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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2017	Feb. 15, 2018	Jun. 30, 2017
Document and Entity Information
Entity Registrant Name	IDERA PHARMACEUTICALS, INC.
Trading Symbol	IDRA
Entity Central Index Key	0000861838
Document Type	10-K
Document Period End Date	Dec. 31, 2017
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			$ 203,037,675
Entity Common Stock, Shares Outstanding		195,635,196
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	FY

CONDENSED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 112,629	$ 80,667
Short-term investments		28,347
Prepaid expenses and other current assets	3,992	2,030
Total current assets	116,621	111,044
Property and equipment, net	1,472	1,853
Restricted cash and other assets	324	334
Total assets	118,417	113,231
Current liabilities:
Accounts payable	1,334	556
Accrued expenses	8,000	7,394
Current portion of note payable	209	292
Current portion of deferred revenue	566	1,111
Total current liabilities	10,109	9,353
Deferred revenue, net of current portion		152
Note payable, net of current portion		209
Other liabilities	613	168
Total liabilities	10,722	9,882
Commitments and contingencies (Note 11)
Stockholders' equity:
Common stock, $0.001 par value, Authorized — 280,000 shares; Issued and outstanding — 195,625 and 149,065 shares at December 31, 2017 and December 31, 2016, respectively	196	149
Additional paid-in capital	711,993	641,687
Accumulated deficit	(604,494)	(538,470)
Accumulated other comprehensive loss		(17)
Total stockholders' equity	107,695	103,349
Total liabilities and stockholders' equity	118,417	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	Dec. 31, 2017	Dec. 31, 2016
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	195,625,000	149,065,000
Common stock, shares outstanding	195,625,000	149,065,000
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

CONDENSED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS
Alliance revenue	$ 902	$ 16,199	$ 249
Operating expenses:
Research and development	50,653	39,824	33,699
General and administrative	16,716	15,132	15,396
Total operating expenses	67,369	54,956	49,095
Loss from operations	(66,467)	(38,757)	(48,846)
Other income (expense):
Interest income	574	415	357
Interest expense	(50)	(80)	(105)
Foreign currency exchange (loss) gain	(41)	33	39
Net loss	(65,984)	(38,389)	(48,555)
Net loss	$ (65,984)	$ (38,389)	$ (48,555)
Net loss per share applicable to common stockholders - basic and diluted (Note 15)	$ (0.42)	$ (0.30)	$ (0.42)
Weighted-average number of common shares used in computing net loss per share applicable to common stockholders - basic and diluted	157,398	127,597	115,092
Net loss	$ (65,984)	$ (38,389)	$ (48,555)
Other comprehensive loss:
Unrealized gain (loss) on available-for-sale securities	17	117	(117)
Total other comprehensive income (loss)	17	117	(117)
Comprehensive loss	$ (65,967)	$ (38,272)	$ (48,672)

STATEMENTS OF STOCKHOLDERS' EQUITY - USD ($) shares in Thousands, $ in Thousands	Common Stock	Additional Paid-in Capital	Accumulated Deficit	Accumulated Other Comprehensive (Loss)/Income	Total
Beginning balance at Dec. 31, 2014	$ 95	$ 494,850	$ (451,526)	$ (17)	$ 43,402
Beginning 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
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	2,170			2,172
Exercise of common stock options, warrants and employee stock purchases, shares	1,491
Issuance of common stock for services		172			172
Issuance of common stock for services, shares	84
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
Cumulative effect from adoption of new accounting standard (Note 2)		40	(40)
Sale of common stock and warrants, net of issuance costs	$ 38	53,708			$ 53,746
Sale of common stock and warrants, shares	38,333
Exercise of common stock options, warrants and employee stock purchases	$ 9	5,688			5,697
Exercise of common stock options, warrants and employee stock purchases, shares	8,146
Issuance of common stock for services		150			150
Issuance of common stock for services, shares	81
Stock-based compensation		10,720			10,720
Unrealized gain (loss) on marketable securities				$ 17	17
Net loss			(65,984)		(65,984)
Ending balance at Dec. 31, 2017	$ 196	$ 711,993	$ (604,494)		$ 107,695
Ending balance, shares at Dec. 31, 2017	195,625				195,625

CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
CONDENSED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Cash Flows from Operating Activities:
Net loss	$ (65,984)	$ (38,389)	$ (48,555)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss from disposition of assets		4
Non-employee stock option expense			143
Stock-based compensation	10,720	6,847	5,442
Issuance of common stock for services rendered	150	172	122
Accretion of discounts and premiums on investments	94	566	599
Depreciation and amortization expense	746	656	488
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(1,962)	1,064	(1,889)
Accounts payable, accrued expenses, and other liabilities	1,674	1,988	(1,709)
Deferred revenue	(697)	(1,111)	2,373
Net cash used in operating activities	(55,259)	(28,203)	(42,986)
Cash Flows from Investing Activities:
Purchases of available-for-sale securities		(2,946)	(63,106)
Proceeds from maturity of available-for-sale securities	28,270	32,746	29,420
Proceeds from sale of available-for-sale securities		1,974	999
Purchases of property and equipment	(206)	(408)	(727)
Net cash provided by (used in) investing activities	28,064	31,366	(33,414)
Cash Flows from Financing Activities:
Proceeds from equity financings, net of issuance costs	53,763	49,014	80,599
Proceeds from exercise of common stock warrants and options and employee stock purchases	5,697	2,172	2,546
Payments on note payable	(292)	(261)	(120)
Payments on capital lease	(11)	(7)	(10)
Net cash provided by financing activities	59,157	50,918	83,015
Net increase in cash and cash equivalents	31,962	54,081	6,615
Cash and cash equivalents, beginning of period	80,667	26,586	19,971
Cash and cash equivalents, end of period	$ 112,629	$ 80,667	$ 26,586

Business and Organization	12 Months Ended
Business and Organization	Dec. 31, 2017
Business and Organization
Business and Organization	Note 1. Business and Organization Business Overview Idera Pharmaceuticals, Inc. (“Idera” or the “Company”), a Delaware corporation, 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 nucleic acid chemistry technology (formerly referred to as the Company’s third generation antisense, or 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 nucleic acid chemistry technology, the Company is developing drug candidates to turn off the messenger RNA (“mRNA”) associated with disease causing genes. The Company believes its nucleic acid chemistry 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 has entered into and may explore additional collaborative alliances to support development and commercialization. Agreement and Plan of Merger As further described in Note 17, in January 2018, the Company entered into an Agreement and Plan of Merger with BioCryst Pharmaceuticals, Inc. and affiliated entities. However, the Company has prepared these financial statements as if the Company will remain an independent company. See Note 17 for further details. Liquidity and Financial Condition As of December 31, 2017, the Company had an accumulated deficit of $604.5 million. The Company expects to incur substantial operating losses in future periods and will require additional capital to advance its drug candidates through development to commercialization. The Company does not expect to generate product revenue, sales-based milestones or royalties until the Company successfully completes development and obtains marketing approval for the Company’s drug candidates, either alone or in collaboration 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. The Company believes, based on its current operating plan, that its existing cash, cash equivalents and investments will enable the Company to fund its operations into the second quarter of 2019. The Company has and will continue to evaluate available alternatives to extend its operations beyond the second quarter of 2019.

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2017

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Note 2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”).

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates, judgements, and assumptions that affect the reported amounts of assets, liabilities, equity, revenues and expenses, and related disclosure of contingencies in the accompanying Financial Statements and these Notes. In addition, management’s assessment of the Company’s ability to continue as a going concern involves the estimation of the amount and timing of future cash inflows and outflows. On an ongoing basis, the Company evaluates its estimates, judgements and methodologies. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable. Actual results could differ materially from those estimates.

Segment Information

Operating segments are defined as components of an enterprise in which separate discrete information is available for evaluation by the chief operating decision maker, or decision-making group, in deciding how to allocate resources and assessing performance. The Company views its operations and manages its business as one operating segment, which is the business of discovering and developing novel oligonucleotide therapeutics for oncology and rare diseases. Additionally, for all periods presented (a) all of the Company's revenues were generated in the United States, (b) all research and development activities occurred in the United States, and (c) all assets were located in the United States.

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 3. 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, 2017 and 2016. As of December 31, 2017 and 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 7, and which includes put and call features, which features 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.

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, 2017, all of the Company’s cash, cash equivalents and investments are held at two financial institutions.

Note 2. Summary of Significant Accounting Policies (Continued)

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 December 31, 2017 and 2016 consisted of cash and money market funds.

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, 2017 and 2016, the restricted cash amounted to $0.3 million and is recorded in “Restricted cash and other assets” in the accompanying balance sheets.

Investments

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, 2017 or 2016. 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 2017, 2016 or 2015. There were no losses or other-than-temporary declines in value included in “Interest income” for any securities for the three years in the period ended December 31, 2017.

Property and Equipment

Property and equipment is carried at acquisition cost less accumulated depreciation, subject to review for impairment whenever events or changes in circumstances indicate that the carrying amount of the asset may not be recoverable as described further under the heading "Impairment of Long-Lived Assets" below. The cost of normal, recurring, or periodic repairs and maintenance activities related to property and equipment are expensed as incurred. The cost for planned major maintenance activities, including the related acquisition or construction of assets, is capitalized if the repair will result in future economic benefits.

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.

When an asset is disposed of, the associated cost and accumulated depreciation is removed from the related accounts on the Company's balance sheet with any resulting gain or loss included in the Company's statement of operations.

Note 2. Summary of Significant Accounting Policies (Continued)

Impairment of Long-Lived Assets

In accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) 360-10-35, Impairment or Disposal of Long-Lived Assets, the Company reviews its long-lived assets and identifiable finite-lived intangible assets for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable (i.e. impaired). Once an impairment is determined, the actual impairment recognized is the difference between the carrying amount and the fair value (less costs to sell for assets to be disposed of) as estimated using one of the following approaches: income, cost and/or market. Fair value using the income approach is determined primarily using a discounted cash flow model that uses the estimated cash flows associated with the asset or asset group under review, discounted at a rate commensurate with the risk involved. Fair value utilizing the cost approach is determined based on the replacement cost of the asset reduced for, among other things, depreciation and obsolescence. Fair value, utilizing the market approach, benchmarks the fair value against the carrying amount. No impairment expense was recognized during the years ended December 31, 2017, 2016 and 2015.

Revenue Recognition

The Company recognizes revenue in accordance with the 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.

Alliance Revenues

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.

See Note 8, “Collaboration and License Agreements” for additional details surrounding the Company’s collaboration arrangements.

Note 2. Summary of Significant Accounting Policies (Continued)

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 the Company’s 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.

Note 2. Summary of Significant Accounting Policies (Continued)

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.

Research and Development Expenses

All research and development expenses 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, 2017 and 2016, the Company recorded approximately $2.6 million and $1.4 million as prepaid research and development, respectively, which is included within prepaid expenses and other current assets in the accompanying balance sheets.

Stock-Based Compensation

The Company accounts for stock-based compensation using ASC 718, Compensation – Stock Compensation (“ASC 718”), or ASC 505-50, Equity – Equity Based Payments to Non-Employees, as applicable. The Company accounts for stock-based awards to employees and non-employee directors using the fair value based method to determine compensation expense for all arrangements where shares of stock or equity instruments are issued for compensation. In addition, the Company accounts for stock-based compensation to other non-employees in accordance with the accounting guidance for equity instruments that are issued to entities or persons other than employees.

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. Vesting is generally four years for employees and one year for directors. The Company uses a Black-Scholes option-pricing model to determine the fair value of each option grant as of the date of grant for expense incurred. The Black-Scholes option pricing model requires inputs for risk-free interest rate, dividend yield, expected stock price volatility and expected term of the options. The value of the award that is ultimately expected to vest based on the achievement of a performance condition (i.e., service period) is recognized as expense on a straight-line basis over the requisite service period. See Note 10, “Stock-based Compensation” for additional details.

Previously, ASC 718 required forfeitures to be estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. In the first quarter of 2017, the Company adopted Accounting Standards Update (“ASU”) 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”), which allows an entity to elect as an accounting policy either to continue to estimate the total number of awards for which the requisite service period will not be rendered or to account for forfeitures when they occur. In connection with the adoption of this ASU, the Company made an accounting policy election to account for forfeitures as they occur and applied this change in accounting policy on a modified retrospective basis. See discussion under Recently Adopted Accounting Pronouncements for the impact this adoption had on the Company’s financial statements.

Note 2. Summary of Significant Accounting Policies (Continued)

Income Taxes

An asset and liability approach is used for financial accounting and reporting for income taxes. Deferred income taxes arise from temporary differences between income tax and financial reporting and principally relate to recognition of revenue and expenses in different periods for financial and tax accounting purposes and are measured using currently enacted tax rates and laws. In addition, a deferred tax asset can be generated by a net operating loss carryover. If it is more likely than not that some portion or all of a deferred tax asset will not be realized, a valuation allowance is recognized.

In the event the Company is charged interest or penalties related to income tax matters, the Company would record such interest as interest expense and would record such penalties as other expense in the Statements of Operations. No such charges have been incurred by the Company. For each of the years ended December 31, 2017, 2016 and 2015, the Company had no uncertain tax positions. See Note 12, “Income Taxes” for additional details.

Net 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, 2017 as the effects of the Company’s potential common stock equivalents are antidilutive (see Note 15).

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, 2017, 2016 and 2015 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. In accordance with ASC Topic 220, Comprehensive Income, the Company has elected to present the components of net income and other comprehensive income as one continuous statement.

New Accounting Pronouncements

Recently Adopted Accounting Pronouncements

In March 2016, the FASB issued ASU No. 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting, which became effective for the Company on January 1, 2017. The Company adopted this ASU during the first quarter of 2017 which had the following impacts on the Company’s 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 Company’s 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 occur and has used the modified retrospective transition method, resulting in less than a $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.

Note 2. Summary of Significant Accounting Policies (Continued)

Recently Issued (Not Yet Adopted) Accounting Pronouncements

In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which was subsequently amended by ASU No. 2015-14, which deferred the effective date, and several other ASU’s related to Topic 606 through December 31, 2017 (e.g. ASU 2016-08, ASU 2016-10, 2016-12 and 2016-20) which clarify various aspects of the new revenue guidance including principal versus agent considerations, identifying performance obligations, and licensing, and include other improvements and practical expedients (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 addition, this ASU addresses contracts with more than one performance obligation, as well as the accounting for 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 guidance is applicable to the Company's fiscal year beginning January 1, 2018 and the Company will adopt ASU 2014-09 in the first quarter of 2018 using the modified retrospective transition method.

To determine revenue recognition for arrangements that an entity determines are within the scope of Topic 606, the entity performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the entity satisfies a performance obligation. To date, the Company has derived its 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 and has been evaluated separately under the new standard.

With respect to its license and collaboration agreements with Vivelix Pharmaceuticals, Ltd. (“Vivelix”) and GlaxoSmithKline Intellectual Property Development Limited (“GSK”), the Company is substantially complete with its assessment and currently estimates that there will be no material impact to Alliance revenues for any of the years presented after the adoption of Topic 606. Additionally, the Company does not expect to revise any balance sheet components of Alliance revenues such as accounts receivable and deferred revenues or beginning retained earnings as of January 1, 2016 as a result of the modified retrospective method of adoption. The Company will continue to monitor additional changes, modifications, clarifications or interpretations being undertaken by the FASB, which may impact the Company’s current conclusion.

In January 2016, the FASB issued ASU No. 2016-01, Recognition and Measurement of Financial Assets and Financial Liabilities (“ASU 2016-01”). The amendments in ASU 2016-01 address certain aspects of recognition, measurement, presentation and disclosure of financial instruments. This guidance is applicable to the Company's fiscal year beginning January 1, 2018 and the Company will adopt this ASU in the first quarter of 2018. Based on the Company’s current investment holdings, the adoption of this new standard is not expected to have a material impact on the Company’s financial position or results of operations.

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 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 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. 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.

Fair Value Measurements

12 Months Ended

Dec. 31, 2017

Fair Value Measurements

Fair Value Measurements

Note 3. Fair Value Measurements

Assets and Liabilities Measured at Fair Value on a Recurring Basis

The Company applies the guidance in ASC 820, Fair Value Measurement, to account for financial assets and liabilities measured on a recurring basis. Fair value is measured 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. As such, fair value is a market-based measurement that is determined based on assumptions that market participants would use in pricing an asset or liability.

The Company uses a fair value hierarchy, which distinguishes between assumptions based on market data (observable inputs) and an entity's own assumptions (unobservable inputs). The guidance requires that fair value measurements be classified and disclosed in one of the following three categories:

Level 1: Unadjusted quoted prices in active markets that are accessible at the measurement date for identical, unrestricted assets or liabilities;

Level 2: Quoted prices in markets that are not active or inputs which are observable, either directly or indirectly, for substantially the full term of the asset or liability;

Level 3: Prices or valuation techniques that require inputs that are both significant to the fair value measurement and unobservable (i.e., supported by little or no market activity).

Determining which category an asset or liability falls within the hierarchy requires significant judgment. The Company evaluates its hierarchy disclosures each reporting period. There were no transfers between Level 1, 2 and 3 during each of the years ended December 31, 2017, 2016 and 2015.

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, 2017 and 2016 categorized by the level of inputs used in the valuation of each asset and liability.



	December 31, 2017
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	66,183	$	66,183	$	—	$	—
Total Assets	$	66,183	$	66,183	$	—	$	—
Total Liabilities	$	—	$	—	$	—	$	—


	December 31, 2016
(In thousands)	Total		Level 1		Level 2		Level 3
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 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. 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.

- 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

12 Months Ended

Dec. 31, 2017

Investments

Investments

Note 4. Investments

The Company held no available-for-sale investments at December 31, 2017. The Company’s available-for-sale investments at December 31, 2016 were as follows:


	December 31, 2016
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
(In thousands)	Cost		(Losses)		Gains		Value
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

Realized gains and losses from available-for-sale securities were immaterial for 2017, 2016 and 2015. Additionally, there were no losses or other-than-temporary declines in value included in the Company’s statements of operations and comprehensive loss for any securities for the three year period ended December 31, 2017. See Note 2, “Summary of Significant Accounting Policies” and Note 3, “Fair Value Measurements” for additional information related to the Company’s investments.

Property and Equipment

12 Months Ended

Dec. 31, 2017

Property and Equipment

Property and Equipment

Note 5. Property and Equipment

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


	December 31,
(In thousands)	2017		2016
Leasehold improvements	$	671	$	671
Laboratory equipment and other		5,261		5,127
Total property and equipment, at cost		5,932		5,798
Less: Accumulated depreciation and amortization		4,460		3,945
Property and equipment, net	$	1,472	$	1,853

Depreciation and amortization expense on Property and equipment was approximately $0.7 million, $0.6 million and $0.5 million in 2017, 2016 and 2015, respectively. See Note 16, “Supplemental Disclosure of Cash Flow Information”, for information related to non-cash property additions.

Accrued Expenses

12 Months Ended

Dec. 31, 2017

Accrued Expenses

Accrued Expenses

Note 6. Accrued Expenses

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


	December 31,
(In thousands)	2017		2016
Payroll and related costs	$	3,108	$	2,498
Clinical and nonclinical trial expenses		3,495		3,577
Professional and consulting fees		1,317		840
Equipment purchase		—		368
Other		80		111
	$	8,000	$	7,394

Included in accrued Payroll and related costs as of December 31, 2017 is the current portion, or $0.6 million, of the remaining $0.9 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 $0.3 million is included within Other liabilities in the Company’s balance sheet as of December 31, 2017. The Equipment purchase relates to equipment received by the Company that was not in service and unpaid as of December 31, 2016.

Note Payable	12 Months Ended
Note Payable	Dec. 31, 2017
Note Payable
Note Payable	Note 7. 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 received total advances of $0.9 million under the loan and security agreement during the draw down period. 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 are being 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, 2017, the total outstanding balance of the note payable to Oxford in the amount of $0.2 million is classified in Current portion of note payable within the accompanying balance sheet. 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.

Collaboration and License Agreements	12 Months Ended
Collaboration and License Agreements	Dec. 31, 2017
Collaboration and License Agreements
Collaboration and License Agreements	Note 8. Collaboration and License Agreements Collaboration with Vivelix In November 2016, the Company entered into an exclusive license and collaboration agreement with Vivelix pursuant to which the Company granted Vivelix worldwide rights to develop and market IMO-9200, an antagonist of TLR7, 8, and 9, for non-malignant gastrointestinal disorders (the GI Field or Field as defined in the Vivelix Agreement), and certain back-up compounds to IMO-9200 (the “Vivelix Agreement”). The Company was previously developing IMO-9200 for potential use in selected autoimmune disease indications. However, the Company determined not to proceed with internal development of IMO-9200 because the large autoimmune disease indications for which IMO-9200 had been developed did not fit within the strategic focus of the Company. Under the terms of the Vivelix Agreement, 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. Note 8. Collaboration and License Agreements (Continued) 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 may last for up to three years. 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, 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, 2017. Affiliates of Baker Brothers constitute two of the four directors on the Board of Directors of Vivelix and two of the seven directors on the Board of Directors of the Company. However, the Boards of the Company and Vivelix share no individual common Board members. Accounting Analysis under ASC 605 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. Note 8. Collaboration and License Agreements (Continued) 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 revenue of less than $0.1 million for the year ended December 31, 2017 and $15.0 million for the year ended December 31, 2016 related to the Vivelix Agreement. This revenue is classified as Alliance revenue in the accompanying statements of operations and comprehensive loss. No such revenues were recognized in 2015. Collaboration with GSK In November 2015, the Company entered into a collaboration and license agreement with GSK to license, research, develop and commercialize pharmaceutical compounds from the Company’s nucleic acid chemistry 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. Note 8. Collaboration and License Agreements (Continued) The GSK Agreement also provided GSK with the option to select up to two additional targets at any time during the first two years of the agreement, for further research under mutually agreed upon research plans. Upon selecting additional targets, GSK then had the option to 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. As of December 31, 2017, GSK had not selected any additional targets for research and the option period in which GSK could select additional targets had expired. 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. Additionally, the Company was eligible to receive a total of up to approximately $100 million in upfront, license, research, clinical development and commercialization milestone payments of which $9 million of these milestone payments would have been payable by GSK upon the identification of the additional targets, the completion of current and future research plans and the designation of development candidates and $89 million would have been payable by GSK upon the achievement of clinical milestones and commercial milestones. As a result of GSK not selecting additional targets during the two-year option period, the Company is eligible to receive a total of up to approximately $20 million in upfront, license, research, clinical development and commercialization milestone payments, of which $1 million of these milestone payments would be payable by GSK upon the designation of a development candidate from the initial target and $17 million would be payable by GSK upon the achievement of clinical milestones and commercial milestones. In addition, the Company is eligible to receive royalty payments based on sales of 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 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 were substantive options. GSK was not contractually obligated to exercise the options and as a result of the uncertain outcome of the research activities, there was significant uncertainty as to whether GSK would decide to exercise its options for any additional targets. Consequently, the Company was at risk with regard to whether GSK would exercise the options. Additionally, the Company 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 were not priced at a significant and incremental discount. During 2017, the two-year option period in which GSK could exercise the options had expired. 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 Note 8. Collaboration and License Agreements (Continued) 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. 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 were considered substantive options as a result of the uncertainties related to the research, development and commercialization activities, and the uncertainty as to whether GSK would exercise the options. Additionally, the substantive options were not priced at a significant incremental discount. Accordingly, the substantive options were not considered deliverables at the inception of the arrangement and the associated option exercise payments were not accounted for at inception of the agreement. Furthermore, GSK did not exercise such options prior to the two-year option period expiration. 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 revenue of $0.9 million, $1.1 million and $0.1 million related to the GSK Agreement during the years ended December 31, 2017, 2016 and 2015, respectively. This revenue is classified as Alliance revenue in the accompanying statements of operations and comprehensive loss. There was $0.5 million of deferred revenue related to the GSK Agreement at December 31, 2017 all classified within the current portion of deferred revenue in the accompanying balance sheet. 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. 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 Note 8. Collaboration and License Agreements (Continued) in Abbott Molecular incurring additional costs. The Company incurred approximately $0.8 million, $0.4 million and $0.9 million in expenses under the Abbott Molecular agreement during the years ended December 31, 2017, 2016 and 2015, respectively. In September 2016, the Company suspended internal clinical development of IMO-8400 for B-cell lymphomas. However, the Company has maintained its relationship with Abbott under the agreement as the Company may explore potential collaborative alliances to support the development of IMO-8400 for B-cell lymphomas.

Stockholders' Equity

12 Months Ended

Dec. 31, 2017

Stockholders' Equity

Stockholders' Equity

Note 9. Stockholders’ Equity

Preferred Stock

The Restated Certificate of Incorporation, as amended, 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, 2017, the Company has designated 1,500,000 shares as Series A convertible preferred stock.

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. 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 convertible 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 convertible 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, 2017 and 2016, there were 655 shares of Series A convertible preferred stock outstanding.

Common Stock

Common Stock Authorized

As of December 31, 2017, the Company had 280,000,000 shares of common stock authorized. In January 2018, the Company’s stockholders approved an amendment to the Company’s Restated Certificate of Incorporation, as amended, in connection with the Company’s proposed reverse stock split, as more fully described in Note 17.

As of December 31, 2017, the Company had 78,662,283 shares of common stock reserved for the issuance upon the exercise of outstanding warrants and options to purchase common stock, the conversion of Series A convertible preferred stock, shares available for grant under the Company’s 2013 Stock Incentive Plan and shares available for purchase under the Company’s 2017 Employee Stock Purchase Plan.

Put Shares

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

Note 9. Stockholders’ Equity (Continued)

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, 2017, 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.

Equity Financings

October 2017 Follow-on Underwritten Public Offering

On October 30, 2017, the Company closed a follow-on underwritten public offering, in which it sold 33,333,334 shares of common stock at a price to the public of $1.50 per share for aggregate gross proceeds of $50.0 million (“2017 Offering”). On November 1, 2017, the Company sold an additional 5,000,000 shares of common stock pursuant to the exercise in full of the underwriters’ 30-day option to purchase additional shares of the Company’s common stock at the public offering price less the underwriting discount. The net proceeds to the Company from the 2017 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 $53.7 million.

Baker Brothers, which is affiliated with two of the Company’s directors, participated in the 2017 Offering and purchased 8,000,000 shares of the Company’s common stock at the price offered to the public.

October 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 a total of 5,125,000 shares in this offering at the $2.00 per share purchase price.

February 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.

Common Stock Warrants

In connection with various financing transactions, the Company has issued warrants to purchase shares of the Company’s common stock. The Company accounts for common stock warrants as equity instruments, derivative liabilities, or liabilities, depending on the specific terms of the warrant agreement. As of December 31, 2017 and 2016, all of the Company’s outstanding common stock warrants were equity-classified.

Note 9. Stockholders’ Equity (Continued)

The following table summarizes outstanding warrants to purchase shares of the Company’s common stock as of December 31, 2017 and 2016:


	Number of Shares
	December 31,		Weighted-Average
Description	2017	2016	Exercise Price		Expiration Date
Issued in Series E Preferred Stock financing	—	7,252,081	$	0.70	Nov 2017
Issued in May 2013 financing	21,606,327	22,306,327		0.47	May 2018
Issued in May 2013 financing (pre-funded)	15,816,327	15,816,327		0.01	May 2020
Issued in September 2013 financing	4,175,975	4,175,975		0.01	Sep 2020
Issued in February 2014 financing (pre-funded)	2,158,750	2,158,750		0.01	Feb 2021
Total	43,757,379	51,709,460

The table below is a summary of the Company's warrant activity for the year ended December 31, 2017.


	Number of	Weighted-Average
	Warrants	Exercise Price
Outstanding at December 31, 2016	51,709,460	$	0.31
Issued	—		—
Exercised (1)	(7,952,081)		0.68
Expired	—		—
Outstanding at December 31, 2017	43,757,379	$	0.24

(1)

During the year ended December 31, 2017, certain related parties exercised warrants as more fully described in Note 14.

Stock-based Compensation

12 Months Ended

Dec. 31, 2017

Stock-based Compensation

Stock-based Compensation

Note 10. Stock-based Compensation

As of December 31, 2017, the only equity compensation plans from which the Company may currently issue new awards are the Company’s 2013 Stock Incentive Plan (as amended to date, the “2013 Plan”) and 2017 Employee Stock Purchase Plan (the “2017 ESPP”), each as more fully described below.

Equity Incentive Plans

2013 Stock Incentive Plan

The Company's board of directors adopted the 2013 Plan, which was approved by the Company’s stockholders effective July 26, 2013. The 2013 Plan is intended to further align the interests of the Company and its stockholders with its employees, including its officers, non-employee directors, consultants and advisers by providing equity-based incentives. The 2013 Plan allows for the issuance of up to such number of shares of the Company’s common stock as equal to (a) 25,224,460 shares of common stock; plus (b) such additional number of shares of common stock (up to 6,946,978 shares) as is equal to the sum of the number of shares of common stock subject to awards granted under the Company’s 2005 Stock Incentive Plan (the “2005 Plan”) or the Company’s 2008 Stock Incentive Plan (the “2008 Plan” and, together with the 2005 Plan, the “Existing Plans”) which awards expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right (subject, however, in the case of Incentive Stock Options to any limitations of the Internal Revenue Code).

Note 10. Stock-based Compensation (Continued)

Under the 2013 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 one to four years, and expire no later than 10 years from the date of grant. 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, 2017, options to purchase a total of 13,524,763 shares of common stock were outstanding and up to 13,043,817 shares of common stock remain available for grant under the 2013 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 Plan, including the Existing Plans. 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, 2017, options to purchase a total of 4,452,437 shares of common stock were outstanding under these earlier plans.

In addition, as of December 31, 2017, non-statutory stock options to purchase an aggregate of 3,425,000 shares of common stock were outstanding that were issued outside of the 2013 Plan to certain employees in 2017, 2015 and 2014 pursuant to the Nasdaq inducement grant exception as a material component of new hires’ employment compensation.

Employee Stock Purchase Plans

1995 Employee Stock Purchase Plan

The Company’s 1995 Employee Stock Purchase Plan (the “1995 ESPP”), as amended, provided for the issuance of up to 500,000 shares of common stock to participating employees of the Company or its subsidiaries. The 1995 ESPP was terminated effective August 31, 2017 as a result of the adoption by the Board and approval of shareholders of the 2017 ESPP, as described below.

2017 Employee Stock Purchase Plan

In March 2017, the Board adopted the 2017 ESPP which was approved by the Company’s stockholders and became effective June 7, 2017. The 2017 ESPP 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. As of December 31, 2017, 456,961 shares remained available for issuance.

Stock Purchase Plan Administration

The 1995 ESPP provided for and 2017 ESPP provides for offerings to employees to purchase common stock with offerings beginning on dates determined by the compensation committee of the Board or on the first business day thereafter. Each offering begins a “plan period” during which payroll deductions are to be made and held for the purchase of common stock at the end of the plan period. The compensation committee may, at its discretion, choose a plan period of 12 months or less for subsequent offerings and/or choose a different commencement date for offerings. During each plan period participating employees may elect to have a portion of their compensation, ranging from 1% to 10% of compensation as defined by the plan, withheld and used for the purchase of common stock at the end of each plan period. The purchase price is equal to 85% of the lower of the fair market value of a share of common stock on the first trading date of each plan period or the fair market value of a share of common stock on the last trading day of the plan period, and is limited by participant to $25,000 in fair value of common stock per year as well as other quarterly plan limitations as defined by each plan.

Note 10. Stock-based Compensation (Continued)

For the years ended December 31, 2017, 2016 and 2015, the Company issued 174,972, 121,460, and 27,951 shares of common stock, respectively, under the Company’s employee stock purchase plans and recognized $0.2 million, $0.1 million and less than $0.1 million, respectively, in related stock-based compensation expense.

Accounting for Stock-based Compensation

The Company recognizes non-cash compensation expense for stock-based awards based on their grant date fair value, determined using the Black-Scholes option-pricing model. During the years ended December 31, 2017, 2016 and 2015, the weighted average fair market value of stock options granted was $1.01, $1.75 and $2.51, respectively.

Total stock-based compensation expense attributable to share-based payments made to employees and directors and included in operating expenses in the Company's statements of operations for the years ended December 31, 2017, 2016 and 2015 was as follows:


(in thousands)	2017		2016		2015
Stock-based Compensation:
Research and development	$	6,494	$	2,719	$	1,688
General and administrative		4,226		4,128		3,754
Total stock-based compensation expense	$	10,720	$	6,847	$	5,442

The 2017 charge to research and development expense includes approximately $4.3 million of additional stock-based compensation recognized as a result of modifications to previously issued stock option awards in connection with the resignation of an executive.

The 2015 charge to general and administrative expense includes approximately $0.3 million of additional stock-based compensation as a result of modifications to previously issued stock option awards in connection with the retirement of a director.

Assumptions Used in Determining Fair Value of Stock Options

Inherent in the Black-Scholes option-pricing model are the following assumptions:

Volatility. The Company estimates stock price volatility based on the Company’s historical stock price performance over a period of time that matches the expected term of the stock options.

Risk-free interest rate. The risk-free interest rate is based on the U.S. Treasury yield curve in effect at the time of grant commensurate with the expected term assumption.

Expected term. The expected term of stock options granted is based on an estimate of when options will be exercised or cancelled in the future.

Dividend rate. The dividend rate is based on the historical rate, which the Company anticipates will remain at zero.

Forfeitures. 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. See Note 2.

The fair value of each option award at the date of grant was estimated using the Black-Scholes option pricing model. All options granted during the three years in the period ended December 31, 2017 were granted at exercise prices equal to the fair market value of the common stock on the dates of grant.

Note 10. Stock-based Compensation (Continued)

The following weighted average assumptions apply to the options to purchase 4,216,500, 3,346,250, and 3,533,250 shares of common stock granted to employees and directors during the years ended December 31, 2017, 2016 and 2015, respectively:




	2017		2016		2015
Average risk free interest rate		1.7%		1.4%		1.4%
Expected dividend yield		—		—		—
Expected lives (years)		4.0		4.2		4.2
Expected volatility		86%		93%		93%
Weighted average exercise price (per share)	$	1.62	$	2.64	$	3.74

Stock Option Activity

The following table summarizes stock option activity for the years ended December 31, 2017, 2016 and 2015.


				Weighted-Average
				Remaining	Aggregate
	Stock	Weighted-Average		Contractual Life	Intrinsic
($ in thousands, except share and per share data)	Options	Exercise Price		(in years)	Value
Outstanding at December 31, 2014	16,950,988	$	3.56
Granted	3,533,250		3.74
Exercised	(405,025)		1.44
Forfeited	(2,518,107)		3.81
Expired	(1,300,354)		5.65
Outstanding at December 31, 2015	16,260,752	$	3.45	7.7	$	8,274
Granted	3,346,250		2.64
Exercised	—		—
Forfeited	(878,579)		3.15
Expired	(726,903)		3.85
Outstanding at December 31, 2016	18,001,520	$	3.30	7.1	$	1,648
Granted	4,216,500		1.62
Exercised	(18,250)		2.04
Forfeited	(460,319)		2.39
Expired	(337,251)		6.22
Outstanding at December 31, 2017 (1)	21,402,200	$	2.94	6.5	$	5,805
Exercisable at December 31, 2017	13,748,469	$	3.25	5.5	$	3,708

(1)

Includes both vested stock options as well as unvested stock options for which the requisite service period has not been rendered but that are expected to vest based on achievement of a service condition.

The fair value of options that vested during 2017, 2016 and 2015 amounted to $7.3 million, $6.9 million and $5.4 million, respectively. As of December 31, 2017, there was $9.1 million of unrecognized compensation cost related to unvested options, which the Company expects to recognize over a weighted average period of 2.0 years.

Commitments and Contingencies

12 Months Ended

Dec. 31, 2017

Commitments and Contingencies

Commitments and Contingencies

Note 11. Commitments and Contingencies

Lease Commitments

The Company leases its facilities in Cambridge, Massachusetts and Exton, Pennsylvania. During 2017, 2016 and 2015, rent expense, including real estate taxes, was $2.4 million, $1.9 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, 2017 and 2016. The leases are classified as operating leases.

Future minimum commitments as of December 31, 2017 under the Company’s lease agreements are approximately:



December 31,	Operating Leases
	(In thousands)
2018	$	2,024
2019		2,084
2020		2,018
2021		1,984
2022		1,348
	$	9,458

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 including a 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.

Income Taxes

12 Months Ended

Dec. 31, 2017

Income Taxes

Income Taxes

Note 12. Income Taxes

In December 2017, the Tax Cuts and Jobs Act (“TCJA”) was signed into law. Among other things, the TCJA permanently lowers the corporate federal income tax rate to 21% from the existing maximum rate of 35%, effective for tax years including or commencing January 1, 2018. As a result of the reduction of the corporate federal income tax rate to 21%, GAAP requires companies to revalue their deferred tax assets and deferred tax liabilities as of the date of enactment, with the resulting tax effects accounted for in the reporting period of enactment. This revaluation resulted in a provision of $27.6 million to income tax expense in and a corresponding reduction in the valuation allowance. As a result, there was no impact to the Company’s statement of operations and comprehensive loss as a result of reduction in tax rates. The Company’s preliminary estimate of the TCJA and the remeasurement of its deferred tax assets and liabilities is subject to the finalization of management’s analysis related to certain matters, such as developing interpretations of the provisions of the TCJA, changes to certain estimates and the filing of the Company’s tax returns. U.S. Treasury regulations, administrative interpretations or court decisions interpreting the TCJA may require further adjustments and changes in the Company’s estimates. The final determination of the TCJA and the remeasurement of the Company’s deferred assets and liabilities will be completed as additional information becomes available, but no later than one year from the enactment of the TCJA.

Certain provisions from the Tax Reform Act of 1986 were not impacted by TCJA, such as those limiting 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, 2017, 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 2017, the Company completed a study which determined that a cumulative three-year ownership change in excess of 50% had occurred in February 2015. The 2017 and 2016 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.

Note 12. Income Taxes (Continued)

As of December 31, 2017, the Company had cumulative federal and state NOLs of approximately $200.4 million and $177.0 million available to reduce federal and state taxable income, respectively. These NOLs expire through 2037. In addition, at December 31, 2017, the Company had cumulative federal and state tax credit carryforwards of $12.7 million and $1.8 million available to reduce federal and state income taxes, respectively, which expire through 2037 and 2032, respectively.

As of December 31, 2017 and 2016, the components of the deferred tax assets are approximately as follows:


	2017		2016
	(In thousands)
Operating loss carryforwards	$	53,276	$	56,832
Tax credit carryforwards		14,099		9,428
Other		7,552		7,710
Total deferred tax assets		74,927		73,970
Valuation allowance		(74,927)		(73,970)
Net deferred tax assets	$	—	$	—

The Company has provided a full valuation allowance for its deferred tax asset due to the uncertainty surrounding the ability to realize these assets.

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, 2017, 2016 and 2015:


	2017		2016		2015
Expected federal income tax rate	(34.0)	%	(34.0)	%	(34.0)	%
Expiring credits and NOLs	—		—		—
Change in valuation allowance	0.9		42.2		39.8
Federal and state credits	(6.9)		(9.9)		(7.4)
State income taxes, net of federal benefit	(3.7)		(3.7)		(4.5)
Permanent differences	2.4		3.5		2.4
Rate change related to TCJA	41.9		—		—
Other	(0.6)		1.9		3.7
Effective tax rate	0.0	%	0.0	%	0.0	%

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, 2017 and 2016.

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, Massachusetts and Pennsylvania jurisdictions. The Company is no longer subject to tax examinations for years before 2014, except to the extent that it utilizes NOLs or tax credit carryforwards that originated before 2014. 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 statements of operations and comprehensive loss as general and administrative expense.

Employee Benefit Plan	12 Months Ended
Employee Benefit Plan	Dec. 31, 2017
Employee Benefit Plan
Employee Benefit Plan	Note 13. 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, $0.3 million and $0.2 million of 401(k) benefits were charged to operating expenses during 2017, 2016 and 2015, respectively.

Related Party Transactions	12 Months Ended
Related Party Transactions	Dec. 31, 2017
Related Party Transactions
Related Party Transactions	Note 14. Related Party Transactions Overview of Related Parties Youssef El Zein, a member of the Company’s Board until his resignation in October 2017, is a director and controlling stockholder of Pillar Invest Corporation (“Pillar Invest”), which is the general partner of Pillar Pharmaceuticals I, L.P. (“Pillar I”), Pillar Pharmaceuticals II, L.P. (“Pillar II”), Pillar Pharmaceuticals III, L.P. (“Pillar III”), Pillar Pharmaceuticals IV, L.P. (“Pillar IV”) and Pillar Pharmaceuticals V, L.P. (“Pillar V”) and limited partner of Pillar I, Pillar II, Pillar III, Pillar IV and Pillar V. Entities affiliated with Pillar Invest and Participations Besancon (“Besancon”), an investment fund advised by Pillar Invest having no affiliation with Mr. El Zein, Pillar I, Pillar II, Pillar III, Pillar IV, Pillar V or Pillar Invest (collectively, the “Pillar Investment Entities”), own approximately 13.1% of the Company's common stock as of December 31, 2017. Julian C. Baker, a member of the Company’s Board, is a principal of Baker Bros. Advisors LP. Baker Bros. Advisors LP, and certain of its affiliated funds, owned approximately 9.4% of the Company's common stock as of December 31, 2017. Additionally, one of the Company’s directors, Kelvin M. Neu, is an employee of Baker Bros. Advisors LP as of December 31, 2017. Pillar Investment Entities During 2017, Pillar II exercised 5,034,061 warrants to purchase shares of the Company’s common stock at a total exercise price of approximately $3.5 million and Besancon exercised 2,918,020 warrants to purchase shares of the Company’s common stock at a total exercise price of approximately $1.9 million. The warrant exercise prices had been established at the time that the warrants were purchased. During 2016, Pillar I exercised 1,370,000 warrants to purchase shares of the Company’s common stock at a total exercise price of approximately $2 million. The warrant exercise prices had been established at the time that the warrants were purchased. Additionally during 2016, investment funds affiliated with Pillar Invest Corporation purchased shares of the Company’s common stock in connection with the 2016 Offering as more fully described in Note 9. During 2015, Pillar II exercised 232,759 warrants to purchase shares of the Company’s common stock at a total exercise price of approximately $0.2 million and Pillar III exercised 2,600,000 warrants to purchase shares of the Company’s common stock at a total exercise price of approximately $1.2 million. The warrant exercise prices had been established at the time that the warrants were purchased. As of December 31, 2017, Besancon held warrants to purchase up to 1,200,000 shares of the Company’s common stock at an exercise price of $0.47 per share. Baker Brothers During 2017, 2016 and 2015, Baker Brothers purchased shares of the Company’s common stock in connection with underwritten public offerings of shares of the Company’s common stock as more fully described in Note 9. As of December 31, 2017, Baker Brothers held 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. Note 14. Related Party Transactions (Continued) Board Fees Paid in Stock Pursuant to the Company’s director compensation program, in lieu of director board and committee fees of approximately $0.1 million, $0.2 million, and $0.1 million incurred during the years ended December 31, 2017, 2016 and 2015, respectively, the Company issued 62,939, 101,239, and 40,934 shares of common stock, respectively, to certain of its directors. Director board and committee fees are paid in arrears and the number of shares issued was calculated based on the market closing price of the Company’s common stock on the issuance date.

Net Loss per Common Share Applicable to Common Stockholders	12 Months Ended
	Dec. 31, 2017
Net Loss per Common Share Applicable to Common Stockholders
Net Loss per Common Share Applicable to Common Stockholders	Note 15. Net Loss per Common Share Applicable to Common Stockholders Basic and diluted net loss per common share applicable to common stockholders is calculated by dividing net loss applicable to common stockholders by the weighted-average number of shares of common stock outstanding during the period, without consideration of common stock equivalents. The Company’s potentially dilutive shares, which include outstanding stock option awards, common stock warrants and convertible preferred stock, are considered to be common stock equivalents and are only included in the calculation of diluted net loss per share when their effect is dilutive. For the years ended December 31, 2017, 2016 and 2015, diluted net loss per common share applicable to common stockholders was 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 that were excluded from the calculation of diluted net loss per share, due to their anti-dilutive effect, were 65,161,505, 69,712,906 and 70,782,788 as of December 31, 2017, 2016 and 2015, respectively, and consisted of stock options, preferred stock and warrants.

Supplemental Disclosure of Cash Flow Information

12 Months Ended

Dec. 31, 2017

Supplemental Disclosure of Cash Flow Information

Supplemental Disclosure of Cash Flow Information

Note 16. Supplemental Disclosure of Cash Flow Information

Supplemental disclosure of cash flow information for the periods presented is as follows:


	Year Ended December 31,
	2017		2016		2015
	(In thousands)
Supplemental disclosure of cash flow information:
Cash paid for interest	$	42	$	72	$	93
Supplemental disclosure of non-cash financing and investing activities:
Non-cash property additions	$	150	$	425	$	123
Accrued financing transaction costs	$	17	$	166	$	—

Subsequent Events	12 Months Ended
Subsequent Events	Dec. 31, 2017
Subsequent Events
Subsequent Events	17. 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. Reverse Stock Split Proposal On January 4, 2018, the Company’s stockholders approved an amendment to the Company’s Restated Certificate of Incorporation, as amended, to effect a reverse stock split of the Company’s issued and outstanding common stock by a whole number ratio of not less than 1-for-4 and not more than 1-for-8, such ratio and the implementation and timing of such reverse stock split to be determined in the discretion of the Board at any time prior to the Company’s 2018 annual meeting of stockholders, and, in connection therewith, to decrease the number of authorized shares of the Company’s common stock on a basis proportional to the reverse stock split ratio. The Company’s stockholders also approved an amendment to the Company’s Restated Certificate of Incorporation, as amended, to set the number of authorized shares of the Company’s common stock at a number determined by calculating the product of 280,000,000 multiplied by two times (2x) the reverse stock split ratio. 17. Subsequent Events (Continued) Agreement and Plan of Merger On January 21, 2018, the Company, BioCryst Pharmaceuticals, Inc., a Delaware corporation (“BioCryst”), Nautilus Holdco, Inc., a Delaware corporation and a direct, wholly owned subsidiary of BioCryst (“Holdco”), Island Merger Sub, Inc., a Delaware corporation and a direct, wholly owned subsidiary of Holdco (“Merger Sub A”), and Boat Merger Sub, Inc., a Delaware corporation and a direct, wholly owned subsidiary of Holdco (“Merger Sub B”), entered into an Agreement and Plan of Merger (the “Merger Agreement”). Pursuant to the Merger Agreement, and subject to the satisfaction or waiver of the conditions specified therein, (a) Merger Sub A will be merged with and into Idera (the “Idera Merger”), with Idera surviving as a wholly owned subsidiary of Holdco, and (b) Merger Sub B will be merged with and into BioCryst (the “BioCryst Merger”, and, together with the Idera Merger, the “Mergers”), with BioCryst surviving as a wholly owned subsidiary of Holdco. Holdco will be renamed prior to the closing of the Mergers. Under the terms of the Merger Agreement, each share of BioCryst common stock will be exchanged for 0.50 shares of the new company stock and each share of Idera common stock will be exchanged for 0.20 shares of the new company stock. The exchange ratio reflects an “at market” combination based upon the approximate 30-day average volume weighted trading prices for each company. On a proforma, fully diluted basis, giving effect to all dilutive stock options, units and warrants, BioCryst stockholders will own 51.6 percent of the stock of the combined company and Idera stockholders will own 48.4 percent. The board of directors of each of Idera and BioCryst has unanimously approved the Merger Agreement and the transactions contemplated thereby. The transaction is subject to approval by the stockholders of both companies, as well as regulatory approvals and satisfaction of other customary closing conditions. A significant stockholder of each company has agreed to enter into a voting and support agreement and has agreed to vote in favor of the transaction. This stockholder owns approximately 9% of Idera shares outstanding and approximately 14% of BioCryst shares outstanding.

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2017

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”).

Use of Estimates

Segment Information

Financial Instruments

Concentration of Credit Risk

Cash and Cash Equivalents

Restricted Cash

Investments

Property and Equipment

Impairment of Long-Lived Assets

Revenue Recognition

The Company recognizes revenue in accordance with the 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.

Alliance Revenues

See Note 8, “Collaboration and License Agreements” for additional details surrounding the Company’s collaboration arrangements.

Note 2. Summary of Significant Accounting Policies (Continued)

The Company’s multiple element revenue arrangements may include the following:

Note 2. Summary of Significant Accounting Policies (Continued)

Research and Development Expenses

Stock-Based Compensation

Income Taxes

Net Loss per Common Share applicable to Common Stockholders

Comprehensive Income (Loss)

New Accounting Pronouncements

Recently Adopted Accounting Pronouncements

Note 2. Summary of Significant Accounting Policies (Continued)

Recently Issued (Not Yet Adopted) Accounting Pronouncements

Accounting for Uncertainty in Income Taxes

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2017

Summary of Significant Accounting Policies

Schedule of weighted average assumptions applied to options




	2017		2016		2015
Average risk free interest rate		1.7%		1.4%		1.4%
Expected dividend yield		—		—		—
Expected lives (years)		4.0		4.2		4.2
Expected volatility		86%		93%		93%
Weighted average exercise price (per share)	$	1.62	$	2.64	$	3.74

Schedule of assets and liabilities measured and recorded in financial statements at fair value on a recurring basis



	December 31, 2017
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	66,183	$	66,183	$	—	$	—
Total Assets	$	66,183	$	66,183	$	—	$	—
Total Liabilities	$	—	$	—	$	—	$	—


	December 31, 2016
(In thousands)	Total		Level 1		Level 2		Level 3
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	$	—	$	—	$	—	$	—

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2017

Fair Value Measurements

Schedule of assets and liabilities measured and recorded in financial statements at fair value on a recurring basis



	December 31, 2017
(In thousands)	Total		Level 1		Level 2		Level 3
Assets
Money market funds	$	66,183	$	66,183	$	—	$	—
Total Assets	$	66,183	$	66,183	$	—	$	—
Total Liabilities	$	—	$	—	$	—	$	—


	December 31, 2016
(In thousands)	Total		Level 1		Level 2		Level 3
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)

12 Months Ended

Dec. 31, 2017

Investments

Schedule of available-for-sale investments at fair value


	December 31, 2016
			Gross		Gross		Estimated
			Unrealized		Unrealized		Fair
(In thousands)	Cost		(Losses)		Gains		Value
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)

12 Months Ended

Dec. 31, 2017

Property and Equipment

Schedule of net property and equipment at cost


	December 31,
(In thousands)	2017		2016
Leasehold improvements	$	671	$	671
Laboratory equipment and other		5,261		5,127
Total property and equipment, at cost		5,932		5,798
Less: Accumulated depreciation and amortization		4,460		3,945
Property and equipment, net	$	1,472	$	1,853

Accrued Expenses (Tables)

12 Months Ended

Dec. 31, 2017

Accrued Expenses

Schedule of accrued expenses


	December 31,
(In thousands)	2017		2016
Payroll and related costs	$	3,108	$	2,498
Clinical and nonclinical trial expenses		3,495		3,577
Professional and consulting fees		1,317		840
Equipment purchase		—		368
Other		80		111
	$	8,000	$	7,394

Stockholders' Equity (Tables)

12 Months Ended

Dec. 31, 2017

Stockholders' Equity

Schedule of warrants outstanding and exercisable for purchase of common stock


	Number of Shares
	December 31,		Weighted-Average
Description	2017	2016	Exercise Price		Expiration Date
Issued in Series E Preferred Stock financing	—	7,252,081	$	0.70	Nov 2017
Issued in May 2013 financing	21,606,327	22,306,327		0.47	May 2018
Issued in May 2013 financing (pre-funded)	15,816,327	15,816,327		0.01	May 2020
Issued in September 2013 financing	4,175,975	4,175,975		0.01	Sep 2020
Issued in February 2014 financing (pre-funded)	2,158,750	2,158,750		0.01	Feb 2021
Total	43,757,379	51,709,460

Summary of warrant activity


	Number of	Weighted-Average
	Warrants	Exercise Price
Outstanding at December 31, 2016	51,709,460	$	0.31
Issued	—		—
Exercised (1)	(7,952,081)		0.68
Expired	—		—
Outstanding at December 31, 2017	43,757,379	$	0.24

During the year ended December 31, 2017, certain related parties exercised warrants as more fully described in Note 14.

- Definition

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2017

Stock-Based Compensation

Schedule of stock-based compensation expense attributable to share-based payments made to employees and directors and included in operating expenses


(in thousands)	2017		2016		2015
Stock-based Compensation:
Research and development	$	6,494	$	2,719	$	1,688
General and administrative		4,226		4,128		3,754
Total stock-based compensation expense	$	10,720	$	6,847	$	5,442

Schedule of weighted average assumptions applied to options




	2017		2016		2015
Average risk free interest rate		1.7%		1.4%		1.4%
Expected dividend yield		—		—		—
Expected lives (years)		4.0		4.2		4.2
Expected volatility		86%		93%		93%
Weighted average exercise price (per share)	$	1.62	$	2.64	$	3.74

Schedule of information related to outstanding and exercisable options


				Weighted-Average
				Remaining	Aggregate
	Stock	Weighted-Average		Contractual Life	Intrinsic
($ in thousands, except share and per share data)	Options	Exercise Price		(in years)	Value
Outstanding at December 31, 2014	16,950,988	$	3.56
Granted	3,533,250		3.74
Exercised	(405,025)		1.44
Forfeited	(2,518,107)		3.81
Expired	(1,300,354)		5.65
Outstanding at December 31, 2015	16,260,752	$	3.45	7.7	$	8,274
Granted	3,346,250		2.64
Exercised	—		—
Forfeited	(878,579)		3.15
Expired	(726,903)		3.85
Outstanding at December 31, 2016	18,001,520	$	3.30	7.1	$	1,648
Granted	4,216,500		1.62
Exercised	(18,250)		2.04
Forfeited	(460,319)		2.39
Expired	(337,251)		6.22
Outstanding at December 31, 2017 (1)	21,402,200	$	2.94	6.5	$	5,805
Exercisable at December 31, 2017	13,748,469	$	3.25	5.5	$	3,708

(1)

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2017

Commitments and Contingencies

Schedule of future minimum commitments under company lease agreements



December 31,	Operating Leases
	(In thousands)
2018	$	2,024
2019		2,084
2020		2,018
2021		1,984
2022		1,348
	$	9,458

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2017

Income Taxes

Schedule of components of deferred tax assets


	2017		2016
	(In thousands)
Operating loss carryforwards	$	53,276	$	56,832
Tax credit carryforwards		14,099		9,428
Other		7,552		7,710
Total deferred tax assets		74,927		73,970
Valuation allowance		(74,927)		(73,970)
Net deferred tax assets	$	—	$	—

Schedule of difference between U.S. federal corporate tax rate and Company effective tax rate


	2017		2016		2015
Expected federal income tax rate	(34.0)	%	(34.0)	%	(34.0)	%
Expiring credits and NOLs	—		—		—
Change in valuation allowance	0.9		42.2		39.8
Federal and state credits	(6.9)		(9.9)		(7.4)
State income taxes, net of federal benefit	(3.7)		(3.7)		(4.5)
Permanent differences	2.4		3.5		2.4
Rate change related to TCJA	41.9		—		—
Other	(0.6)		1.9		3.7
Effective tax rate	0.0	%	0.0	%	0.0	%

Supplemental Disclosure of Cash Flow Information (Tables)

12 Months Ended

Dec. 31, 2017

Supplemental Disclosure of Cash Flow Information

Schedule of supplemental disclosure of cash flow information


	Year Ended December 31,
	2017		2016		2015
	(In thousands)
Supplemental disclosure of cash flow information:
Cash paid for interest	$	42	$	72	$	93
Supplemental disclosure of non-cash financing and investing activities:
Non-cash property additions	$	150	$	425	$	123
Accrued financing transaction costs	$	17	$	166	$	—

Business and Organization (Details) $ in Thousands	12 Months Ended
Business and Organization (Details) $ in Thousands	Dec. 31, 2017 USD ($) item	Dec. 31, 2016 USD ($)
Business and Organization
Number of technology platforms to develop drug candidates \| item	2
Accumulated deficit \| $	$ 604,494	$ 538,470

Summary of Significant Accounting Policies - Additional Information (Details) $ in Thousands	12 Months Ended			36 Months Ended
	Dec. 31, 2017 USD ($) segment item	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2017 USD ($)
Accounting Policies
Number of operating segments \| segment	1
Number of financial institutions \| item	2
Restricted cash and other assets	$ 324	$ 334		$ 324
Held-to-maturity investments	0	0		0
Realized gains or losses from available-for-sale securities	0	0	$ 0
Losses from investments				0
Impairment expense recognized	0	0	0
Stock-based compensation	10,720	6,847	5,442
Remaining performance obligation	0
Uncertain tax positions	0	0	$ 0	0
Prepaid expenses research and development	$ 2,600	$ 1,400		$ 2,600
Employees
Accounting Policies
Stock options, vesting period	4 years
Board of Director
Accounting Policies
Stock options, vesting period	1 year
Minimum
Accounting Policies
Equipment depreciation period	3 years
Stock options, vesting period	3 years
Maximum
Accounting Policies
Equipment depreciation period	5 years
Stock options, vesting period	4 years

Summary of Significant Accounting Policies - New Accounting Pronouncements (Details) $ in Millions		1 Months Ended
	Jan. 01, 2017 USD ($)	Feb. 29, 2016	May 31, 2014 agreement
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
Effect of recently adopted accounting pronouncements	$ 1.4
Accounting Standards Update 2016-09 \| Additional Paid-in Capital
New Accounting Pronouncements or Change in Accounting Principle
Effect of recently adopted accounting pronouncements	$ 0.1
Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle
Number of performance obligations \| agreement			1

Fair Value Measurements - Transfers Between Levels (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Fair Value Measurements
Fair value of assets transfers from level 1 to level 2	$ 0	$ 0	$ 0
Fair value of assets transfers from level 2 to level 1	0	0	0
Fair value of liabilities transfers from level 1 to level 2	0	0	0
Fair value of liabilities transfers from level 2 to level 1	0	0	0
Fair value of assets transfers into level 3	0	0	0
Fair value of assets transfers out of level 3	0	0	0
Fair value of liabilities transfers into level 3	0	0	0
Fair value of liabilities transfers out of level 3	$ 0	$ 0	$ 0

Fair Value Measurements - Assets and Liabilities at Fair Value on Recurring Basis (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Short-term investments		$ 28,347
Fair value on a recurring basis
Fair Value of Assets and Liabilities Measured at Fair Value on a Recurring Basis
Money market funds	$ 66,183	67,580
Total Assets	66,183	95,927
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		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
Money market funds	66,183	67,580
Total Assets	$ 66,183	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		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		$ 8,618

Investments - Summary of Available-for-Sale Investments at Fair Value (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Schedule of Available-for-sale Securities
Cost		$ 28,364
Gross Unrealized (Losses)		(17)
Estimated Fair Value	$ 0	28,347
Estimated Fair Value - Short-term investments		28,347
Short-term investments
Schedule of Available-for-sale Securities
Cost		28,364
Gross Unrealized (Losses)		(17)
Estimated Fair Value		28,347
Short-term investments \| Corporate bonds
Schedule of Available-for-sale Securities
Cost		19,740
Gross Unrealized (Losses)		(11)
Estimated Fair Value		19,729
Short-term investments \| Municipal bonds
Schedule of Available-for-sale Securities
Cost		8,624
Gross Unrealized (Losses)		(6)
Estimated Fair Value		$ 8,618

Investments - Additional Information (Details) - USD ($) $ in Thousands	36 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Investments
Available-for-sale investments	$ 0	$ 28,347
Losses from investments	$ 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	Dec. 31, 2017	Dec. 31, 2016
Property, Plant and Equipment
Total property and equipment, at cost	$ 5,932	$ 5,798
Less: accumulated depreciation and amortization	4,460	3,945
Property and equipment, net	1,472	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	$ 5,261	$ 5,127

Property and Equipment - Depreciation and Amortization Expense (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Property and Equipment
Depreciation and amortization expense on property and equipment	$ 0.7	$ 0.6	$ 0.5

Accrued Expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Payroll and related costs	$ 3,108	$ 2,498
Clinical and nonclinical trial expenses	3,495	3,577
Cost of regaining rights to cancer program	1,317	840
Professional and consulting fees		368
Other	80	111
Total accrued expenses	8,000	$ 7,394
Former Executive
Payroll and related costs	600
Salary continuation severance benefits	900
Long-term portion of other liabilities	$ 300

Note Payable (Details) $ in Thousands	12 Months Ended	15 Months Ended
Note Payable (Details) $ in Thousands	Dec. 31, 2017 USD ($) installment	Dec. 31, 2015 USD ($)	Dec. 31, 2016 USD ($)
Debt Instrument
Current portion of note payable	$ 209		$ 292
Advance received under loan and security agreement	$ 900
Oxford
Debt Instrument
Borrowing capacity under the loan and security agreement		$ 3,000
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%
Current portion of note payable	$ 200
Maximum prepayment fee interest rate percentage	3.00%
Outstanding loan balance, default interest rate	5.00%
Oxford \| Three months US LIBOR
Debt Instrument
Basis spread on fixed interest rate set at time of advance		7.27%
Description of interest rate	three-month U.S. Libor Rate

Collaboration and License Agreements (Details) $ in Thousands	1 Months Ended			3 Months Ended	12 Months Ended
	Nov. 30, 2016 USD ($) director	Nov. 30, 2015 USD ($) item person	May 31, 2014 USD ($)	Jun. 30, 2017	Dec. 31, 2017 USD ($) item	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Remaining performance obligation					$ 0
Number of board director seats held \| director	2
Total number of board director seats \| director	7
Number of common board of directors \| director	0
Collaboration revenue					902	$ 16,199	$ 249
Current portion of deferred revenue					566	1,111
long-term deferred revenue						152
Expenses					67,369	54,956	49,095
Baker Bros. Advisors LP
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Common stock ownership percentage under the collaboration agreement	7.00%
Abbott Molecular
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Paid or expects to pay for external development expenses			$ 6,700
Expenses					800	400	900
Expected agreement term			5 years
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%
Deferred revenue					$ 900	1,100	100
Expected agreement term		27 months
Revised, increased research period				36 months
GSK Agreement \| License, Research, Clinical Development and Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 100,000			20,000
GSK Agreement \| Research and Development Plans and Designation of Development Candidates
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		9,000			1,000
GSK Agreement \| Clinical and Commercial Milestones
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments		$ 89,000			$ 17,000
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
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Number of units of accounting in connection of agreements \| item					3
Number of board director seats held \| director	2
Total number of board director seats \| director	4
Number of common board of directors \| director	0
Collaboration revenue						$ 15,000	$ 0
Vivelix \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Milestone payments	$ 140,000
Collaboration revenue					$ 100
Vivelix \| Maximum \| Back-up compounds
Collaborative Arrangements and Non-collaborative Arrangement Transactions
Anticipated initial collaboration term	3 years
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 - Preferred Stock (Details) - $ / shares	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Class of Stock
Preferred stock, shares authorized	5,000,000
Preferred stock, par value	$ 0.01
Series A Preferred Stock
Class of Stock
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, par value	$ 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
Series A preferred stock liquidation preference per share	$ 1
Series A Preferred stock conversion price per share	$ 34.00
Preferred stock, shares issued	1,000	1,000

Stockholders’ Equity - Common Stock (Details) $ / shares in Units, $ in Millions							12 Months Ended
	Nov. 01, 2017 USD ($) shares	Oct. 30, 2017 USD ($) person $ / shares shares	Oct. 28, 2016 USD ($) person $ / shares shares	Oct. 13, 2016 USD ($) $ / shares shares	Feb. 19, 2015 USD ($) person $ / shares shares	May 05, 1998 $ / shares shares	Dec. 31, 2017 $ / shares shares	Dec. 31, 2016 shares
Class of Stock
Common stock, shares authorized							280,000,000	280,000,000
Common stock, shares reserved for future issuance							78,662,283
Common Stock
Class of Stock
Stock issued (in shares)	5,000,000	33,333,334	1,225,243	25,000,000	23,000,000	1,199,684
Sale price of common shares subject to the liquidation put \| $ / shares						$ 16.00
Minimum closing sales price of common stock to issue termination notice to put holders \| $ / shares							$ 32.00
Price exceeds on number of days							20 days
Liquidation put shares no longer held by original holders							399,950
Shares held by put holders							35,780
Put Rights outstanding							0
Remaining shares of common stock subject to the liquidation put							763,954
Number of days underwriters have to purchase additional shares	30 days		30 days
Net proceeds from offering of common stock \| $	$ 53.7		$ 48.8		$ 80.6
Stock price (in dollars per share) \| $ / shares		$ 1.50		$ 2.00	$ 3.75
Gross proceeds from offering of common stock \| $		$ 50.0		$ 50.0	$ 86.3
Common Stock \| Investor
Class of Stock
Number of people \| person			2
Common Stock \| Investor \| Board of Director
Class of Stock
Stock issued (in shares)			5,125,000		5,333,333
Stock price (in dollars per share) \| $ / shares			$ 2.00		$ 3.75
Number of people \| person					2
Common Stock \| Baker Bros. Advisors LP
Class of Stock
Stock issued (in shares)		8,000,000
Number of people \| person		2

Stockholders’ Equity - Common Stock Warrants (Details) - $ / shares	Dec. 31, 2017	Dec. 31, 2016
Class of Warrant or Right
Number of Warrants	43,757,379	51,709,460
Warrant exercise price per share	$ 0.24	$ 0.31
Expiration Date - November 2017
Class of Warrant or Right
Number of Warrants		7,252,081
Warrant exercise price per share	$ 0.68	$ 0.70
Expiration Date - May 2018
Class of Warrant or Right
Number of Warrants	21,606,327	22,306,327
Warrant exercise price per share	$ 0.47	$ 0.47
Expiration Date - May 2020
Class of Warrant or Right
Number of Warrants	15,816,327	15,816,327
Warrant exercise price per share	$ 0.01	$ 0.01
Expiration Date - September 2020
Class of Warrant or Right
Number of Warrants	4,175,975	4,175,975
Warrant exercise price per share	$ 0.01	$ 0.01
Expiration Date - February 2021
Class of Warrant or Right
Number of Warrants	2,158,750	2,158,750
Warrant exercise price per share	$ 0.01	$ 0.01

Stockholders’ Equity - Common Stock Warrant Activity (Details) - $ / shares	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Class of Warrant or Right [Line Items]
Outstanding warrants, beginning of period	51,709,460
Outstanding warrants, end of period	43,757,379
Warrant exercise price per share	$ 0.24	$ 0.31
Expiration Date - November 2017
Class of Warrant or Right [Line Items]
Outstanding warrants, beginning of period	7,252,081
Exercised (1)	(7,952,081)
Warrant exercise price per share	$ 0.68	$ 0.70

Stock-based Compensation - Equity Incentive Plans (Details) - shares		12 Months Ended
	Jul. 26, 2013	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Class of Stock
Common stock, shares reserved for future issuance		78,662,283
Minimum option exercise price as a percentage of market value of common stock		100.00%
Common stock options outstanding		21,402,200	18,001,520	16,260,752	16,950,988
Options outstanding under earlier plans		4,452,437
Grant of inducement stock option		3,425,000
2013 Stock Incentive Plan
Class of Stock
Maximum number of additional common shares	6,946,978
Maximum number of shares that may be granted to any one individual in single year		1,500,000
Common stock options outstanding		13,524,763
Common shares available for grant	25,224,460	13,043,817
Minimum
Class of Stock
Stock options, vesting period		3 years
Minimum \| 2013 Stock Incentive Plan
Class of Stock
Stock options, vesting period		1 year
Maximum
Class of Stock
Stock options, vesting period		4 years
Stock options, expiration period		10 years
Maximum \| 2013 Stock Incentive Plan
Class of Stock
Stock options, vesting period		4 years
Stock options, expiration period		10 years

Stock-based Compensation - Employee Stock Purchase Plans (Details) - USD ($)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
1995 Employee Stock Purchase Plan \| Maximum
Class of Stock
Common stock shares authorized for issuance under stock purchase plan	500,000
2017 Employee Stock Purchase Plan
Class of Stock
Maximum percentage of total combined voting power or value of the stock of the Company after the grant	5.00%
Common shares available for grant	456,961
2017 Employee Stock Purchase Plan \| Maximum
Class of Stock
Common stock shares authorized for issuance under stock purchase plan	500,000
Employee Stock Purchase Plans
Class of Stock
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 fair market value of common stock for the ESPP option price	85.00%
Annual maximum a participant may purchase under the employee stock purchase plan	$ 25,000
Common stock share issued	174,972	121,460	27,951
Defined Contribution Plan, Cost	$ 200,000	$ 100,000
Employee Stock Purchase Plans \| Maximum
Class of Stock
Subsequent offering period as established by the compensation committee	12 months
Defined Contribution Plan, Cost			$ 100,000

Stock-Based Compensation - Accounting for Stock-based Compensation (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Share-based Compensation Arrangement by Share-based Payment Award
Weighted average grant date fair value of options granted during the period (per share)	$ 1.01	$ 1.75	$ 2.51
Stock-based compensation	$ 10,720	$ 6,847	$ 5,442
Research and development
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation	6,494	2,719	1,688
Research and development \| Former Executive
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation	4,300
General and administrative
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation	$ 4,226	$ 4,128	3,754
General and administrative \| Retiring Director
Share-based Compensation Arrangement by Share-based Payment Award
Stock-based compensation			$ 300

Stock-based Compensation - Assumptions Used in Determining Fair Value of Stock Options (Details) - $ / shares	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Summary of Significant Accounting Policies
Dividend rate	0.00%
Options to purchase common stock granted to employees and directors	4,216,500	3,346,250	3,533,250
Average risk free interest rate	1.70%	1.40%	1.40%
Expected lives (years)	4 years	4 years 2 months 12 days	4 years 2 months 12 days
Expected volatility	86.00%	93.00%	93.00%
Weighted average exercise price of options granted during the period (per share)	$ 1.62	$ 2.64	$ 3.74

Stock-based Compensation - Stock Option Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Stockholders' Equity
Options, Outstanding, Beginning Balance	18,001,520	16,260,752	16,950,988
Granted	4,216,500	3,346,250	3,533,250
Exercised	(18,250)		(405,025)
Forfeited	(460,319)	(878,579)	(2,518,107)
Expired	(337,251)	(726,903)	(1,300,354)
Options, Outstanding, Ending Balance	21,402,200	18,001,520	16,260,752
Exercisable, Ending Balance	13,748,469
Weighted Average Exercise Price, Beginning Balance	$ 3.30	$ 3.45	$ 3.56
Granted, Weighted Average Exercise Price	1.62	2.64	3.74
Exercised, Weighted Average Exercise Price	2.04		1.44
Forfeited, Weighted Average Exercise Price	2.39	3.15	3.81
Expired, Weighted Average Exercise Price	6.22	3.85	5.65
Weighted Average Exercise Price, Ending Balance	2.94	$ 3.30	$ 3.45
Exercisable, Weighted Average Exercise Price	$ 3.25
Outstanding, Ending balance, Weighted Average Remaining Contractual Term	6 years 6 months	7 years 1 month 6 days	7 years 8 months 12 days
Exercisable Ending Balance, Weighted Average Remaining Contractual Term	5 years 6 months
Outstanding, Intrinsic Value, Ending Balance	$ 5,805	$ 1,648	$ 8,274
Exercisable, Ending Balance, Intrinsic Value	3,708
Fair value of options, vested	7,300	$ 6,900	$ 5,400
Unrecognized compensation cost related to nonvested stock-based compensation	$ 9,100
Weighted average remaining period over which unrecognized compensation expense will be recognized	2 years

Commitments and Contingencies - Rent Expense and Lease Information (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Lease Commitments
Rent expense, including real estate taxes	$ 2.4	$ 1.9	$ 1.7
Cash restricted for a security deposit	$ 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 Contingencies - Future Minimum Commitments Under Lease Agreements (Details) $ in Thousands	Dec. 31, 2017 USD ($)
Commitments and Contingencies
2018	$ 2,024
2019	2,084
2020	2,018
2021	1,984
2022	1,348
Total	$ 9,458

Income Taxes - Tax Cuts and Jobs Act (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Corporate federal income tax rate		34.00%	34.00%	34.00%
TCJA of 2017 provisional income tax expense		$ 27.6
Forecast
Corporate federal income tax rate	21.00%
Maximum
Corporate federal income tax rate		35.00%

Income Taxes - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	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%
Unrecognized tax benefits from uncertain tax	$ 0	$ 0	$ 0
Period over which material changes in unrecognized tax positions are not expected	12 months
Federal
Income Taxes
Cumulative net operating loss carryforwards	$ 200,400
Tax credit carryforwards	12,700
State
Income Taxes
Cumulative net operating loss carryforwards	177,000
Tax credit carryforwards	$ 1,800

Income Taxes - Components of the Deferred Tax Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Income Taxes
Operating loss carryforwards	$ 53,276	$ 56,832
Tax credit carryforwards	14,099	9,428
Other	7,552	7,710
Deferred Tax Assets, Gross	74,927	73,970
Valuation allowance	$ (74,927)	$ (73,970)

Income Taxes - Difference Between U.S. Federal Corporate Tax Rate and Company's Effective Tax Rate (Details)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Taxes
Expected federal income tax rate	(34.00%)	(34.00%)	(34.00%)
Change in valuation allowance	0.90%	42.20%	39.80%
Federal and state credits	(6.90%)	(9.90%)	(7.40%)
State income taxes, net of federal benefit	(3.70%)	(3.70%)	(4.50%)
Permanent differences	2.40%	3.50%	2.40%
Rate change related to TCJA	41.90%
Other	(0.60%)	1.90%	3.70%
Effective tax rate	0.00%	0.00%	0.00%

Employee Benefit Plan (Details) - USD ($) $ in Millions	12 Months Ended
Employee Benefit Plan (Details) - USD ($) $ in Millions	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
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	$ 0.3	$ 0.2

Related Party Transactions - Overview of Related Parties (Details) - USD ($) $ / shares in Units, $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015	Jan. 21, 2018
Related Party Transactions
Ownership percentage				48.40%
Number of Warrants	43,757,379	51,709,460
Exercise price of warrants	$ 0.24	$ 0.31
Common stock issued in lieu of board fees	62,939	101,239	40,934
Proceeds from issuance of common stock in lieu of director board and committee fees	$ 0.1	$ 0.2	$ 0.1
Common Stock \| Board of Director
Related Party Transactions
Ownership percentage	9.40%
Pillar I
Related Party Transactions
Number of warrants exercised		1,370,000
Proceeds from exercise of warrants		$ 2.0
Pillar II
Related Party Transactions
Number of warrants exercised	5,034,061		232,759
Proceeds from exercise of warrants	$ 3.5		$ 0.2
Pillar III
Related Party Transactions
Number of warrants exercised			2,600,000
Proceeds from exercise of warrants			$ 1.2
Pillar Investment Entities \| Common Stock
Related Party Transactions
Ownership percentage	13.10%
Besancon
Related Party Transactions
Number of warrants exercised	2,918,020
Proceeds from exercise of warrants	$ 1.9
Number of Warrants	1,200,000
Exercise price of warrants	$ 0.47
Baker Bros. Advisors LP
Related Party Transactions
Number of Warrants	20,316,327
Exercise price of warrants	$ 0.47
Baker Bros. Advisors LP \| Pre-funded Warrants
Related Party Transactions
Number of Warrants	22,151,052
Exercise price of warrants	$ 0.01

Net Loss per Common Share (Details) - shares	12 Months Ended
Net Loss per Common Share (Details) - shares	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Net Loss per Common Share Applicable to Common Stockholders
Total antidilutive securities	65,161,505	69,712,906	70,782,788

Supplemental Disclosure of Cash Flow Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 42	$ 72	$ 93
Supplemental disclosure of non-cash financing and investing activities:
Non-cash property additions	150	425	$ 123
Accrued financing transaction costs	$ 17	$ 166

Subsequent Events (Details)	Jan. 21, 2018 shares	Jan. 04, 2018 shares	Dec. 31, 2017 shares	Dec. 31, 2016 shares
Subsequent Events
Common stock, shares authorized			280,000,000	280,000,000
Ownership percentage of new company	48.40%
Common stock, shares issued			195,625,000	149,065,000
BioCryst
Subsequent Events
Ownership percentage of new company	51.60%
Subsequent Events
Subsequent Events
Common stock, shares authorized		280,000,000
Multiplier used for the reverse stock split ratio		2
Number of shares received from new company	0.20
Number of days in average volume weighted trading prices	30 days
Subsequent Events \| Minimum
Subsequent Events
Reverse stock split conversion ratio		1
Subsequent Events \| Maximum
Subsequent Events
Reverse stock split conversion ratio		1
Subsequent Events \| BioCryst
Subsequent Events
Number of shares received from new company	0.50
Subsequent Events \| Investor
Subsequent Events
Common stock, shares issued	9
Subsequent Events \| Investor \| BioCryst
Subsequent Events
Common stock, shares issued	14