Aceragen (ACGN) 10-K 15 Mar 17 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($)	12 Months Ended
	Dec. 31, 2016	Feb. 15, 2017	Jun. 30, 2016
Document and Entity Information
Entity Registrant Name	IDERA PHARMACEUTICALS, INC.
Trading Symbol	IDRA
Entity Central Index Key	861,838
Document Type	10-K
Document Period End Date	Dec. 31, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 145,406,315
Entity Common Stock, Shares Outstanding		149,093,717
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY

BALANCE SHEETS

BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 80,667	$ 26,586
Short-term investments	28,347	33,574
Prepaid expenses and other current assets	2,030	3,082
Total current assets	111,044	63,242
Long-term investments		26,997
Property and equipment, net	1,853	1,692
Restricted cash and other assets	334	345
Total assets	113,231	92,276
Current liabilities:
Accounts payable	556	1,169
Accrued expenses	7,394	4,274
Current portion of note payable	292	261
Current portion of deferred revenue	1,111	1,111
Total current liabilities	9,353	6,815
Deferred revenue, net of current portion	152	1,262
Note payable, net of current portion	209	501
Other liabilities	168	116
Total liabilities	9,882	8,694
Commitments and contingencies
Stockholders' equity:
Common stock, $0.001 par value, Authorized — 280,000 shares; Issued and outstanding — 149,065 and 121,265 shares at December 31, 2016 and December 31, 2015, respectively	149	121
Additional paid-in capital	641,687	583,676
Accumulated deficit	(538,470)	(500,081)
Accumulated other comprehensive loss	(17)	(134)
Total stockholders' equity	103,349	83,582
Total liabilities and stockholders' equity	113,231	92,276
Series A Preferred Stock
Stockholders' equity:
Preferred stock, $0.01 par value, Authorized — 5,000 shares: Series A convertible preferred stock; Designated — 1,500 shares, Issued and outstanding — 1 share

BALANCE SHEETS (Parenthetical)

BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
Preferred stock, par value	$ 0.01
Preferred stock, shares authorized	5,000,000
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	280,000,000	280,000,000
Common stock, shares issued	149,065,000	121,265,000
Common stock, shares outstanding	149,065,000	121,265,000
Series A Preferred Stock
Preferred stock, par value	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares designated	1,500,000	1,500,000
Preferred stock, shares issued	1,000	1,000
Preferred stock, shares outstanding	1,000	1,000

STATEMENTS OF OPERATIONS AND CO

STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
Alliance revenue	$ 16,199	$ 249	$ 73
Operating expenses:
Research and development	39,824	33,699	27,493
General and administrative	15,132	15,396	11,332
Total operating expenses	54,956	49,095	38,825
Loss from operations	(38,757)	(48,846)	(38,752)
Other income (expense):
Interest income	415	357	66
Interest expense	(80)	(105)	(27)
Foreign currency exchange gain	33	39	71
Net loss	(38,389)	(48,555)	(38,642)
Loss on extinguishment of convertible preferred stock and preferred stock dividends			519
Net loss	$ (38,389)	$ (48,555)	$ (38,642)
Basic and diluted net loss per common share (Note 12)	$ (0.30)	$ (0.42)	$ (0.47)
Shares used in computing basic and diluted net loss per common share	127,597	115,092	82,827
Net loss	$ (38,389)	$ (48,555)	$ (39,161)
Other comprehensive gain (loss):
Unrealized gain (loss) on available-for-sale securities	117	(117)	(10)
Other comprehensive loss	117	(117)	(10)
Comprehensive loss	$ (38,272)	$ (48,672)	$ (38,652)

STATEMENTS OF STOCKHOLDERS' EQU

STATEMENTS OF STOCKHOLDERS' EQUITY - USD ($) shares in Thousands, $ in Thousands	Common StockSeries E Convertible Preferred Stock	Common StockSeries D Convertible Preferred Stock	Common Stock	Additional Paid-in CapitalSeries E Convertible Preferred Stock	Additional Paid-in CapitalSeries D Convertible Preferred Stock	Additional Paid-in CapitalSeries E Preferred Stock	Additional Paid-in CapitalSeries D Preferred Stock	Additional Paid-in Capital	Accumulated Deficit	Accumulated Other Comprehensive (Loss)/Income	Series E Convertible Preferred Stock	Series D Convertible Preferred Stock	Series E Preferred Stock	Series D Preferred Stock	Total
Beginning balance at Dec. 31, 2013			$ 66					$ 434,285	$ (412,884)	$ (7)	$ 5,528	$ 5,464			$ 32,452
Beginning balance, shares at Dec. 31, 2013			66,252								424	1,124
Sale of common stock and warrants, net of issuance costs			$ 8					37,229							37,237
Sale of common stock and warrants, shares			7,867
Exercise of common stock options, warrants and employee stock purchases			$ 6					8,450							8,456
Exercise of common stock options, warrants and employee stock purchases, shares			5,932
Issuance of common stock for services								82							82
Issuance of common stock for services, shares			27
Non-employee stock option expense								24							24
Stock-based compensation								4,322							4,322
Convertible preferred stock dividends						$ (453)	$ (66)						$ (453)	$ (66)
Unrealized gain (loss) on marketable securities										(10)					(10)
Conversion of preferred stock to common	$ 9	$ 6		$ 5,519	$ 5,458						$ (5,528)	$ (5,464)
Conversion of preferred stock to common, shares	(8,485)	(6,266)									(424)	(1,124)
Net loss									(38,642)						(38,642)
Ending balance at Dec. 31, 2014			$ 95					494,850	(451,526)	(17)					43,402
Ending balance, shares at Dec. 31, 2014			94,829
Sale of common stock and warrants, net of issuance costs			$ 23					80,576							80,599
Sale of common stock and warrants, shares			23,000
Exercise of common stock options, warrants and employee stock purchases			$ 3					2,543							2,546
Exercise of common stock options, warrants and employee stock purchases, shares			3,402
Issuance of common stock for services								122							122
Issuance of common stock for services, shares			34
Non-employee stock option expense								143							143
Stock-based compensation								5,442							5,442
Unrealized gain (loss) on marketable securities										(117)					(117)
Net loss									(48,555)						(48,555)
Ending balance at Dec. 31, 2015			$ 121					583,676	(500,081)	(134)					$ 83,582
Ending balance, shares at Dec. 31, 2015			121,265												121,265
Sale of common stock and warrants, net of issuance costs			$ 26					48,822							$ 48,848
Sale of common stock and warrants, shares			26,225
Exercise of common stock options, warrants and employee stock purchases			$ 2					2,342							2,344
Exercise of common stock options, warrants and employee stock purchases, shares			1,575
Stock-based compensation								6,847							6,847
Unrealized gain (loss) on marketable securities										117					117
Net loss									(38,389)						(38,389)
Ending balance at Dec. 31, 2016			$ 149					$ 641,687	$ (538,470)	$ (17)					$ 103,349
Ending balance, shares at Dec. 31, 2016			149,065												149,065

STATEMENTS OF CASH FLOWS

STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Cash Flows from Operating Activities:
Net loss	$ (38,389)	$ (48,555)	$ (38,642)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss from disposition of assets	4		1
Non-employee stock option expense		143	24
Stock-based compensation	6,847	5,442	4,322
Issuance of common stock for services rendered	172	122	82
Accretion of premiums and discounts on investments	566	599	213
Depreciation and amortization expense	656	488	206
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	1,064	(1,889)	(329)
Accounts payable, accrued expenses, and other liabilities	1,988	(1,709)	2,802
Deferred revenue	(1,111)	2,373
Net cash used in operating activities	(28,203)	(42,986)	(31,321)
Cash Flows from Investing Activities:
Purchases of available-for-sale securities	(2,946)	(63,106)	(23,623)
Proceeds from maturity of available-for-sale securities	32,746	29,420	4,115
Proceeds from sale of available-for-sale securities	1,974	999
Purchases of property and equipment	(408)	(727)	(1,093)
Net cash provided by (used in) investing activities	31,366	(33,414)	(20,601)
Cash Flows from Financing Activities:
Sale of common stock and warrants, net of issuance costs	49,014	80,599	37,137
Proceeds from issuance of note payable			825
Proceeds from exercise of common stock warrants and options and employee stock purchases	2,172	2,546	8,456
Dividends paid			(798)
Payments on note payable	(261)	(120)
Payments on capital lease	(7)	(10)	(5)
Net cash provided by financing activities	50,918	83,015	45,615
Net increase (decrease) in cash and cash equivalents	54,081	6,615	(6,307)
Cash and cash equivalents, beginning of period	26,586	19,971	26,278
Cash and cash equivalents, end of period	$ 80,667	$ 26,586	$ 19,971

Organization

Organization	12 Months Ended
	Dec. 31, 2016
Organization
Organization	1. Idera Pharmaceuticals, Inc. (“Idera” or the “Company”) is a clinical-stage biopharmaceutical company focused on the discovery, development and commercialization of novel therapeutics for oncology and rare diseases. The Company uses two distinct proprietary drug discovery technology platforms to design and develop drug candidates: Toll-like receptor (“TLR”) targeting technology and third-generation antisense (“3GA”) technology. The Company developed these platforms based on its scientific expertise and pioneering work with synthetic oligonucleotides as therapeutic agents. Using its TLR targeting technology, the Company designs synthetic oligonucleotide-based drug candidates to modulate the activity of specific TLRs. In addition, using its 3GA technology, the Company is developing drug candidates to turn off the messenger RNA (“mRNA”) associated with disease causing genes. The Company believes that its 3GA technology may potentially reduce the immunotoxicity and increase the potency of earlier generation antisense and RNA interference (“RNAi”) technologies. Idera is focused on the clinical development of drug candidates for oncology and rare diseases characterized by small, well-defined patient populations with serious unmet medical needs. The Company believes it can develop and commercialize these targeted therapies on its own. To the extent the Company seeks to develop drug candidates for broader disease indications, it may explore potential collaborative alliances to support development and commercialization. The Company’s pipeline of drug candidates includes IMO-2125, IMO-8400 and IDRA-008. TLRs are key receptors of the immune system and play a role in innate and adaptive immunity. As a result, the Company believes TLRs are potential therapeutic targets for the treatment of a broad range of diseases. Using its chemistry-based platform, the Company has designed TLR agonists and antagonists to act by modulating the activity of targeted TLRs. A TLR agonist is a compound that stimulates an immune response through the targeted TLR. A TLR antagonist is a compound that inhibits an immune response by blocking the targeted TLR. The Company’s TLR agonist lead drug candidate IMO-2125 is an agonist of TLR9. The Company is evaluating IMO-2125 for the treatment by intra-tumoral injection of multiple oncology indications both in combination with checkpoint inhibitors and as monotherapy. The Company is initially developing IMO-2125 for use in combination with checkpoint inhibitors for the treatment of patients with anti-PD1 refractory metastatic melanoma. The Company’s TLR antagonist lead drug candidate is IMO-8400, which is an antagonist of TLR7, TLR8 and TLR9. The Company is developing IMO-8400 for the treatment of a rare disease called dermatomyositis. The Company selected this indication for development based on the reported increase in TLR expression in this disease state, expression of cytokines indicative of key TLR-mediated pathways and the presence of auto-antibodies that can induce TLR-mediated immune responses. The Company is developing its 3GA technology to “turn off” the mRNA associated with disease causing genes. The Company designed 3GA oligonucleotides to specifically address challenges associated with earlier generation antisense and RNAi technologies. Although currently used technologies to silence RNA have demonstrated the ability to inhibit the expression of disease-associated proteins, the Company believes that to reach their full therapeutic potential, gene silencing technologies need to achieve an improved therapeutic index with efficient systemic delivery, reduced immunotoxicity and increased potency. The Company has designed its 3GA oligonucleotides to provide these attributes. As of December 31, 2016 the Company had an accumulated deficit of $538.5 million. The Company expects to incur substantial operating losses in future periods. The Company does not expect to generate significant product revenue, sales-based milestones or royalties until the Company successfully completes development and obtains marketing approval for drug candidates, either alone or in collaborations with third parties, which the Company expects will take a number of years. In order to commercialize its drug candidates, the Company needs to complete clinical development and comply with comprehensive regulatory requirements. The Company is subject to a number of risks and uncertainties similar to those of other companies of the same size within the biotechnology industry, such as uncertainty of clinical trial outcomes, uncertainty of additional funding, and history of operating losses.

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2016
Summary of Significant Accounting Policies
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies (a) Basis of Presentation The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates. (b) Cash, Cash Equivalents and Investments The Company considers all highly liquid investments with maturities of 90 days or less when purchased to be “cash equivalents.” Cash and cash equivalents at December 31, 2016 and 2015 consisted of cash and money market funds. Management determines the appropriate classification of marketable securities at the time of purchase. Investments that the Company does not have the positive intent to hold to maturity are classified as “available-for-sale” and reported at fair market value. Available-for-sale investments are classified as long-term if their contractual maturity is greater than one year at the balance sheet date and the Company does not have the intent to sell them in order to fund current operations. Unrealized gains and losses associated with available-for-sale investments are recorded in “Accumulated other comprehensive income” on the accompanying balance sheets. The amortization of premiums and accretion of discounts, and any realized gains and losses and declines in value judged to be other-than-temporary, and interest and dividends for all available-for-sale securities are included in “Interest income” on the accompanying statements of operations. Investments that the Company intends to hold to maturity are classified as “held-to-maturity” investments. The Company had no “held-to-maturity” investments at either December 31, 2016 or 2015. The cost of securities sold is based on the specific identification method. The Company had no realized gains or losses from available-for-sale securities in 2016, 2015 or 2014. There were no losses or other-than-temporary declines in value included in “Interest income” for any securities for the three years ended December 31, 2016. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and investments will enable the Company to fund its operations into the second quarter of 2018. The Company has and will continue to evaluate available alternatives to extend its operations beyond the second quarter of 2018. (c) Restricted Cash As part of the Company’s lease arrangement for its office and laboratory facility in Cambridge, Massachusetts, the Company is required to restrict cash held in a certificate of deposit securing a line of credit for the lessor. As of December 31, 2016 and 2015, the restricted cash amounted to $0.3 million held in certificates of deposit securing a line of credit for the lessor. (d) Depreciation and Amortization Depreciation and amortization are computed using the straight-line method based on the estimated useful lives of the related assets. Laboratory and other equipment are depreciated over three to five years. Leasehold improvements are amortized over the remaining lease term or the related useful life, if shorter. (e) Revenue Recognition The Company recognizes revenue in accordance with the Financial Accounting Standards Board’s (FASB) Accounting Standards Codification (“ASC”) Topic 605, Revenue Recognition . Accordingly, revenue is recognized for each unit of accounting when all of the following criteria are met: · persuasive evidence of an arrangement exists; · delivery has occurred or services have been rendered; · the seller’s price to the buyer is fixed or determinable; and · collectability is reasonably assured. Amounts received prior to satisfying the revenue recognition criteria are recognized as deferred revenue in the Company’s balance sheet. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, current. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion. The Company’s revenues have primarily been generated through collaborative research, development and/or commercialization agreements. The terms of these agreements typically may include payment to the Company of one or more of the following: nonrefundable, up-front license fees, research, development and commercial milestone payments, other contingent payments due based on the activities of the counterparty or the reimbursement by licensees of costs associated with patent maintenance. Each of these types of revenue are recorded as Alliance revenues in the Company’s statement of operations. For each collaborative research, development and/or commercialization agreement, which results in revenues, the Company determines (i) whether multiple deliverables exist, (ii) whether the delivered elements have value to the customer on a stand-alone basis, (iii) how the deliverables should be separated or combined and (iv) how the consideration should be allocated to the deliverables. Arrangement consideration that is fixed or determinable is allocated among the separate units of accounting using the relative selling price method. Then, the applicable revenue recognition criteria in ASC 605 are applied to each of the separate units of accounting in determining the appropriate period and pattern of recognition. The Company determines the selling price of a unit of accounting following the hierarchy of evidence prescribed by ASC 605-25. Accordingly, the Company determines the estimated selling price for units of accounting within each arrangement using vendor-specific objective evidence (“VSOE”) of selling price, if available, third-party evidence (“TPE”) of selling price if VSOE is not available, or best estimate of selling price (“BESP”) if neither VSOE nor TPE is available. The Company typically uses BESP to estimate the selling price, since the Company generally does not have VSOE or TPE of selling price for its units of accounting. Determining the BESP for a unit of accounting requires significant judgment. In developing the BESP for a unit of accounting, the Company considers applicable market conditions and relevant entity-specific factors, including factors that were contemplated in negotiating the agreement with the customer and estimated costs. The Company validates the BESP for units of accounting by evaluating whether changes in the key assumptions used to determine the BESP will have a significant effect on the allocation of arrangement consideration between multiple units of accounting. Options are considered substantive if, at the inception of the arrangement, this Company is at risk as to whether the collaborator will choose to exercise the option. Factors that the Company considers in evaluating whether an option is substantive include the overall objective of the arrangement, the benefit the collaborator might obtain from the arrangement without exercising the option, the cost to exercise the option and the likelihood that the option will be exercised. For arrangements under which an option is considered substantive, the Company does not consider the item underlying the option to be a deliverable at the inception of the arrangement and the associated option fees are not included in allocable arrangement consideration, assuming the option is not priced at a significant and incremental discount. Conversely, for arrangements under which an option is not considered substantive or if an option is priced at a significant and incremental discount, the Company would consider the item underlying the option to be a deliverable at the inception of the arrangement and a corresponding amount would be included in allocable arrangement consideration. The Company recognizes arrangement consideration allocated to each unit of accounting when all of the revenue recognition criteria in ASC 605 are satisfied for that particular unit of accounting. The Company will recognize as revenue arrangement consideration attributed to licenses that have standalone value from the other deliverables to be provided in an arrangement upon delivery. The Company will recognize as revenue arrangement consideration attributed to licenses that do not have standalone value from the other deliverables to be provided in an arrangement over our estimated performance period as the arrangement would be accounted for as a single unit of accounting. The Company’s multiple element revenue arrangements may include the following: Up-front License Fees: If a license does not have stand-alone value, the Company recognizes revenues from nonrefundable, up-front license fees on a straight-line basis over the contracted or estimated period of performance of the services under the related agreement, unless evidence suggests that revenue is earned or obligations are fulfilled in a different pattern. The Company evaluates the period of performance each reporting period and adjusts the period of performance on a prospective basis if there are changes to be made. If a license were to have stand-alone value and the other criteria of revenue recognition were satisfied, then revenue would be recognized in the period earned. Milestone Payments: At the inception of an agreement that includes research and development milestone payments, the Company evaluates whether each milestone is substantive or represents a deliverable of the counterparty to the agreement. The Company recognized revenues related to substantive milestones in full in the period in which the substantive milestone is achieved if payment is reasonably assured. If a milestone is a deliverable of the counterparty to the agreement, it is considered contingent revenue and is recognized when the Company is informed by the counterparty that they have achieved it and such amount is reasonably assured of payment. Research and Development Activities: If the Company is entitled to reimbursement from its collaborators for specified research and development activities or the reimbursement of costs associated with patent maintenance, the Company determines whether such funding would result in alliance revenues or an offset to research and development expenses. Reimbursement of patent maintenance costs are recognized during the period in which the related expenses are incurred as alliance revenues in the Company’s statement of operations. Royalties : If the Company is entitled to receive royalties from its collaborator for product sales, the Company will recognize royalty revenue in the period of sale of the related product(s), based on the underlying contract terms, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, assuming all other revenue recognition criteria are met. Under the terms of the Company’s exclusive license and collaboration agreement with Vivelix Pharmaceuticals, Ltd. (“Vivelix”) which granted Vivelix worldwide rights to develop and market IMO-9200, an antagonist of TLR7, 8, and 9, for non-malignant gastrointestinal disorders, and certain back-up compounds to IMO-9200 (the “Vivelix Agreement”), the Company received an upfront, non-refundable fee of $15 million. In addition, the Company will be eligible for future IMO-9200 related development, regulatory and sales milestone payments totaling up to $140 million, including development and regulatory milestones totaling up to $65 million and sales milestones totaling up to $75 million, and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. As it relates to back-up compounds, the Company will be eligible for related designation payments and development, regulatory sales and milestone payments totaling up to $52.5 million, including development and regulatory milestones totaling up to $35 million and sales milestones totaling up to $17.5 million and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. Under the terms of the Company’s collaboration and license agreement with GlaxoSmithKline Intellectual Property Development Limited (“GSK”) to license, research, develop and commercialize pharmaceutical compounds from the Company’s 3GA technology for the treatment of selected targets in renal disease (the “GSK Agreement”), the Company is eligible to receive up to approximately $100 million in license, research, clinical development and commercialization milestone payments, including a $2.5 million upfront, non-refundable, non-creditable cash payment. Approximately $9 million of the milestone payments are payable by GSK upon the identification of additional targets, the completion of current and future research plans and the designation of development candidates. Approximately $89 million is payable by GSK upon the achievement of clinical milestones and commercial milestones. In addition, the Company is eligible to receive royalty payments based on net sales of licensed products following commercialization at varying rates of up to five percent on annual net sales, as defined in the GSK Agreement. (f) Financial Instruments The fair value of the Company’s financial instruments is determined and disclosed in accordance with the three-tier fair value hierarchy specified in Note 2(m). The Company is required to disclose the estimated fair values of its financial instruments. The Company’s financial instruments consist of cash, cash equivalents, available-for-sale investments, receivables and a note payable. The estimated fair values of these financial instruments approximate their carrying values as of December 31, 2016 and 2015. As of December 31, 2016 and 2015, the Company did not have any derivatives, hedging instruments or other similar financial instruments except for the note issued under the Company’s loan and security agreement, which is discussed in Note 5(a), including put and call features which the Company determined are clearly and closely associated with the debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial. (g) Comprehensive Income (Loss) Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions and other events and circumstances from non-owner sources. Comprehensive income (loss) for the years ended December 31, 2016, 2015 and 2014 is comprised of reported net income (loss) and any change in net unrealized gains and losses on investments during each year, which is included in “Accumulated other comprehensive income” on the accompanying balance sheets. The Company applies Accounting Standards Update (“ASU”) No. 2011-05, “Comprehensive Income” by presenting the components of net income and other comprehensive income as one continuous statement. The following table includes the changes in the accumulated balance of the component of other comprehensive loss for the years ended December 31, 2016, 2015 and 2014: Year Ended December 31, (In thousands) 2016 2015 2014 Accumulated unrealized loss on available-for-sale securities at beginning of period $ $ $ Change during the period Accumulated unrealized loss on available-for-sale securities at end of period $ $ $ (h) Net Income (Loss) per Common Share applicable to Common Stockholders Basic and diluted net loss per common share applicable to common stockholders is computed using the weighted average number of shares of common stock outstanding during the period. Diluted net loss per common share applicable to common stockholders is the same as basic net loss per common share applicable to common stockholders for each of the three years in the period ended December 31, 2016 as the effects of the Company’s potential common stock equivalents are antidilutive (see Note 12). (i) Segment Reporting The Company views its operations and manages its business as one operating segment. Accordingly, the Company operates in one segment, which is the business of discovering and developing novel therapeutics that modulate immune responses through TLRs. As a result, the financial information disclosed herein represents all of the material financial information related to the Company’s principal operating segment. For all of the periods presented, all of the Company’s revenues were generated in the United States. As of December 31, 2016 and 2015, all assets were located in the United States. (j) Stock-Based Compensation The Company recognizes all share-based payments to employees and directors as expense in the statements of operations and comprehensive loss based on their fair values. The Company records compensation expense over an award’s requisite service period, or vesting period, based on the award’s fair value at the date of grant. The Company’s policy is to charge the fair value of stock options as an expense, adjusted for forfeitures, on a straight-line basis over the vesting period, which is generally four years for employees and three years for directors. The Company recorded charges of $6.8 million, $5.4 million and $4.3 million for the years ended December 31, 2016, 2015 and 2014, respectively, for stock-based compensation expense attributable to share-based payments made to employees and directors. The 2015 charge includes approximately $0.3 million of stock-based compensation in connection with the recognition of additional expense associated with the acceleration of vesting and extension of the exercise period of a retiring director’s stock options as a result of a modification to such director’s stock options. The 2014 charge includes approximately $1.3 million for the recognition of amortization associated with an employee’s options that were subject to accelerated vesting as a result of a modification to such employee’s stock options. The fair value of each option award is estimated on the date of grant using the Black-Scholes option pricing model. The following weighted average assumptions apply to the options to purchase 3,346,250, 3,533,750, and 8,232,424 shares of common stock granted to employees and directors during the years ended December 31, 2016, 2015 and 2014, respectively: 2016 2015 2014 Average risk free interest rate Expected dividend yield — — — Expected lives (years) Expected volatility Weighted average grant date fair value of options granted during the period (per share) $ $ $ Weighted average exercise price of options granted during the period (per share) $ $ $ The expected lives of the options and the expected volatility are based on historical experience. All options granted during the three years in the period ended December 31, 2016 were granted at exercise prices equal to the fair market value of the common stock on the dates of grant . The fair value of options that vested during 2016, 2015 and 2014 amounted to $6.9 million, $5.4 million and $4.2 million, respectively. There were no options exercised in 2016. The intrinsic value of options exercised amounted to $0.8 million and $0.6 million during 2015 and 2014, respectively. As of December 31, 2016, there was $13.4 million of unrecognized compensation cost related to nonvested stock-based compensation arrangements, which the Company expects to recognize over a weighted average period of 2.4 years. (k) Research and Development Expenses All research and development expenses, including amounts funded by research collaborations, are expensed as incurred. Research and development expenses are comprised of costs incurred in performing research and development activities, including drug development trials and studies, drug manufacturing, laboratory supplies, external research, payroll including stock-based compensation and overhead. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are deferred and capitalized. The capitalized amounts are expensed as the related goods are accepted by the Company or the services are performed. As of December 31, 2016 and 2015, the Company recorded approximately $1.4 million and $2.3 million as prepaid research and development, respectively. (l) Concentration of Credit Risk Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents and available-for-sale investments. The Company’s credit risk is managed by investing its cash and cash equivalents and marketable securities in highly rated money market instruments, certificates of deposit, corporate bonds, and debt securities. Due to these factors, no significant additional credit risk is believed by management to be inherent in the Company’s assets. As of December 31, 2016, all of the Company’s cash, cash equivalents and investments are held at two financial institutions. (m) Fair Value of Assets and Liabilities The Company measures fair value at the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date using assumptions that market participants would use in pricing the asset or liability (the “inputs”) into a three-tier fair value hierarchy. This fair value hierarchy gives the highest priority (Level 1) to quoted prices in active markets for identical assets or liabilities and the lowest priority (Level 3) to unobservable inputs in which little or no market data exists, requiring companies to develop their own assumptions. Observable inputs that do not meet the criteria of Level 1, and include quoted prices for similar assets or liabilities in active markets or quoted prices for identical assets and liabilities in markets that are not active, are categorized as Level 2. Level 3 inputs are those that reflect the Company’s estimates about the assumptions market participants would use in pricing the asset or liability, based on the best information available in the circumstances. Valuation techniques for assets and liabilities measured using Level 3 inputs may include unobservable inputs such as projections, estimates and management’s interpretation of current market data. These unobservable Level 3 inputs are only utilized to the extent that observable inputs are not available or cost-effective to obtain. The Company applies ASU No. 2011-04, “Fair Value Measurement (Topic 820),” in its fair value measurements and disclosures. The table below presents the assets and liabilities measured and recorded in the financial statements at fair value on a recurring basis at December 31, 2016 and 2015 categorized by the level of inputs used in the valuation of each asset and liability. Quoted Prices in Active Markets Significant for Identical Other Significant Assets or Observable Unobservable Liabilities Inputs Inputs (In thousands) Total (Level 1) (Level 2) (Level 3) December 31, 2016 Assets Money market funds $ $ $ — $ — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ — December 31, 2015 Assets Money market funds $ $ $ — $ — Short-term investments – commercial paper — — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Long-term investments – corporate bonds — — Long-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ — The Level 1 assets consist of money market funds, which are actively traded daily. The Level 2 assets consist of corporate bond, commercial paper, and municipal bond investments whose fair value may not represent actual transactions of identical securities. The fair value of corporate and municipal bonds is generally determined from quoted market prices received from pricing services based upon quoted prices from active markets and/or other significant observable market transactions at fair value. The fair value of commercial paper is generally determined based on the relationship between the investment’s discount rate and the discount rates of the same issuer’s commercial paper available in the market which may not be actively traded daily. Since these fair values may not be based upon actual transactions of identical securities, they are classified as Level 2. Since any investments are classified as available-for-sale securities, any unrealized gains or losses are recorded in accumulated other comprehensive income or loss within stockholders’ equity on the balance sheet. The Company did not elect to measure any other financial assets or liabilities at fair value at December 31, 2016 or 2015. (n) New Accounting Pronouncements — Recently Issued In May 2014, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) No. 2014-09, Revenue from Contracts with Customers (Topic 606), which was amended by ASU No. 2015-14. ASU No. 2014-09, as amended by ASU No. 2015-14, requires an entity to recognize revenue from the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. In particular, this ASU addresses contracts with more than one performance obligation, as well as the accounting for some costs to obtain or fulfill a contract with a customer, and provides for additional disclosures with respect to revenues and cash flows arising from contracts with customers. This ASU will be effective for fiscal years beginning after December 15, 2017, including interim periods within that fiscal year. Early adoption of this ASU is permitted only for fiscal years beginning after December 15, 2016, including interim periods within that fiscal year. The Company expects to adopt ASU 2014-09 in the first quarter of 2018 and is currently determining the transition method it will adopt. The adoption of ASU 2014-09 may have a material effect on our financial statements, including the footnote disclosures. To date, we have derived our revenues from a limited number of license and collaboration agreements. The consideration we are eligible to receive under these agreements includes upfront payments, research and development funding, contingent revenues in the form of commercial and development milestones and option payments and royalties. Each of our license and collaboration agreements has unique terms that will need to be evaluated separately under the new standard. We have started our preliminary assessment of our active license and collaboration agreements. ASU 2014-09 differs from the current accounting standard in many respects, such as in the accounting for variable consideration, including milestone payments. Accordingly, we expect that our evaluation of the accounting for collaboration agreements under the new revenue standard could identify material changes from the current accounting treatment. In addition, the current accounting standards include a presumption that revenue from upfront non-refundable fees are recognized ratably over the performance period, unless another attribution method is determined to more closely approximate the delivery of the goods or services to the customer. The new accounting standard will require entities to determine an appropriate attribution method using either output or input methods and does not include a presumption that entities would default to a ratable attribution approach. These factors could materially impact the amount and timing of our revenue recognition from our license and collaboration agreements under the new revenue standard. In August 2014, the FASB issued ASU No. 2014-15, Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern. ASU 2014-15 amends FASB ASC 205-40, Presentation of Financial Statements – Going Concern, by providing guidance on determining when and how reporting entities must disclose going-concern uncertainties in their financial statements, including requiring management to perform interim and annual assessments of an entity’s ability to continue as a going concern within one year of the date of issuance of the entity’s financial statements and providing certain disclosures if there is substantial doubt about the entity’s ability to continue as a going concern. ASU 2014-15 will be effective for fiscal years ending after December 15, 2016 and for interim periods thereafter. Early adoption of ASU 2014-15 is permitted. The Company has adopted this standard, which has not had a material impact on its financial statements. In January 2016, the FASB issued ASU No. 2016-01, Recognition and Measurement of Financial Assets and Financial Liabilities. The amendments in ASU 2016-01 address certain aspects of recognition, measurement, presentation and disclosure of financial instruments. ASU 2016-01 will be effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. Early adoption of some of the amendments included in ASU 2016-01 for financial statements of fiscal years or interim periods that have not yet been issued is permitted as of the beginning of the fiscal year of adoption. The Company is currently evaluating the effect that the adoption of ASU 2016-01 will have on its financial statements. In February 2016, the FASB issued ASU No. 2016-02, Leases. The amendments in ASU 2016-02 will require organizations that lease assets, with lease terms of more than 12 months, to recognize on the balance sheet the assets and liabilities for the rights and obligations created by those leases. Consistent with current U.S. Generally Accepted Accounting Principles (“U.S. GAAP”), the recognition, measurement, and presentation of expenses and cash flows arising from a lease by a lessee primarily will depend on its classification as a finance or operating lease. However, unlike current U.S. GAAP which requires only capital leases to be recognized on the balance sheet, ASU No. 2016-02 will require both types of leases to be recognized on the balance sheet. ASU 2016-02 will be effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the effect that the adoption of ASU 2016-02 will have on its financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (Topic 718). ASU 2016-09 will require organizations to recognize all income tax effects of awards in the statement of operations when the awards vest or are settled. ASU 2016-09 will also allow organizations to repurchase more shares from employees than they could previously purchase for tax withholding purposes without triggering liability accounting and to make a policy election to account for forfeitures as they occur. ASU 2016-09 will be effective for fiscal years beginning after December 15, 2016, and interim periods within those fiscal years. Early adoption is permitted in any interim or annual period. The Company is currently evaluating the effect that the adoption of ASU 2016-09 will have on its financial statements.

Investments

Investments	12 Months Ended
	Dec. 31, 2016
Investments
Investments	3. Investments The Company’s available-for-sale investments at fair value consisted of the following at December 31, 2016 and 2015: December 31, 2016 Gross Gross Estimated Unrealized Unrealized Fair Cost (Losses) Gain Value (In thousands) Short-term investments – corporate bonds $ $ $ — $ Short-term investments – municipal bonds — Total short-term investments — Total investments $ $ $ — $ December 31, 2015 Gross Gross Estimated Unrealized Unrealized Fair Cost (Losses) Gains Value (In thousands) Short-term investments – commercial paper $ $ — $ $ Short-term investments – corporate bonds — Short-term investments – municipal bonds — — Total short-term investments Long-term investments – corporate bonds — Long-term investments – municipal bonds Total long-term investments Total investments $ $ $ $ The Company had no realized gains or losses from available-for-sale securities in 2016, 2015 or 2014. There were no losses or other-than-temporary declines in value included in “Interest income” for any securities for the three years ended December 31, 2016. The Company had no auction rate securities as of December 31, 2016 and 2015. See Notes 2(f) and 2(m).

Property and Equipment

Property and Equipment	12 Months Ended
	Dec. 31, 2016
Property and Equipment
Property and Equipment	4. Property and Equipment At December 31, 2016 and 2015, net property and equipment at cost consisted of the following: December 31, (In thousands) 2016 2015 Leasehold improvements $ $ Laboratory equipment and other Total property and equipment, at cost Less: Accumulated depreciation and amortization Property and equipment, net $ $ Depreciation and amortization expense on Property and equipment was approximately $0.6 million, $0.5 million and $0.2 million in 2016, 2015 and 2014, respectively. As of December 31, 2016, Property and equipment includes $0.4 million of equipment that was received in December 2016, but was not in service as of December 31, 2016. As this equipment was unpaid at December 31, 2016, the $0.4 million payment due is reported in Accrued expenses.

Note Payable and Accrued Expens

Note Payable and Accrued Expenses	12 Months Ended
	Dec. 31, 2016
Note Payable and Accrued Expenses
Note Payable and Accrued Expenses	5. Note Payable and Accrued Expenses (a) Note Payable On September 30, 2014, the Company executed a loan and security agreement with Oxford Finance LLC (“Oxford”). Under the agreement, Oxford committed to lend the Company up to an aggregate principal amount of $3 million, through December 31, 2015, in one or more advances each of which is to be evidenced by a promissory note. The Company’s obligations to Oxford are secured by the specific laboratory, manufacturing, office or computer equipment financed under the agreement. Each equipment advance includes interest at a fixed interest rate equal to the greater of 7.50% per annum and 7.27% plus the three-month U.S. Libor Rate per annum, set at the time of funding. The principal amount of each equipment advance will be repaid in 36 monthly installments commencing on the applicable amortization date, which was July 1, 2015 for any equipment advance made on or before June 30, 2015. Monthly installments payable prior to July 1, 2015 consisted of interest only and monthly installments payable on or after July 1, 2015 consist of principal and accrued interest. The Company is required to pay a final payment in an amount equal to 5.7% of the aggregate advanced amount under each equipment advance at the time that the final monthly installment is due or such earlier date as specified in the loan and security agreement. The final payments will be accrued as interest expense over the term of each equipment advance using the effective interest method. The weighted average annual effective interest rate on the notes payable based on the amount advanced through December 31, 2015, including accrual of the final payment, is 11.1%. If the Company prepays all or a portion of the principal amount of any equipment advance prior to maturity, it will be required to pay Oxford a prepayment fee of between 1% and 3% of the principal amount of such equipment advance. As of December 31, 2016, the Company had received approximately $0.9 million in advances under the loan and security agreement and additional advances were not available under the agreement because the draw down period had expired. Aggregate future minimum payments, reflecting payments on outstanding principal plus interest, due under the loan and security agreement as of December 31, 2016, were as follows (in thousands): Year Ended December 31, 2017 $ 2018 Total minimum payments Less amount representing interest Notes payable, gross Unamortized facility fee Accrual of final payment Notes payable, balance Less current portion of notes payable Non-current portion of notes payable $ The loan and security agreement includes standard affirmative and restrictive covenants, but does not include any covenants to attain or maintain any financial metrics, and also includes standard events of default, including payment defaults, breaches of covenants following any applicable cure period, a material impairment in the perfection or priority of Oxford’s security interest or in the value of the collateral, a material impairment of the prospect of repayment of the loans and a material adverse change in the business, operations or conditions of the Company. Upon the occurrence of an event of default and following any applicable cure periods, a default interest rate of an additional 5% may be applied to the outstanding loan balances, and Oxford may declare all outstanding obligations immediately due and payable and take such other actions as set forth in the loan and security agreement. The Company assessed all terms and features of the note that the Company issued under its loan and security agreement in order to identify any potential embedded features that would require bifurcation. As part of this analysis, the Company assessed the economic characteristics and risks of the note, including put and call features. The Company determined that all features of the note are clearly and closely associated with a debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial. The Company will continue to reassess the features to determine if they require separate accounting on a quarterly basis. (b) Accrued Expenses At December 31, 2016 and 2015, accrued expenses consisted of the following: December 31, 2016 2015 (In thousands) Payroll and related costs $ $ Clinical and nonclinical trial expenses Professional and consulting fees Equipment purchase — Other $ $ The Equipment purchase relates to equipment received by the Company that was not in service and unpaid as of December 31, 2016.

Collaboration and License Agree

Collaboration and License Agreements	12 Months Ended
	Dec. 31, 2016
Collaboration and License Agreements
Collaboration and License Agreements	6. Collaboration and License Agreements (a) Collaboration with Vivelix In November 2016, the Company entered into the Vivelix Agreement. Under the terms of the agreement, the Company granted Vivelix worldwide rights to develop and market IMO-9200 and certain back-up compounds to IMO-9200. Vivelix is solely responsible for the development and commercialization of IMO-9200 and any designated back-up compounds. In connection with the Vivelix Agreement, Idera also transferred certain drug material to Vivelix for Vivelix’s use in its development activities. In accordance with the Vivelix Agreement, a Joint Research Committee (“JRC”) was formed with equal representation from Idera and Vivelix. The responsibilities of the JRC, include, but are not limited to monitoring the progress of the research program, advising on the designation of back-up compounds, sharing information between the parties and dealing with disputes that may arise between the parties. If a dispute cannot be resolved by the JRC, Vivelix has final decision making authority. If requested by Vivelix pursuant to the Vivelix Agreement, Idera will create, characterize and perform research on back-up compounds. Such activity is to be mutually agreed upon and moderated by the JRC. The research period commenced with the execution of the agreement and will last for one year. Vivelix may extend the research period by up to two one year periods. During the research period, the parties will agree on the number of full time equivalents to work on the program. Vivelix will reimburse Idera at an annual market rate for the services rendered. Vivelix has certain rights under the agreement whereby it may (i) exercise the right of first refusal, (ii) the right of first negotiation to obtain an exclusive license for any compound controlled by Idera that has activity in the field of inflammatory bowel disease and (iii) the right to request an expanded Field beyond the GI Field. The Company has determined that these rights are substantive options. Under the terms of the Vivelix Agreement, the Company received an upfront, non-refundable fee of $15 million. In addition, the Company will be eligible for future IMO-9200 related development, regulatory and sales milestone payments totaling up to $140 million, including development and regulatory milestones totaling up to $65 million and sales milestones totaling up to $75 million, and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. As it relates to back-up compounds, the Company will be eligible for related designation payments and development, regulatory sales and milestone payments totaling up to $52.5 million, including development and regulatory milestones totaling up to $35 million and sales milestones totaling up to $17.5 million and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. Under the terms of the agreement and if requested by and at Vivelix’s expense, the Company is responsible for performing research services related to the back-up compounds. At the effective date of the Vivelix Agreement and as of December 31, 2016, Baker Bros. Advisors LP and certain of its affiliated funds (“Baker Brothers”) beneficially owned approximately 7.0% of the Company’s outstanding common stock. Baker Brothers also owned a controlling financial interest of Vivelix at the effective date of the Vivelix Agreement and as of December 31, 2016. Baker Brothers holds two of the four board seats on the Board of Directors of Vivelix and two of the nine board seats on the Board of Directors of the Company. However, the Boards of the Company and Vivelix share no individual common Board members. Accounting Analysis The Company evaluated the Vivelix Agreement in accordance with the provisions of ASC 605-25. The Vivelix Agreement contains the following initial deliverables: (i) a research and commercialization license for IMO-9200 and back-up compounds to IMO-9200 (the “IMO-9200 License”), (ii) drug materials transferred, and (iii) participation in the JRC (the “JRC Deliverable”). The Company has determined that Vivelix’s right of first refusal, the right of first negotiation and the right to request an expanded field are substantive options. Vivelix is not contractually obligated to exercise the options and Idera is not contractually obligated to perform. Accordingly, the substantive options are not considered deliverables at the inception of the arrangement and the associated payments are not accounted for at inception of the agreement. The Company concluded that the IMO-9200 License has standalone value from the undelivered elements as Vivelix could benefit from the IMO-9200 License on a standalone basis as they would be able to sell the compound in the market without any additional involvement or participation from Idera. Idera has no further obligations related to the IMO-9200 License. In the event that Vivelix does not make a designated compound payment, the license to back-up compounds reverts back to Idera at the end of the research term at no cost or payment by either party. The research and development services in the Vivelix Agreement relate to the back-up compounds and Vivelix would be able to conduct research and development activities with external third parties, as IMO-9200 is at an advanced enough stage where Idera’s expertise would not be required. Accordingly, the IMO-9200 License is a separate unit of accounting. The Company concluded that the materials transferred identified at the inception and the JRC Deliverable of the Vivelix Agreement also have standalone value from the other deliverables based on their nature. In the case of the materials transferred, it was noted that Vivelix would not be able to realize any of the value associated without the IMO-9200 License; however, the IMO-9200 License was provided at the inception of the arrangement and therefore, this determination is not relevant. Therefore, the Company has identified three units of accounting in connection with its initial deliverables under the Vivelix Agreement as follows: (i) the IMO-9200 License, (ii) drug materials transferred, and (iii) the JRC Deliverable. Allocable arrangement consideration at inception of the Vivelix Agreement is comprised of the up-front payment of $15 million. The $15 million was allocated based on the relative values of the best estimate of selling price of the units of accounting. Allocated revenue associated with the IMO-9200 License was recognized at the inception of the Vivelix Agreement in the fourth quarter of 2016 as Vivelix was granted an exclusive, perpetual license to develop and commercialize IMO-9200 and certain back-up compounds to IMO-9200, subject to certain designation milestone and royalty payments, and the performance obligations of Idera under the agreement are extinguished at that point. Allocable revenue associated with drug materials transferred shortly after the inception of the agreement was recognized upon delivery, in the fourth quarter of 2016. The JRC deliverable was deemed to be de minimus and no amount separately accounted for. The development and commercial milestones provided for in the Vivelix Agreement are all performance obligations of Vivelix occurring after the Company has completed its obligations. As a result, they represent contingent revenue to the Company and will be accounted for at the time the contingencies are resolved. The Company will recognize royalty revenue in the period of sale of the related product(s), based on the underlying contract terms, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, assuming all other revenue recognition criteria are met. The Company recognized as Alliance revenue $15.0 million in the Statement of Operations for the year ended December 31, 2016. (b) Collaboration with GSK In November 2015, the Company entered into the GSK Agreement. The initial collaboration term is currently anticipated to last between two and four years. In connection with the GSK Agreement, GSK identified an initial target for the Company to attempt to identify a potential population of development candidates to address such target under a mutually agreed upon research plan, currently estimated to take 27 months to complete. From the population of identified development candidates, GSK may designate one development candidate in its sole discretion to move forward into clinical development. Once GSK designates a development candidate, GSK would be solely responsible for the development and commercialization activities for that designated development candidate. At any time during the first two years of the GSK Agreement, GSK has the option to select up to two additional targets, for further research under mutually agreed upon research plans. GSK may then designate one development candidate for each additional target, at which time GSK would have sole responsibility to develop and commercialize each such designated development candidate. In accordance with the GSK Agreement, a Joint Steering Committee (“JSC”) was formed with equal representation from Idera and GSK. The responsibilities of the JSC, include, but are not limited to monitoring the progress of the collaboration, reviewing research plans and dealing with disputes that may arise between the parties. If a dispute cannot be resolved by the JSC, GSK has final decision making authority. Under the terms of the GSK Agreement, the Company received a $2.5 million upfront, non-refundable, non-creditable cash payment upon the execution of the GSK Agreement. The Company is eligible to receive up to approximately $100 million in license, research, clinical development and commercialization milestone payments. Approximately $9 million of these milestone payments are payable by GSK upon the identification of the additional targets, the completion of current and future research plans and the designation of development candidates. Approximately $89 million is payable by GSK upon the achievement of clinical milestones and commercial milestones. In addition, the Company is eligible to receive royalty payments based on net sales upon licensed products following commercialization at varying rates of up to five percent on annual net sales, as defined in the GSK Agreement. Accounting Analysis The Company evaluated the GSK Agreement in accordance with the provisions of ASC 605-25. The GSK Agreement contains the following initial deliverables: (i) a collaboration license for Idera’s proprietary technology related to the initial target (the “Collaboration License”), (ii) research services (the “Research Services”), and (iii) participation in the JSC (the “JSC Deliverable”). The Company has determined that GSK’s options to choose up to two additional targets and to purchase additional collaboration licenses for the Company’s proprietary technology related to each additional target are substantive options. GSK is not contractually obligated to exercise the options. Moreover, as a result of the uncertain outcome of the research activities, there is significant uncertainty as to whether GSK will decide to exercise its options for any additional targets. Consequently, the Company is at risk with regard to whether GSK will exercise the options. The Company has determined that GSK’s options to choose up to two additional targets and to purchase additional collaboration licenses for the Company’s proprietary technology related to each additional target are not priced at a significant and incremental discount. The Company has concluded that the Collaboration License does not qualify for separation from the Research Services. As it relates to the assessment of standalone value, the Company has determined that GSK cannot fully exploit the value of the Collaboration License without receipt of the Research Services from the Company. The Research Services involve unique skills and specialized expertise, particularly as it relates to the Company’s proprietary technology, which is not available in the marketplace. Accordingly, GSK must obtain the Research Services from the Company which significantly limits the ability for GSK to utilize the Collaboration License for its intended purpose on a standalone basis. Therefore, the Collaboration License does not have standalone value from the Research Services. As a result, the Collaboration License and the Research Services have been combined as a single unit of accounting (the R&D Services Unit of Accounting). The Company has concluded that the JSC Deliverable identified at the inception of the arrangement has standalone value from the other deliverables noted based on its nature. Factors considered in this determination included, among other things, the capabilities of the collaborator, whether any other vendor sells the item separately, whether the value of the deliverable is dependent on the other elements in the arrangement, whether there are other vendors that can provide the items and if the customer could use the item for its intended purpose without the other deliverables in the arrangement. Therefore, the Company has identified two units of accounting in connection with its initial deliverables under the GSK Agreement as follows: (i) R&D Services Unit of Accounting, and (ii) JSC Deliverable. Allocable arrangement consideration at inception of the GSK Agreement is comprised of the up-front payment of $2.5 million, which was allocated to the R&D Services Unit of Accounting. No amount was allocated to the JSC Deliverable because the related best estimate of selling price was determined to be de minimis. The $2.5 million was recorded as deferred revenue in the Company’s balance sheet and is being recognized as revenue on a straight line basis as the Research Services are delivered over the estimated 27 month research plan period. Payments to be received in connection with GSK’s identification of additional targets and designation of development candidates are considered substantive options as a result of the uncertainties related to the research, development and commercialization activities, and the uncertainty as to whether GSK will exercise the options. The substantive options are not priced at a significant incremental discount. Accordingly, the substantive options are not considered deliverables at the inception of the arrangement and the associated option exercise payments are not accounted for at inception of the agreement. The clinical and commercial milestones provided for in the GSK Agreement are all performance obligations of GSK occurring after the Company has completed its obligations. As a result, they represent contingent revenue to the Company and will be accounted for at the time the contingencies are resolved. The Company will recognize royalty revenue in the period of sale of the related product(s), based on the underlying contract terms, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, assuming all other revenue recognition criteria are met. The Company recognized as revenue approximately $1.1 million and $0.1 million of deferred revenue related to the GSK Agreement during the years ended December 31, 2016 and 2015, respectively. This revenue is classified as alliance revenue in the accompanying statements of operations and comprehensive loss. There was approximately $1.3 million of deferred revenue related to the GSK Agreement at December 31, 2016, including approximately $1.1 million classified as current portion of deferred revenue in the accompanying balance sheet. (c) Collaboration with Abbott Molecular Inc. In May 2014, the Company entered into a development and commercialization agreement with Abbott Molecular, Inc. (“Abbott Molecular”) for the development of an in vitro companion diagnostic for use in the Company’s clinical development programs to treat certain genetically defined forms of B-cell lymphoma with IMO-8400, the Company’s TLR antagonist lead drug candidate. The agreement provides for the development and subsequent commercialization by Abbott Molecular of a companion diagnostic test utilizing polymerase chain reaction technology to identify with high sensitivity and specificity the presence in tumor biopsy samples of the oncogenic mutation referred to scientifically as MYD88 L265P. Under the agreement, Abbott Molecular is primarily responsible for developing and obtaining regulatory approvals for the companion diagnostic in accordance with an agreed development plan and regulatory plan and for making the companion diagnostic test commercially available in accordance with an agreed commercialization plan. Abbott Molecular will retain all proceeds from commercialization of the companion diagnostic test. Subject to the terms of the agreement, the Company will pay Abbott Molecular fees and fund Abbott Molecular’s development of the companion diagnostic test in an approximate aggregate amount of $6.7 million over an approximately five year development period, which includes clinical trial site costs and Abbott Molecular’s costs of preparation and filing fees for regulatory submissions for the companion diagnostic with the U.S. Food and Drug Administration (“FDA”). This amount is subject to increase if Abbott Molecular incurs additional expenses in order to meet unexpected material requirements or obligations not included in the agreement or if the Company is required to conduct additional or different clinical trials which result in Abbott Molecular incurring additional costs. The Company incurred approximately $0.4 million, $0.9 million and $2.2 million in expenses under the Abbott Molecular agreement during the years ended December 31, 2016, 2015 and 2014, respectively. (d) Collaboration and License Agreement with Merck & Co. In April 2014, the Company entered into an amendment of its December 2006 exclusive, worldwide license and research collaboration agreement with Merck & Co. to research, develop, and commercialize vaccine products containing the Company’s TLR7, TLR8, and TLR9 agonists in the fields of cancer, infectious diseases, and Alzheimer’s disease. As a result of this amendment, Merck & Co.’s rights to a number of the Company’s TLR7, TLR8 and TLR9 agonists under the agreement have been limited to specified TLR7, TLR8, and TLR9 agonists that Merck & Co. selected in January 2012, and the Company regained the rights to pursue its other independently discovered TLR7, TLR8, and TLR9 agonists for use as vaccine adjuvants in the fields of cancer, infectious diseases and Alzheimer’s disease so that it now has the right to pursue its TLR7, TLR8, and TLR9 agonists for use as vaccine adjuvants in all fields. Merck & Co.’s obligations under the agreement to pay the Company milestone payments and royalties continue in effect with respect to the specified TLR7, TLR8, and TLR9 agonists. However, in connection with this amendment, the Company agreed that, to the extent that the Company licenses to third parties any TLR7, TLR8, and TLR9 agonists for use as vaccine adjuvants in the fields of cancer, infectious diseases and Alzheimer’s disease and receives income under such licenses, Merck & Co. may credit against any milestone payments and royalties it owes to the Company an amount equal to 15% of the license income received by the Company under the third-party licenses, up to a maximum of $60.0 million in credits. (e) Other License Agreements The Company has out-licensed and in-licensed therapies related to antisense technology. In 2001, Idera entered into an agreement with Ionis Pharmaceuticals, Inc. (“Ionis”), formerly Isis Pharmaceuticals, Inc., under which the Company granted Ionis a license (with the right to sublicense) to its second-generation antisense chemistry and delivery patents and patent applications, but the Company retained the right to use these patents and applications in its own drug discovery and development efforts and in collaborations with third parties.

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2016
Stockholders' Equity
Stockholders' Equity	7. Stockholders’ Equity (a) Common Stock Pursuant to the terms of a unit purchase agreement dated as of May 5, 1998, the Company issued and sold a total of 1,199,684 shares of common stock (the “Put Shares”) at a price of $16.00 per share. Under the terms of the unit purchase agreement, the initial purchasers (the “Put Holders”) of the Put Shares have the right (the “Put Right”) to require the Company to repurchase the Put Shares. The Put Right may not be exercised by any Put Holder unless: (1) the Company liquidates, dissolves or winds up its affairs pursuant to applicable bankruptcy law, whether voluntarily or involuntarily; (2) all of the Company’s indebtedness and obligations, including without limitation the indebtedness under the Company’s then outstanding notes, has been paid in full; and (3) all rights of the holders of any series or class of capital stock ranking prior and senior to the common stock with respect to liquidation, including without limitation the Series A convertible preferred stock, have been satisfied in full. The Company may terminate the Put Right upon written notice to the Put Holders if the closing sales price of its common stock exceeds $32.00 per share for the twenty consecutive trading days prior to the date of notice of termination. Because the Put Right is not transferable, in the event that a Put Holder has transferred Put Shares since May 5, 1998, the Put Right with respect to those shares has terminated. As a consequence of the Put Right, in the event the Company is liquidated, holders of shares of common stock that do not have Put Rights with respect to such shares may receive smaller distributions per share upon the liquidation than if there were no Put Rights outstanding. As of December 31, 2016, the Company has repurchased or received documentation of the transfer of 399,950 Put Shares and 35,780 of the Put Shares continued to be held in the name of Put Holders. The Company cannot determine at this time what portion of the Put Rights of the remaining 763,954 Put Shares have terminated. As of December 31, 2016, the Company had 76,137,792 shares reserved for issuance upon the exercise of outstanding warrants and options to purchase common stock, employee and director stock purchases, conversion of Series A convertible preferred stock, and additional shares available for grant under the 2013 Stock Incentive Plan. (b) Warrants The Company has the following warrants outstanding and exercisable for the purchase of common stock at December 31, 2016: Expiration Date Shares Weighted Average Exercise Price Per Share November 9, 2017 $ May 7, 2018 May 7, 2020 September 30, 2020 February 10, 2021 Total $ (c) Stock Options Under the Company’s 2013 Stock Incentive Plan (the “2013 Stock Incentive Plan”), the Company may grant options to purchase common stock, stock appreciation rights, restricted stock awards and other forms of stock-based compensation. Stock options generally vest over three to four years, and expire no later than 10 years from the date of grant. A total of 15,224,460 shares of common stock, plus such additional number of shares of common stock (up to 6,946,975) as is equal to the number of shares of common stock subject to awards granted under the Company’s 2005 Stock Incentive Plan or 2008 Stock Incentive Plan which awards expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right may be issued pursuant to awards granted under the 2013 Stock Incentive Plan subject to reduction in the event that there are any “full-value awards,” as defined in the plan. The maximum number of shares of common stock with respect to which awards may be granted to any participant under the plan is 1,500,000 per calendar year. The compensation committee of the board of directors has the authority to select the employees to whom options are granted and determine the terms of each option, including (i) the number of shares of common stock subject to the option; (ii) when the option becomes exercisable, which generally may be no earlier than the first anniversary of the date of grant; (iii) the option exercise price, which must be at least 100% of the fair market value of the common stock as of the date of grant; and (iv) the duration of the option, which may not exceed 10 years. Stock options may not be re-priced without shareholder approval. Discretionary awards to non-employee directors are granted and administered by a committee comprised of independent directors. As of December 31, 2016, options to purchase a total of 10,235,083 shares of common stock were outstanding under the 2013 Stock Incentive Plan. As of December 31, 2016, 6,275,852 shares of common stock remain available for grant under the 2013 Stock Incentive Plan. The Company is no longer granting stock options or other awards pursuant to the share-based compensation plans that were utilized prior to the approval of the 2013 Stock Incentive Plan. Under these earlier plans, stock options generally vested over three to four years and expired no later than 10 years from the date of grant. As of December 31, 2016, options to purchase a total of 4,616,437 shares of common stock were outstanding under these earlier plans. During 2015, the Company also granted as inducement grants non-statutory stock options to purchase an aggregate of 1,150,000 shares of common stock. The inducement grant awards were made outside of the 2013 Stock Incentive Plan pursuant to the NASDAQ inducement grant exception as a material component of new hires’ employment compensation. Options to purchase 3,150,000 shares as inducement grants remained outstanding at December 31, 2016. The balance of the inducement options were forfeited. The following table summarizes information related to the outstanding and exercisable options during 2016 (in thousands, except per share amounts and years): Weighted-Average Remaining Aggregate Stock Weighted-Average Contractual Life Intrinsic Options Exercise Price (in years) Value Outstanding at December 31, 2015 $ Granted Exercised — — Forfeited Expired Outstanding at December 31, 2016 $ Exercisable at December 31, 2016 Total exercisable or expected to vest (d) Employee Stock Purchase Plan The Company’s 1995 Employee Stock Purchase Plan (the “Stock Purchase Plan”), as amended, provides for the issuance of up to 500,000 shares of common stock to participating employees of the Company or its subsidiaries. Participation is limited to employees that would not own 5% or more of the total combined voting power or value of the stock of the Company after the grant. Under the Stock Purchase Plan, on the first day of a designated payroll deduction period, the “Offering Period,” the Company will grant to each eligible employee who has elected to participate in the Stock Purchase Plan an option to purchase shares of common stock as follows: the employee may authorize an amount, a whole percentage from 1% to 10% of such employee’s regular pay, to be deducted by the Company from such pay during the Offering Period. On the last day of the Offering Period, the employee is deemed to have exercised the option, at the option exercise price, to the extent of accumulated payroll deductions. Under the terms of the Stock Purchase Plan, the option price is an amount equal to 85% of the fair market value per share of the common stock on either the first day or the last day of the Offering Period, whichever is lower. In no event may an employee purchase in any one Offering Period a number of shares that is more than 15% of the employee’s annualized base pay divided by 85% of the market value of a share of common stock on the commencement date of the Offering Period. The compensation committee may, in its discretion, choose an Offering Period of 12 months or less for each of the Offerings and choose a different Offering Period for each Offering. Offering periods are three months in duration and commence on March 1, June 1, September 1, and December 1. In 2016, 2015, and 2014, the Company issued 121,460, 27,951, and 13,844 shares of common stock, respectively, under the Stock Purchase Plan. (e) Preferred Stock The Restated Certificate of Incorporation of the Company permits its board of directors to issue up to 5,000,000 shares of preferred stock, par value $0.01 per share, in one or more series, to designate the number of shares constituting such series, and fix by resolution, the powers, privileges, preferences and relative, optional or special rights thereof, including liquidation preferences and dividends, and conversion and redemption rights of each such series. As of December 31, 2016, the Company has designated 1,500,000 shares as Series A convertible preferred stock. (f) Series A Convertible Preferred Stock The dividends on the Series A convertible preferred stock are payable semi-annually in arrears at the rate of 1% per annum, at the election of the Company, either in cash or additional duly designated, fully paid and nonassessable shares of Series A preferred stock. The Company paid dividends in stock until 2004 when it elected to pay further dividends in cash. In the event of liquidation, dissolution or winding up of the Company, after payment of debts and other liabilities of the Company, the holders of the Series A convertible preferred stock then outstanding will be entitled to a distribution of $1 per share out of any assets available to shareholders. The Series A preferred stock is non-voting. All remaining shares of Series A preferred stock rank as to payment upon the occurrence of any liquidation event senior to the common stock. Shares of Series A preferred stock are convertible, in whole or in part, at the option of the holder into fully paid and nonassessable shares of common stock at $34.00 per share, subject to adjustment. As of December 31, 2016 and 2015, there were 655 shares of Series A convertible preferred stock outstanding. (g) Series D Convertible Preferred Stock On January 10, 2014, the Company notified Pillar Pharmaceuticals I, L.P. (“Pillar I”), an investment partnership managed by one of the Company’s directors and significant stockholders and the holder of all 1,124,260 shares of the Company’s issued and outstanding Series D redeemable convertible preferred stock (“Series D preferred stock”), of its intention to redeem the Series D preferred stock on February 10, 2014 in accordance with the terms of the Certificate of Designations, Preference and Rights of Series D Preferred Stock of the Company (the “Series D Certificate of Designations”). On February 6, 2014, Pillar I converted such shares into 6,266,175 shares of the Company’s common stock in accordance with the terms of the Series D Certificate of Designations. As a result of the conversion, no shares of the Company’s Series D preferred stock remain outstanding. On March 28, 2014, the Company filed a Certificate of Elimination of Number of Shares of Preferred Stock Designated as Series D Convertible Preferred Stock with the State of Delaware Secretary of State which eliminated the designation of the shares of Series D preferred stock. (h) Series E Convertible Preferred Stock In December 2014, the holders of all of the 424,242 shares of Series E convertible preferred stock (“Series E preferred stock”) converted such shares into 8,484,840 shares of common stock in accordance with the terms of the Certificate of Designations, Preferences and Rights of Series E Preferred Stock (the “Series E Certificate of Designations”). As a result of this conversion, no shares of Series E preferred stock remain outstanding. On March 12, 2015, the Company filed a Certificate of Elimination of Number of Shares of Preferred Stock Designated as Series E Convertible Preferred Stock with the State of Delaware Secretary of State which eliminated the designation of the shares of Series E preferred stock.

Common Stock Warrant and Option

Common Stock Warrant and Option Exercises and Employee Stock Purchases	12 Months Ended
	Dec. 31, 2016
Common Stock Warrant and Option Exercises and Employee Stock Purchases
Common Stock Warrant and Option Exercises and Employee Stock Purchases	8. Common Stock Warrant and Option Exercises and Employee Stock Purchases The Company issued 1,491,000, 3,402,000, and 5,932,000 shares of common stock and received total proceeds of $2.2 million, $2.5 million, and $8.5 million for warrant and stock option exercises and employee stock purchases under the Stock Purchase Plan during the years ended December 31, 2016, 2015 and 2014, respectively, as follows: 2016 2015 2014 (In thousands) Shares Proceeds Shares Proceeds Shares Proceeds Warrant exercises $ $ $ Stock option exercises — — Employee stock purchases Total $ $ $

Commitments and Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies.
Commitments and Contingencies	9. Commitments and Contingencies (a) Lease Commitments The Company leases its facilities in Cambridge, Massachusetts and Exton, Pennsylvania. During 2016, 2015 and 2014, rent expense, including real estate taxes, was $1.9 million, $1.7 million and $1.7 million, respectively. As part of the Cambridge facility lease, the Company is required to restrict approximately $0.3 million of cash for a security deposit as of December 31, 2016 and 2015. The leases are classified as operating leases. Future minimum commitments as of December 31, 2016 under the Company’s lease agreements are approximately: December 31, Operating Lease (In thousands) 2017 $ 2018 2019 2020 2021 Thereafter $ The Cambridge facility lease was amended on November 17, 2016 to, among other things, extend the expiration date to August 31, 2022 subject to a five-year renewal option exercisable by the Company. The Cambridge facility lease amendment includes certain lease incentives in the form of premises improvement allowance of up to $0.3 million. Amounts will be recorded in future periods when such premises improvements are made. The Company entered into the Exton facility lease on April 1, 2015 and amended it on September 23, 2015 to include additional space. The Exton facility lease term ends on May 31, 2020 subject to a three-year renewal option exercisable by the Company. (c) Contract Obligations The Company has employment agreements with its executive officers that include future minimum commitments of approximately $2.7 million per year. In the normal course of business, the Company enters into contracts with clinical research organizations, drug manufacturers and other vendors for preclinical and clinical research studies, research and development supplies and other services and products for operating purposes. These contracts generally provide for termination on notice, and therefore are cancellable contracts and not included in contract obligations. (d) Related-Party Transactions In November 2011, the Company issued and sold, for an aggregate purchase price of $9.5 million, 1,124,260 shares of Series D preferred stock and warrants to purchase 2,810,650 shares of its common stock with an exercise price of $1.63 per share (“Series D warrants”) pursuant to a Convertible Preferred Stock and Warrant Purchase Agreement with Pillar I, an investment partnership managed by one of the Company’s current directors and significant shareholders. The Series D warrants expired on November 4, 2016. As a result of an anti-dilution adjustment triggered by the sale of the Company’s Series E preferred stock in November, 2012, the exercise price of the Series D warrants was reduced to $1.46 per share. As discussed in Note 7(g), all shares of Series D preferred stock were converted to 6,266,175 shares of common stock in February, 2014. In November 2012, the Company issued and sold, for an aggregate purchase price of $7.0 million, 424,242 shares of Series E preferred stock and warrants to purchase 8,484,840 shares of its common stock with an exercise price of $0.70 per share (“Series E warrants”) pursuant to a Convertible Preferred Stock and Warrant Purchase Agreement with Pillar Pharmaceuticals II, L.P. (“Pillar II”), an investment partnership managed by two of the Company’s directors (one of the Company’s current directors) and one of its significant shareholders and an entity affiliated with Pillar II (together with Pillar II, the “Pillar II Entities”). The Series E warrants expire on November 9, 2017. As discussed in Note 7(h), all shares of Series E preferred stock were converted to 8,484,840 shares of common stock in December 2014. In connection with the Company’s follow-on underwritten public offering on May 7, 2013, the Company sold 5,000,000 shares of common stock and warrants to purchase 5,000,000 shares of common stock at $0.47 per share for an aggregate purchase price of $2,500,000 to Pillar Pharmaceuticals III, L.P. (“Pillar III”) and an entity affiliated with Pillar III (together with Pillar III, the “Pillar III Entities”), which is described in Note 14. In connection with the Company’s follow-on underwritten public offering on September 30, 2013, the Company sold 1,774,193 shares of common stock for an aggregate purchase price of $2,750,000 to Pillar Pharmaceuticals IV, L.P. (“Pillar IV”) and an entity affiliated with Pillar IV (together with Pillar IV, the “Pillar IV Entities”), which is described in Note 14. Youssef El Zein, a member of the Company’s board of directors, is a director and controlling stockholder of Pillar Invest Corporation (“Pillar Invest”), which is the general partner of Pillar I, Pillar II, Pillar III and Pillar IV. Mr. El Zein has voting and investment control over the securities beneficially owned by the Pillar III Entities and the Pillar IV Entities. In addition, Abdul-Wahab Umari, who was also a member of the Company’s board of directors until June 2014, is a managing partner of Pillar Invest. During 2016, the Pillar I exercised 1,370,000 warrants to purchase common stock at a total exercise price of $2,000,200. The warrant exercise prices had been established at the time that the warrants were purchased. During 2015, the Pillar II Entities exercised 232,759 warrants to purchase common stock at a total exercise price of $163,000 and the Pillar III Entities exercised 2,600,000 warrants to purchase common stock at a total exercise price of $1,222,000. The warrant exercise prices had been established at the time that the warrants were purchased. During 2014, Pillar I exercised 1,575,758 warrants to purchase common stock at a total exercise price of $1,065,000, the Pillar II Entities exercised 1,424,242 warrants to purchase common stock at a total exercise price of $1,035,000 and the Pillar III Entities exercised 500,000 warrants to purchase common stock at a total exercise price of $235,000. The warrant exercise prices had been established at the time that the warrants were purchased. The Company issued common stock in lieu of director board and committee fees of approximately $172,000, $122,000, and $82,000 during 2016, 2015 and 2014, respectively. Such shares were issued at the market closing price on the purchase date. Additional information on related party transactions associated with the April 2013 agreements between the Company and the Pillar Entities (as defined in Note 14) is included in Note 14. See also Note 6, “Collaboration and License Agreements” and Note 14, “Financings,” for additional information on related party transactions.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2016
Income Taxes
Income Taxes	10. Income Taxes The Tax Reform Act of 1986 contains provisions that limit the amount of net operating loss carryforwards (“NOLs”) and tax credit carryforwards that companies may utilize in any one year in the event of cumulative changes in ownership over a three-year period in excess of 50%. The Company has completed several financings since the effective date of the Tax Reform Act of 1986, which as of December 31, 2016, have resulted in ownership changes in excess of 50% that will significantly limit the Company’s ability to utilize its NOL and tax credit carryforwards. In December, 2014, the Company completed a study which determined that a cumulative three-year ownership change in excess of 50% had occurred in November 2012. The 2016 and 2015 federal and state NOLs, tax credit carryforwards and related deferred tax assets shown below have been adjusted to reflect the ownership change limitations that resulted from this study. The Company has entered into additional equity transactions since November 2012 that could result in ownership changes that further limit its ability to utilize its NOL and tax credit carryforwards. The Company has not determined whether any additional ownership change limitations have resulted from equity transactions that have occurred after November 2012. As of December 31, 2016, the Company had cumulative federal and state NOLs of approximately $149.3 million and $138.2 million available to reduce federal and state taxable income, respectively. These NOLs expire through 2036. In addition, at December 31, 2016, the Company had cumulative federal and state tax credit carryforwards of $8.4 million and $1.6 million, respectively, available to reduce federal and state income taxes, respectively, which expire through 2036 and 2031, respectively. The federal and state NOLs include approximately $1.0 million and $0.7 million, respectively, of deductions related to the exercise of stock options subsequent to the adoption of ASC 718, “Stock Compensation.” These amounts represent excess tax benefits as defined under ASC 718 and have not been included in the gross deferred tax asset reflected for NOLs. However, the Company intends to adopt ASU 2016-09, Improvements to Employee Share-Based Payment Accounting, during the quarter ended March 31, 2017. As a result of the adoption, it is anticipated that the net operating losses deferred tax assets will increase by $1.4 million and will be offset by a corresponding increase in the valuation allowance. The Company does not anticipate that the adoption of ASU 2016-09 will have an impact on the Company’s Financial statements. As of December 31, 2016 and 2015, the components of the deferred tax assets are approximately as follows: 2016 2015 (In thousands) Operating loss carryforwards $ $ Tax credit carryforwards Other Valuation allowance $ — $ — The Company has provided a valuation allowance for its deferred tax asset due to the uncertainty surrounding the ability to realize this asset. The difference between the 34% U.S. federal corporate tax rate and the Company’s effective tax rate is as follows for the years ended December 31, 2016, 2015 and 2014: 2016 2015 2014 Expected federal income tax rate % % % Expiring credits and NOLs — — — Change in valuation allowance Federal and state credits State income taxes, net of federal benefit Permanent differences Section 382 limitation — — Other Effective tax rate % % % The Company applies ASC 740-10, “Accounting for Uncertainty in Income Taxes, an interpretation of ASC 740.” ASC 740-10 clarifies the accounting for uncertainty in income taxes recognized in financial statements and requires the impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. The Company had no unrecognized tax benefits resulting from uncertain tax positions at December 31, 2016 and 2015. The Company has not, as of yet, conducted a study of its research and development credit carryforwards. Such a study might result in an adjustment to the Company’s research and development credit carryforwards, however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position under ASC 740-10. A full valuation allowance has been provided against the Company’s research and development credits and, if an adjustment is required, this adjustment would be offset by an adjustment to the valuation allowance. Thus, there would be no impact to the statements of operations and comprehensive loss if an adjustment was required. The Company files income tax returns in the U.S. federal and Massachusetts jurisdictions. The Company is no longer subject to tax examinations for years before 2013, except to the extent that it utilizes NOLs or tax credit carryforwards that originated before 2013. The Company does not believe there will be any material changes in its unrecognized tax positions over the next 12 months. The Company has not incurred any interest or penalties. In the event that the Company is assessed interest or penalties at some point in the future, they will be classified in the Statement of Operations and comprehensive loss as general and administrative expense. In November 2015, the FASB released ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes. ASU No. 2015-17 requires that all deferred income tax assets, liabilities and valuation allowances applicable to the same taxing jurisdiction be presented as noncurrent in a classified statement of financial position. ASU No. 2015-17 permits early application on a prospective or retrospective basis. The Company elected to early adopt ASU No. 2015-17 on a prospective basis in its 2015 financial statements because this change in accounting principal will allow the Company to benefit from the simplified presentation of deferred income taxes. Prior period financial statements have not been retrospectively adjusted to reflect the adoption of ASU No. 2015-17.

Employee Benefit Plan

Employee Benefit Plan	12 Months Ended
	Dec. 31, 2016
Employee Benefit Plan
Employee Benefit Plan	11. Employee Benefit Plan The Company has an employee benefit plan under Section 401(k) of the Internal Revenue Code. The plan allows employees to make contributions up to a specified percentage of their compensation. Under the plan, the Company matches a portion of the employees’ contributions up to a defined maximum. The Company is currently contributing up to 3% of employee base salary, by matching 50% of the first 6% of annual base salary contributed by each employee. Approximately $0.3 million, $0.2 million and $0.1 million of 401(k) benefits were charged to operating expenses during 2016, 2015 and 2014, respectively.

Net Loss per Common Share Appli

Net Loss per Common Share Applicable to Common Stockholders	12 Months Ended
	Dec. 31, 2016
Net Loss per Common Share Applicable to Common Stockholders
Net Loss per Common Share Applicable to Common Stockholders	12. Net Loss per Common Share Applicable to Common Stockholders For the years ended December 31, 2016, 2015 and 2014, basic and diluted net loss per common share applicable to common stockholders is computed using the weighted average number of shares of common stock outstanding during the period. Diluted net loss per common share applicable to common stockholders is the same as basic net loss per common share applicable to common stockholders as the effects of the Company’s potential common stock equivalents are antidilutive. Total antidilutive securities were 69,712,906, 70,782,788 and 74,640,383 at December 31, 2016, 2015 and 2014, respectively, and consisted of stock options, preferred stock and warrants.

Supplemental Disclosure of Cash

Supplemental Disclosure of Cash Flow Information	12 Months Ended
	Dec. 31, 2016
Supplemental Disclosure of Cash Flow Information
Supplemental Disclosure of Cash Flow Information	13. Supplemental Disclosure of Cash Flow Information Supplemental disclosure of cash flow information for the periods presented is as follows: Year Ended December 31, 2016 2015 2014 (In thousands) Supplemental disclosure of cash flow information: Cash paid for interest $ $ $ Supplemental disclosure of non-cash financing and investing activities: Conversion of Series D preferred stock to common stock $ — $ — $ Conversion of Series E preferred stock to common stock $ — $ — $ Non-cash property additions $ $ $ Accrued 2016 financing transaction costs paid in 2017 $ $ — $ —

April 2013 Pillar Agreements

April 2013 Pillar Agreements	12 Months Ended
	Dec. 31, 2016
April 2013 Pillar Agreements
April 2013 Pillar Agreements	14. April 2013 Pillar Agreements In April 2013, the Company entered into two agreements (the “Pillar Agreements”) with Pillar I, Pillar II and an entity affiliated with Pillar I and Pillar II (together with Pillar I and Pillar II, the “Pillar Entities”). The agreements, including the Company’s obligations to issue the warrants under the Pillar Agreements, became effective upon the consummation of the follow-on underwritten public offering of the Company’s securities on May 7, 2013. Mr. El Zein, a member of the Company’s board of directors, is a director and controlling stockholder of Pillar Invest, which is the general partner of Pillar I and Pillar II, and is a limited partner of Pillar I and Pillar II. Mr. El Zein has voting and investment control over the securities beneficially owned by the Pillar Entities. In addition, Mr. Umari, who was also a member of the Company’s board of directors until June 2014, is a managing partner of Pillar Invest. Under the first agreement entered into with Pillar I and Pillar II (the “April 22, 2013 Pillar Agreement”), Pillar I, as the sole holder of the Company’s Series D preferred stock, irrevocably waived and agreed to not exercise the rights, powers, preferences and other terms of the Series D preferred stock under Section 6 of the Series D Certificate of Designations, including without limitation the right to require the Company to purchase all or any portion of the shares of its Series D preferred stock at a price equal to the original Series D preferred stock purchase price per share plus all accrued or declared but unpaid dividends thereon upon the occurrence of specified fundamental changes such as mergers, consolidations, business combinations, stock purchases or similar transactions resulting in a person or group unaffiliated with any holder of Series D preferred stock owning 66.67% or more of the outstanding voting securities of the Company or successor entity (the “Series D Redemption Rights”). Under the April 22, 2013 Pillar Agreement, the Company agreed to seek approval and each of Pillar I and Pillar II agreed to vote in favor, of the following proposals at the Company’s 2013 annual meeting of stockholders held on July 26, 2013 (“Annual Meeting”): · amendments to the Series D Certificate of Designations for the Series D preferred stock to: · modify the dividend provisions of the Series D Certificate of Designations to change the date after which the Company may elect to pay dividends in shares of its common stock from December 31, 2014 to October 1, 2013, and to allow for the payment of such dividends in shares of a to-be-created new series of non-voting preferred stock in the event that payment of such dividends may not be made in shares of its common stock as a result of the application of the beneficial ownership and voting power limitations set forth the Series D Certificate of Designations; and · modify the Series D Certificate of Designations to provide, in the event of a sale of the Company, for the distribution of any assets that remain available for distribution to its stockholders, after payment to the holders of its Series A convertible preferred stock and any other class of its capital stock that ranks senior to its Series D preferred stock, to the holders of the Company’s Series D preferred stock on a pro rata basis with the holders of its common stock, Series E preferred stock and such new series of non-voting preferred stock; and · amendments to the Series E Certificate of Designations to: · modify the dividend provisions of the Series E Certificate of Designations to allow for the payment of dividends in shares of its common stock commencing October 1, 2013; and · allow for the payment of dividends in shares of a to-be-created new series of non-voting preferred stock in the event that payment of such dividends may not be made in shares of its common stock as a result of the application of the beneficial ownership and voting power limitations set forth in the Series E Certificate of Designations. Under the second agreement with the Pillar Entities (the “April 30, 2013 Pillar Agreement”), Pillar I irrevocably waived the right of the holders of the Series D preferred stock under Section 2.1 of the Series D Certificate of Designations to receive, in the event of a voluntary or involuntary liquidation, dissolution or winding up of the Company (a “Liquidation”), an amount per share of Series D preferred stock equal to the original issue price of such share of Series D preferred stock plus any dividends accrued or declared but unpaid thereon to the extent such amount is greater than the amount that would have been payable with respect to such share had all shares of Series D preferred stock been converted into shares of the Company’s common stock immediately prior to such Liquidation, and that upon a Liquidation the holders of the Series D preferred stock will receive an amount per share of Series D preferred stock equal to the amount that would be payable with respect to such share had all shares of Series D preferred stock been converted into shares of common stock immediately prior to such Liquidation. In addition, under the April 30, 2013 Pillar Agreement, Pillar II and the entity affiliated with Pillar I and Pillar II, as the holders of 100% of the Company’s Series E preferred stock, irrevocably waived the right of the holders of the Series E preferred stock under Section 2.1.1 of the Series E Certificate of Designations to receive, in the event of a Liquidation, an amount per share of Series E preferred stock equal to the original issue price of such share of Series E preferred stock plus any dividends accrued or declared but unpaid thereon to the extent such amount is greater than the amount that would have been payable with respect to such share had all shares of Series E preferred stock been converted into shares of common stock immediately prior to such Liquidation, and that upon a Liquidation the holders of the Series E preferred stock will receive under Section 2.1 of the Series E Certificate of Designations an amount per share of Series E preferred stock equal to the amount that would be payable with respect to such share had all shares of Series E preferred stock been converted into shares of common stock immediately prior to such Liquidation. In accordance with the terms of the Pillar Agreements, the Company sought approval from its stockholders of amendments to the Series D Certificate of Designations and Series E Certificate of Designations to effect the changes described above to the dividend and liquidation provisions of the Company’s Series D preferred stock and Series E preferred stock, the redemption rights of the holders of its Series D preferred stock and the rights of the holders of its Series D preferred stock to distributions in the event of a sale of the Company. These matters were approved at the 2013 Annual Meeting. Under the April 22, 2013 Pillar Agreement, in consideration of the agreements of Pillar I and II under the April 22, 2013 Pillar Agreement and the delivery of the waiver by Pillar I, and for no additional cash consideration, the Company issued to Pillar I warrants, the “Pillar I Warrants,” to purchase up to 1,000,000 shares of the Company’s common stock at an exercise price of $0.61 per share. In addition, under the April 30, 2013 Pillar Agreement, in consideration of the agreements of the Pillar Entities under the April 30, 2013 Pillar Agreement and the delivery of the waivers by the Pillar Entities, and for no additional cash consideration, the Company issued to the Pillar Entities warrants (the “Additional Pillar Warrants,” and together with the Pillar I Warrants, the “Pillar Warrants”), to purchase up to an aggregate of 1,000,000 shares of the Company’s common stock at an exercise price of $0.79 per share. The Pillar Warrants became exercisable immediately upon issuance. The Pillar I Warrants will expire if not exercised on or prior to the fifth anniversary from the date of issuance and the Additional Pillar Warrants will expire if not exercised on or prior to June 1, 2014. The Pillar I Warrants provide that, after the second anniversary of the date of issuance, the Company may redeem such Pillar I Warrants for $0.01 per share of common stock issuable on exercise of such Pillar I Warrants following notice to the holder thereof if the closing price of its common stock for 20 or more trading days in a period of 30 consecutive trading days is greater than or equal to $2.80 per share. In connection with the Pillar Agreements, the Company filed a registration statement that became effective on July 10, 2013, registering the resale of the shares of common stock issuable upon exercise of the Pillar Warrants. All of the Pillar I Warrants and the Additional Pillar Warrants were exercised during 2014. The amendments to the Series D Certificate of Designations and Series E Certificate of Designations did not become effective until the amendments were approved by the Company’s stockholders at the 2013 Annual Meeting. As discussed in Note 7(g), all shares of Series D preferred stock were converted to common stock in February, 2014. As discussed in Note 7(h), all shares of Series E preferred stock were converted to common stock in December 2014. Since Pillar I irrevocably waived and agreed to not exercise the Series D Redemption Rights, the Company reassessed its accounting in May 2013 for the Series D preferred stock, which had been classified as temporary equity in the Company’s condensed balance sheet because the Series D Redemption Rights represented a contingent put feature that was outside the Company’s control. Upon effectiveness of this waiver, the contingent put feature ceased to exist. In addition, the Pillar Entities irrevocably waived the liquidation preferences of both the Series D preferred stock and the Series E preferred stock. The Company concluded that these irrevocable waivers of the Series D Redemption Rights and the Series D and Series E liquidation preferences, which became effective on May 7, 2013, represented changes to the fundamental terms of both the Series D preferred stock and the Series E preferred stock. As a result, the Company has accounted for these irrevocable waivers as an extinguishment of the Series D preferred stock and the Series E preferred stock and changed the classification of the Series D preferred stock from temporary equity to permanent equity. The Company compared (1) the sum of the fair values of the Series D preferred stock, the Series E preferred stock and the Pillar Warrants immediately after the effectiveness of the waivers to (2) the sum of the carrying values of the Series D preferred stock and Series E preferred stock immediately prior to the effectiveness of the waivers on May 7, 2013. The Company recorded the excess of the aggregate fair value of the preferred stock plus the Pillar Warrants immediately after the effectiveness of the waivers over the aggregate carrying value of the preferred stock immediately prior to May 7, 2013 as a loss on extinguishment and classified the fair values, immediately after the effectiveness of the waivers, of the Series D preferred stock, the Series E preferred stock and the Pillar Warrants within permanent equity on its balance sheet. The effect of this extinguishment accounting on the Company’s financial statements was to (1) remove the $5,921,000 carrying value of the Series D preferred stock immediately prior to the extinguishment from temporary equity; (2) record the $5,464,000 fair value of the Series D preferred stock immediately after the extinguishment in permanent equity (“equity”); (3) remove the $3,701,000 carrying value of the Series E preferred stock immediately prior to the extinguishment from equity; (4) record the $5,528,000 fair value of the Series E preferred stock immediately after the extinguishment in equity; (5) record the $380,000 fair value of the Pillar Warrants in equity; and (6) record a $1,750,000 extinguishment loss to net loss applicable to common stockholders. These accounting entries resulted in a $5,921,000 net increase in stockholders’ equity on its balance sheet. The Company determined the fair value of the Series D preferred stock and the Series E preferred stock as of May 7, 2013, the date the above described waivers became effective, based on the Option Pricing Method (“OPM”) which is a market based approach to imply the aggregate equity value of the Company by using the closing price of the Company’s publicly traded common stock as of the May 7, 2013 valuation date. Under the OPM, the fair value of preferred stock and common stock are determined based on the net value of a series of call options representing the present value of the expected future returns to each shareholder class. Essentially, the rights of the common stock are equivalent to a call option on any value of the Company above any cumulative preferred stock liquidation preference. The analysis involves calculating the equity value breakeven points at which the various equity classes would participate, or convert in the case of preferred stock, or exercise in the case of stock options and warrants. The Company used the Black-Scholes option pricing model to compute the fair value of the Pillar Warrants as of the May 7, 2013 effective date on which the Pillar Warrants were issued based on the following assumptions and other inputs: Pillar I Warrants Additional Pillar Warrants Common stock price $ $ Warrant exercise price $ $ Term of warrant (years) Expected volatility % % Average risk free interest rate % % Expected dividend yield — — Expected percentage of warrants to be exercised % % The closing price of the Company’s common stock is readily determinable since it is publicly traded. The warrant exercise prices and the warrant terms are readily determinable from the warrant agreements. The expected volatility is based on the actual stock-price volatility over a period equal to the greater of the term of the warrant or three years. The assumed risk-free interest rate is based on the U.S. Treasury security rate with a term equal to the term of the warrant. The assumed dividend yield of zero is based on the fact that the Company has never paid cash dividends to common stockholders and has no present intention to pay cash dividends to common stockholders. The Company assumed that future financings would dilute the warrant holder’s ownership in the Company such that the 19.99% ownership limitation would not prevent the warrant holder from exercising all of the warrants during the term of the warrants.

Financings

Financings	12 Months Ended
	Dec. 31, 2016
Financings
Financings	15. Financings October 13, 2016 Follow-on Underwritten Public Offering On October 13, 2016, the Company closed a follow-on underwritten public offering, in which it sold 25,000,000 shares of common stock at a price to the public of $2.00 per share for aggregate gross proceeds of $50.0 million. On October 28, 2016, the Company sold an additional 1,225,243 shares of common stock pursuant to the underwriters’ 30-day option to purchase additional shares at the public offering price less the underwriting discount. The net proceeds to the Company from the offering, including the exercise by the underwriters of their option to purchase additional shares and after deducting underwriters’ discounts and commissions and other offering costs and expenses, were approximately $48.8 million. Investment funds affiliated with Baker Brothers and Pillar Invest Corporation, two of the Company’s principal stockholders, and certain members of the Company’s board of directors, purchased 5,125,000 shares in this offering at the $2.00 per share purchase price. February 19, 2015 Follow-on Underwritten Public Offering On February 19, 2015, the Company closed a follow-on underwritten public offering, in which it sold 23,000,000 shares of common stock at a price to the public of $3.75 per share for aggregate gross proceeds of $86.3 million. The net proceeds to the Company from the offering, after deducting underwriters’ discounts and commissions and other offering costs and expenses, were $80.6 million. Investment funds affiliated with Baker Brothers and two members of the Company’s board of directors purchased 5,333,333 shares in this offering at the $3.75 per share purchase price. On February 19, 2015, Baker Brothers held 6,965,432 shares of the Company’s common stock, warrants to purchase up to 20,316,327 shares of the Company’s common stock at an exercise price of $0.47 per share and pre-funded warrants to purchase up to 22,151,052 shares of the Company’s common stock at an exercise price of $0.01 per share. February 10, 2014 Follow-on Underwritten Public Offering On February 10, 2014, the Company closed a follow-on underwritten public offering, in which it sold 7,867,438 shares of common stock at a price to the public of $4.00 per share and pre-funded warrants to purchase up to 2,158,750 shares of common stock at a price to the public of $3.99 per share for aggregate gross proceeds of $40.1 million. The pre-funded warrants have an exercise price of $0.01 per share and will expire if not exercised by February 10, 2021. The net proceeds to the Company from the offering, after deducting underwriters’ discounts and commissions and other offering costs and expenses and excluding the proceeds of the exercise of the warrants, if any, were approximately $37.2 million.

Subsequent Event

Subsequent Event	12 Months Ended
	Dec. 31, 2016
Subsequent Event.
Subsequent Event	16. Subsequent Event 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.

Summary of Significant Accoun23

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2016
Summary of Significant Accounting Policies
Basis of Presentation	(a) Basis of Presentation The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.
Cash, Cash Equivalents and Investments	(b) Cash, Cash Equivalents and Investments The Company considers all highly liquid investments with maturities of 90 days or less when purchased to be “cash equivalents.” Cash and cash equivalents at December 31, 2016 and 2015 consisted of cash and money market funds. Management determines the appropriate classification of marketable securities at the time of purchase. Investments that the Company does not have the positive intent to hold to maturity are classified as “available-for-sale” and reported at fair market value. Available-for-sale investments are classified as long-term if their contractual maturity is greater than one year at the balance sheet date and the Company does not have the intent to sell them in order to fund current operations. Unrealized gains and losses associated with available-for-sale investments are recorded in “Accumulated other comprehensive income” on the accompanying balance sheets. The amortization of premiums and accretion of discounts, and any realized gains and losses and declines in value judged to be other-than-temporary, and interest and dividends for all available-for-sale securities are included in “Interest income” on the accompanying statements of operations. Investments that the Company intends to hold to maturity are classified as “held-to-maturity” investments. The Company had no “held-to-maturity” investments at either December 31, 2016 or 2015. The cost of securities sold is based on the specific identification method. The Company had no realized gains or losses from available-for-sale securities in 2016, 2015 or 2014. There were no losses or other-than-temporary declines in value included in “Interest income” for any securities for the three years ended December 31, 2016. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and investments will enable the Company to fund its operations into the second quarter of 2018. The Company has and will continue to evaluate available alternatives to extend its operations beyond the second quarter of 2018.
Restricted Cash	(c) Restricted Cash As part of the Company’s lease arrangement for its office and laboratory facility in Cambridge, Massachusetts, the Company is required to restrict cash held in a certificate of deposit securing a line of credit for the lessor. As of December 31, 2016 and 2015, the restricted cash amounted to $0.3 million held in certificates of deposit securing a line of credit for the lessor.
Depreciation and Amortization	(d) Depreciation and Amortization Depreciation and amortization are computed using the straight-line method based on the estimated useful lives of the related assets. Laboratory and other equipment are depreciated over three to five years. Leasehold improvements are amortized over the remaining lease term or the related useful life, if shorter.
Revenue Recognition	(e) Revenue Recognition The Company recognizes revenue in accordance with the Financial Accounting Standards Board’s (FASB) Accounting Standards Codification (“ASC”) Topic 605, Revenue Recognition . Accordingly, revenue is recognized for each unit of accounting when all of the following criteria are met: · persuasive evidence of an arrangement exists; · delivery has occurred or services have been rendered; · the seller’s price to the buyer is fixed or determinable; and · collectability is reasonably assured. Amounts received prior to satisfying the revenue recognition criteria are recognized as deferred revenue in the Company’s balance sheet. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, current. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion. The Company’s revenues have primarily been generated through collaborative research, development and/or commercialization agreements. The terms of these agreements typically may include payment to the Company of one or more of the following: nonrefundable, up-front license fees, research, development and commercial milestone payments, other contingent payments due based on the activities of the counterparty or the reimbursement by licensees of costs associated with patent maintenance. Each of these types of revenue are recorded as Alliance revenues in the Company’s statement of operations. For each collaborative research, development and/or commercialization agreement, which results in revenues, the Company determines (i) whether multiple deliverables exist, (ii) whether the delivered elements have value to the customer on a stand-alone basis, (iii) how the deliverables should be separated or combined and (iv) how the consideration should be allocated to the deliverables. Arrangement consideration that is fixed or determinable is allocated among the separate units of accounting using the relative selling price method. Then, the applicable revenue recognition criteria in ASC 605 are applied to each of the separate units of accounting in determining the appropriate period and pattern of recognition. The Company determines the selling price of a unit of accounting following the hierarchy of evidence prescribed by ASC 605-25. Accordingly, the Company determines the estimated selling price for units of accounting within each arrangement using vendor-specific objective evidence (“VSOE”) of selling price, if available, third-party evidence (“TPE”) of selling price if VSOE is not available, or best estimate of selling price (“BESP”) if neither VSOE nor TPE is available. The Company typically uses BESP to estimate the selling price, since the Company generally does not have VSOE or TPE of selling price for its units of accounting. Determining the BESP for a unit of accounting requires significant judgment. In developing the BESP for a unit of accounting, the Company considers applicable market conditions and relevant entity-specific factors, including factors that were contemplated in negotiating the agreement with the customer and estimated costs. The Company validates the BESP for units of accounting by evaluating whether changes in the key assumptions used to determine the BESP will have a significant effect on the allocation of arrangement consideration between multiple units of accounting. Options are considered substantive if, at the inception of the arrangement, this Company is at risk as to whether the collaborator will choose to exercise the option. Factors that the Company considers in evaluating whether an option is substantive include the overall objective of the arrangement, the benefit the collaborator might obtain from the arrangement without exercising the option, the cost to exercise the option and the likelihood that the option will be exercised. For arrangements under which an option is considered substantive, the Company does not consider the item underlying the option to be a deliverable at the inception of the arrangement and the associated option fees are not included in allocable arrangement consideration, assuming the option is not priced at a significant and incremental discount. Conversely, for arrangements under which an option is not considered substantive or if an option is priced at a significant and incremental discount, the Company would consider the item underlying the option to be a deliverable at the inception of the arrangement and a corresponding amount would be included in allocable arrangement consideration. The Company recognizes arrangement consideration allocated to each unit of accounting when all of the revenue recognition criteria in ASC 605 are satisfied for that particular unit of accounting. The Company will recognize as revenue arrangement consideration attributed to licenses that have standalone value from the other deliverables to be provided in an arrangement upon delivery. The Company will recognize as revenue arrangement consideration attributed to licenses that do not have standalone value from the other deliverables to be provided in an arrangement over our estimated performance period as the arrangement would be accounted for as a single unit of accounting. The Company’s multiple element revenue arrangements may include the following: Up-front License Fees: If a license does not have stand-alone value, the Company recognizes revenues from nonrefundable, up-front license fees on a straight-line basis over the contracted or estimated period of performance of the services under the related agreement, unless evidence suggests that revenue is earned or obligations are fulfilled in a different pattern. The Company evaluates the period of performance each reporting period and adjusts the period of performance on a prospective basis if there are changes to be made. If a license were to have stand-alone value and the other criteria of revenue recognition were satisfied, then revenue would be recognized in the period earned. Milestone Payments: At the inception of an agreement that includes research and development milestone payments, the Company evaluates whether each milestone is substantive or represents a deliverable of the counterparty to the agreement. The Company recognized revenues related to substantive milestones in full in the period in which the substantive milestone is achieved if payment is reasonably assured. If a milestone is a deliverable of the counterparty to the agreement, it is considered contingent revenue and is recognized when the Company is informed by the counterparty that they have achieved it and such amount is reasonably assured of payment. Research and Development Activities: If the Company is entitled to reimbursement from its collaborators for specified research and development activities or the reimbursement of costs associated with patent maintenance, the Company determines whether such funding would result in alliance revenues or an offset to research and development expenses. Reimbursement of patent maintenance costs are recognized during the period in which the related expenses are incurred as alliance revenues in the Company’s statement of operations. Royalties : If the Company is entitled to receive royalties from its collaborator for product sales, the Company will recognize royalty revenue in the period of sale of the related product(s), based on the underlying contract terms, provided that the reported sales are reliably measurable and the Company has no remaining performance obligations, assuming all other revenue recognition criteria are met. Under the terms of the Company’s exclusive license and collaboration agreement with Vivelix Pharmaceuticals, Ltd. (“Vivelix”) which granted Vivelix worldwide rights to develop and market IMO-9200, an antagonist of TLR7, 8, and 9, for non-malignant gastrointestinal disorders, and certain back-up compounds to IMO-9200 (the “Vivelix Agreement”), the Company received an upfront, non-refundable fee of $15 million. In addition, the Company will be eligible for future IMO-9200 related development, regulatory and sales milestone payments totaling up to $140 million, including development and regulatory milestones totaling up to $65 million and sales milestones totaling up to $75 million, and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. As it relates to back-up compounds, the Company will be eligible for related designation payments and development, regulatory sales and milestone payments totaling up to $52.5 million, including development and regulatory milestones totaling up to $35 million and sales milestones totaling up to $17.5 million and escalating royalties ranging from the mid single-digits to low double-digits of global net sales, which percentages are subject to reduction under agreed upon circumstances. Under the terms of the Company’s collaboration and license agreement with GlaxoSmithKline Intellectual Property Development Limited (“GSK”) to license, research, develop and commercialize pharmaceutical compounds from the Company’s 3GA technology for the treatment of selected targets in renal disease (the “GSK Agreement”), the Company is eligible to receive up to approximately $100 million in license, research, clinical development and commercialization milestone payments, including a $2.5 million upfront, non-refundable, non-creditable cash payment. Approximately $9 million of the milestone payments are payable by GSK upon the identification of additional targets, the completion of current and future research plans and the designation of development candidates. Approximately $89 million is payable by GSK upon the achievement of clinical milestones and commercial milestones. In addition, the Company is eligible to receive royalty payments based on net sales of licensed products following commercialization at varying rates of up to five percent on annual net sales, as defined in the GSK Agreement.
Financial Instruments	(f) Financial Instruments The fair value of the Company’s financial instruments is determined and disclosed in accordance with the three-tier fair value hierarchy specified in Note 2(m). The Company is required to disclose the estimated fair values of its financial instruments. The Company’s financial instruments consist of cash, cash equivalents, available-for-sale investments, receivables and a note payable. The estimated fair values of these financial instruments approximate their carrying values as of December 31, 2016 and 2015. As of December 31, 2016 and 2015, the Company did not have any derivatives, hedging instruments or other similar financial instruments except for the note issued under the Company’s loan and security agreement, which is discussed in Note 5(a), including put and call features which the Company determined are clearly and closely associated with the debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial.
Comprehensive Income (Loss)	(g) Comprehensive Income (Loss) Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions and other events and circumstances from non-owner sources. Comprehensive income (loss) for the years ended December 31, 2016, 2015 and 2014 is comprised of reported net income (loss) and any change in net unrealized gains and losses on investments during each year, which is included in “Accumulated other comprehensive income” on the accompanying balance sheets. The Company applies Accounting Standards Update (“ASU”) No. 2011-05, “Comprehensive Income” by presenting the components of net income and other comprehensive income as one continuous statement. The following table includes the changes in the accumulated balance of the component of other comprehensive loss for the years ended December 31, 2016, 2015 and 2014: Year Ended December 31, (In thousands) 2016 2015 2014 Accumulated unrealized loss on available-for-sale securities at beginning of period $ $ $ Change during the period Accumulated unrealized loss on available-for-sale securities at end of period $ $ $
Net Income (Loss) per Common Share applicable to Common Stockholders	(h) Net Income (Loss) per Common Share applicable to Common Stockholders Basic and diluted net loss per common share applicable to common stockholders is computed using the weighted average number of shares of common stock outstanding during the period. Diluted net loss per common share applicable to common stockholders is the same as basic net loss per common share applicable to common stockholders for each of the three years in the period ended December 31, 2016 as the effects of the Company’s potential common stock equivalents are antidilutive (see Note 12).
Segment Reporting	(i) Segment Reporting The Company views its operations and manages its business as one operating segment. Accordingly, the Company operates in one segment, which is the business of discovering and developing novel therapeutics that modulate immune responses through TLRs. As a result, the financial information disclosed herein represents all of the material financial information related to the Company’s principal operating segment. For all of the periods presented, all of the Company’s revenues were generated in the United States. As of December 31, 2016 and 2015, all assets were located in the United States.
Stock-Based Compensation	(j) Stock-Based Compensation The Company recognizes all share-based payments to employees and directors as expense in the statements of operations and comprehensive loss based on their fair values. The Company records compensation expense over an award’s requisite service period, or vesting period, based on the award’s fair value at the date of grant. The Company’s policy is to charge the fair value of stock options as an expense, adjusted for forfeitures, on a straight-line basis over the vesting period, which is generally four years for employees and three years for directors. The Company recorded charges of $6.8 million, $5.4 million and $4.3 million for the years ended December 31, 2016, 2015 and 2014, respectively, for stock-based compensation expense attributable to share-based payments made to employees and directors. The 2015 charge includes approximately $0.3 million of stock-based compensation in connection with the recognition of additional expense associated with the acceleration of vesting and extension of the exercise period of a retiring director’s stock options as a result of a modification to such director’s stock options. The 2014 charge includes approximately $1.3 million for the recognition of amortization associated with an employee’s options that were subject to accelerated vesting as a result of a modification to such employee’s stock options. The fair value of each option award is estimated on the date of grant using the Black-Scholes option pricing model. The following weighted average assumptions apply to the options to purchase 3,346,250, 3,533,750, and 8,232,424 shares of common stock granted to employees and directors during the years ended December 31, 2016, 2015 and 2014, respectively: 2016 2015 2014 Average risk free interest rate Expected dividend yield — — — Expected lives (years) Expected volatility Weighted average grant date fair value of options granted during the period (per share) $ $ $ Weighted average exercise price of options granted during the period (per share) $ $ $ The expected lives of the options and the expected volatility are based on historical experience. All options granted during the three years in the period ended December 31, 2016 were granted at exercise prices equal to the fair market value of the common stock on the dates of grant . The fair value of options that vested during 2016, 2015 and 2014 amounted to $6.9 million, $5.4 million and $4.2 million, respectively. There were no options exercised in 2016. The intrinsic value of options exercised amounted to $0.8 million and $0.6 million during 2015 and 2014, respectively. As of December 31, 2016, there was $13.4 million of unrecognized compensation cost related to nonvested stock-based compensation arrangements, which the Company expects to recognize over a weighted average period of 2.4 years.
Research and Development Expenses	(k) Research and Development Expenses All research and development expenses, including amounts funded by research collaborations, are expensed as incurred. Research and development expenses are comprised of costs incurred in performing research and development activities, including drug development trials and studies, drug manufacturing, laboratory supplies, external research, payroll including stock-based compensation and overhead. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are deferred and capitalized. The capitalized amounts are expensed as the related goods are accepted by the Company or the services are performed. As of December 31, 2016 and 2015, the Company recorded approximately $1.4 million and $2.3 million as prepaid research and development, respectively.
Concentration of Credit Risk	(l) Concentration of Credit Risk Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents and available-for-sale investments. The Company’s credit risk is managed by investing its cash and cash equivalents and marketable securities in highly rated money market instruments, certificates of deposit, corporate bonds, and debt securities. Due to these factors, no significant additional credit risk is believed by management to be inherent in the Company’s assets. As of December 31, 2016, all of the Company’s cash, cash equivalents and investments are held at two financial institutions.
Fair Value of Assets and Liabilities	(m) Fair Value of Assets and Liabilities The Company measures fair value at the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date using assumptions that market participants would use in pricing the asset or liability (the “inputs”) into a three-tier fair value hierarchy. This fair value hierarchy gives the highest priority (Level 1) to quoted prices in active markets for identical assets or liabilities and the lowest priority (Level 3) to unobservable inputs in which little or no market data exists, requiring companies to develop their own assumptions. Observable inputs that do not meet the criteria of Level 1, and include quoted prices for similar assets or liabilities in active markets or quoted prices for identical assets and liabilities in markets that are not active, are categorized as Level 2. Level 3 inputs are those that reflect the Company’s estimates about the assumptions market participants would use in pricing the asset or liability, based on the best information available in the circumstances. Valuation techniques for assets and liabilities measured using Level 3 inputs may include unobservable inputs such as projections, estimates and management’s interpretation of current market data. These unobservable Level 3 inputs are only utilized to the extent that observable inputs are not available or cost-effective to obtain. The Company applies ASU No. 2011-04, “Fair Value Measurement (Topic 820),” in its fair value measurements and disclosures. The table below presents the assets and liabilities measured and recorded in the financial statements at fair value on a recurring basis at December 31, 2016 and 2015 categorized by the level of inputs used in the valuation of each asset and liability. Quoted Prices in Active Markets Significant for Identical Other Significant Assets or Observable Unobservable Liabilities Inputs Inputs (In thousands) Total (Level 1) (Level 2) (Level 3) December 31, 2016 Assets Money market funds $ $ $ — $ — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ — December 31, 2015 Assets Money market funds $ $ $ — $ — Short-term investments – commercial paper — — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Long-term investments – corporate bonds — — Long-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ — The Level 1 assets consist of money market funds, which are actively traded daily. The Level 2 assets consist of corporate bond, commercial paper, and municipal bond investments whose fair value may not represent actual transactions of identical securities. The fair value of corporate and municipal bonds is generally determined from quoted market prices received from pricing services based upon quoted prices from active markets and/or other significant observable market transactions at fair value. The fair value of commercial paper is generally determined based on the relationship between the investment’s discount rate and the discount rates of the same issuer’s commercial paper available in the market which may not be actively traded daily. Since these fair values may not be based upon actual transactions of identical securities, they are classified as Level 2. Since any investments are classified as available-for-sale securities, any unrealized gains or losses are recorded in accumulated other comprehensive income or loss within stockholders’ equity on the balance sheet. The Company did not elect to measure any other financial assets or liabilities at fair value at December 31, 2016 or 2015.
New Accounting Pronouncements - Recently Issued	(n) New Accounting Pronouncements — Recently Issued In May 2014, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) No. 2014-09, Revenue from Contracts with Customers (Topic 606), which was amended by ASU No. 2015-14. ASU No. 2014-09, as amended by ASU No. 2015-14, requires an entity to recognize revenue from the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. In particular, this ASU addresses contracts with more than one performance obligation, as well as the accounting for some costs to obtain or fulfill a contract with a customer, and provides for additional disclosures with respect to revenues and cash flows arising from contracts with customers. This ASU will be effective for fiscal years beginning after December 15, 2017, including interim periods within that fiscal year. Early adoption of this ASU is permitted only for fiscal years beginning after December 15, 2016, including interim periods within that fiscal year. The Company expects to adopt ASU 2014-09 in the first quarter of 2018 and is currently determining the transition method it will adopt. The adoption of ASU 2014-09 may have a material effect on our financial statements, including the footnote disclosures. To date, we have derived our revenues from a limited number of license and collaboration agreements. The consideration we are eligible to receive under these agreements includes upfront payments, research and development funding, contingent revenues in the form of commercial and development milestones and option payments and royalties. Each of our license and collaboration agreements has unique terms that will need to be evaluated separately under the new standard. We have started our preliminary assessment of our active license and collaboration agreements. ASU 2014-09 differs from the current accounting standard in many respects, such as in the accounting for variable consideration, including milestone payments. Accordingly, we expect that our evaluation of the accounting for collaboration agreements under the new revenue standard could identify material changes from the current accounting treatment. In addition, the current accounting standards include a presumption that revenue from upfront non-refundable fees are recognized ratably over the performance period, unless another attribution method is determined to more closely approximate the delivery of the goods or services to the customer. The new accounting standard will require entities to determine an appropriate attribution method using either output or input methods and does not include a presumption that entities would default to a ratable attribution approach. These factors could materially impact the amount and timing of our revenue recognition from our license and collaboration agreements under the new revenue standard. In August 2014, the FASB issued ASU No. 2014-15, Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern. ASU 2014-15 amends FASB ASC 205-40, Presentation of Financial Statements – Going Concern, by providing guidance on determining when and how reporting entities must disclose going-concern uncertainties in their financial statements, including requiring management to perform interim and annual assessments of an entity’s ability to continue as a going concern within one year of the date of issuance of the entity’s financial statements and providing certain disclosures if there is substantial doubt about the entity’s ability to continue as a going concern. ASU 2014-15 will be effective for fiscal years ending after December 15, 2016 and for interim periods thereafter. Early adoption of ASU 2014-15 is permitted. The Company has adopted this standard, which has not had a material impact on its financial statements. In January 2016, the FASB issued ASU No. 2016-01, Recognition and Measurement of Financial Assets and Financial Liabilities. The amendments in ASU 2016-01 address certain aspects of recognition, measurement, presentation and disclosure of financial instruments. ASU 2016-01 will be effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. Early adoption of some of the amendments included in ASU 2016-01 for financial statements of fiscal years or interim periods that have not yet been issued is permitted as of the beginning of the fiscal year of adoption. The Company is currently evaluating the effect that the adoption of ASU 2016-01 will have on its financial statements. In February 2016, the FASB issued ASU No. 2016-02, Leases. The amendments in ASU 2016-02 will require organizations that lease assets, with lease terms of more than 12 months, to recognize on the balance sheet the assets and liabilities for the rights and obligations created by those leases. Consistent with current U.S. Generally Accepted Accounting Principles (“U.S. GAAP”), the recognition, measurement, and presentation of expenses and cash flows arising from a lease by a lessee primarily will depend on its classification as a finance or operating lease. However, unlike current U.S. GAAP which requires only capital leases to be recognized on the balance sheet, ASU No. 2016-02 will require both types of leases to be recognized on the balance sheet. ASU 2016-02 will be effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the effect that the adoption of ASU 2016-02 will have on its financial statements. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (Topic 718). ASU 2016-09 will require organizations to recognize all income tax effects of awards in the statement of operations when the awards vest or are settled. ASU 2016-09 will also allow organizations to repurchase more shares from employees than they could previously purchase for tax withholding purposes without triggering liability accounting and to make a policy election to account for forfeitures as they occur. ASU 2016-09 will be effective for fiscal years beginning after December 15, 2016, and interim periods within those fiscal years. Early adoption is permitted in any interim or annual period. The Company is currently evaluating the effect that the adoption of ASU 2016-09 will have on its financial statements.
Accounting for Uncertainty in Income Taxes	The Company applies ASC 740-10, “Accounting for Uncertainty in Income Taxes, an interpretation of ASC 740.” ASC 740-10 clarifies the accounting for uncertainty in income taxes recognized in financial statements and requires the impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. The Company had no unrecognized tax benefits resulting from uncertain tax positions at December 31, 2016 and 2015.

Summary of Significant Accoun24

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2016
Summary of Significant Accounting Policies
Schedule of changes in accumulated balance of the component of other comprehensive (loss)	Year Ended December 31, (In thousands) 2016 2015 2014 Accumulated unrealized loss on available-for-sale securities at beginning of period $ $ $ Change during the period Accumulated unrealized loss on available-for-sale securities at end of period $ $ $
Schedule of weighted average assumptions applied to options	2016 2015 2014 Average risk free interest rate Expected dividend yield — — — Expected lives (years) Expected volatility Weighted average grant date fair value of options granted during the period (per share) $ $ $ Weighted average exercise price of options granted during the period (per share) $ $ $
Schedule of assets and liabilities measured and recorded in financial statements at fair value on a recurring basis	Quoted Prices in Active Markets Significant for Identical Other Significant Assets or Observable Unobservable Liabilities Inputs Inputs (In thousands) Total (Level 1) (Level 2) (Level 3) December 31, 2016 Assets Money market funds $ $ $ — $ — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ — December 31, 2015 Assets Money market funds $ $ $ — $ — Short-term investments – commercial paper — — Short-term investments – corporate bonds — — Short-term investments – municipal bonds — — Long-term investments – corporate bonds — — Long-term investments – municipal bonds — — Total Assets $ $ $ $ — Total Liabilities $ — $ — $ — $ —

Investments (Tables)

Investments (Tables)	12 Months Ended
	Dec. 31, 2016
Investments
Schedule of available-for-sale investments at fair value	December 31, 2016 Gross Gross Estimated Unrealized Unrealized Fair Cost (Losses) Gain Value (In thousands) Short-term investments – corporate bonds $ $ $ — $ Short-term investments – municipal bonds — Total short-term investments — Total investments $ $ $ — $ December 31, 2015 Gross Gross Estimated Unrealized Unrealized Fair Cost (Losses) Gains Value (In thousands) Short-term investments – commercial paper $ $ — $ $ Short-term investments – corporate bonds — Short-term investments – municipal bonds — — Total short-term investments Long-term investments – corporate bonds — Long-term investments – municipal bonds Total long-term investments Total investments $ $ $ $

Property and Equipment (Tables)

Property and Equipment (Tables)	12 Months Ended
	Dec. 31, 2016
Property and Equipment
Schedule of net property and equipment at cost	December 31, (In thousands) 2016 2015 Leasehold improvements $ $ Laboratory equipment and other Total property and equipment, at cost Less: Accumulated depreciation and amortization Property and equipment, net $ $

Note Payable and Accrued Expe27

Note Payable and Accrued Expenses (Tables)	12 Months Ended
	Dec. 31, 2016
Note Payable and Accrued Expenses
Schedule of aggregate future minimum payments, reflecting payments on outstanding principal plus interest, due under the loan and security agreement	Year Ended December 31, 2017 $ 2018 Total minimum payments Less amount representing interest Notes payable, gross Unamortized facility fee Accrual of final payment Notes payable, balance Less current portion of notes payable Non-current portion of notes payable $
Schedule of accrued expenses	December 31, 2016 2015 (In thousands) Payroll and related costs $ $ Clinical and nonclinical trial expenses Professional and consulting fees Equipment purchase — Other $ $

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2016
Stockholders' Equity
Schedule of warrants outstanding and exercisable for purchase of common stock	Expiration Date Shares Weighted Average Exercise Price Per Share November 9, 2017 $ May 7, 2018 May 7, 2020 September 30, 2020 February 10, 2021 Total $
Schedule of information related to outstanding and exercisable options	Weighted-Average Remaining Aggregate Stock Weighted-Average Contractual Life Intrinsic Options Exercise Price (in years) Value Outstanding at December 31, 2015 $ Granted Exercised — — Forfeited Expired Outstanding at December 31, 2016 $ Exercisable at December 31, 2016 Total exercisable or expected to vest

Common Stock Warrant and Opti29

Common Stock Warrant and Option Exercises and Employee Stock Purchases (Tables)	12 Months Ended
	Dec. 31, 2016
Common Stock Warrant and Option Exercises and Employee Stock Purchases
Schedule of common stock a result of warrant exercises, stock option exercises and employee stock purchases	2016 2015 2014 (In thousands) Shares Proceeds Shares Proceeds Shares Proceeds Warrant exercises $ $ $ Stock option exercises — — Employee stock purchases Total $ $ $

Commitments and Contingencies (

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies.
Schedule of future minimum commitments under company lease agreements	December 31, Operating Lease (In thousands) 2017 $ 2018 2019 2020 2021 Thereafter $

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2016
Income Taxes
Schedule of components of deferred tax assets	2016 2015 (In thousands) Operating loss carryforwards $ $ Tax credit carryforwards Other Valuation allowance $ — $ —
Schedule of difference between U.S. federal corporate tax rate and Company effective tax rate	2016 2015 2014 Expected federal income tax rate % % % Expiring credits and NOLs — — — Change in valuation allowance Federal and state credits State income taxes, net of federal benefit Permanent differences Section 382 limitation — — Other Effective tax rate % % %

Supplemental Disclosure of Ca32

Supplemental Disclosure of Cash Flow Information (Tables)	12 Months Ended
	Dec. 31, 2016
Supplemental Disclosure of Cash Flow Information
Schedule of supplemental disclosure of cash flow information	Year Ended December 31, 2016 2015 2014 (In thousands) Supplemental disclosure of cash flow information: Cash paid for interest $ $ $ Supplemental disclosure of non-cash financing and investing activities: Conversion of Series D preferred stock to common stock $ — $ — $ Conversion of Series E preferred stock to common stock $ — $ — $ Non-cash property additions $ $ $ Accrued 2016 financing transaction costs paid in 2017 $ $ — $ —

April 2013 Pillar Agreements (T

April 2013 Pillar Agreements (Tables)	12 Months Ended
	Dec. 31, 2016
April 2013 Pillar Agreements
Schedule of assumptions and other inputs used to compute fair value of agreement warrants	Pillar I Warrants Additional Pillar Warrants Common stock price $ $ Warrant exercise price $ $ Term of warrant (years) Expected volatility % % Average risk free interest rate % % Expected dividend yield — — Expected percentage of warrants to be exercised % %

Organization (Details)

Organization (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2016USD ($)item	Dec. 31, 2015USD ($)
Organization
Number of technology platforms to develop drug candidates | item	2
Accumulated deficit | $	$ 538,470	$ 500,081

Summary of Significant Accoun35

Summary of Significant Accounting Policies - Additional Information (Details) $ in Thousands	12 Months Ended			36 Months Ended
	Dec. 31, 2016USD ($)segmentshares	Dec. 31, 2015USD ($)shares	Dec. 31, 2014USD ($)shares	Dec. 31, 2016USD ($)
Accounting Policies
Held-to-maturity investments	$ 0	$ 0		$ 0
Realized gains or losses from available-for-sale securities	0	0	$ 0
Losses from investments	0	0	0	0
Total restricted cash	$ 300	300		300
Number of operating segments | segment	1
Stock-based compensation	$ 6,847	$ 5,442	4,322
Accelerated amortization expense associated to employee's option			$ 1,300
Options to purchase common stock granted to employees and directors | shares	3,346,250	3,533,750	8,232,424
Fair value of options, vested	$ 6,900	$ 5,400	$ 4,200
Stock option exercises, Shares | shares	0	406,000	374,000
Intrinsic value of options exercised		$ 800	$ 600
Unrecognized compensation cost related to nonvested stock-based compensation	$ 13,400			13,400
Period for recognition of cost related to nonvested stock-based compensation arrangements	2 years 4 months 24 days
Prepaid expenses research and development	$ 1,400	$ 2,300		$ 1,400
Employees
Accounting Policies
Stock options, vesting period	4 years
Directors
Accounting Policies
Stock options, vesting period	3 years
Retiring Director's Stock Options
Accounting Policies
Stock-based compensation	$ 300
Minimum
Accounting Policies
Equipment depreciation period	3 years
Maximum
Accounting Policies
Equipment depreciation period	5 years

Summary of Significant Accoun36

Summary of Significant Accounting Policies - Royalties (Details) $ in Thousands	1 Months Ended				12 Months Ended
	Nov. 30, 2016USD ($)	Nov. 30, 2015USD ($)itemperson	May 31, 2014USD ($)	Apr. 30, 2014USD ($)	Dec. 31, 2016USD ($)item	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Remaining performance obligation					$ 0
Alliance revenue					16,199	$ 249	$ 73
Deferred revenue, current portion					1,111	1,111
Abbott Molecular
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Paid or expects to pay for external development expenses			$ 6,700
Expected agreement term			5 years
Merck & Co.
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Maximum amount that may be credited towards any amount due from collaborator for third-party license income received by the Company				$ 60,000
Percentage of third-party license income received by the Company that is credited towards any amount due from collaborator				15.00%
GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Number of optional additional targets | person		2
Number of development candidates | person		1
Number of units of accounting in connection of agreements | item		2
Remaining performance obligation					$ 0
Maximum royalty percentage on net sales					5.00%
Alliance revenue					$ 1,100
Deferred revenue					1,300	$ 100
Deferred revenue, current portion					1,100
Expected agreement term		27 months
GSK Agreement | License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 100,000			100,000
GSK Agreement | Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments					9,000
GSK Agreement | Clinical and Commercial Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments					$ 89,000
GSK Agreement | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		4 years
Number of optional additional targets | item					2
GSK Agreement | Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		2 years
Vivelix | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 140,000
Vivelix | Maximum | Development and Regulatory Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	65,000
Vivelix | Maximum | Sales Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	75,000
Up-front Payment Arrangement | GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement					$ 2,500
Up-front Payment Arrangement | Vivelix
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement	15,000
Back-up compounds | Vivelix | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	52,500
Back-up compounds | Vivelix | Maximum | Development and Regulatory Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	35,000
Back-up compounds | Vivelix | Maximum | Sales Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 17,500

Summary of Significant Accoun37

Summary of Significant Accounting Policies - Change in Accumulated Balance of the Component of Other Comprehensive Loss (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Summary of Significant Accounting Policies
Accumulated unrealized loss on available-for-sale securities at beginning of period	$ (134)	$ (17)	$ (7)
Change during the period	117	(117)	(10)
Accumulated unrealized loss on available-for-sale securities at end of period	$ (17)	$ (134)	$ (17)

Summary of Significant Accoun38

Summary of Significant Accounting Policies - Schedule of Assumptions Used to Determine Fair Value of Stock Options Granted During Period (Details) - $ / shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Summary of Significant Accounting Policies
Average risk free interest rate	1.40%	1.40%	1.40%
Expected lives (years)	4 years 2 months 12 days	4 years 2 months 12 days	4 years 4 months 24 days
Expected volatility	93.00%	93.00%	86.00%
Weighted average grant date fair value of options granted during the period (per share)	$ 1.75	$ 2.51	$ 2.36
Weighted average exercise price of options granted during the period (per share)	$ 2.64	$ 3.74	$ 3.69

Summary of Significant Accoun39

Summary of Significant Accounting Policies - Assets and Liabilities Measured at Fair Value on a Recurring Basis (Details) - Fair value on a recurring basis - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	$ 95,927	$ 86,627
Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	67,580	26,056
Short-term investments | Short-term investments – commercial paper
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		3,974
Short-term investments | Short-term investments – certificate of deposit
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		24,575
Short-term investments | Corporate bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	19,729	5,025
Short-term investments | Municipal bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	8,618	21,186
Long-term investments
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		5,811
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1)
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	67,580	26,056
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1) | Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	67,580	26,056
Significant Other Observable Inputs (Level 2)
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	28,347	60,571
Significant Other Observable Inputs (Level 2) | Short-term investments | Short-term investments – commercial paper
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		3,974
Significant Other Observable Inputs (Level 2) | Short-term investments | Short-term investments – certificate of deposit
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		24,575
Significant Other Observable Inputs (Level 2) | Short-term investments | Corporate bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	19,729	5,025
Significant Other Observable Inputs (Level 2) | Short-term investments | Municipal bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure	$ 8,618	21,186
Significant Other Observable Inputs (Level 2) | Long-term investments
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Assets, Fair Value Disclosure		$ 5,811

Investments - Summary of Availa

Investments - Summary of Available-for-Sale Investments at Fair Value (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities
Cost	$ 28,364	$ 60,705
Gross Unrealized (Losses)	(17)	(137)
Gross Unrealized Gains		3
Estimated Fair Value	28,347	60,571
Estimated Fair Value - Short-term investments	28,347	33,574
Estimated Fair Value - Long-term investments		26,997
Short-term investments
Schedule of Available-for-sale Securities
Cost	28,364	33,598
Gross Unrealized (Losses)	(17)	(25)
Gross Unrealized Gains		1
Estimated Fair Value	28,347	33,574
Short-term investments | Other cash equivalents – commercial paper
Schedule of Available-for-sale Securities
Cost		3,973
Gross Unrealized Gains		1
Estimated Fair Value		3,974
Short-term investments | Corporate bonds
Schedule of Available-for-sale Securities
Cost	19,740	24,600
Gross Unrealized (Losses)	(11)	(25)
Estimated Fair Value	19,729	24,575
Short-term investments | Municipal bonds
Schedule of Available-for-sale Securities
Cost	8,624	5,025
Gross Unrealized (Losses)	(6)
Estimated Fair Value	$ 8,618	5,025
Long-term investments
Schedule of Available-for-sale Securities
Cost		27,107
Gross Unrealized (Losses)		(112)
Gross Unrealized Gains		2
Estimated Fair Value		26,997
Long-term investments | Corporate bonds
Schedule of Available-for-sale Securities
Cost		21,289
Gross Unrealized (Losses)		(103)
Estimated Fair Value		21,186
Long-term investments | Municipal bonds
Schedule of Available-for-sale Securities
Cost		5,818
Gross Unrealized (Losses)		(9)
Gross Unrealized Gains		2
Estimated Fair Value		$ 5,811

Investments - Additional Inform

Investments - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended			36 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2016
Investments
Realized gains or losses from available-for-sale securities	$ 0	$ 0	$ 0
Losses from investments	0	$ 0	$ 0	$ 0
Auction rate securities, noncurrent	$ 0			$ 0

Property and Equipment - Net Pr

Property and Equipment - Net Property and Equipment at Cost (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Property, Plant and Equipment
Total property and equipment, at cost	$ 5,798	$ 5,146
Less: accumulated depreciation and amortization	3,945	3,454
Property and equipment, net	1,853	1,692
Leasehold improvements
Property, Plant and Equipment
Total property and equipment, at cost	671	603
Laboratory equipment and other
Property, Plant and Equipment
Total property and equipment, at cost	$ 5,127	$ 4,543

Property and Equipment - Additi

Property and Equipment - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Depreciation and amortization expense on property and equipment	$ 600	$ 500	$ 200
Accrued Liabilities, Current	7,394	$ 4,274
Accrued expenses
Accrued Liabilities, Current	$ 400

Note Payable and Accrued Expe44

Note Payable and Accrued Expenses - Additional Information (Details) - Oxford $ in Millions	12 Months Ended	15 Months Ended
	Dec. 31, 2016USD ($)installment	Dec. 31, 2015USD ($)
Debt Instrument
Borrowing capacity under the loan & security agreement		$ 3
Minimum interest rate		7.50%
Number of debt instrument payments | installment	36
Final payment of additional interest as a percentage of aggregate amount advanced	5.70%
Weighted average annual effective interest rate	11.10%
Minimum prepayment fee interest rate percentage	1.00%
Maximum prepayment fee interest rate percentage	3.00%
Advance received under loan and security agreement	$ 0.9
Outstanding loan balance, default interest rate	5.00%
Three months US LIBOR
Debt Instrument
Basis spread on fixed interest rate set at time of advance		7.27%

Note Payable and Accrued Expe45

Note Payable and Accrued Expenses - Schedule of Aggregate Future Minimum Payments Due Under Loan and Security Agreement (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Note Payable and Accrued Expenses
2,016	$ 333
2,017	219
Total minimum payments	552
Less amount representing interest	(80)
Notes payable, gross	472
Unamortized facility fee	(7)
Accrual of final payment	36
Notes payable, balance	501
Less current portion of notes payable	(292)	$ (261)
Non-current portion of notes payable	$ 209	$ 501

Note Payable and Accrued Expe46

Note Payable and Accrued Expenses - Accrued Expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Note Payable and Accrued Expenses
Payroll and related costs	$ 2,498	$ 2,325
Clinical and nonclinical trial expenses	3,577	1,339
Cost of regaining rights to cancer program	840	425
Professional and consulting fees	368
Other	111	185
Total accrued expenses	$ 7,394	$ 4,274

Collaboration and License Agr47

Collaboration and License Agreements (Details) $ in Thousands	1 Months Ended				12 Months Ended
	Nov. 30, 2016USD ($)	Nov. 30, 2015USD ($)itemperson	May 31, 2014USD ($)	Apr. 30, 2014USD ($)	Dec. 31, 2016USD ($)item	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Remaining performance obligation					$ 0
Alliance revenue					16,199	$ 249	$ 73
Deferred revenue, current portion					1,111	1,111
Deferred Revenue, Noncurrent					152	1,262
Expenses					54,956	49,095	38,825
Abbott Molecular
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Paid or expects to pay for external development expenses			$ 6,700
Expenses					400	900	$ 2,200
Expected agreement term			5 years
Merck & Co.
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Maximum amount that may be credited towards any amount due from collaborator for third-party license income received by the Company				$ 60,000
Percentage of third-party license income received by the Company that is credited towards any amount due from collaborator				15.00%
GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Number of optional additional targets | person		2
Number of development candidates | person		1
Number of units of accounting in connection of agreements | item		2
Remaining performance obligation					$ 0
Maximum royalty percentage on net sales					5.00%
Alliance revenue					$ 1,100
Deferred revenue					1,300	$ 100
Deferred revenue, current portion					1,100
Expected agreement term		27 months
GSK Agreement | License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 100,000			100,000
GSK Agreement | Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments					9,000
GSK Agreement | Clinical and Commercial Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments					$ 89,000
GSK Agreement | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		4 years
Number of optional additional targets | item					2
GSK Agreement | Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term		2 years
Vivelix | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 140,000
Vivelix | Maximum | Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	52,500
Vivelix | Maximum | Development and Regulatory Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	65,000
Vivelix | Maximum | Development and Regulatory Milestones | Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	35,000
Vivelix | Maximum | Sales Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	75,000
Vivelix | Maximum | Sales Milestones | Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	17,500
Up-front Payment Arrangement | GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement					$ 2,500
Up-front Payment Arrangement | Vivelix
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement	$ 15,000
R&D Services Unit of Accounting | GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement		$ 2,500
JSC Deliverable | GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement		$ 0

Stockholders' Equity - Common S

Stockholders' Equity - Common Stock (Details) - $ / shares	Oct. 28, 2016	Oct. 13, 2016	Feb. 19, 2015	Feb. 10, 2014	May 05, 1998	Dec. 31, 2016
Class of Stock
Minimum closing sales price of common stock to issue termination notice to put holders						$ 32
Shares held by put holders						35,780
Put Rights outstanding						0
Remaining shares of common stock subject to the liquidation put						763,954
Common stock, shares reserved for future issuance						76,137,792
Common Stock
Class of Stock
Stock issued (in shares)	1,225,243	25,000,000	23,000,000	7,867,438	1,199,684
Sale price of common shares subject to the liquidation put						$ 16
Price exceeds on number of days						20 days
Liquidation put shares no longer held by original holders						399,950

Stockholders' Equity - Warrants

Stockholders' Equity - Warrants Outstanding and Exercisable for the Purchase of Common Stock (Details)	Dec. 31, 2016$ / sharesshares
Class of Warrant or Right
Shares | shares	51,709,460
Weighted Average Exercise Price Per Share | $ / shares	$ 0.31
Warrant Expiration of November 9, 2017
Class of Warrant or Right
Shares | shares	7,252,081
Weighted Average Exercise Price Per Share | $ / shares	$ 0.70
Warrant Expiration of May 7, 2018
Class of Warrant or Right
Shares | shares	22,306,327
Weighted Average Exercise Price Per Share | $ / shares	$ 0.47
Warrant Expiration of May 7, 2020
Class of Warrant or Right
Shares | shares	15,816,327
Weighted Average Exercise Price Per Share | $ / shares	$ 0.01
Warrant Expiration of September 30, 2020
Class of Warrant or Right
Shares | shares	4,175,975
Weighted Average Exercise Price Per Share | $ / shares	$ 0.01
Warrant Expiration of February 10, 2021
Class of Warrant or Right
Shares | shares	2,158,750
Weighted Average Exercise Price Per Share | $ / shares	$ 0.01

Stockholders' Equity - Stock Op

Stockholders' Equity - Stock Options (Details) - shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Class of Stock
Common stock, shares reserved for future issuance	76,137,792
Maximum number of additional common shares	6,946,975
Minimum option exercise price as a percentage of market value of common stock	100.00%
Common stock options outstanding	18,002,000	16,261,000
Options outstanding under earlier plans	4,616,437
Grant of inducement stock option	1,150,000
Inducement grants outstanding shares	3,150,000
2013 Stock Incentive Plan
Class of Stock
Stock options, expiration period	10 years
Common stock, shares reserved for future issuance	15,224,460
Maximum number of shares that may be granted to any one individual in single year	1,500,000
Common stock options outstanding	10,235,083
Common shares available for grant	6,275,852
Minimum | 2013 Stock Incentive Plan
Class of Stock
Stock options, vesting period	3 years
Maximum | 2013 Stock Incentive Plan
Class of Stock
Stock options, vesting period	4 years

Stockholders' Equity - Summary

Stockholders' Equity - Summary of Stock Options (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Stockholders' Equity
Options, Outstanding, Beginning Balance	16,261
Granted	3,346
Exercised	0	(406)	(374)
Forfeited	(878)
Expired	(727)
Options, Outstanding, Ending Balance	18,002	16,261
Exercisable, Ending Balance	10,522
Total exercisable or expected to vest	17,283
Weighted Average Exercise Price, Beginning Balance	$ 3.45
Granted, Weighted Average Exercise Price	2.64	$ 3.74	$ 3.69
Forfeited, Weighted Average Exercise Price	3.15
Expired, Weighted Average Exercise Price	3.85
Weighted Average Exercise Price, Ending Balance	3.30	$ 3.45
Exercisable, Weighted Average Exercise Price	3.41
Total exercisable or expected to vest, Weighted Average Exercise Price	$ 3.31
Outstanding, Ending balance, Weighted Average Remaining Contractual Term	7 years 1 month 21 days
Exercisable Ending Balance, Weighted Average Remaining Contractual Term	6 years 2 months 5 days
Total exercisable or expected to vest, Weighted Average Remaining Contractual Term	7 years 29 days
Outstanding, Intrinsic Value, Ending Balance	$ 1,648
Exercisable, Ending Balance, Intrinsic Value	1,536
Total exercisable or expected to vest, Aggregate Intrinsic Value	$ 1,637

Stockholders' Equity - Employee

Stockholders' Equity - Employee Stock Purchase Plan (Details) - shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Class of Stock
Maximum percentage of total combined voting power or value of the stock of the Company after the grant	5.00%
Maximum percentage of employee defined annualized base pay that may be used to purchase stock under employee stock purchase plan	15.00%
Employee Stock Purchase Plan
Class of Stock
Percentage of fair market value of common stock for the ESPP option price	85.00%
Minimum percentage in payroll of deduction base salary to acquire shares of common stock	1.00%
Maximum percentage in payroll of deduction base salary to acquire shares of common stock	10.00%
Percentage of market value of common stock on the commencement of offering period	85.00%
Common stock share issued	121,460	27,951	13,844
Employee Stock Purchase Plan | Maximum
Class of Stock
Common stock shares authorized for issuance under stock purchase plan	500,000

Stockholders' Equity - Preferre

Stockholders' Equity - Preferred Stock (Details)	Feb. 06, 2014shares	Jan. 10, 2014personshares	Dec. 31, 2014shares	Dec. 31, 2016$ / sharesshares	Dec. 31, 2015$ / sharesshares	Nov. 30, 2012shares	Nov. 30, 2011shares
Class of Stock
Preferred stock, shares authorized				5,000,000
Preferred stock, par value | $ / shares				$ 0.01
Series A preferred stock liquidation preference per share | $ / shares				1
Series A Preferred stock conversion price per share | $ / shares				$ 34
Series A Preferred Stock
Class of Stock
Preferred stock, shares authorized				5,000,000	5,000,000
Preferred stock, par value | $ / shares				$ 0.01	$ 0.01
Preferred stock, shares designated				1,500,000	1,500,000
Annual percentage of dividend of preferred stock				1.00%
Preferred stock, shares outstanding				1,000	1,000
Preferred stock, shares issued				1,000	1,000
Series D Convertible Preferred Stock
Class of Stock
Preferred stock, shares outstanding		1,124,260
Number of people | person		1
Preferred stock, shares issued		1,124,260
Series D Convertible Preferred Stock | Pillar I
Class of Stock
Preferred stock, shares outstanding	0
Preferred stock, shares issued							1,124,260
Shares of common stock issued upon conversion	6,266,175
Series E Convertible Preferred Stock | Pillar II
Class of Stock
Preferred stock, shares outstanding			0
Preferred stock, shares issued			424,242			424,242
Shares of common stock issued upon conversion			8,484,840

Common Stock Warrant and Opti54

Common Stock Warrant and Option Exercises and Employee Stock Purchases (Details) - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Common Stock Warrant and Option Exercises and Employee Stock Purchases
Warrant exercises, Shares	1,370	2,968	5,544
Stock option exercises, Shares	0	406	374
Employee stock purchases, Shares	121	28	14
Total, Shares	1,491	3,402	5,932
Warrant exercises	$ 2,000	$ 1,888	$ 7,534
Stock option exercises		584	890
Employee stock purchases	172	74	32
Total, Proceeds	$ 2,172	$ 2,546	$ 8,456

Commitments and Contingencies -

Commitments and Contingencies - Rent Expense and Lease Information (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Lease Commitments
Rent expense, including real estate taxes	$ 1.9	$ 1.7	$ 1.7
Cash restricted for a security deposit	$ 0.3	$ 0.3
Cambridge Facility
Lease Commitments
Renewal option period exercisable by the Company	5 years
Cambridge Facility | Maximum
Lease Commitments
Premises improvements	$ 0.3
Exton Facility
Lease Commitments
Renewal option period exercisable by the Company	3 years

Commitments and Contingencies56

Commitments and Contingencies - Future Minimum Commitments Under Lease Agreements (Details) $ in Thousands	Dec. 31, 2016USD ($)
Commitments and Contingencies.
2,017	$ 1,842
2,018	2,024
2,019	2,084
2,020	2,018
2,021	1,984
Thereafter	1,348
Total	$ 11,300

Commitments and Contingencies57

Commitments and Contingencies - External Collaborations and Contract Obligations (Details) $ in Millions	Dec. 31, 2016USD ($)
Commitments and Contingencies.
Future minimum commitments under agreement, total	$ 2.7

Commitments and Contingencies58

Commitments and Contingencies - Related-Party Transactions (Details)	Jan. 10, 2014personshares	Sep. 30, 2013USD ($)shares	May 07, 2013USD ($)$ / sharesshares	Dec. 31, 2014shares	Feb. 28, 2014shares	Nov. 30, 2012USD ($)$ / sharesshares	Nov. 30, 2012person$ / sharesshares	Nov. 30, 2011USD ($)person$ / sharesshares	Dec. 31, 2016USD ($)shares	Dec. 31, 2015USD ($)shares	Dec. 31, 2014USD ($)shares
Related Party Transactions
Warrant to purchase common stock									51,709,460
Proceeds from exercise of warrants | $									$ 2,000,000	$ 1,888,000	$ 7,534,000
Proceeds from issuance of common stock in lieu of director board and committee fees | $									$ 172,000	$ 122,000	$ 82,000
Series E Convertible Preferred Stock
Related Party Transactions
Conversion of preferred stock to common, shares											424,000
Series D Convertible Preferred Stock
Related Party Transactions
Preferred stock, shares issued	1,124,260
Number of people | person	1
Conversion of preferred stock to common, shares											1,124,000
Common Stock | Series E Convertible Preferred Stock
Related Party Transactions
Conversion of preferred stock to common, shares											8,485,000
Common Stock | Series D Convertible Preferred Stock
Related Party Transactions
Conversion of preferred stock to common, shares											6,266,000
Pillar I
Related Party Transactions
Shares issued on exercise of warrants during the period									1,370,000		1,575,758
Proceeds from exercise of warrants | $									$ 2,000,200		$ 1,065,000
Pillar I | Series D Convertible Preferred Stock
Related Party Transactions
Preferred stock, shares issued								1,124,260
Aggregate purchase price under agreement | $								$ 9,500,000
Conversion of preferred stock to common, shares					6,266,175
Pillar I | Common Stock | Series D Warrant
Related Party Transactions
Warrant to purchase common stock								2,810,650
Exercise price of warrants | $ / shares						$ 1.46	$ 1.46	$ 1.63
Pillar I | Common Stock | Series D Warrant | Current Director
Related Party Transactions
Number of people | person								1
Pillar II
Related Party Transactions
Shares issued on exercise of warrants during the period										232,759	1,424,242
Proceeds from exercise of warrants | $										$ 163,000	$ 1,035,000
Pillar II | Series E Convertible Preferred Stock
Related Party Transactions
Preferred stock, shares issued				424,242		424,242	424,242				424,242
Aggregate purchase price under agreement | $						$ 7,000,000
Conversion of preferred stock to common, shares				8,484,840
Pillar II | Common Stock | Series E Warrant
Related Party Transactions
Warrant to purchase common stock						8,484,840	8,484,840
Exercise price of warrants | $ / shares						$ 0.70	$ 0.70
Pillar II | Common Stock | Series E Warrant | Directors
Related Party Transactions
Number of people | person							2
Pillar II | Common Stock | Series E Warrant | Current Director
Related Party Transactions
Number of people | person							1
Pillar II | Common Stock | Series E Warrant | Significant Shareholder
Related Party Transactions
Number of people | person							1
Pillar III
Related Party Transactions
Exercise price of warrants | $ / shares			$ 0.47
Proceeds from equity financings, net of issuance costs | $			$ 2,500,000
Shares issued on exercise of warrants during the period										2,600,000	500,000
Proceeds from exercise of warrants | $										$ 1,222,000	$ 235,000
Pillar III | Common Stock and Matching Warrants Sold
Related Party Transactions
Warrant to purchase common stock			5,000,000
Number of shares of common stock sold in financing			5,000,000
Pillar IV
Related Party Transactions
Number of shares of common stock sold in financing		1,774,193
Proceeds from equity financings, net of issuance costs | $		$ 2,750,000

Income Taxes - Additional Infor

Income Taxes - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Income Taxes
Period over which NOL and tax credit carryforward limitations are applied	1 year
Period of cumulative changes in ownership	3 years
Cumulative changes in ownership	50.00%
Operating loss carryforwards	$ 56,832	$ 46,432
Deferred Tax Assets, Valuation Allowance, Total	73,970	57,757
Unrecognized tax benefits from uncertain tax	$ 0	$ 0
Period over which material changes in unrecognized tax positions are not expected	12 months
ASU 2016-09
Income Taxes
Operating loss carryforwards	$ 1,400
Deferred Tax Assets, Valuation Allowance, Total	1,400
Federal
Income Taxes
Cumulative net operating loss carryforwards	149,300
Tax credit carryforwards	8,400
Excess tax benefit deductions related to the exercise of stock options	1,000
State
Income Taxes
Cumulative net operating loss carryforwards	138,200
Tax credit carryforwards	1,600
Excess tax benefit deductions related to the exercise of stock options	$ 700

Income Taxes - Components of th

Income Taxes - Components of the Deferred Tax Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Income Taxes
Operating loss carryforwards	$ 56,832	$ 46,432
Tax credit carryforwards	9,428	5,627
Other	7,710	5,698
Deferred Tax Assets, Gross	73,970	57,757
Valuation allowance	$ (73,970)	$ (57,757)

Income Taxes - Difference Betwe

Income Taxes - Difference Between U.S. Federal Corporate Tax Rate and Company's Effective Tax Rate (Details)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Taxes
Expected federal income tax rate	(34.00%)	(34.00%)	(34.00%)
Change in valuation allowance	42.20%	39.80%	(115.30%)
Federal and state credits	(9.90%)	(7.40%)	(4.00%)
State income taxes, net of federal benefit	(3.70%)	(4.50%)	(5.10%)
Permanent differences	3.50%	2.40%	0.80%
Section 382 limitation			157.50%
Other	1.90%	3.70%	0.10%
Effective tax rate	0.00%	0.00%	0.00%

Employee Benefit Plan - Additio

Employee Benefit Plan - Additional Information (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Employee Benefit Plan
Maximum employer match as a percentage of base pay	3.00%
Percentage the employer matches of employee contributions	50.00%
Portion of the employee's base salary that the Company matches	6.00%
Employer matching contributions to the plan	$ 0.3	$ 0.2	$ 0.1

Net Loss per Common Share App63

Net Loss per Common Share Applicable to Common Stockholders (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Net Loss per Common Share Applicable to Common Stockholders
Total antidilutive securities	69,712,906	70,782,788	74,640,383
Preferred stock dividends			$ 519

Supplemental Disclosure of Ca64

Supplemental Disclosure of Cash Flow Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 72	$ 93	$ 49
Supplemental disclosure of non-cash financing and investing activities:
Non-cash property additions	425	$ 123	324
Accrued 2013 financing transaction costs paid in 2014	$ 166
Series D Convertible Preferred Stock
Supplemental disclosure of non-cash financing and investing activities:
Conversion of preferred stock to common stock			5,464
Series E Convertible Preferred Stock
Supplemental disclosure of non-cash financing and investing activities:
Conversion of preferred stock to common stock			$ 5,528

April 2013 Pillar Agreements -

April 2013 Pillar Agreements - Additional Information (Details)	May 07, 2013USD ($)$ / shares	Apr. 30, 2013USD ($)agreement$ / sharesshares	Apr. 22, 2013USD ($)$ / sharesshares	Apr. 30, 2013agreement$ / sharesshares	Dec. 31, 2016shares
Effects of Agreements
Shares of common stock that may be purchased upon exercise of warrants issued | shares					51,709,460
Fair value of the Pillar Warrants in equity	$ 380,000
Extinguishment loss which was immediately charged to net loss applicable to common stockholders	1,750,000
Increase in stockholders equity resulting from preferred stock extinguishment and warrant issuance	$ 5,921,000
Minimum period for determining expected volatility					3 years
Percentage of holding by affiliates above which warrants may not be exercised					19.99%
Pillar I Warrants
Effects of Agreements
Exercise price of warrants | $ / shares	$ 0.61		$ 0.61
Additional cash consideration			$ 0
Consecutive trading days			30 days
Minimum closing price to redeem the warrants | $ / shares			$ 2.80
Redemption price per share of warrants | $ / shares			$ 0.01
Pillar I Warrants | Minimum
Effects of Agreements
Number of trading days			20 days
Pillar I Warrants | Maximum
Effects of Agreements
Shares of common stock that may be purchased upon exercise of warrants issued | shares			1,000,000
Additional Pillar Warrants
Effects of Agreements
Shares of common stock that may be purchased upon exercise of warrants issued | shares		1,000,000		1,000,000
Exercise price of warrants | $ / shares	$ 0.79	$ 0.79		$ 0.79
Additional cash consideration		$ 0
Final exercise date of warrant				Jun. 1, 2014
Series D Convertible Preferred Stock
Effects of Agreements
Carrying value of preferred stock prior to extinguishment	$ 5,921,000
Value of preferred stock immediately after the extinguishment of equity	5,464,000
Series E Convertible Preferred Stock
Effects of Agreements
Carrying value of preferred stock prior to extinguishment	3,701,000
Value of preferred stock immediately after the extinguishment of equity	$ 5,528,000
April 2013 Pillar Agreements
Effects of Agreements
Number of agreements | agreement		2		2
April 2013 Pillar Agreements | Series D Convertible Preferred Stock | Minimum
Effects of Agreements
Unaffiliated ownership percent that would trigger the right to require the Company to repurchase stock that was waived by Pillar Agreement				66.67%
April 2013 Pillar Agreements | Series D And Series E Preferred Stock
Effects of Agreements
Percentage of preferred stock holders who waived right to receive specified amount in liquidation				100.00%

April 2013 Pillar Agreements 66

April 2013 Pillar Agreements - Schedule of Assumptions and Other Inputs Used to Compute Fair Value of Agreement Warrants (Details) - $ / shares	May 07, 2013	Apr. 30, 2013	Apr. 22, 2013
Pillar I Warrants
Assumptions used to compute fair value of Pillar warrants
Stock price (in dollars per share)	$ 0.57
Warrant exercise price per share	$ 0.61		$ 0.61
Term of warrant (years)	5 years
Expected volatility	62.00%
Average risk free interest rate	0.80%
Expected percentage of warrants to be exercised	100.00%
Additional Pillar Warrants
Assumptions used to compute fair value of Pillar warrants
Stock price (in dollars per share)	$ 0.57
Warrant exercise price per share	$ 0.79	$ 0.79
Term of warrant (years)	1 year 1 month 6 days
Expected volatility	67.00%
Average risk free interest rate	0.10%
Expected percentage of warrants to be exercised	100.00%

Financings - October 2016 Follo

Financings - October 2016 Follow-on Underwritten Public Offering (Details) $ / shares in Units, $ in Millions	Oct. 28, 2016USD ($)person$ / sharesshares	Oct. 13, 2016USD ($)$ / sharesshares	Feb. 19, 2015USD ($)person$ / sharesshares	Feb. 10, 2014$ / sharesshares	May 05, 1998shares	Dec. 31, 2016shares
Class of Stock
Number of days underwriters have to purchase additional shares	30 days
Shares of common stock that may be purchased upon exercise of warrants | shares						51,709,460
Common Stock
Class of Stock
Stock issued (in shares) | shares	1,225,243	25,000,000	23,000,000	7,867,438	1,199,684
Common stock, price per share		$ 2	$ 3.75	$ 4
Gross proceeds from offering of common stock | $		$ 50	$ 86.3
Net proceeds from offering of common stock | $	$ 48.8		$ 80.6
Pre-funded Warrants
Class of Stock
Common stock, price per share				3.99
Warrant exercise price per share				$ 0.01
Investment Funds
Class of Stock
Number of people | person	2
Investment Funds | Directors
Class of Stock
Stock issued (in shares) | shares	5,125,000
Common stock, price per share	$ 2
Investment Funds | Directors | Common Stock
Class of Stock
Stock issued (in shares) | shares			5,333,333
Common stock, price per share			$ 3.75
Number of people | person			2
Baker Bros. Advisors LP
Class of Stock
Common stock, price per share			$ 0.47
Common stock held, shares | shares			6,965,432
Shares of common stock that may be purchased upon exercise of warrants | shares			20,316,327
Baker Bros. Advisors LP | Pre-funded Warrants
Class of Stock
Warrant exercise price per share			$ 0.01

Financings - February 2015 Foll

Financings - February 2015 Follow-on Underwritten Public Offering (Details) $ / shares in Units, $ in Millions	Oct. 28, 2016USD ($)person$ / sharesshares	Oct. 13, 2016USD ($)$ / sharesshares	Feb. 19, 2015USD ($)person$ / sharesshares	Feb. 10, 2014$ / sharesshares	May 05, 1998shares	Dec. 31, 2016shares
Class of Stock
Shares of common stock that may be purchased upon exercise of warrants						51,709,460
Common Stock
Class of Stock
Stock issued (in shares)	1,225,243	25,000,000	23,000,000	7,867,438	1,199,684
Common stock, price per share | $ / shares		$ 2	$ 3.75	$ 4
Gross proceeds from offering of common stock | $		$ 50	$ 86.3
Net proceeds from offering of common stock | $	$ 48.8		$ 80.6
Pre-funded Warrants
Class of Stock
Common stock, price per share | $ / shares				3.99
Warrant exercise price per share | $ / shares				$ 0.01
Pre-funded Warrants | Maximum
Class of Stock
Stock issued (in shares)				2,158,750
Investment Funds
Class of Stock
Number of people | person	2
Investment Funds | Directors
Class of Stock
Stock issued (in shares)	5,125,000
Common stock, price per share | $ / shares	$ 2
Investment Funds | Directors | Common Stock
Class of Stock
Stock issued (in shares)			5,333,333
Common stock, price per share | $ / shares			$ 3.75
Number of people | person			2
Baker Bros. Advisors LP
Class of Stock
Common stock, price per share | $ / shares			$ 0.47
Common stock held, shares			6,965,432
Shares of common stock that may be purchased upon exercise of warrants			20,316,327
Baker Bros. Advisors LP | Pre-funded Warrants
Class of Stock
Warrant exercise price per share | $ / shares			$ 0.01
Baker Bros. Advisors LP | Pre-funded Warrants | Maximum
Class of Stock
Shares of common stock that may be purchased upon exercise of warrants			22,151,052

Financings - February 2014 Foll

Financings - February 2014 Follow-on Underwritten Public Offering (Details) - USD ($) $ / shares in Units, $ in Millions	Oct. 28, 2016	Oct. 13, 2016	Feb. 19, 2015	Feb. 10, 2014	May 05, 1998	Dec. 31, 2016
Class of Stock
Shares of common stock that may be purchased upon exercise of warrants issued						51,709,460
Net proceeds from sale of common stock and warrants excluding the proceeds from exercise of the warrants, if any				$ 37.2
Common Stock
Class of Stock
Stock issued (in shares)	1,225,243	25,000,000	23,000,000	7,867,438	1,199,684
Stock price (in dollars per share)		$ 2	$ 3.75	$ 4
Pre-funded Warrants
Class of Stock
Gross proceeds from sale of common stock and warrants excluding the proceeds from exercise of the warrants, if any				$ 40.1
Exercise price of warrants				$ 0.01
Stock price (in dollars per share)				$ 3.99
Pre-funded Warrants | Maximum
Class of Stock
Stock issued (in shares)				2,158,750