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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2017	Oct. 31, 2017
Document and Entity Information [Abstract]
Entity Registrant Name	NEWLINK GENETICS CORP
Entity Central Index Key	0001126234
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Sep. 30, 2017
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Common Stock, Shares Outstanding		37,077,159

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 120,702	$ 131,490
Prepaid expenses and other current assets	2,701	5,921
Income tax receivable	114	5,975
Other receivables	10,670	24,526
Total current assets	134,187	167,912
Property and equipment, net	5,527	6,835
Total assets	139,714	174,747
Current liabilities:
Accounts payable	11,860	22,883
Accrued expenses	13,832	14,309
Current portion of unearned revenue	112	391
Current portion of deferred rent	93	90
Current portion of notes payable and obligations under capital leases	194	232
Total current liabilities	26,091	37,905
Long-term liabilities:
Royalty obligation payable to Iowa Economic Development Authority	6,000	6,000
Notes payable and obligations under capital leases	138	285
Deferred rent	1,021	1,091
Total long-term liabilities	7,159	7,376
Total liabilities	33,250	45,281
Stockholders' equity:
Blank check preferred stock, $0.01 par value: Authorized shares — 5,000,000 at September 30, 2017 and December 31, 2016; issued and outstanding shares — 0 at September 30, 2017 and December 31, 2016	0	0
Common stock, $0.01 par value: Authorized shares — 75,000,000 at September 30, 2017 and December 31, 2016; issued 31,375,528 and 29,193,718 at September 30, 2017 and December 31, 2016, respectively, and outstanding 31,319,751 and 29,163,673 at September 30, 2017 and December 31, 2016, respectively	314	292
Additional paid-in capital	331,036	295,535
Treasury stock, at cost: 55,777 and 30,045 shares at September 30, 2017 and December 31, 2016, respectively	(1,113)	(853)
Accumulated deficit	(223,773)	(165,508)
Total stockholders' equity	106,464	129,466
Total liabilities and stockholders' equity	$ 139,714	$ 174,747

Condensed Consolidated Balance Sheets (Parentheticals) - $ / shares	Sep. 30, 2017	Dec. 31, 2016
Stockholders' Equity:
Blank check preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Blank check preferred stock, authorized shares	5,000,000	5,000,000
Blank check preferred stock, issued shares	0	0
Blank check preferred stock, outstanding shares	0	0
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, authorized shares	75,000,000	75,000,000
Common stock, issued shares	31,375,528	29,193,718
Common stock, outstanding shares	31,319,751	29,163,673
Treasury stock, shares	55,777	30,045

Condensed Consolidated Statements of Operations - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Income Statement [Abstract]
Grant revenue	$ 5,379,000	$ 14,457,000	$ 18,279,000	$ 20,057,000
Licensing and collaboration revenue	103,000	888,000	334,000	3,008,000
Total operating revenues	5,482,000	15,345,000	18,613,000	23,065,000
Operating expenses:
Research and development	18,480,000	24,463,000	52,405,000	73,810,000
General and administrative	7,907,000	7,749,000	25,038,000	26,043,000
Total operating expenses	26,387,000	32,212,000	77,443,000	99,853,000
Loss from operations	(20,905,000)	(16,867,000)	(58,830,000)	(76,788,000)
Other income and expense:
Miscellaneous income (expense)	12,000	(44,000)	(101,000)	(44,000)
Interest income	151,000	68,000	353,000	180,000
Interest expense	(3,000)	(5,000)	(116,000)	(18,000)
Other income, net	160,000	19,000	136,000	118,000
Net loss before taxes	(20,745,000)	(16,848,000)	(58,694,000)	(76,670,000)
Income tax benefit	119,000	1,308,000	429,000	5,021,000
Net loss	$ (20,626,000)	$ (15,540,000)	$ (58,265,000)	$ (71,649,000)
Basic and diluted loss per share (in dollars per share)	$ (0.69)	$ (0.54)	$ (1.98)	$ (2.48)
Basic and diluted average shares outstanding (in shares)	29,939,823	28,983,561	29,462,226	28,911,042

Condensed Consolidated Statement of Stockholders' Equity - 9 months ended Sep. 30, 2017 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Treasury Stock	Accumulated Deficit
Balance at beginning of period at Dec. 31, 2016	$ 129,466	$ 292	$ 295,535	$ (853)	$ (165,508)
Balance at beginning of period (shares) at Dec. 31, 2016	29,163,673	29,163,673
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	$ 14,938		14,938
Exercise of stock options and restricted stock vested	925	$ 2	923
Exercise of stock options and restricted stock vested (shares)		189,155
Sales of shares under stock purchase plan	326		325
Sales of shares under stock purchase plan (shares)		51,999
Repurchase of common stock	(260)			(260)
Issuance of common stock under the ATM Offering (net of offering costs of $561)	19,334	$ 19	19,315
Issuance of common stock under the ATM Offering (net of offering costs of $561) (shares)		1,940,656
Repurchase of common stock (shares)		(25,732)
Net loss	(58,265)				(58,265)
Balance at end of period at Sep. 30, 2017	$ 106,464	$ 314	$ 331,036	$ (1,113)	$ (223,773)
Balance at end of period (shares) at Sep. 30, 2017	31,319,751	31,319,751

Condensed Consolidated Statement of Stockholders' Equity (Parentheticals) $ in Thousands	9 Months Ended
	Sep. 30, 2017 USD ($)
Statement of Stockholders' Equity [Abstract]
Stock issuance costs	$ 561

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Cash Flows From Operating Activities
Net loss	$ (58,265)	$ (71,649)
Adjustments to reconcile net loss to net cash used in operating activities:
Share-based compensation	14,938	13,119
Depreciation and amortization	1,064	1,536
Forgiveness of debt	0	(397)
Tax shortfall associated with employee stock plans	0	(640)
Impairment of fixed assets	0	3,976
Loss on sale of fixed assets	102	0
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	3,220	(5,734)
Other receivables	13,856	(9,607)
Accounts payable and accrued expenses	(11,500)	27,204
Income taxes receivable	5,861	(6,056)
Unearned revenue	(279)	(606)
Deferred rent	(67)	(79)
Net cash used in operating activities	(31,070)	(48,933)
Cash Flows From Investing Activities
Maturity of certificates of deposit	0	2,180
Purchase of equipment	(43)	(2,069)
Proceeds on sale of equipment	185	0
Net cash provided by investing activities	142	111
Cash Flows From Financing Activities
Issuance of common stock, net of offering costs	20,585	1,686
Repurchase of common stock	(260)	(13)
Payments under capital lease obligations and principal payments on notes payable	(185)	(195)
Net cash provided by financing activities	20,140	1,478
Net decrease in cash and cash equivalents	(10,788)	(47,344)
Cash and cash equivalents at beginning of period	131,490	195,620
Cash and cash equivalents at end of period	120,702	148,276
Supplemental disclosure of cash flows information:
Cash paid for interest	11	18
Cash (refunds received) paid for taxes, net	(6,261)	1,022
Noncash financing and investing activities:
Equipment acquired by capital lease	0	231
Forgiveness of debt	$ 0	$ 397

Description of Business	9 Months Ended
Description of Business	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Description of Business	Description of Business On June 4, 1999, NewLink Genetics Corporation (NewLink) was incorporated as a Delaware corporation. NewLink was formed for the purpose of developing treatments for patients with cancer and other diseases. NewLink initiated operations in April 2000. NewLink and its subsidiaries (the Company) are devoting substantially all of their efforts toward research and development. The Company has never earned revenue from commercial sales of its drugs. The Company incurred a net loss of $20.6 million and $58.3 million for the three and nine months ended September 30, 2017. In July 2017, the Company undertook an organizational realignment to refocus its clinical development efforts and align the Company's resources to focus on the Company's highest value opportunities. The Company's restructuring activities included a reduction of its workforce by approximately 50%, which consisted primarily of clinical and research and development staff, as well as stopping additional research on the Zika virus. Refer to Note 9 for more information. The accompanying condensed consolidated financial statements as of September 30, 2017 and for the three and nine months ended have been prepared assuming the Company will continue as a going concern. The Company successfully raised net proceeds of $37.6 million from its IPO, completed a follow-on offering of its common stock raising net proceeds of $49.0 million, and raised an additional $58.7 million in net proceeds from an at the market (ATM) offering completed in 2015. On November 29, 2016, the Company entered into a Sales Agreement with Cantor Fitzgerald & Co. (Cantor) under which the Company may sell up to $40.0 million of its common stock in one or more placements at prevailing market prices in an ATM offering. The Company launched this ATM offering in June 2017. During the three months ended September 30, 2017, 1,940,656 shares of the Company's common stock were sold under this ATM, with aggregate net proceeds of $19.3 million after commissions of $398,000 paid to Cantor as the placement agent, and other costs of $163,000 . Subsequent to September 30, 2017, the Company sold 5,750,000 of its shares of common stock in a public offering for aggregate net proceeds of $55.2 million after underwriters' discounts, commissions and other expenses of $3.7 million. In connection with two license and collaboration agreements the Company entered into during 2014, the Company received a nonrefundable upfront cash payment of $150.0 million from Genentech Inc., a member of the Roche Group, or Genentech, in 2014, and a nonrefundable upfront cash payment of $30.0 million from Merck, Sharpe and Dohme Corp., or Merck, in 2014, as well as a milestone payment of $20.0 million from Merck in February 2015. The Company's cash and cash equivalents after these agreements and the offerings are expected to be adequate to satisfy the Company's liquidity requirements into the second quarter of 2020. If available liquidity becomes insufficient to meet the Company’s operating obligations as they come due, the Company's plans include pursuing alternative funding arrangements and/or reducing expenditures as necessary to meet the Company’s cash requirements. However, there is no assurance that, if required, the Company will be able to raise additional capital or reduce discretionary spending to provide the required liquidity. Failure by the Company to successfully execute its plans or otherwise address its liquidity needs may have a material adverse effect on its business and financial position, and may materially affect the Company’s ability to continue as a going concern.

Basis of Presentation	9 Months Ended
Basis of Presentation	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Basis of Presentation	Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared and presented by the Company in accordance with U.S. generally accepted accounting principles (U.S. GAAP) and the rules and regulations of the U.S. Securities and Exchange Commission (the SEC), and, in management’s opinion, reflect all adjustments necessary to present fairly the Company’s interim condensed financial information. Certain information and footnote disclosures normally included in the Company’s annual financial statements prepared in accordance with U.S. GAAP have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2016, included in the Company’s Annual Report on Form 10-K. There were no significant changes in the Company’s accounting policies since the end of fiscal 2016. The financial results for any interim period are not necessarily indicative of financial results for the full year.

Significant Accounting Policies	9 Months Ended
Significant Accounting Policies	Sep. 30, 2017
Accounting Policies [Abstract]
Significant Accounting Policies	Significant Accounting Policies Use of Estimates The preparation of the condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates. Principles of Consolidation The condensed consolidated financial statements include the financial statements of NewLink and its wholly owned subsidiaries. All significant intercompany balances and transactions have been eliminated in consolidation. Financial Instruments and Concentrations of Credit Risk Cash and cash equivalents, receivables, and accounts payable are recorded at cost, which approximates fair value based on the short-term nature of these financial instruments. The carrying value of notes payable and capital lease obligations was $332,000 and $517,000 as of September 30, 2017 and December 31, 2016, respectively, which approximate fair value using Level 2 inputs (computed in accordance with ASC 820). The Company is unable to estimate the fair value of the royalty obligation based on future product sales, as the timing of payments, if any, is uncertain. Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash and cash equivalents. Cash and cash equivalents are held by financial institutions and are federally insured up to certain limits. At times, the Company’s cash and cash equivalents balance exceeds the federally insured limits. To limit the credit risk, the Company invests its excess cash primarily in high-quality securities such as certificates of deposit and money market funds. Property and equipment Property and equipment are capitalized as the Company believes they have alternative future uses and are stated at cost, less accumulated depreciation of $6.7 million and $5.7 million as of September 30, 2017 and December 31, 2016, respectively. Equipment under capital leases is stated at the present value of minimum lease payments. Depreciation on all property and equipment is calculated on the straight-line method over the shorter of the lease term or estimated useful life of the asset. Computer equipment has useful lives of three to five years, lab equipment has a useful life of five years and contract manufacturing organization equipment has a useful life of five years. Revenue Recognition The Company receives payments from government entities under its grants and contracts with the Department of Defense and the United States Department of Health and Human Services. These agreements provide the Company cost reimbursement plus a percentage for certain types of expenditures in return for research and development activities over a contractually defined period. Grant revenues are recognized in the period during which the related costs are incurred, provided that the conditions under which the costs submitted or to be submitted for reimbursement have been met and the Company has only perfunctory obligations outstanding. The Company had $10.1 million and $23.9 million of receivables from the government contracts recorded in other receivables and $1.5 million and $4.3 million of unbilled expenses relating to the government contracts recorded in prepaid expenses and other current assets on the balance sheet as of September 30, 2017 and December 31, 2016, respectively. The Company had $1.4 million and $2.9 million of accrued expenses for subcontractor fees incurred under the government contracts as of September 30, 2017 and December 31, 2016, respectively. Recent Accounting Pronouncements On May 28, 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers, which requires an entity to recognize the amount of revenue to which it expects to be entitled for the transfer of promised goods or services to customers. The ASU will replace most existing revenue recognition guidance in U.S. GAAP when it becomes effective. The new standard is effective for the Company on January 1, 2018. The standard permits the use of either the retrospective or cumulative effect transition method. The Company plans to adopt the standard on a modified retrospective basis at January 1, 2018, with an adjustment for the cumulative effect of all changes recognized in beginning retained earnings. The Company does not expect to record any adjustment relating to the Company’s licensing and collaboration agreements. The Company continues to assess the impact adoption will have on the government grant revenue contracts.

Long-Term Debt	9 Months Ended
Long-Term Debt	Sep. 30, 2017
Debt Disclosure [Abstract]
Long-Term Debt	Long-Term Debt March 2010 City of Ames Forgivable Loan In March 2010, the Company entered into a $400,000 forgivable loan agreement with the City of Ames, Iowa and the Ames Chamber of Commerce, jointly, as lenders. The project provided the Company with financial assistance to construct new facilities within the Ames city limits. The project required the Company to create or retain at least 150 full-time positions located in Ames, Iowa by March 10, 2016. The agreement required the Company to enter into a five-year building lease with the option for extension for an additional five years of not less than 20,000 square feet within the corporate limits of the City of Ames by March 10, 2015, which requirement was met prior to the deadline of March 10, 2015. As of March 10, 2016, the Company had satisfactorily fulfilled all of the above terms of the loan agreement and the loan was forgiven. Accordingly, the entire outstanding loan amount of $397,000 was derecognized with a corresponding amount recorded in grant revenue for the three months ended March 31, 2016.

License and Research Collaboration Agreements	9 Months Ended
License and Research Collaboration Agreements	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Licensing and Research Collaboration Agreements	License and Research Collaboration Agreements Genentech, a Member of the Roche Group In October 2014, the Company entered into an exclusive worldwide collaboration and license agreement with Genentech, or the Genentech Agreement, for the development and commercialization of navoximod (GDC-0919), one of the Company's clinical stage IDO pathway inhibitors. The parties also entered into a research collaboration for the discovery of next generation IDO and TDO pathway inhibitors to be developed and commercialized under this agreement. Under the terms of the Genentech Agreement, the Company received a nonrefundable upfront cash payment of $150.0 million from Genentech in 2014 and is eligible to receive additional milestone payments of up to $561.0 million upon achieving certain Next Generation Product Development regulatory development, international patent acceptance, country marketing approval, and sales-based milestones. The Company retains the right to exercise an option to co-promote any products for the U.S. market and is also eligible to receive escalating royalty payments on potential commercial sales of products by Genentech. On June 6, 2017, the Company received a formal notice of Genentech’s intent to terminate the Genentech Agreement with respect to navoximod with such termination to be effective no later than December 6, 2017. Discussions regarding the termination are ongoing. The Genentech Agreement continues with regards to any Next Generation Products as defined under the Genentech Agreement. For the three and nine months ended September 30, 2017, the Company recognized license and collaboration revenue under the Genentech Agreement of $56,000 and $279,000, respectively, for providing an alliance manager. For the three months ended September 30, 2016, the Company recognized license and collaboration revenue under the Genentech Agreement of $687,000, including $486,000 for amounts received as reimbursement for the Company's employees working on the project, and $201,000 for providing an alliance manager. For the nine months ended September 30, 2016, the Company recognized license and collaboration revenue under the Genentech Agreement of $2.2 million, including $1.6 million for amounts received as reimbursement for the Company's employees working on the project, $502,000 for providing an alliance manager, and $101,000 for participation in the joint research committee. In accordance with the Company’s continuing performance obligation, $112,000 of the $150.0 million upfront payment remains deferred as of September 30, 2017 and will be recognized during the remainder of 2017. The upfront payment provides no general right of return for any non-contingent deliverable and no portion of any revenue recognized is refundable. Merck Sharp & Dohme Corp. In November 2014, the Company entered into a licensing and collaboration agreement with Merck, or the Merck Agreement, to develop, manufacture and commercialize rVSV-ZEBOV GP, an Ebola vaccine the Company licensed from the Public Health Agency of Canada, or PHAC. Under the terms of the Merck Agreement, the Company granted Merck an exclusive, royalty bearing license to rVSV-ZEBOV GP and related technology. Under the Merck Agreement, the Company received a $30.0 million non-refundable, upfront payment in December 2014, and a one-time $20.0 million non-refundable milestone payment in February 2015 upon the initiation of the pivotal clinical trial using the current rVSV-ZEBOV GP vaccine product as one arm of the trial. In addition, the Company can receive escalating royalties on potential commercial sales by Merck of the current product candidate ranging from single digit to double digits on the rVSV-ZEBOV GP license agreement product sales and escalating royalties on potential commercial sales by Merck of products other than current products within the Company’s patent rights ranging from low to high single digit, on increasing levels of annual net sales worldwide. Merck will lead the development of rVSV-ZEBOV GP and any other rVSV-based viral hemorrhagic fever vaccine product candidates in order to create a marketable product safe for human use. The Company completed all deliverables under the Merck Agreement in their entirety during the year ended December 31, 2016. For the three months ended September 30, 2016, the Company recognized no revenues under the Merck Agreement. For the nine months ended September 30, 2016, the Company recognized license and collaboration revenues under the Merck Agreement of $764,000, for the reimbursement of costs not covered under government contracts.

Common Stock Equity Incentive Plan

9 Months Ended

Sep. 30, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Common Stock Equity Incentive Plan

2009 Equity Incentive Plan

In April 2000, the stockholders approved the Company's 2000 Equity Incentive Plan, or the 2000 Plan, and in July 2009, the stockholders approved the Company's 2009 Equity Incentive Plan, or the 2009 Plan. Following the approval of the 2009 Plan, all options outstanding under the 2000 Plan are effectively included under the 2009 Plan. Under the provisions of the 2009 Plan, the Company may grant the following types of common stock awards:


•	Incentive Stock Options


•	Nonstatutory Stock Options


•	Restricted Stock Awards


•	Stock Appreciation Rights

Awards under the 2009 Plan, as amended, may be made to officers, employees, members of the Board of Directors, advisors, and consultants to the Company. As of September 30, 2017, there were 10,238,220 shares of common stock authorized for the 2009 Plan and 1,094,264 shares remained available for issuance.

The following table summarizes the authorized increases of common stock under the 2009 Plan:



Date Authorized		Authorized Shares Added
May 15, 2010		1,238,095
January 7, 2011		714,286
January 1, 2013		838,375
January 1, 2014		1,066,340
January 1, 2015		1,119,255
January 1, 2016		1,152,565
January 1, 2017		1,166,546

The increases in the authorized shares of common stock under the 2009 Plan in 2010 and 2011 were approved by the Company’s stockholders. The increases in the authorized shares of common stock under the 2009 Plan in 2012 through 2017 were made pursuant to an “evergreen provision,” in accordance with which, on January 1 of each year, from 2012 to (and including) 2019, a number of shares of common stock in an amount equal to 4% of the total number of shares of common stock outstanding on December 31 of the preceding calendar year, or such lesser amount of shares (or no shares) approved by the Company's Board of Directors, was added or will be added to the shares reserved under the 2009 Plan.

2010 Non-Employee Directors' Stock Award Plan

Under the terms of the Company’s 2010 Non-Employee Directors’ Stock Award Plan, or the Directors’ Plan, which became effective on November 10, 2011, 238,095 shares of common stock were reserved for future issuance. On May 9, 2013, an additional 161,905 shares of common stock were added to the shares reserved for future issuance under the Directors' Plan. As of September 30, 2017, no shares remained available for issuance under the Directors' Plan.

2010 Employee Stock Purchase Plan

Under the terms of the Company’s 2010 Employee Stock Purchase Plan, or the 2010 Purchase Plan, which became effective on November 10, 2011, 214,285 shares of common stock were reserved for future issuance. On May 9, 2013, an additional 185,715 shares of common stock were added to the shares reserved for future issuance under the 2010 Purchase Plan. As of September 30, 2017, 120,784 shares remained available for issuance under the 2010 Purchase Plan.

Share-based Compensation

Share-based compensation expense for the three months ended September 30, 2017 and 2016 was $4.4 million and $3.9 million, respectively, and was $14.9 million and $13.1 million, respectively, for nine months ended September 30, 2017 and 2016. Share-based compensation expense is allocated between research and development and general and administrative expenses within the condensed consolidated statements of operations.

As of September 30, 2017, the total compensation cost related to nonvested option awards not yet recognized was $19.9 million and the weighted-average period over which it is expected to be recognized is 2.1 years.

Stock Options and Performance Stock Options

The following table summarizes the stock option activity, including options with performance conditions, for the nine months ended September 30, 2017:



	Number of options		Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	6,278,542		$	14.93	5.8
Options granted	1,439,287		11.78
Options exercised	(108,775	)	8.51
Options forfeited	(277,443	)	20.13
Options expired	(17,605	)	42.00
Outstanding at end of period	7,314,006		$	14.15	5.5
Options exercisable at end of period	5,456,602		$	12.65	4.4

The Company estimates the fair value of each stock option grant on the date of grant using a Black-Scholes option pricing model. For stock option grants issued with a market condition, the Company used a Monte Carlo simulation valuation model to determine the grant date fair value.

The following table summarizes the range of assumptions used to estimate the fair value of stock options granted, including those options granted with a market condition, during the nine months ended September 30, 2017:



Risk-free interest rate		1.9% to 2.2%
Expected dividend yield		—%
Expected volatility		68.9% to 73.2%
Expected term (in years)		6.5 to 7.8
Weighted-average grant-date fair value per share		$7.81

The intrinsic value of options exercised during the nine months ended September 30, 2017 was $924,164. The fair value of awards vested during the nine months ended September 30, 2017 was $12.4 million.

During the nine months ended September 30, 2017, the Company’s Board of Directors approved and granted 388,144 shares of compensation and equity awards to certain executives with either market or performance conditions. The compensation and equity awards had a weighted average grant date fair value per share of $6.73. The compensation and equity awards will vest upon the achievement of certain performance conditions. During the nine months ended September 30, 2017, certain conditions were met which resulted in the vesting of 194,070 shares and the recognition of $1.2 million in stock compensation expense.

Restricted Stock and Performance Restricted Stock

Restricted stock is common stock that is subject to restrictions, including risks of forfeiture, determined by the plan committee of the Board of Directors in its sole discretion, for as long as such common stock remains subject to any such restrictions. A holder of restricted stock has all rights of a stockholder with respect to such stock, including the right to vote and to receive dividends thereon, except as otherwise provided in the award agreement relating to such award. Restricted stock awards are classified as equity within the consolidated balance sheets. The fair value of each restricted stock grant is estimated on the date of grant using the closing price of the Company's common stock on the NASDAQ Stock Market on the date of grant.

A summary of the Company's unvested restricted stock, including restricted stock with performance conditions, at September 30, 2017 and changes during the nine months ended September 30, 2017 are as follows:



	Number of restricted stock shares		Weighted average grant date fair value
Unvested at beginning of period	288,964			$	34.94
Granted	—			—
Vested	(80,380	)		35.04
Forfeited/cancelled	(27,248	)		33.84
Unvested at end of period	181,336			$	35.05

As of September 30, 2017, the total remaining unrecognized compensation cost related to restricted stock was approximately $4.4 million and is expected to be recognized over a weighted-average period of 1.8 years. As of September 30, 2017, there remains approximately $6.4 million of unrecognized compensation cost related to the issuance of performance restricted stock. The fair value of awards vested during the nine months ended September 30, 2017 was $814,000.

The Company does not have a formal policy regarding the source of shares issued upon exercise of stock options or issuance of restricted stock. The Company expects shares issued to be issued from treasury shares or new shares.

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2017
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes For the three and nine months ended September 30, 2017, the Company recorded an income tax benefit of $119,000 and $429,000, respectively. For the three and nine months ended September 30, 2016, the Company recorded an income tax benefit of $1.3 million and $5.0 million, respectively. The income tax benefit for the three and nine months ended September 30, 2017 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to the limited potential to carry back losses to 2015 and the net loss generated by NewLink's foreign subsidiary. Income tax benefit for the three and nine months ended September 30, 2016 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to the ability to carry back losses to 2014 and the net loss generated by the NewLink's foreign subsidiary. In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected taxable income, and tax planning strategies in making this assessment. Valuation allowances have been established for the entire amount of the net deferred tax assets as of September 30, 2017 and December 31, 2016, respectively, due to the uncertainty of future recoverability. The Company has a reserve for uncertain tax positions related to state tax matters of $843,000 as of September 30, 2017 recorded within Accrued Expenses in the condensed consolidated balance sheet, which includes the accrual of interest and penalties. The Company does not expect the amount to change significantly within the next 12 months.

Net Loss per Common Share

9 Months Ended

Sep. 30, 2017

Earnings Per Share [Abstract]

Net Loss per Common Share

Basic loss per share is based upon the weighted-average number of common shares outstanding during the period, without consideration of common stock equivalents. Diluted loss per share is based upon the weighted-average number of common shares outstanding during the period plus additional weighted-average potentially dilutive common stock equivalents during the period when the effect is dilutive.

The following table presents the computation of basic and diluted loss per common share (in thousands, except share and per share data):



	Three Months Ended September 30,						Nine Months Ended September 30,
	2017			2016			2017			2016
Loss attributable to common stockholders	$	(20,626	)	$	(15,540	)	$	(58,265	)	$	(71,649	)

Basic and diluted weighted-average shares outstanding	29,939,823			28,983,561			29,462,226			28,911,042

Basic and diluted loss per share	$	(0.69	)	$	(0.54	)	$	(1.98	)	$	(2.48	)

All common stock equivalents are excluded from the computation of diluted loss per share during periods in which losses are reported since the result would be anti-dilutive. As of September 30, 2017, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 7,314,006 and 181,336, respectively. As of September 30, 2016, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 6,453,331 and 307,079, respectively.

Restructuring Charges

9 Months Ended

Sep. 30, 2017

Restructuring and Related Activities [Abstract]

Restructuring Charges

The Company records liabilities for costs associated with exit or disposal activities in the period in which the liability is incurred. Employee severance costs are accrued when the restructuring actions are probable and estimable. Costs for one-time termination benefits in which the employee is required to render service until termination in order to receive the benefits are recognized ratably over the future service period. The Company also records costs incurred with contract terminations associated with restructuring activities.

In July 2017, the Company undertook an organizational realignment to refocus its clinical development efforts and align the Company's resources to focus on the Company's highest value opportunities. The Company's restructuring activities included a reduction of its workforce by approximately 50%, which consisted primarily of clinical and research and development staff, as well as stopping additional research on the Zika virus. Restructuring charges recorded during the three and nine months ended September 30, 2017 included $1.7 million in employee severance cost, which is comprised of one-time employee termination benefits and certain expenses related to contractual termination benefits for employees with pre-existing severance arrangements.

In May 2016, the Company announced that its Phase 3 clinical trial Immunotherapy for Pancreatic RESectable cancer Study, or IMPRESS, of algenpantucel-L for patients with resected pancreatic cancer did not achieve its primary endpoint and in order to reduce costs associated with algenpantucel-L and the HyperAcute® Cellular Immunotherapy platform technology, the Company's management adopted a restructuring plan in May 2016 which included a reduction in the Company's workforce; the exit or reduction of certain leased facilities; and the renegotiation or termination of contracts with certain third parties. As a result of the restructuring, the Company also impaired fixed assets which management determined had no or limited future use. The fair value of impaired fixed assets was determined based on management’s estimate of market resale value. Restructuring charges recorded during 2016 were $12.3 million, of which $500,000 is included within general and administrative expenses and $11.8 million is included within the research and development expenses in the condensed consolidated statement of operations. Included in the $12.3 million of charges is non-cash asset impairment charges of $4.0 million. No additional charges related to the 2016 restructuring were recorded during the three and nine months ended September 30, 2017 and all amounts accrued as of December 31, 2016 were paid by the end of the first quarter of 2017.

The following table shows the amount accrued for restructuring activities which is recorded within Accrued Expenses in the condensed consolidated balance sheet:



	Employee Severance Cost		Total
Balance as of December 31, 2016	$	42	$	42
Expensed	1,695		1,695
Cash Payments	1,085		1,085
Balance as of September 30, 2017	$	652	$	652

The majority of the charges are expected to be paid by the end of the year.

Commitments and Contingencies	9 Months Ended
Commitments and Contingencies	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies Disclosure	Commitments and Contingencies From time to time, claims are asserted against the Company arising in the ordinary course of business. In the opinion of management, liabilities, if any, arising from existing claims are not expected to have a material effect on the Company's earnings, financial position, or liquidity. On or about May 12, 2016, Trevor Abramson filed a putative securities class action lawsuit in the United States District Court for the Southern District of New York, or the Court, captioned Abramson v. NewLink Genetics Corp., et al., Case 1:16-cv-3545, or the Securities Action. Subsequently, the Court appointed Michael and Kelly Nguyen as lead plaintiffs and approved their selection of Kahn, Swick & Foti, LLC as lead counsel in the Securities Action. On October 31, 2016, the lead plaintiffs filed an amended complaint which asserts claims under the federal securities laws against the Company, the Company’s Chief Executive Officer Charles J. Link, Jr., and the Company’s Chief Medical Officer and President Nicholas Vahanian, or collectively, the Defendants. The amended complaint alleges the Defendants made material false and/or misleading statements that caused losses to the Company’s investors. In particular, the lead plaintiffs allege that the Defendants made material misstatements or omissions related to the Phase II and III trials and efficacy of the product candidate algenpantucel-L. The lead plaintiffs do not quantify any alleged damages in the amended complaint but, in addition to attorneys’ fees and costs, they seek to recover damages on behalf of themselves and other persons who purchased or otherwise acquired the Company’s stock during the putative class period of September 17, 2013 through May 9, 2016, inclusive, at allegedly inflated prices and purportedly suffered financial harm as a result. On April 27, 2017, the Court granted the parties’ request for leave to brief a motion to dismiss the amended complaint, and ordered the parties to file a stipulation and proposed order setting forth a schedule for the briefing of that motion. On May 15, 2017, the Court ordered the following briefing schedule: motion to dismiss due July 14, 2017, opposition due September 12, 2017, and reply due September 26, 2017. The Defendants filed a motion to dismiss on July 14, 2017. The lead plaintiffs filed an opposition to the motion to dismiss on September 12, 2017. The Defendants filed a reply in support of the motion to dismiss on September 26, 2017. Oral argument was held on October 19, 2017, after which the Court reserved decision. The Company disputes the claims in the Securities Action and intends to defend against them vigorously. On or about April 26, 2017, Ronald Morrow filed a shareholder derivative lawsuit on behalf of the Company in the United States District Court for the Southern District of New York, or the Court, against the Company’s Chief Executive Officer Charles J. Link, Jr., the Company’s Chief Medical Officer and President Nicholas Vahanian, and Company directors Thomas A. Raffin, Joseph Saluri, Ernest J. Talarico, III, Paul R. Edick, Paolo Pucci, and Lota S. Zoth, or collectively, the Morrow Defendants, captioned Morrow v. Link., et al., Case 1:17-cv-03039, or the Morrow Action. The complaint alleges that the Morrow Defendants caused the Company to issue false statements in its 2016 proxy statement regarding risk management and compensation matters in violation of federal securities law. The complaint also asserts state law claims against the Morrow Defendants for breaches of fiduciary duties, unjust enrichment, abuse of control, insider trading, gross mismanagement, and corporate waste, alleging that the Morrow Defendants made material misstatements or omissions related to the Phase II and III trials and efficacy of the product candidate algenpantucel-L, awarded themselves excessive compensation, engaged in illegal insider trading, and grossly mismanaged the Company. The plaintiff does not quantify any alleged damages in the complaint but seeks restitution for damages to the Company, attorneys’ fees, costs, and expenses, as well as an order directing that proposals for strengthening board oversight be put to a vote of the Company’s shareholders. The language for such proposals is not specified in the complaint. The plaintiff also contemporaneously filed a statement of relatedness, informing the Court that the Morrow Action is related to Abramson v. NewLink Genetics Corp., et al., Case 1:16-cv-3545. On May 19, 2017, the plaintiff dismissed the Morrow Action without prejudice. Also on May 19, 2017, plaintiffs’ counsel in the Morrow Action filed a new shareholder derivative complaint that is substantively identical to the Morrow Action, except that the plaintiff is Rickey Ely. The latter action is captioned Ely v. Link, et al., Case 17-cv-3799, or the Ely Action. By agreement of the parties and order dated June 26, 2017, the Court temporarily stayed the Ely Action until the Securities Action is dismissed or otherwise resolved. Under the terms of the stay, the plaintiff in the Ely Action will be provided with any discovery that is provided in the Securities Action, and given an opportunity to participate in any mediation or settlement efforts in the Securities Action. The Company disputes the claims in the Ely Action and intends to defend against them vigorously.

Subsequent Events	9 Months Ended
Subsequent Events	Sep. 30, 2017
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events On October 6, 2017, the Company sold 5,750,000 shares of its common stock for total proceeds of $55.2 million, net of offering expenses of $3.7 million. Net proceeds from the offering will be used to further advance its pipeline of product candidates, including the continued clinical development of indoximod, and for working capital and other general corporate purposes.

Significant Accounting Policies (Policies)	9 Months Ended
Significant Accounting Policies (Policies)	Sep. 30, 2017
Accounting Policies [Abstract]
Use of Estimates	Use of Estimates The preparation of the condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.
Principles of Consolidation	Principles of Consolidation The condensed consolidated financial statements include the financial statements of NewLink and its wholly owned subsidiaries. All significant intercompany balances and transactions have been eliminated in consolidation.
Financial Instruments	Financial Instruments and Concentrations of Credit Risk Cash and cash equivalents, receivables, and accounts payable are recorded at cost, which approximates fair value based on the short-term nature of these financial instruments. The carrying value of notes payable and capital lease obligations was $332,000 and $517,000 as of September 30, 2017 and December 31, 2016, respectively, which approximate fair value using Level 2 inputs (computed in accordance with ASC 820). The Company is unable to estimate the fair value of the royalty obligation based on future product sales, as the timing of payments, if any, is uncertain.
Concentration of Credit Risk	Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash and cash equivalents. Cash and cash equivalents are held by financial institutions and are federally insured up to certain limits. At times, the Company’s cash and cash equivalents balance exceeds the federally insured limits. To limit the credit risk, the Company invests its excess cash primarily in high-quality securities such as certificates of deposit and money market funds.
Property and equipment	Property and equipment Property and equipment are capitalized as the Company believes they have alternative future uses and are stated at cost, less accumulated depreciation of $6.7 million and $5.7 million as of September 30, 2017 and December 31, 2016, respectively. Equipment under capital leases is stated at the present value of minimum lease payments. Depreciation on all property and equipment is calculated on the straight-line method over the shorter of the lease term or estimated useful life of the asset. Computer equipment has useful lives of three to five years, lab equipment has a useful life of five years and contract manufacturing organization equipment has a useful life of five years.
Revenue Recognition	Revenue Recognition The Company receives payments from government entities under its grants and contracts with the Department of Defense and the United States Department of Health and Human Services. These agreements provide the Company cost reimbursement plus a percentage for certain types of expenditures in return for research and development activities over a contractually defined period. Grant revenues are recognized in the period during which the related costs are incurred, provided that the conditions under which the costs submitted or to be submitted for reimbursement have been met and the Company has only perfunctory obligations outstanding. The Company had $10.1 million and $23.9 million of receivables from the government contracts recorded in other receivables and $1.5 million and $4.3 million of unbilled expenses relating to the government contracts recorded in prepaid expenses and other current assets on the balance sheet as of September 30, 2017 and December 31, 2016, respectively. The Company had $1.4 million and $2.9 million of accrued expenses for subcontractor fees incurred under the government contracts as of September 30, 2017 and December 31, 2016, respectively.
Recent Accounting Pronouncements	Recent Accounting Pronouncements On May 28, 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers, which requires an entity to recognize the amount of revenue to which it expects to be entitled for the transfer of promised goods or services to customers. The ASU will replace most existing revenue recognition guidance in U.S. GAAP when it becomes effective. The new standard is effective for the Company on January 1, 2018. The standard permits the use of either the retrospective or cumulative effect transition method. The Company plans to adopt the standard on a modified retrospective basis at January 1, 2018, with an adjustment for the cumulative effect of all changes recognized in beginning retained earnings. The Company does not expect to record any adjustment relating to the Company’s licensing and collaboration agreements. The Company continues to assess the impact adoption will have on the government grant revenue contracts.

Common Stock Equity Incentive Plan (Tables)

9 Months Ended

Sep. 30, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Authorized Increases of Common Stock under the 2009 Plan

The following table summarizes the authorized increases of common stock under the 2009 Plan:



Date Authorized		Authorized Shares Added
May 15, 2010		1,238,095
January 7, 2011		714,286
January 1, 2013		838,375
January 1, 2014		1,066,340
January 1, 2015		1,119,255
January 1, 2016		1,152,565
January 1, 2017		1,166,546

Stock Option Activity

The following table summarizes the stock option activity, including options with performance conditions, for the nine months ended September 30, 2017:



	Number of options		Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	6,278,542		$	14.93	5.8
Options granted	1,439,287		11.78
Options exercised	(108,775	)	8.51
Options forfeited	(277,443	)	20.13
Options expired	(17,605	)	42.00
Outstanding at end of period	7,314,006		$	14.15	5.5
Options exercisable at end of period	5,456,602		$	12.65	4.4

Assumptions Used in Black-Scholes Pricing Model for New Grants



Risk-free interest rate		1.9% to 2.2%
Expected dividend yield		—%
Expected volatility		68.9% to 73.2%
Expected term (in years)		6.5 to 7.8
Weighted-average grant-date fair value per share		$7.81

Restricted Stock Activity



	Number of restricted stock shares		Weighted average grant date fair value
Unvested at beginning of period	288,964			$	34.94
Granted	—			—
Vested	(80,380	)		35.04
Forfeited/cancelled	(27,248	)		33.84
Unvested at end of period	181,336			$	35.05

Net Loss per Common Share (Tables)

9 Months Ended

Sep. 30, 2017

Earnings Per Share [Abstract]

Basic and Diluted Net Loss per Common Share

The following table presents the computation of basic and diluted loss per common share (in thousands, except share and per share data):



	Three Months Ended September 30,						Nine Months Ended September 30,
	2017			2016			2017			2016
Loss attributable to common stockholders	$	(20,626	)	$	(15,540	)	$	(58,265	)	$	(71,649	)

Basic and diluted weighted-average shares outstanding	29,939,823			28,983,561			29,462,226			28,911,042

Basic and diluted loss per share	$	(0.69	)	$	(0.54	)	$	(1.98	)	$	(2.48	)

Restructuring Charges (Tables)

9 Months Ended

Sep. 30, 2017

Restructuring and Related Activities [Abstract]

Restructuring and Related Costs

The following table shows the amount accrued for restructuring activities which is recorded within Accrued Expenses in the condensed consolidated balance sheet:



	Employee Severance Cost		Total
Balance as of December 31, 2016	$	42	$	42
Expensed	1,695		1,695
Cash Payments	1,085		1,085
Balance as of September 30, 2017	$	652	$	652

Description of Business (Details)			1 Months Ended			3 Months Ended		9 Months Ended		12 Months Ended
Description of Business (Details)	Oct. 06, 2017 USD ($) shares	Nov. 29, 2016 USD ($)	Aug. 02, 2017 USD ($) shares	Jul. 31, 2017	Feb. 28, 2015 USD ($)	Sep. 30, 2017 USD ($)	Sep. 30, 2016 USD ($)	Sep. 30, 2017 USD ($)	Sep. 30, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($) arrangement
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Net loss						$ (20,626,000)	$ (15,540,000)	$ (58,265,000)	$ (71,649,000)
Percentage reduction in force				50.00%
Financings
Number of license and collaboration arrangements \| arrangement											2
License and Collaborative Arrangement \| Genentech
Financings
Upfront cash payments											$ 150,000,000
License and Collaborative Arrangement \| Merck
Financings
Upfront cash payments					$ 20,000,000						$ 30,000,000
IPO [Member]
Financings
FInancing proceeds										$ 37,600,000
Follow-on Offering
Financings
FInancing proceeds										49,000,000
ATM Offering
Financings
FInancing proceeds			$ 19,300,000							$ 58,700,000
Maximum available under ATM offering		$ 40,000,000
Number of shares of common stock sold \| shares			1,940,656
Commissions paid			$ 398,000
Other costs			$ 163,000
Subsequent event \| Public Offering [Member]
Financings
FInancing proceeds	$ 55,200,000
Fees and commissions	$ 3,700,000
Number of shares issued \| shares	5,750,000

Significant Accounting Policies (Details) - USD ($)	9 Months Ended
Significant Accounting Policies (Details) - USD ($)	Sep. 30, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Fair Value Disclosure of notes payable and capital lease obligations	$ 332,000	$ 517,000
Accumulated depreciation	6,700,000	5,700,000
Property, Plant and Equipment [Line Items]
Government contract receivable	10,100,000	23,900,000
Unbilled contracts receivable	1,500,000	4,300,000
Accrued expenses for subcontractor fees incurred under government contracts	$ 1,400,000	$ 2,900,000
Computer Equipment \| Minimum
Property, Plant and Equipment [Line Items]
Useful life	3 years
Computer Equipment \| Maximum
Property, Plant and Equipment [Line Items]
Useful life	5 years
Lab Equipment
Property, Plant and Equipment [Line Items]
Useful life	5 years
Contract Manufacturing Organization Equipment
Property, Plant and Equipment [Line Items]
Useful life	5 years

Long-Term Debt (Details)	1 Months Ended	3 Months Ended			9 Months Ended
Long-Term Debt (Details)	Mar. 31, 2010 USD ($)	Sep. 30, 2017 USD ($) ft² position	Sep. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Sep. 30, 2017 USD ($) ft² position	Sep. 30, 2016 USD ($)
Debt Instrument
Grant revenue		$ 5,379,000	$ 14,457,000		$ 18,279,000	$ 20,057,000
City of Ames Forgivable Loan 2010
Debt Instrument
Grant revenue				$ 397,000
Loans Payable \| City of Ames Forgivable Loan 2010
Debt Instrument
Original Available Balance	$ 400,000
Full-time position requirement (in positions) \| position		150			150
Term of lease	5 years
Lease extension term	5 years
Lease square feet \| ft²		20,000			20,000

License and Research Collaboration Agreements (Details) - USD ($)	1 Months Ended	3 Months Ended		9 Months Ended		12 Months Ended
	Feb. 28, 2015	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2014
Deferred Revenue Arrangement [Line Items]
Licensing and collaboration revenue		$ 103,000	$ 888,000	$ 334,000	$ 3,008,000
License and Collaborative Arrangement \| Merck
Deferred Revenue Arrangement [Line Items]
Upfront cash payments	$ 20,000,000					$ 30,000,000
Licensing and collaboration revenue			0		764,000
License and Collaborative Arrangement \| Genentech
Deferred Revenue Arrangement [Line Items]
Upfront cash payments						$ 150,000,000
Genentech potential milestones		561,000,000		561,000,000
Licensing and collaboration revenue		56,000	687,000	279,000	2,200,000
Reimbursement for direct labor			486,000		1,600,000
Alliance manager			$ 201,000		502,000
Participation in JRC					$ 101,000
Deferred revenue		$ 112,000		$ 112,000

Common Stock Equity Incentive Plan (Narrative)(Details) - USD ($)									3 Months Ended		9 Months Ended
	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	May 09, 2013	Jan. 01, 2013	Jan. 07, 2011	May 15, 2010	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Nov. 10, 2011
Share-based Compensation Arrangement by Share-based Payment Award
Share-based compensation expense									$ 4,400,000	$ 3,900,000	$ 14,900,000	$ 13,100,000
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized									10,238,220		10,238,220
Number of shares remained available for issuance									1,094,264		1,094,264
Increase in number of shares authorized	1,166,546	1,152,565	1,119,255	1,066,340		838,375	714,286	1,238,095
Evergreen increase (percent)											4.00%
2010 Non-Employee Directors' Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized													238,095
Number of shares remained available for issuance									0		0
Increase in number of shares authorized					161,905
2010 Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized													214,285
Number of shares remained available for issuance									120,784		120,784
Increase in number of shares authorized					185,715
Stock Option
Share-based Compensation Arrangement by Share-based Payment Award
Total compensation cost related to non-vested option awards									$ 19,900,000		$ 19,900,000
Weighted average vesting period for non-vested option awards, in years											2 years 1 month 24 days
Intrinsic value of options exercised											$ 924,164
Fair value of awards vested											12,400,000
Performance Stock
Share-based Compensation Arrangement by Share-based Payment Award
Share-based compensation expense											$ 1,200,000
Granted (in shares)											388,144
Weighted average grant-date fair value per share (in dollars per share)											$ 6.73
Options exercisable at end of period (in shares)											194,070
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award
Weighted average vesting period for non-vested option awards, in years											1 year 9 months 7 days
Granted (in shares)											0
Weighted average grant-date fair value per share (in dollars per share)											$ 0.00
Options exercisable at end of period (in shares)											80,380
Unrecognized compensation cost									4,400,000		$ 4,400,000
Performance Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award
Unrecognized compensation cost									$ 6,400,000		6,400,000
Fair value of restricted stock awards vested											$ 814,000

Common Stock Equity Incentive Plan (Authorized Increases of Common Stock) (Details) - shares	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	Jan. 01, 2013	Jan. 07, 2011	May 15, 2010
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Authorized Shares Added	1,166,546	1,152,565	1,119,255	1,066,340	838,375	714,286	1,238,095

Common Stock Equity Incentive Plan (Stock Option Activity) (Details) - Stock Option - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2017	Dec. 31, 2016
Number of options
Outstanding at beginning of period (in shares)	6,278,542
Options granted (in shares)	1,439,287
Options exercised (in shares)	(108,775)
Options forfeited (in shares)	(277,443)
Options expired (in shares)	(17,605)
Outstanding at end of period (in shares)	7,314,006	6,278,542
Weighted average exercise price
Outstanding, weighted average exercise price at beginning of period (in dollars per share)	$ 14.93
Granted, weighted average exercise price (in dollars per share)	11.78
Exercised, weighted average exercise price (in dollars per share)	8.51
Forfeitured, weighted average exercise price (in dollars per share)	20.13
Expired, weighted average exercise price (in dollars per share)	42.00
Outstanding, weighted average exercise price at end of period (in dollars per share)	$ 14.15	$ 14.93
Options exercisable at end of period (in shares)	5,456,602
Exercisable, weighted average exercise price (in dollars per share)	$ 12.65
Outstanding, weighted average remaining contractual term, in years	5 years 6 months 15 days	5 years 9 months 18 days
Exercisable, weighted average remaining contractual term, in years	4 years 5 months 12 days

Common Stock Equity Incentive Plan (Range of Assumptions Used) (Details) - Stock Option	9 Months Ended
	Sep. 30, 2017 $ / shares
Share-based Compensation Arrangement by Share-based Payment Award
Risk-free interest rate, minimum (percent)	1.90%
Risk free interest rate, maximum (percent)	2.20%
Expected dividend rate (percent)	0.00%
Volatility rate, minimum (percent)	68.90%
Volatility rate, maximum (percent)	73.20%
Weighted average grant-date fair value per share (in dollars per share)	$ 7.81
Minimum
Share-based Compensation Arrangement by Share-based Payment Award
Expected Term (in years)	6 years 6 months
Maximum
Share-based Compensation Arrangement by Share-based Payment Award
Expected Term (in years)	7 years 9 months 18 days

Common Stock Equity Incentive Plan (Restricted Stock Activity) (Details) - Restricted Stock	9 Months Ended
	Sep. 30, 2017 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Non-Option Equity Instruments, Outstanding [Roll Forward]
Unvested at beginning of period (in shares) \| shares	288,964
Granted (in shares) \| shares	0
Vested (in shares) \| shares	(80,380)
Forfeited / cancelled (in shares) \| shares	(27,248)
Unvested at end of period (in shares) \| shares	181,336
Share-based Compensation Arrangement by Share-based Payment Award, Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted average grant date fair value at beginning of period (in dollars per share) \| $ / shares	$ 34.94
Weighted average grant-date fair value per share (in dollars per share) \| $ / shares	0.00
Vested, weighted average grant date fair value (in dollars per share) \| $ / shares	35.04
Forfeited/cancelled, weighted average grant date fair value (in dollars per share) \| $ / shares	33.84
Weighted average grant date fair value at end of period (in dollars per share) \| $ / shares	$ 35.05

Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended
Income Taxes (Details) - USD ($)	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Income Tax Disclosure [Abstract]
Income tax benefit	$ 119,000	$ 1,308,000	$ 429,000	$ 5,021,000
Uncertain tax positions	$ 843,000		$ 843,000

Net Loss per Common Share (Net Loss Per Share Computation) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Earnings Per Share [Abstract]
Loss attributable to common stockholders	$ (20,626)	$ (15,540)	$ (58,265)	$ (71,649)
Basic and diluted weighted-average shares outstanding (in shares)	29,939,823	28,983,561	29,462,226	28,911,042
Basic and diluted loss per share (in dollars per share)	$ (0.69)	$ (0.54)	$ (1.98)	$ (2.48)

Net Loss per Common Share (Antidilutive Securities) (Details) - shares	3 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Stock Option
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	7,314,006	6,453,331
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	181,336	307,079

Restructuring Charges (Details) - USD ($)	1 Months Ended	3 Months Ended	9 Months Ended	12 Months Ended
Restructuring Charges (Details) - USD ($)	Jul. 31, 2017	Sep. 30, 2017	Sep. 30, 2017	Dec. 31, 2016
Restructuring Charges
Percentage reduction in force	50.00%
Asset impairment charges				$ 4,000,000
Restructuring Reserve [Roll Forward]
Balance at beginning of period			$ 42,000
Expensed			1,695,000	12,300,000
Cash Payments			1,085,000
Balance at end of period		$ 652,000	652,000	42,000
General and Administrative Expense [Member]
Restructuring Reserve [Roll Forward]
Expensed				500,000
Research and Development Expense [Member]
Restructuring Reserve [Roll Forward]
Expensed				11,800,000
Employee Severance Cost
Restructuring Reserve [Roll Forward]
Balance at beginning of period			42,000
Expensed		1,700,000	1,695,000
Cash Payments			1,085,000
Balance at end of period		652,000	652,000	$ 42,000
2016 Restructuring Plan
Restructuring Reserve [Roll Forward]
Expensed		$ 0	$ 0

Subsequent Events (Details) - Subsequent event - Public Offering [Member] $ in Millions	Oct. 06, 2017 USD ($) shares
Subsequent Event [Line Items]
Number of shares issued \| shares	5,750,000
FInancing proceeds	$ 55.2
Fees and commissions	$ 3.7