations — 90,789 — 90,789 U.S. Treasury securities — 37,057 — 37,057 Certificates of deposit — 31,154 — 31,154 Mortgage and other asset backed securities — 61,498 — 61,498 Restricted cash 946 — — 946 Total assets $ 27,557 $ 220,498 $ — $ 248,055 Liabilities: Warrants to purchase common stock $ — $ — $ 12,161 $ 12,161 Total liabilities $ — $ — $ 12,161 12,161 December 31, 2015 Quoted Prices in Active Markets for Identical Items (Level 1) Significant other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Total Assets: Money market funds $ 24,811 $ — $ — $ 24,811 Corporate obligations — 67,706 — 67,706 U.S. Treasury securities — 10,991 — 10,991 Certificates of deposit — 16,776 — 16,776 Mortgage and other asset backed securities — 13,228 — 13,228 Restricted cash 796 — — 796 Total assets $ 25,607 $ 108,701 $ — $ 134,308 Liabilities: Warrants to purchase common stock $ — $ — $ 17,187 $ 17,187 Total liabilities $ — $ — $ 17,187 $ 17,187
Summary of changes in the fair value of the preferred and common stock warrant liability	The following table sets forth a summary of changes in the fair value of the Company’s common stock warrant liability, which has been classified within Level 3 of the fair value hierarchy, wherein fair value is estimated using significant unobservable inputs (in thousands): Nine Months Ended September 30, 2016 2015 Beginning balance $ 17,187 $ 14,124 Change in fair value (5,026 ) (5,595 ) Exercises — (465 ) Ending balance $ 12,161 $ 8,064

Net Loss Per Share (Tables)

Net Loss Per Share (Tables)	9 Months Ended
	Sep. 30, 2016
Earnings Per Share [Abstract]
Schedule of anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share	The following common stock equivalents were excluded from the calculation of diluted net loss per share for the periods indicated because their inclusion would have had an anti-dilutive effect (in thousands): Three Months Ended Nine Months Ended 2016 2015 2016 2015 Outstanding stock options 3,193 3,328 3,193 3,328 Common stock warrants 397 398 397 398 Shares issuable under employee stock purchase plan 18 19 18 19 Restricted stock units 670 524 670 524 4,278 4,269 4,278 4,269

Warrants (Tables)

Warrants (Tables)	9 Months Ended
	Sep. 30, 2016
Warrants and Rights Note Disclosure [Abstract]
Summary of the number of shares issuable upon exercise of outstanding warrants and the terms and accounting treatment for the outstanding warrants	Below is a summary of the number of shares issuable upon exercise of outstanding warrants and the terms and accounting treatment for the outstanding warrants (in thousands, except per share data): Warrants as of Weighted- Average Exercise Balance Sheet Classification September 30, 2016 December 31, 2015 Price Per Share Expiration September 30, 2016 December 31, 2015 Warrants to purchase common stock 393 393 $ 5.88 June 10, 2020 - July 9, 2020 Liability Liability Warrants to purchase common stock 4 5 4.00 - 7.40 March 28, 2017 - December 31, 2017 Equity(1) (2) Equity(2) All warrants 397 398 $ 5.88 (1) In March 2016, the warrant holders exercised warrants to purchase 1,317 shares of Common Stock on a net basis, resulting in the issuance of 1,109 shares of Common Stock. (2) Warrants to purchase common stock were issued in connection with various debt financing transactions that were consummated in periods prior to December 31, 2012. See discussion below for further details.

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Compensation Costs Recognized	Total compensation cost recognized for all stock-based compensation awards in the consolidated statements of operations and comprehensive loss is as follows (in thousands): Three Months Ended Nine Months Ended 2016 2015 2016 2015 Research and development $ 1,942 $ 1,201 $ 5,617 $ 3,302 General and administrative 2,646 1,863 7,770 4,993 $ 4,588 $ 3,064 $ 13,387 $ 8,295
Schedule of Weighted-Average Assumptions Used for Estimating Fair Value	The fair value of each stock option issued to employees was estimated at the date of grant using the Black-Scholes option pricing model with the following weighted-average assumptions: Three Months Ended Nine Months Ended 2016 2015 2016 2015 Expected volatility 65.4 % 66.0 % 64.5 % 67.1 % Expected term (in years) 6.0 6.0 5.9 6.0 Risk-free interest rate 1.2 % 1.7 % 1.4 % 1.7 % Expected dividend yield — % — % — % — %
Summary of Stock Option Activity	The following table summarizes the stock option activity under the Company’s 2003 Stock Option and Restricted Stock Plan and 2013 Equity Incentive Plan during the nine months ended September 30, 2016 (in thousands): Number of Grants Weighted- Average Exercise Price Per Share Weighted- Average Contractual Life (in years) Aggregate Intrinsic Value(1) Outstanding at December 31, 2015 3,191 $ 18.85 6.31 Granted 639 $ 28.69 Exercised (606 ) $ 5.82 Canceled or forfeited (31 ) $ 36.28 Outstanding at September 30, 2016 3,193 $ 23.12 6.69 $ 46,294 Exercisable at September 30, 2016 1,932 $ 16.72 5.37 $ 39,724 Vested and expected to vest at September 30, 2016 (2) 3,147 $ 22.97 6.65 $ 46,058 (1) The aggregate intrinsic value is calculated as the difference between the exercise price of the underlying options and the estimated fair value of the common stock for the options that were in the money at September 30, 2016 . (2) This represents the number of vested options at September 30, 2016 , plus the number of unvested options expected to vest at September 30, 2016 , based on the unvested options outstanding at September 30, 2016 , adjusted for the estimated forfeiture rate.
Schedule of Nonvested Restricted Stock Units Activity	The following table summarizes the restricted stock unit (RSU) activity under the 2013 Equity Incentive Plan during the nine months ended September 30, 2016 (in thousands): Number Weighted- Unvested balance at December 31, 2015 521 $ 31.57 Granted 158 30.17 Vested — — Forfeited (9 ) 34.01 Unvested balance at September 30, 2016 670 $ 31.22

Nature of Business (Details)

Nature of Business (Details)	9 Months Ended
	Sep. 30, 2016protein_therapeutic
Nature of Business
Number of therapeutics candidates discovered	4

Basis of Presentation Narrative

Basis of Presentation Narrative (Details) $ / shares in Units, $ in Millions	Jan. 11, 2016USD ($)$ / sharesshares
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Number of shares issued in transaction (in shares) | shares	3,750,000
Price per share (in dollars per share) | $ / shares	$ 40
Consideration received on transaction | $	$ 140.3

Segment Information (Details)

Segment Information (Details)	9 Months Ended
	Sep. 30, 2016segment
Segment Information
Number of operating segments	1

Cash Equivalents and Short-te34

Cash Equivalents and Short-term and Long-term Investments (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015	Sep. 30, 2015	Dec. 31, 2014
Schedule of Available-for-sale Securities [Line Items]
Cash and cash equivalents due in 90 days or less	$ 31,016	$ 27,783	$ 43,438	$ 176,460
Available-for-sale securities:
Amortized Cost	220,075	108,418
Gross Unrealized Gains	61	0
Gross Unrealized Losses	(129)	(220)
Estimated Fair Value	220,007	108,198
Total cash, cash equivalents and available-for-sale securities
Amortized Cost	251,091	136,201
Gross Unrealized Gains	61	0
Gross Unrealized Losses	(129)	(220)
Estimated Fair Value	251,023	135,981
Corporate obligations due in one year or less
Available-for-sale securities:
Amortized Cost	42,643	53,243
Gross Unrealized Gains	1	0
Gross Unrealized Losses	(23)	(81)
Estimated Fair Value	42,621	53,162
Corporate obligations due in more than one year
Available-for-sale securities:
Amortized Cost	48,203	14,112
Gross Unrealized Gains	31	0
Gross Unrealized Losses	(66)	(72)
Estimated Fair Value	48,168	14,040
U.S. Treasury securities due in one year or less
Available-for-sale securities:
Amortized Cost	22,985	6,016
Gross Unrealized Gains	10	0
Gross Unrealized Losses	0	(4)
Estimated Fair Value	22,995	6,012
U.S. Treasury securities due in more than one year
Available-for-sale securities:
Amortized Cost	14,048	4,995
Gross Unrealized Gains	14	0
Gross Unrealized Losses	(1)	(15)
Estimated Fair Value	14,061	4,980
Certificates of deposit due in one year or less
Available-for-sale securities:
Amortized Cost	20,385	11,890
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	20,385	11,890
Certificates of deposit due in more than one year
Available-for-sale securities:
Amortized Cost	10,280	4,886
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(1)	0
Estimated Fair Value	10,279	4,886
Mortgage and other asset backed securities due in one year or less
Available-for-sale securities:
Amortized Cost	21,278	6,010
Gross Unrealized Gains	4	0
Gross Unrealized Losses	(4)	(10)
Estimated Fair Value	21,278	6,000
Mortgage and other asset backed securities due in more than one year
Available-for-sale securities:
Amortized Cost	40,253	7,266
Gross Unrealized Gains	1	0
Gross Unrealized Losses	(34)	(38)
Estimated Fair Value	$ 40,220	$ 7,228

Cash Equivalents and Short-te35

Cash Equivalents and Short-term and Long-term Investments - Narrative (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Cash and Cash Equivalents [Abstract]
Unrealized loss position, less than twelve months, fair value	$ 106,700	$ 89,700
Continuous unrealized loss position, twelve months or longer, fair value	5,500
Continuous unrealized loss position, fair value	$ 5

Restricted Cash (Details)

Restricted Cash (Details) - Letter of Credit - USD ($) $ in Millions	Sep. 30, 2016	Dec. 31, 2015
Certificates of Deposits and Money Market Funds
Accounts, Notes, Loans and Financing Receivable [Line Items]
Letters of credit held in the form of a money market account as collateral for lease obligations and credit cards	$ 0.9
Certificates of deposit
Accounts, Notes, Loans and Financing Receivable [Line Items]
Letters of credit held in the form of a money market account as collateral for lease obligations and credit cards		$ 0.8

Fair Value Measurements Financi

Fair Value Measurements Financial Instrument at Fair Value Schedule (Details) - USD ($)	9 Months Ended	12 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Liabilities:
Fair value measurement transfers between levels	$ 0	$ 0
Recurring
Assets:
Total assets	248,055,000	134,308,000
Liabilities:
Total liabilities	12,161,000	17,187,000
Recurring | Common stock warrants
Liabilities:
Total liabilities	12,161,000	17,187,000
Recurring | Money market funds
Assets:
Total assets	26,611,000	24,811,000
Recurring | Corporate obligations
Assets:
Total assets	90,789,000	67,706,000
Recurring | U.S. Treasury securities
Assets:
Total assets	37,057,000	10,991,000
Recurring | Certificates of deposit
Assets:
Total assets	31,154,000	16,776,000
Recurring | Mortgage and other asset backed securities
Assets:
Total assets	61,498,000	13,228,000
Recurring | Restricted cash
Assets:
Total assets	946,000	796,000
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1)
Assets:
Total assets	27,557,000	25,607,000
Liabilities:
Total liabilities	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Common stock warrants
Liabilities:
Total liabilities	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Money market funds
Assets:
Total assets	26,611,000	24,811,000
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Corporate obligations
Assets:
Total assets	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | U.S. Treasury securities
Assets:
Total assets	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Certificates of deposit
Assets:
Total assets	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Mortgage and other asset backed securities
Assets:
Total assets	0	0
Recurring | Quoted Prices in Active Markets for Identical Items (Level 1) | Restricted cash
Assets:
Total assets	946,000	796,000
Recurring | Significant Other Observable Inputs (Level 2)
Assets:
Total assets	220,498,000	108,701,000
Liabilities:
Total liabilities	0	0
Recurring | Significant Other Observable Inputs (Level 2) | Common stock warrants
Liabilities:
Total liabilities	0	0
Recurring | Significant Other Observable Inputs (Level 2) | Money market funds
Assets:
Total assets	0	0
Recurring | Significant Other Observable Inputs (Level 2) | Corporate obligations
Assets:
Total assets	90,789,000	67,706,000
Recurring | Significant Other Observable Inputs (Level 2) | U.S. Treasury securities
Assets:
Total assets	37,057,000	10,991,000
Recurring | Significant Other Observable Inputs (Level 2) | Certificates of deposit
Assets:
Total assets	31,154,000	16,776,000
Recurring | Significant Other Observable Inputs (Level 2) | Mortgage and other asset backed securities
Assets:
Total assets	61,498,000	13,228,000
Recurring | Significant Other Observable Inputs (Level 2) | Restricted cash
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3)
Assets:
Total assets	0	0
Liabilities:
Total liabilities	12,161,000	17,187,000
Recurring | Significant Unobservable Inputs (Level 3) | Common stock warrants
Liabilities:
Total liabilities	12,161,000	17,187,000
Recurring | Significant Unobservable Inputs (Level 3) | Money market funds
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Corporate obligations
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3) | U.S. Treasury securities
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Certificates of deposit
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Mortgage and other asset backed securities
Assets:
Total assets	0	0
Recurring | Significant Unobservable Inputs (Level 3) | Restricted cash
Assets:
Total assets	$ 0	$ 0

Fair Value Measurements Preferr

Fair Value Measurements Preferred and Common Stock Warrant Liability Rollforward (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Summary of changes in the fair value of the preferred and common stock warrant liability classified within Level 3 of the fair value hierarchy
Beginning balance	$ 17,187	$ 14,124
Change in fair value	(5,026)	(5,595)
Exercises	0	(465)
Ending balance	$ 12,161	$ 8,064

Net Loss Per Share (Details)

Net Loss Per Share (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Net Income (Loss) Per Share
Anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share (in shares)	4,278	4,269	4,278	4,269
Outstanding stock options
Net Income (Loss) Per Share
Anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share (in shares)	3,193	3,328	3,193	3,328
Common stock warrants
Net Income (Loss) Per Share
Anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share (in shares)	397	398	397	398
Shares issuable under employee stock purchase plan
Net Income (Loss) Per Share
Anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share (in shares)	18	19	18	19
Restricted stock units
Net Income (Loss) Per Share
Anti-dilutive common stock equivalents excluded from the calculation of diluted net loss per share (in shares)	670	524	670	524

Warrants (Details)

Warrants (Details) - USD ($) $ / shares in Units, $ in Thousands		Jul. 31, 2010	Mar. 31, 2016	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Warrants
Number of shares issuable upon exercise of outstanding warrants (in shares)				397,000		397,000		398,000
Weighted-average exercise price per share (in dollars per share)				$ 5.88		$ 5.88
Class of warrant or right number of warrants exercised on net basis (in shares)			1,317
Stock issued during period shares warrants exercise on net basis (in shares)			1,109
Increase (decrease) in fair value of warrants						$ (5,026)	$ (5,595)
Warrants to purchase Common stock expiring between June 10, 2020 to July 9, 2020
Warrants
Number of shares issuable upon exercise of outstanding warrants (in shares)				393,000		393,000		393,000
Weighted-average exercise price per share (in dollars per share)				$ 5.88		$ 5.88
Increase (decrease) in fair value of warrants				$ 800	$ (2,600)	$ (5,000)	$ (5,600)
Warrants to purchase Common stock expiring between June 10, 2020 to July 9, 2020 | Warrants issued in connection with financing transactions
Warrants
Number of shares issuable upon exercise of outstanding warrants (in shares)		871,580
Expiration period		10 years
Warrants to purchase Common stock expiring between June 10, 2020 to July 9, 2020 | Series E Preferred Stock
Warrants
Discount recorded to the preferred stock issued		$ 3,000
Warrants to purchase Common stock expiring between March 28, 2017 to December 31, 2017
Warrants
Number of shares issuable upon exercise of outstanding warrants (in shares)	[1],[2]			4,000		4,000		5,000
Minimum | Warrants to purchase Common stock expiring between March 28, 2017 to December 31, 2017
Warrants
Weighted-average exercise price per share (in dollars per share)	[1],[2]			$ 4		$ 4
Maximum | Warrants to purchase Common stock expiring between March 28, 2017 to December 31, 2017
Warrants
Weighted-average exercise price per share (in dollars per share)	[1],[2]			$ 7.40		$ 7.40
[1]	In March 2016, the warrant holders exercised warrants to purchase 1,317 shares of Common Stock on a net basis, resulting in the issuance of 1,109 shares of Common Stock.
[2]	Warrants to purchase common stock were issued in connection with various debt financing transactions that were consummated in periods prior to December 31, 2012. See discussion below for further details.

Significant Agreements - Celgen

Significant Agreements - Celgene (Details) $ in Thousands	Feb. 20, 2008discovery_stage_compound	Sep. 30, 2016USD ($)	Sep. 30, 2015USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2015USD ($)
Significant Agreements
Cost-sharing, net		$ 2,870	$ 3,950	$ 8,987	$ 13,286
Investor | Collaboration, License, and Option Agreement
Significant Agreements
Deferred revenue recognized		100	200	400	1,000
Cost-sharing, net		2,900	$ 3,900	9,000	$ 13,300
Investor | Collaboration, License, and Option Agreement | Sotarcept
Significant Agreements
Number of license options granted | discovery_stage_compound	3
Payments received				43,500
Investor | Collaboration, License, and Option Agreement | Luspatercept
Significant Agreements
Payments received				$ 84,500
Investor | Collaboration, License, and Option Agreement | Sotarcept and Luspatercept
Significant Agreements
Percentage of development costs for which collaborator is responsible				100.00%
Investor | Collaboration, License, and Option Agreement | Clinical milestones | Sotarcept
Significant Agreements
Milestone payment receivable on commencement of Phase 2b clinical trial		10,000		$ 10,000
Investor | Collaboration, License, and Option Agreement | Clinical milestones | Luspatercept
Significant Agreements
Milestone payment receivable on commencement of Phase 2b clinical trial		$ 25,000		$ 25,000
Investor | Collaboration, License, and Option Agreement | Weighted Average | Sotarcept and Luspatercept
Significant Agreements
Potential royalty rate (as a percent)				20.00%

Significant Agreements - Other

Significant Agreements - Other Agreements (Details) - USD ($)	1 Months Ended	3 Months Ended		9 Months Ended		12 Months Ended
	May 31, 2014	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2012	Dec. 31, 2004
Significant Agreements
Milestones and fees		$ 17,102,000	$ 13,335,000	$ 49,492,000	$ 42,261,000
License agreement with research institution
Significant Agreements
Milestones and fees expensed		0	0	0	0
License Agreement | Common Stock | License agreement with a non-profit institution
Significant Agreements
Number of shares issued as compensation for licenses (in shares)							62,500
Fair value of shares issued as compensation for licenses							$ 25,000
License Agreement | Minimum | License agreement with a non-profit institution
Significant Agreements
Milestone fees payable as percentage of research and U.S. development progress and sublicensing revenue							10.00%
Royalty payable as percentage of net sales							1.00%
License Agreement | Maximum | License agreement with a non-profit institution
Significant Agreements
Milestone fees payable as percentage of research and U.S. development progress and sublicensing revenue							25.00%
Royalty payable as percentage of net sales							3.50%
License Agreement | Dalantercept | License agreement with certain individuals
Significant Agreements
Percentage of reduction in royalty rate for a period of time after patent expiration							50.00%
Milestones and fees expensed		0	0	0	0
License Agreement | Dalantercept | License agreement with research institution
Significant Agreements
Royalty payable as percentage of net sales						1.50%
Annual payment upon first commercial sale						$ 25,000
License Agreement | Development milestone | Sotarcept | Maximum | License agreement with a non-profit institution
Significant Agreements
Total potential milestone payments							$ 2,000,000
License Agreement | Development milestone | Luspatercept | Maximum | License agreement with a non-profit institution
Significant Agreements
Total potential milestone payments							700,000
License Agreement | Development and sales milestone | Dalantercept | Maximum | License agreement with certain individuals
Significant Agreements
Total potential milestone payments							$ 1,000,000
License Agreement | Development and commercial milestone | Dalantercept | Maximum | License agreement with research institution
Significant Agreements
Total potential milestone payments						$ 1,000,000
Collaborative Arrangement | License agreement with antibody technology company
Significant Agreements
Milestones and fees expensed	$ 300,000	0	0	1,000,000	100,000
Non-collaborative Arrangement Transactions | License Agreement with Non Profit Institution
Significant Agreements
Milestones and fees		$ 400,000	$ 200,000	$ 900,000	$ 1,000,000

Stock-Based Compensation (Detai

Stock-Based Compensation (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation expense	$ 4,588	$ 3,064	$ 13,387	$ 8,295
Employee Stock Purchase Plan 2013
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation expense	$ 100	$ 100	$ 200	$ 200

Stock-Based Compensation - Sche

Stock-Based Compensation - Schedule of Stock-Based Compensation Costs Recognized (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost
Stock-based compensation expense	$ 4,588	$ 3,064	$ 13,387	$ 8,295
Research and Development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost
Stock-based compensation expense	1,942	1,201	5,617	3,302
General and Administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost
Stock-based compensation expense	$ 2,646	$ 1,863	$ 7,770	$ 4,993

Stock-Based Compensation - Sc45

Stock-Based Compensation - Schedule of Weighted-Average Assumptions Used for Estimating Fair Value (Details) - Stock Option	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award
Expected volatility	65.40%	66.00%	64.50%	67.10%
Expected term (in years)	6 years	6 years	5 years 11 months 9 days	6 years
Risk-free interest rate	1.20%	1.70%	1.40%	1.70%
Expected dividend yield	0.00%	0.00%	0.00%	0.00%

Stock-Based Compensation - Summ

Stock-Based Compensation - Summary of Stock Option Activity (Details) - USD ($) $ / shares in Units, $ in Thousands		9 Months Ended	12 Months Ended
		Sep. 30, 2016	Dec. 31, 2015
Number of Grants
Granted (in shares)		639,070
Exercised (in shares)		(605,558)
Aggregate Intrinsic Value
Weighted average grant date fair value (in usd per share)		$ 28.69
Total proceeds from options exercised		$ 3,500
Aggregate intrinsic value of options exercised		$ 16,700
Stock Option
Number of Grants
Outstanding at the beginning of period (in shares)		3,191,000
Granted (in shares)		639,000
Exercised (in shares)		(606,000)
Canceled or forfeited (in shares)		(31,000)
Outstanding at the end of the period (in shares)		3,193,000	3,191,000
Exercisable at the end of the period (in shares)		1,932,000
Vested and expected to vest at the end of the period (in shares)	[1]	3,147,000
Weighted- Average Exercise Price Per Share
Outstanding at the beginning of period (in usd per share)		$ 18.85
Granted (in usd per share)		28.69
Exercised (in usd per share)		5.82
Canceled or forfeited (in usd per share)		36.28
Outstanding at the end of the period (in usd per share)		23.12	$ 18.85
Exercisable at the end of the period (in usd per share)		16.72
Vested and expected to vest at the end of the period (in usd per share)	[1]	$ 22.97
Weighted- Average Contractual Life
Outstanding at the beginning of the period (in years)		6 years 8 months 9 days	6 years 3 months 23 days
Outstanding at the end of the period (in years)		6 years 8 months 9 days	6 years 3 months 23 days
Exercisable at the end of the period (in years)		5 years 4 months 13 days
Vested and expected to vest at the end of the period (in years)	[1]	6 years 7 months 24 days
Aggregate Intrinsic Value
Outstanding at the end of the period (in usd)	[2]	$ 46,294
Exercisable at the end of the period (in usd)	[2]	39,724
Vested and expected to vest at the end of the period (in usd)	[1],[2]	46,058
Unrecognized compensation expense		$ 21,500
Weighted-average period for recognition (in years)		2 years 5 months 5 days
[1]	This represents the number of vested options at September 30, 2016, plus the number of unvested options expected to vest at September 30, 2016, based on the unvested options outstanding at September 30, 2016, adjusted for the estimated forfeiture rate.
[2]	The aggregate intrinsic value is calculated as the difference between the exercise price of the underlying options and the estimated fair value of the common stock for the options that were in the money at September 30, 2016.

Stock-Based Compensation - Sc47

Stock-Based Compensation - Schedule of Nonvested Restricted Stock Activity (Details) - USD ($) $ / shares in Units, $ in Millions	9 Months Ended	12 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Restricted stock units
Number of Grants
Unvested balance at beginning of the period (in shares)	521,000
Granted (in shares)	158,000
Vested (in shares)	0
Forfeited (in shares)	(9,000)
Unvested balance at end of the period (in shares)	670,000	521,000
Weighted- Average Grant Date Fair Value
Unvested balance at beginning of the period (in usd per share)	$ 31.57
Granted (in usd per share)	30.17
Vested (in usd per share)	0
Forfeited (in usd per share)	34.01
Unvested balance at end of the period (in usd per share)	$ 31.22	$ 31.57
Certain Individuals | Restricted stock units
Number of Grants
Granted (in shares)	133,980
Unvested balance at end of the period (in shares)	181,710
Weighted- Average Grant Date Fair Value
Unrecognized compensation cost	$ 4.7
Weighted-average period for recognition (in years)	2 years 2 months 23 days
Certain Individuals | Performance-Based Restricted Stock Units
Number of Grants
Granted (in shares)	23,977	464,000
Unvested balance at end of the period (in shares)	487,977
Weighted- Average Grant Date Fair Value
Unrecognized compensation cost	$ 9.5
Weighted-average period for recognition (in years)	2 years 29 days

Income Taxes (Details)

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Income Tax Disclosure [Abstract]
Income tax benefit	$ 20	$ 0	$ 20	$ 0
Unrealized holding gain (loss) on securities, tax	53	$ 0	53	$ 0
Accrued tax provision	$ 17		$ 17

Related Party Transactions (Det

Related Party Transactions (Details) - Celgene - USD ($) $ in Millions	Sep. 30, 2016	Dec. 31, 2015
Related Party Transactions
Ownership percentage of entity's fully diluted equity	12.90%	12.30%
Deferred revenue	$ 4.4