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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2017	Jul. 31, 2017
Document and Entity Information
Entity Registrant Name	IDERA PHARMACEUTICALS, INC.
Trading Symbol	IDRA
Entity Central Index Key	0000861838
Document Type	10-Q
Document Period End Date	Jun. 30, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		149,631,783
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q2

CONDENSED BALANCE SHEETS - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 74,659	$ 80,667
Short-term investments	2,576	28,347
Prepaid expenses and other current assets	4,209	2,030
Total current assets	81,444	111,044
Property and equipment, net	1,600	1,853
Restricted cash and other assets	329	334
Total assets	83,373	113,231
Current liabilities:
Accounts payable	529	556
Accrued expenses	5,950	7,394
Current portion of note payable	309	292
Current portion of deferred revenue	563	1,111
Total current liabilities	7,351	9,353
Deferred revenue, net of current portion	235	152
Note payable, net of current portion	50	209
Other liabilities	865	168
Total liabilities	8,501	9,882
Commitments and contingencies
Stockholders' equity:
Common stock, $0.001 par value, Authorized — 280,000 shares; Issued and outstanding — 149,606 and 149,065 shares at June 30, 2017 and December 31, 2016, respectively	150	149
Additional paid-in capital	649,761	641,687
Accumulated deficit	(575,038)	(538,470)
Accumulated other comprehensive loss	(1)	(17)
Total stockholders' equity	74,872	103,349
Total liabilities and stockholders' equity	83,373	113,231
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

CONDENSED BALANCE SHEETS (Parenthetical) - $ / shares shares in Thousands	Jun. 30, 2017	Dec. 31, 2016
Preferred stock, par value	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000	5,000
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	280,000	280,000
Common stock, shares issued	149,606	149,065
Common stock, shares outstanding	149,606	149,065
Series A Preferred Stock
Preferred stock, shares designated	1,500	1,500
Preferred stock, shares issued	1	1
Preferred stock, shares outstanding	1	1

CONDENSED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
Alliance revenue	$ 187	$ 301	$ 565	$ 595
Operating expenses:
Research and development	17,891	10,128	29,376	19,424
General and administrative	3,888	3,778	7,969	7,694
Total operating expenses	21,779	13,906	37,345	27,118
Loss from operations	(21,592)	(13,605)	(36,780)	(26,523)
Other income (expense):
Interest income	144	110	297	230
Interest expense	(13)	(21)	(29)	(44)
Foreign currency exchange gain (loss)	(10)	31	(16)	29
Net loss	$ (21,471)	$ (13,485)	$ (36,528)	$ (26,308)
Basic and diluted net loss per common share (Note 14)	$ (0.14)	$ (0.11)	$ (0.24)	$ (0.22)
Shares used in computing basic and diluted net loss per common share	149,412	121,323	149,257	121,304
Net loss	$ (21,471)	$ (13,485)	$ (36,528)	$ (26,308)
Other comprehensive gain (loss):
Unrealized gain on available-for-sale securities		12	16	146
Comprehensive loss	$ (21,471)	$ (13,473)	$ (36,512)	$ (26,162)

CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	6 Months Ended
CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	Jun. 30, 2017	Jun. 30, 2016
Cash Flows from Operating Activities:
Net loss	$ (36,528)	$ (26,308)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	7,542	3,497
Issuance of common stock for services rendered	74	64
Accretion of discounts and premiums on investments	92	360
Depreciation and amortization expense	368	317
Other		2
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(2,179)	(12)
Accounts payable, accrued expenses, and other liabilities	(779)	121
Deferred revenue	(465)	(555)
Net cash used in operating activities	(31,875)	(22,514)
Cash Flows from Investing Activities:
Purchases of available-for-sale securities		(2,946)
Proceeds from maturity of available-for-sale securities	25,695	21,296
Proceeds from sale of available-for-sale securities		1,974
Purchases of property and equipment	(100)	(267)
Net cash provided by investing activities	25,595	20,057
Cash Flows from Financing Activities:
Proceeds from exercise of common stock warrants and options and employee stock purchases	419	67
Payments on note payable	(142)	(127)
Payments on capital lease	(5)	(5)
Net cash provided by (used in) financing activities	272	(65)
Net decrease in cash and cash equivalents	(6,008)	(2,522)
Cash and cash equivalents, beginning of period	80,667	26,586
Cash and cash equivalents, end of period	$ 74,659	$ 24,064

Organization	6 Months Ended
Organization	Jun. 30, 2017
Organization
Organization	(1) Organization Idera Pharmaceuticals, Inc. (“Idera” or the “Company”) is a clinical-stage biopharmaceutical company focused on the discovery, development and commercialization of novel oligonucleotide therapeutics for oncology and rare diseases. The Company uses two distinct proprietary drug discovery technology platforms to design and develop drug candidates: its Toll-like receptor (“TLR”) targeting technology and its 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 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. Toll-Like Receptors 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 IMO-8400 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. Third-Generation Antisense 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 is designing its 3GA oligonucleotides to have these attributes. The Company has selected IDRA-008 as its first 3GA candidate to enter clinical development. The Company is planning to develop IDRA-008 for a well-established liver target with available pre-clinical animal models and well-known clinical endpoints. The Company believes that IDRA-008 has potential for both broad and rare disease applications At June 30, 2017, the Company had an accumulated deficit of $575.0 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 or its collaborators successfully complete development and obtain marketing approval for drug candidates, 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. The Company believes, based on its current operating plan, its existing cash, cash equivalents and investments will enable the Company to fund its operations into the fourth quarter of 2018. The Company has and will continue to evaluate available alternatives to extend its operations beyond the fourth quarter of 2018.

New Accounting Pronouncements	6 Months Ended
New Accounting Pronouncements	Jun. 30, 2017
New Accounting Pronouncements
New Accounting Pronouncements	(2) New Accounting Pronouncements Recently Adopted Accounting Pronouncements In March 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) No. 2016-09, Compensation – Stock Compensation (Topic 718), which is effective for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years. As of January 1, 2017, the Company adopted this standard, which had the following impacts on its financial statements. (1) ASU 2016-09 requires organizations to recognize all income tax effects of awards in the statement of operations when the awards vest or are settled. The Company’s net operating loss deferred tax assets increased by $1.4 million and were offset by a corresponding increase in the valuation allowance given the Company’s continued loss position. Accordingly, the adoption of this portion of ASU 2016-09 had no impact on the Accumulated deficit. (2) ASU 2016-09 allows organizations to repurchase more shares from employees than they could previously purchase for tax withholding purposes without triggering liability accounting. The adoption of this portion of ASU 2016-09 had no impact on the Company’s financial statements. (3) ASU 2016-09 allows companies to make a policy election to account for forfeitures as they occur. The Company has made the policy election to account for forfeitures as they occurred and has used the modified retrospective transition method, resulting in less than $0.1 million reduction in Additional paid-in capital and an increase in Accumulated deficit as of January 1, 2017, to reflect the cumulative effect of previously estimated forfeitures. Recently Issued Accounting Pronouncements In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which was amended by ASU No. 2015-14 (as amended, “ASU 2014-09”). ASU No. 2014-09 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 is effective for public business entities 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. This guidance is applicable to the Company's fiscal year beginning January 1, 2018 and the Company expects to adopt ASU 2014-09 in the first quarter of 2018 using the modified retrospective transition method. The adoption of ASU 2014-09 may have a material effect on the Company’s financial statements, including the footnote disclosures. To date, the Company has derived our revenues from a limited number of license and collaboration agreements. The consideration the Company is 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 the Company’s license and collaboration agreements has unique terms that will need to be evaluated separately under the new standard. The Company is in process of assessing its two 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 the timing of recognition of certain milestone payments. Accordingly, the Company expects its 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 certain 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. ASU 2014-09 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 the Company’s revenue recognition from its license and collaboration agreements under ASU 2014-09. In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (“ASU 2016-02”). ASU 2016-02 requires 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 is effective for public business entities for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. This guidance is applicable to the Company's fiscal year beginning January 1, 2019. The Company is currently evaluating the effect that the adoption of ASU 2016-02 will have on its financial statements.

Unaudited Interim Financial Statements	6 Months Ended
Unaudited Interim Financial Statements	Jun. 30, 2017
Unaudited Interim Financial Statements
Unaudited Interim Financial Statements	(3) Unaudited Interim Financial Statements The accompanying unaudited financial statements included herein have been prepared by the Company in accordance with U.S. GAAP for interim financial information and pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”). Accordingly, certain information and footnote disclosures normally included in financial statements prepared in accordance with U.S. GAAP have been condensed or omitted pursuant to such rules and regulations. In the opinion of management, all adjustments, consisting of normal recurring adjustments, and disclosures considered necessary for a fair presentation of interim period results have been included. Interim results for the three and six months ended June 30, 2017 are not necessarily indicative of results that may be expected for the year ending December 31, 2017. For further information, refer to the financial statements and footnotes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2016, which was filed with the SEC on March 15, 2017.

Financial Instruments	6 Months Ended
Financial Instruments	Jun. 30, 2017
Financial Instruments
Financial Instruments	(4) 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 6, “Fair Value of Assets and Liabilities.” 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 and a note payable. The estimated fair values of these financial instruments approximate their carrying values as of June 30, 2017 and December 31, 2016. As of June 30, 2017 and December 31, 2016, 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) to the financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, 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.

Cash and Cash Equivalents	6 Months Ended
Cash and Cash Equivalents	Jun. 30, 2017
Cash and Cash Equivalents
Cash and Cash Equivalents	(5) Cash and Cash Equivalents 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 June 30, 2017 and December 31, 2016 consisted of cash and money market funds.

Fair Value of Assets and Liabilities

6 Months Ended

Jun. 30, 2017

Fair Value of Assets and Liabilities

Fair Value of Assets and Liabilities

(6) 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 June 30, 2017 and December 31, 2016 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)
June 30, 2017
Assets
Money market funds	$	73,136	$	73,136	$	—	$	—
Short-term investments – municipal bonds		2,576		—		2,576		—
Total Assets	$	75,712	$	73,136	$	2,576	$	—
Total Liabilities	$	—	$	—	$	—	$	—

December 31, 2016
Assets
Money market funds	$	67,580	$	67,580	$	—	$	—
Short-term investments – corporate bonds		19,729		—		19,729		—
Short-term investments – municipal bonds		8,618		—		8,618		—
Total Assets	$	95,927	$	67,580	$	28,347	$	—
Total Liabilities	$	—	$	—	$	—	$	—

The Level 1 assets consist of money market funds, which are actively traded daily. The Level 2 assets consist of corporate bond and municipal bond investments, the fair value of which 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. Since these fair values may not be based upon actual transactions of identical securities, they are classified as Level 2. Since all 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 June 30, 2017 or December 31, 2016.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Investments

6 Months Ended

Jun. 30, 2017

Investments

Investments

(7) Investments

The Company’s available-for-sale investments at fair value consisted of the following at June 30, 2017 and December 31, 2016:


	June 30, 2017
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
	Cost		(Losses)		Gains		Value
	(In thousands)
Short-term investments – municipal bonds	$	2,577	$	(1)	$	—	$	2,576
Total short-term investments		2,577		(1)		—		2,576
Total investments	$	2,577	$	(1)	$	—	$	2,576


	December 31, 2016
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
	Cost		(Losses)		Gains		Value
	(In thousands)
Short-term investments – corporate bonds	$	19,740	$	(11)	$	—	$	19,729
Short-term investments – municipal bonds		8,624		(6)		—		8,618
Total short-term investments		28,364		(17)		—		28,347
Total investments	$	28,364	$	(17)	$	—	$	28,347

The Company had no realized gains or losses from available-for-sale securities during the six months ended June 30, 2017 and 2016. There were no losses or other-than-temporary declines in value included in “Interest income” on the Company’s statements of operations and comprehensive loss for any securities for the six months ended June 30, 2017 and 2016. See Note 4, “Financial Instruments,” and Note 6, “Fair Value of Assets and Liabilities” for additional information related to the Company’s investments.

Property and Equipment

6 Months Ended

Jun. 30, 2017

Property and Equipment

Property and Equipment

(8) Property and Equipment

At June 30, 2017 and December 31, 2016, net property and equipment at cost consisted of the following:


	June 30,		December 31,
(In thousands)	2017		2016
Leasehold improvements	$	671	$	671
Laboratory equipment and other		5,158		5,127
Total property and equipment, at cost		5,829		5,798
Less: Accumulated depreciation and amortization		4,229		3,945
Property and equipment, net	$	1,600	$	1,853

Depreciation and amortization expense on property and equipment was approximately $0.2 million for both the three months ended June 30, 2017 and 2016, and $0.4 million and $0.3 million for the six months ended June 30, 2017 and 2016, respectively. There were less than $0.1 million in non-cash property additions during both the three months and six months ended June 30, 2017 and 2016.

Restricted Cash	6 Months Ended
Restricted Cash	Jun. 30, 2017
Restricted Cash
Restricted Cash	(9) 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 June 30, 2017 and December 31, 2016, the restricted cash amounted to $0.3 million held in certificates of deposit securing a line of credit for the lessor. The lease expires August 2022.

Accrued Expenses

6 Months Ended

Jun. 30, 2017

Accrued Expenses

Accrued Expenses

(10) Accrued Expenses

At June 30, 2017 and December 31, 2016, accrued expenses consisted of the following:



	June 30,		December 31,
(In thousands)	2017		2016
Payroll and related costs	$	2,056	$	2,498
Clinical and nonclinical trial expenses		3,392		3,577
Professional and consulting fees		424		840
Equipment purchase		—		368
Other		78		111
	$	5,950	$	7,394

Included in accrued payroll and related costs as of June 30, 2017 is the current portion, or $0.6 million, of the $1.2 million of salary continuation severance benefits to be paid in equal installments through May 31, 2019 to a former executive. The long-term portion of $0.6 million is included within Other liabilities in the Company’s balance sheet as of June 30, 2017.

Comprehensive Income (Loss)

6 Months Ended

Jun. 30, 2017

Comprehensive Income (Loss)

Comprehensive Income (Loss)

(11) 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 loss for the six months ended June 30, 2017 and 2016 is comprised of reported net loss and any change in net unrealized gains and losses on investments during each period, which is included in accumulated other comprehensive income (loss) on the accompanying balance sheets.

The following table includes the changes in the accumulated balance of the component of other comprehensive income (loss) for the six months ended June 30, 2017 and 2016:


	Six Months Ended		Six Months Ended
	June 30,		June 30,
(In thousands)	2017		2016
Accumulated unrealized loss on available-for-sale securities at beginning of period	$	(17)	$	(134)
Change during the period		16		146
Accumulated unrealized loss on available-for-sale securities at end of period	$	(1)	$	12

Collaboration with GlaxoSmithKline Intellectual Property Development Limited	6 Months Ended
	Jun. 30, 2017
Collaboration with GlaxoSmithKline Intellectual Property Development Limited
Collaboration with GlaxoSmithKline Intellectual Property Development Limited	(12) Collaboration with GlaxoSmithKline Intellectual Property Development Limited In November 2015, the Company entered into a 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 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 36 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 on sales upon 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) the R&D Services Unit of Accounting, and (ii) the 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 over the Company’s estimate of the period over which the Research Services are delivered. In the second quarter of 2017, the Company revised its estimate of the research period from 27 months to 36 months, which is being accounted for on a prospective basis. 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 $0.2 million and $0.3 million of deferred revenue related to the GSK Agreement during the three months ended June 30, 2017 and 2016, respectively, and $0.5 million and $0.6 million of deferred revenue for the six months ended June 30, 2017 and 2016, respectively. This revenue is classified as alliance revenue in the accompanying statements of operations and comprehensive loss. There was $0.8 million of deferred revenue related to the GSK Agreement at June 30, 2017, of which $0.6 million is reflected in current portion of deferred revenue and $0.2 million is reflected as long-term deferred revenue in the accompanying balance sheet.

Stock-Based Compensation

6 Months Ended

Jun. 30, 2017

Stock-Based Compensation

Stock-Based Compensation

(13) Stock-Based Compensation

The Company recognizes all stock-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 on a straight-line basis over the vesting period, which is generally four years for employees and three years for directors. The Company accounts for forfeitures when they occur. Ultimately, the actual expense recognized over the vesting period will be for only those shares that vest.

Total stock-based compensation expense recognized using the straight-line attribution method and included in operating expenses in the Company’s statements of operations and comprehensive loss was $5.8 million and $1.8 million for the three months ended June 30, 2017 and 2016, respectively, and $7.5 million and $3.5 million for the six months ended June 30, 2017 and 2016, respectively. Included in the $5.8 million and $7.5 million recognized during the three and six months ended June 30, 2017, respectively, is $4.3 million of stock-based compensation resulting from modifications to previously issued stock option awards in connection with the resignation of an executive, which is recorded in Research and development expense. Additionally, as of June 30, 2017, there was approximately $12.5 million of unrecognized compensation expense related to non-vested stock options which is expected to be recognized over a weighted-average period of 2.3 years.

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 3,911,500 and 3,161,000 shares of common stock granted to employees and directors during the six months ended June 30, 2017 and 2016, respectively:


	Six Months Ended
	June 30,
	2017		2016
Average risk free interest rate		1.7%		1.4%
Expected dividend yield		—		—
Expected lives (years)		4.0		4.2
Expected volatility		86.9%		93.0%
Weighted average grant date fair value (per share)	$	1.00	$	1.79
Weighted average exercise price (per share)	$	1.60	$	2.68

The expected lives and the expected volatility of the options granted during the six months ended June 30, 2017 and 2016 are based on historical experience. All options granted during the six months ended June 30, 2017 and 2016 were granted at exercise prices equal to the fair market value of the common stock on the dates of grant.

Net Loss per Common Share	6 Months Ended
Net Loss per Common Share	Jun. 30, 2017
Net Loss per Common Share
Net Loss per Common Share	(14) Net Loss per Common Share For the three and six months ended June 30, 2017 and 2016, basic and diluted net loss per common share is computed using the weighted average number of shares of common stock outstanding during the period. Diluted net loss per common share is the same as basic net loss per common share as the effects of the Company’s potential common stock equivalents are antidilutive. Total antidilutive securities were 72,809,539 and 73,369,852 for the six months ended June 30, 2017 and 2016, respectively, and consist of stock options, convertible preferred stock and warrants.

Stockholders’ Equity

6 Months Ended

Jun. 30, 2017

Stockholders’ Equity

Stockholders’ Equity

(15) Stockholders’ Equity

Common Stock Warrant Exercises, Stock Option Exercises and Employee Stock Purchases

The Company issued common stock as a result of stock option exercises and employee stock purchases as follows during the six months ended June 30, 2017 and 2016:


	Six Months Ended			Six Months Ended
	June 30, 2017			June 30, 2016
(In thousands)	Shares	Proceeds		Shares	Proceeds
Warrant exercises	409	$	287	—	$	—
Stock option exercises	7		17	—		—
Employee stock purchases	83		115	47		67
Total	499	$	419	47	$	67

Related Party Transactions	6 Months Ended
Related Party Transactions	Jun. 30, 2017
Related Party Transactions
Related Party Transactions	(16) Related Party Transactions The Company issued 41,302 and 26,973 shares of common stock during the six months ended June 30, 2017 and 2016, respectively, in lieu of director board and committee fees of less than $0.1 million for each six-month period, pursuant to the Company’s director compensation program. The number of shares issued was calculated based on the market closing price of the Company’s common stock on the issuance date.

Deferred Tax Assets	6 Months Ended
Deferred Tax Assets	Jun. 30, 2017
Deferred Tax Assets
Deferred Tax Assets	(17) Deferred Tax Assets The Company’s deferred tax assets are determined based on temporary differences between the financial reporting and tax bases of assets and are measured using the enacted tax rates and laws that will be in effect when the differences are expected to reverse. A valuation allowance is recorded against deferred tax assets if it is more likely than not that some portion or all of the deferred tax assets will not be realized. For the six months ended June 30, 2017 and 2016, the Company did not record any current or deferred income tax provisions or benefits. Due to the uncertainty surrounding the future realization of the deferred tax assets, the Company has recorded full valuation allowances against its otherwise recognizable deferred tax assets at June 30, 2017 and December 31, 2016.

Subsequent Events	6 Months Ended
Subsequent Events	Jun. 30, 2017
Subsequent Events.
Subsequent Events	(18) Subsequent Events The Company considers events or transactions that occur after the balance sheet date but prior to the issuance of the financial statements to provide additional evidence relative to certain estimates or to identify matters that require additional disclosure.

Fair Value of Assets and Liabilities (Tables)

6 Months Ended

Jun. 30, 2017

Fair Value of Assets and Liabilities

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)
June 30, 2017
Assets
Money market funds	$	73,136	$	73,136	$	—	$	—
Short-term investments – municipal bonds		2,576		—		2,576		—
Total Assets	$	75,712	$	73,136	$	2,576	$	—
Total Liabilities	$	—	$	—	$	—	$	—

December 31, 2016
Assets
Money market funds	$	67,580	$	67,580	$	—	$	—
Short-term investments – corporate bonds		19,729		—		19,729		—
Short-term investments – municipal bonds		8,618		—		8,618		—
Total Assets	$	95,927	$	67,580	$	28,347	$	—
Total Liabilities	$	—	$	—	$	—	$	—

Investments (Tables)

6 Months Ended

Jun. 30, 2017

Investments

Schedule of available-for-sale investments at fair value


	June 30, 2017
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
	Cost		(Losses)		Gains		Value
	(In thousands)
Short-term investments – municipal bonds	$	2,577	$	(1)	$	—	$	2,576
Total short-term investments		2,577		(1)		—		2,576
Total investments	$	2,577	$	(1)	$	—	$	2,576


	December 31, 2016
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
	Cost		(Losses)		Gains		Value
	(In thousands)
Short-term investments – corporate bonds	$	19,740	$	(11)	$	—	$	19,729
Short-term investments – municipal bonds		8,624		(6)		—		8,618
Total short-term investments		28,364		(17)		—		28,347
Total investments	$	28,364	$	(17)	$	—	$	28,347

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References + Details

Property and Equipment (Tables)

6 Months Ended

Jun. 30, 2017

Property and Equipment

Schedule of net property and equipment at cost


	June 30,		December 31,
(In thousands)	2017		2016
Leasehold improvements	$	671	$	671
Laboratory equipment and other		5,158		5,127
Total property and equipment, at cost		5,829		5,798
Less: Accumulated depreciation and amortization		4,229		3,945
Property and equipment, net	$	1,600	$	1,853

Accrued Expenses (Tables)

6 Months Ended

Jun. 30, 2017

Accrued Expenses

Schedule of Accrued Expenses



	June 30,		December 31,
(In thousands)	2017		2016
Payroll and related costs	$	2,056	$	2,498
Clinical and nonclinical trial expenses		3,392		3,577
Professional and consulting fees		424		840
Equipment purchase		—		368
Other		78		111
	$	5,950	$	7,394

Comprehensive Income (Loss) (Tables)

6 Months Ended

Jun. 30, 2017

Comprehensive Income (Loss)

Schedule of changes in accumulated balance of the component of other comprehensive income (loss)


	Six Months Ended		Six Months Ended
	June 30,		June 30,
(In thousands)	2017		2016
Accumulated unrealized loss on available-for-sale securities at beginning of period	$	(17)	$	(134)
Change during the period		16		146
Accumulated unrealized loss on available-for-sale securities at end of period	$	(1)	$	12

Stock-Based Compensation (Tables)

6 Months Ended

Jun. 30, 2017

Stock-Based Compensation

Schedule of weighted average assumptions applied to options


	Six Months Ended
	June 30,
	2017		2016
Average risk free interest rate		1.7%		1.4%
Expected dividend yield		—		—
Expected lives (years)		4.0		4.2
Expected volatility		86.9%		93.0%
Weighted average grant date fair value (per share)	$	1.00	$	1.79
Weighted average exercise price (per share)	$	1.60	$	2.68

Stockholders’ Equity (Tables)

6 Months Ended

Jun. 30, 2017

Stockholders’ Equity

Schedule of common stock a result of warrant exercises, stock option exercises and employee stock purchases


	Six Months Ended			Six Months Ended
	June 30, 2017			June 30, 2016
(In thousands)	Shares	Proceeds		Shares	Proceeds
Warrant exercises	409	$	287	—	$	—
Stock option exercises	7		17	—		—
Employee stock purchases	83		115	47		67
Total	499	$	419	47	$	67

Organization (Details) $ in Thousands	6 Months Ended
Organization (Details) $ in Thousands	Jun. 30, 2017 USD ($) item	Dec. 31, 2016 USD ($)
Organization
Number of technology platforms to develop drug candidates \| item	2
Accumulated deficit \| $	$ 575,038	$ 538,470

New Accounting Pronouncements (Details) $ in Millions		1 Months Ended
New Accounting Pronouncements (Details) $ in Millions	Jan. 01, 2017 USD ($)	Feb. 29, 2016	May 31, 2014 item agreement
New Accounting Pronouncements or Change in Accounting Principle
Number Of Agreements \| agreement			2
Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle
Number Of Performance Obligations \| item			1
Accounting Standards Update 2016-02 \| Minimum
New Accounting Pronouncements or Change in Accounting Principle
Lease term		12 months
Accounting Standards Update 2016-09 \| Long-term deferred tax assets, net
New Accounting Pronouncements or Change in Accounting Principle
New Accounting Pronouncement or Change in Accounting Principle, Effect of Adoption, Quantification	$ 1.4
Accounting Standards Update 2016-09 \| Additional Paid-in Capital
New Accounting Pronouncements or Change in Accounting Principle
New Accounting Pronouncement or Change in Accounting Principle, Effect of Adoption, Quantification	$ 0.1

Fair Value of Assets and Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments	$ 2,576	$ 28,347
Short-term investments
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments	2,576	28,347
Short-term investments \| Corporate bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments		19,729
Short-term investments \| Municipal bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments	2,576	8,618
Fair value on a recurring basis
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Total Assets	75,712	95,927
Fair value on a recurring basis \| Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Money market funds	73,136	67,580
Fair value on a recurring basis \| Short-term investments \| Corporate bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments		19,729
Fair value on a recurring basis \| Short-term investments \| Municipal bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments	2,576	8,618
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1) \| Fair value on a recurring basis
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Total Assets	73,136	67,580
Quoted Prices in Active Markets for Identical Assets or Liabilities (Level 1) \| Fair value on a recurring basis \| Money market funds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Money market funds	73,136	67,580
Significant Other Observable Inputs (Level 2) \| Fair value on a recurring basis
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Total Assets	2,576	28,347
Significant Other Observable Inputs (Level 2) \| Fair value on a recurring basis \| Short-term investments \| Corporate bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments		19,729
Significant Other Observable Inputs (Level 2) \| Fair value on a recurring basis \| Short-term investments \| Municipal bonds
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments	$ 2,576	$ 8,618

Investments - Summary of Available-for-Sale Investments at Fair Value (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Schedule of Available-for-sale Securities
Cost	$ 2,577	$ 28,364
Gross Unrealized (Losses)	(1)	(17)
Estimated Fair Value	2,576	28,347
Estimated Fair Value - Short-term investments	2,576	28,347
Short-term investments
Schedule of Available-for-sale Securities
Cost	2,577	28,364
Gross Unrealized (Losses)	(1)	(17)
Estimated Fair Value - Short-term investments	2,576	28,347
Short-term investments \| Corporate bonds
Schedule of Available-for-sale Securities
Cost		19,740
Gross Unrealized (Losses)		(11)
Estimated Fair Value - Short-term investments		19,729
Short-term investments \| Municipal bonds
Schedule of Available-for-sale Securities
Cost	2,577	8,624
Gross Unrealized (Losses)	(1)	(6)
Estimated Fair Value - Short-term investments	$ 2,576	$ 8,618

Investments - Additional Information (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Investments
Realized gains or losses from available-for-sale securities	$ 0	$ 0
Losses from investments	$ 0	$ 0

- Definition

This item represents the net total realized and unrealized gain (loss) included in earnings for the period as a result of selling or holding marketable securities categorized as trading, available-for-sale, or held-to-maturity, including the unrealized holding gain (loss) of held-to-maturity securities transferred to the trading security category and the cumulative unrealized gain (loss) which was included in other comprehensive income (a separate component of shareholders' equity) for available-for-sale securities transferred to trading securities during the period. Additionally, this item would include any gains (losses) realized during the period from the sale of investments accounted for under the cost method of accounting and losses recognized for other than temporary impairments (OTTI) of the subject investments.

+ References + Details

Property and Equipment - Net Property and Equipment at Cost (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Property, Plant and Equipment
Total property and equipment, at cost	$ 5,829	$ 5,798
Less: accumulated depreciation and amortization	4,229	3,945
Property and equipment, net	1,600	1,853
Leasehold improvements
Property, Plant and Equipment
Total property and equipment, at cost	671	671
Laboratory equipment and other
Property, Plant and Equipment
Total property and equipment, at cost	$ 5,158	$ 5,127

Property and Equipment - Additional Information (Details) - USD ($) $ in Millions	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Property and Equipment
Depreciation and amortization expense on property and equipment	$ 0.2	$ 0.2	$ 0.4	$ 0.3
Non-cash property additions	$ 0.1	$ 0.1	$ 0.1	$ 0.1

Restricted Cash (Details) - USD ($) $ in Millions	Jun. 30, 2017	Dec. 31, 2016
Restricted Cash
Total restricted cash	$ 0.3	$ 0.3

Accrued Expenses - (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Accrued Expenses
Payroll and related costs	$ 2,056	$ 2,498
Clinical and nonclinical trial expenses	3,392	3,577
Professional and consulting fees	424	840
Equipment purchase		368
Other	78	111
Total accrued expenses	5,950	$ 7,394
Salary continuation severance benefits	1,200
Long-term portion of other liabilities	$ 600

Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Comprehensive Income (Loss)
Accumulated unrealized loss on available-for-sale securities at beginning of period		$ (17)	$ (134)
Change during the period	$ 12	16	146
Accumulated unrealized loss on available-for-sale securities at end of period	$ 12	$ (1)	$ 12

Collaboration with GlaxoSmithKline Intellectual Property Development Limited (Details)	1 Months Ended	3 Months Ended		6 Months Ended
	Nov. 30, 2015 person	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2017 USD ($)	Jun. 30, 2017 USD ($) item	Jun. 30, 2017 USD ($) agreement	Jun. 30, 2017 USD ($)	Jun. 30, 2016 USD ($)	Dec. 31, 2016 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Alliance revenue		$ 187,000	$ 301,000				$ 565,000	$ 595,000
Current portion of deferred revenue		563,000		$ 563,000	$ 563,000	$ 563,000	563,000		$ 1,111,000
Long-term deferred revenue		235,000		235,000	$ 235,000	235,000	235,000		$ 152,000
Operating expenses		21,779,000	13,906,000				37,345,000	27,118,000
Operating expense
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Operating expenses		5,800,000	1,800,000				7,500,000	3,500,000
GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Deferred revenue recognition period	36 months
Number of development candidates	1				1
Number of units of accounting in connection of agreements \| item					2
Alliance revenue		200,000	$ 300,000				500,000	$ 600,000
Deferred revenue		$ 800,000		800,000	$ 800,000	800,000	800,000
Research period		27 months
Current portion of deferred revenue		$ 600,000		600,000	600,000	600,000	600,000
Long-term deferred revenue		$ 200,000		$ 200,000	$ 200,000	$ 200,000	200,000
Additional extended research period		36 months
GSK Agreement \| Clinical and Commercial Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments							89
GSK Agreement \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term	4 years
Number of optional additional targets					2	2
Maximum royalty percentage on net sales				5.00%
GSK Agreement \| Maximum \| License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments							100,000,000
GSK Agreement \| Maximum \| Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments							9
GSK Agreement \| Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term	2 years
R&D Services Unit of Accounting \| Up-front Payment Arrangement \| GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement							2,500,000
JSC Deliverable \| Up-front Payment Arrangement \| GSK Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Upfront payment received under collaboration agreement							$ 0

Stock-Based Compensation - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation		$ 7,542	$ 3,497
Options to purchase common stock granted to employees and directors		3,911,500	3,161,000
Unrecognized compensation expense	$ 12,500	$ 12,500
Weighted average remaining period over which unrecognized compensation expense will be recognized		2 years 3 months 18 days
Research and Development Expense
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation	$ 4,300	$ 4,300
Employees
Share-based Compensation Arrangement by Share-based Payment Award
Stock options, vesting period		4 years
Directors
Share-based Compensation Arrangement by Share-based Payment Award
Stock options, vesting period		3 years

Stock-Based Compensation - Schedule of Assumptions Used to Determine Fair Value of Stock Options Granted During Period (Details) - $ / shares	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Stock-Based Compensation
Average risk free interest rate	1.70%	1.40%
Expected lives (years)	4 years	4 years 2 months 12 days
Expected volatility	86.90%	93.00%
Weighted average grant date fair value of options granted during the period (per share)	$ 1.00	$ 1.79
Granted, Weighted Average Exercise Price	$ 1.60	$ 2.68

Net Loss per Common Share (Details) - shares	6 Months Ended
Net Loss per Common Share (Details) - shares	Jun. 30, 2017	Jun. 30, 2016
Net Loss per Common Share
Total antidilutive securities	72,809,539	73,369,852

Stockholders’ Equity (Details) - USD ($) shares in Thousands, $ in Thousands	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Stockholders’ Equity
Warrant exercises, Shares	409
Warrant exercises, Proceeds	$ 287
Stock option exercises, Shares	7
Stock option exercises, Proceeds	$ 17
Employee stock purchases, Shares	83	47
Employee stock purchases, Proceeds	$ 115	$ 67
Total, Shares	499	47
Total, Proceeds	$ 419	$ 67

Related Party Transactions (Details) - Directors - USD ($) $ in Millions	6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016
Related Party Transactions
Common stock issued in lieu of board fees	41,302	26,973
Issuance of common stock for services	$ 0.1	$ 0.1