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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2016	Nov. 02, 2016
Entity Information [Line Items]
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, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Common Stock, Shares Outstanding		29,134,623
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 148,276	$ 195,620
Certificates of deposit	0	2,180
Prepaid expenses and other current assets	10,688	4,954
Income tax receivable	5,197	0
Other receivables	14,995	5,388
Total current assets	179,156	208,142
Property and equipment, net	7,188	10,400
Total assets	186,344	218,542
Current liabilities:
Accounts payable	2,367	3,661
Accrued expenses	37,259	8,761
Income taxes payable	0	859
Current portion of unearned revenue	693	892
Current portion of deferred rent	81	96
Current portion of notes payable and obligations under capital leases	245	571
Total current liabilities	40,645	14,840
Long-term liabilities:
Royalty obligation payable to Iowa Economic Development Authority	6,000	6,000
Notes payable and obligations under capital leases	333	368
Unearned revenue	0	407
Deferred rent	1,089	1,153
Total long-term liabilities	7,422	7,928
Total liabilities	48,067	22,768
Stockholders' equity:
Blank check preferred stock, $0.01 par value: Authorized shares — 5,000,000 at September 30, 2016 and December 31, 2015; issued and outstanding shares — 0 at September 30, 2016 and December 31, 2015	0	0
Common stock, $0.01 par value: Authorized shares — 75,000,000 at September 30, 2016 and December 31, 2015; issued 29,116,879 and 28,838,176 at September 30, 2016 and December 31, 2015, respectively, and outstanding 29,091,652 and 28,814,142 at September 30, 2016 and December 31, 2015, respectively	291	288
Additional paid-in capital	290,772	276,610
Treasury stock, at cost: 25,227 and 24,034 shares at September 30, 2016 and December 31, 2015, respectively	(784)	(771)
Accumulated deficit	(152,002)	(80,353)
Total stockholders' equity	138,277	195,774
Total liabilities and stockholders' equity	$ 186,344	$ 218,542

Consolidated Balance Sheets (Parentheticals) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Stockholders' Equity:
Blank check preferred stock, par value	$ 0.01	$ 0.01
Blank check preferred stock, authorized shares	5,000,000	5,000,000
Blank check preferred stock, issued shares	0.00	0.00
Blank check preferred stock, outstanding shares	0	0
Common stock, par value	$ 0.01	$ 0.01
Common stock, $0.01 par value: Authorized shares — 75,000,000 at September 30, 2016 and December 31, 2015; issued 29,116,879 and 28,838,176 at September 30, 2016 and December 31, 2015, respectively, and outstanding 29,091,652 and 28,814,142 at September 30, 2016 and December 31, 2015, respectively	75,000,000	75,000,000
Common stock, issued shares	29,116,879	28,838,176
Common stock, outstanding shares	29,091,652	28,814,142
Treasury stock, at cost: 25,227 and 24,034 shares at September 30, 2016 and December 31, 2015, respectively	25,227	24,034

Condensed Consolidated Statements of Operations - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Grant revenue	$ 14,457,000	$ 13,365,000	$ 20,057,000	$ 26,294,000
Licensing and collaboration revenue	888,000	844,000	3,008,000	34,555,000
Total operating revenues	15,345,000	14,209,000	23,065,000	60,849,000
Operating expenses:
Research and development	24,463,000	22,508,000	73,810,000	56,619,000
General and administrative	7,749,000	7,384,000	26,043,000	23,007,000
Total operating expenses	32,212,000	29,892,000	99,853,000	79,626,000
Loss from operations	(16,867,000)	(15,683,000)	(76,788,000)	(18,777,000)
Other income and expense:
Miscellaneous expense	(44,000)		(44,000)
Interest income	68,000	25,000	180,000	68,000
Interest expense	(5,000)	(88,000)	(18,000)	(98,000)
Other income (expense), net	19,000	(63,000)	118,000	(30,000)
Net loss before taxes	(16,848,000)	(15,746,000)	(76,670,000)	(18,807,000)
Income tax benefit (expense)	1,308,000	(160,000)	5,021,000	0
Net loss	$ (15,540,000)	$ (15,906,000)	$ (71,649,000)	$ (18,807,000)
Basic and diluted loss per share	$ (0.54)	$ (0.55)	$ (2.48)	$ (0.66)
Basic and diluted average shares outstanding	28,983,561	28,734,768	28,911,042	28,518,503

Consolidated Statement of Stockholders' Equity (Deficit) - 9 months ended Sep. 30, 2016 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Treasury Stock	Accumulated Deficit
Balance at December 31, 2015 at Dec. 31, 2015	$ 195,774	$ 288	$ 276,610	$ (771)	$ (80,353)
Balance at December 31, 2015 (shares) at Dec. 31, 2015	28,814,142
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	$ 13,119		13,119
Exercise of stock options and restricted stock vested	$ 1,323	3	1,320
Exercise of stock options and restricted stock vested (shares)	240,815
Sale of shares under stock purchase plan	$ 363		363
Sale of shares under stock purchase plan (shares)	37,888
Shares withheld for statutory tax withholding	$ (13)			(13)
Shares withheld for statutory tax withholding (shares)	(1,193)
Tax shortfall from employee stock plan awards	$ (640)		(640)
Net loss	$ (71,649)				(71,649)
Balance at September 30, 2016 (shares) at Sep. 30, 2016	29,091,652
Balance at September 30, 2016 at Sep. 30, 2016	$ 138,277	$ 291	$ 290,772	$ (784)	$ (152,002)

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash Flows From Operating Activities
Net loss	$ (71,649)	$ (18,807)
Adjustments to reconcile net loss to net cash used in operating activities:
Share-based compensation	13,119	12,394
Depreciation and amortization	1,536	1,071
Forgiveness of debt	(397)	0
Impairment of fixed assets	3,976	0
Tax shortfall associated with employee stock plan awards	(640)	0
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(5,734)	6,565
Other receivables	(9,607)	(11,261)
Accounts payable and accrued expenses	27,204	(1,780)
Income taxes receivable	(6,056)	8,687
Unearned revenue	(606)	(12,542)
Deferred rent	(79)	(62)
Net cash used in operating activities	(48,933)	(15,735)
Cash Flows From Investing Activities
Maturity of certificates of deposit	2,180	9,177
Purchase of equipment	(2,069)	(3,450)
Net cash provided by investing activities	111	5,727
Cash Flows From Financing Activities
Issuance of common stock, net of offering costs	1,686	17,230
Repurchase of common stock	(13)	(341)
Payments under capital lease obligations and principal payments on notes payable	(195)	(144)
Net cash provided by financing activities	1,478	16,745
Net (decrease) increase in cash and cash equivalents	(47,344)	6,737
Cash and cash equivalents at beginning of period	195,620	190,404
Cash and cash equivalents at end of period	148,276	197,141
Supplemental disclosure of cash flows information:
Cash paid for interest	18	37
Cash paid for taxes	1,022	4,808
Noncash financing and investing activities:
Equipment acquired by capital lease	231	0
Forgiveness of debt	$ 397	$ 0

Description of Business (Notes)	9 Months Ended
Description of Business (Notes)	Sep. 30, 2016
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. In 2005, NewLink created a partially owned subsidiary, BioProtection Systems Corporation (BPS). NewLink contributed certain licensing agreements and other intangible assets for BPS to create vaccines against potential biological terror threats. On January 7, 2011, NewLink acquired all of the minority interest in BPS by merging a newly formed subsidiary of NewLink with BPS, with BPS as the surviving corporation, resulting in NewLink owning all the outstanding capital stock of BPS. In 2013, NewLink created a wholly-owned subsidiary, NewLink International (NI). NewLink plans to conduct all or a portion of its operations outside of the United States through NI. In 2014, NewLink created another wholly owned subsidiary, NewLink Global (NG), which was subsequently merged into NewLink during 2014. 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 $15.5 million and $71.6 million for the three and nine months ended September 30, 2016, respectively. In May 2016, the Company announced that its Phase 3 clinical trial IMPRESS (IMmunotherapy for Pancreatic RESectable cancer Study) of algenpantucel-L for patients with resected pancreatic cancer did not achieve its primary endpoint and the Company's management adopted a restructuring plan designed to better align the Company's workforce and operating costs to its revised pipeline development plans and operating needs. The restructuring plan 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. In connection with the restructuring plan, the Company also discontinued the development of its commercial manufacturing capabilities for algenpantucel-L, discontinued programs supporting the future commercialization of algenpantucel-L, and recorded an impairment charge to fixed assets. The Company has retained some internal manufacturing ability to support the development of clinical supplies for its ongoing clinical trials of the other HyperAcute Cellular Immunotherapy product candidates. Refer to Note 9 for more information. The accompanying condensed consolidated financial statements as of September 30, 2016 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 the at the market (ATM) offering. 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 offerings are expected to be adequate to satisfy the Company's liquidity requirements through 2018. 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 (Notes)	9 Months Ended
Basis of Presentation (Notes)	Sep. 30, 2016
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, 2015, 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 2015. The financial results for any interim period are not necessarily indicative of financial results for the full year.

Significant Accounting Policies (Notes)	9 Months Ended
Significant Accounting Policies (Notes)	Sep. 30, 2016
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, certificates of deposit, 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 $578,000 and $939,000 as of September 30, 2016 and December 31, 2015, respectively, which approximate fair value using Level 2 inputs. 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 $5.2 million and $6.5 million as of September 30, 2016 and December 31, 2015, 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 $14.0 million and $4.1 million of receivables from the government contracts recorded in other receivables and $9.7 million and $3.6 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, 2016 and December 31, 2015, respectively. The Company had $18.3 million and $1.1 million of accrued expenses for subcontractor fees incurred under the government contracts as of September 30, 2016 and December 31, 2015, respectively. Recent Accounting Pronouncements In February 2016, the Financial Accounting Standards Board, or the FASB, issued ASU No. 2016-02, Leases, to improve financial reporting for leasing transactions. The new standard requires lessees to recognize on the balance sheet a right of use asset and related lease liability for all leases with terms greater than twelve months. The ASU also requires disclosures about the amount, timing, and uncertainty of cash flows arising from leases. The effective date for public entities is fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted for all entities. The Company is currently evaluating any impact this standard may have on its consolidated financial statements and related disclosures. In March 2016, the FASB issued ASU No, 2016-09, Compensation—Stock Compensation: Improvements to Employee Share-Based Payment Accounting. The ASU includes multiple provisions intended to simplify various aspects of the accounting for share-based payments. While aimed at reducing the cost and complexity of the accounting for share-based payments, the amendments are expected to significantly impact net income, earnings per share, and the statement of cash flows. The effective date for public entities is for fiscal years beginning after December 15, 2016. Early adoption is permitted in any interim period provided that the entire ASU is adopted. The Company is currently evaluating any impact this standard may have on its consolidated financial statements and related disclosures. In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows, Classification of Certain Cash Receipts and Cash Payments, which addresses eight specific cash flow issues with the objective of reducing the existing diversity in practice. The guidance will be effective for the fiscal year beginning after December 15, 2017, including interim periods within that year. The Company does not expect the adoption of this standard to have an impact on its condensed consolidated financial statements.

Long-Term Debt (Notes)	9 Months Ended
Long-Term Debt (Notes)	Sep. 30, 2016
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 nine months ended September 30, 2016.

License and Research Collaboration Agreements (Notes)	9 Months Ended
License and Research Collaboration Agreements (Notes)	Sep. 30, 2016
Revenue Recognition [Abstract]
Licensing and Research Collaboration Agreements [Text Block]	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 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 payments of over $1.0 billion upon achieving certain GDC-0919 and 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 GDC-0919 and any subsequent products for the U.S. market and is also eligible to receive escalating double digit royalty payments on potential commercial sales of multiple products by Genentech. For the three and nine months ended September 30, 2016, the Company recognized license and collaboration revenue under the Genentech Agreement of $687,000 and $2.2 million, respectively, 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 (JRC). For the three and nine months ended September 30, 2015, the Company recognized license and collaboration revenue under the Genentech agreement of $808,000 and $14.4 million, respectively, including $2.0 million for amounts received as reimbursement for the Company's employees working on the project, $11.9 million for program materials and technology transfer, $335,000 for providing an alliance manager, and $118,000 for participation in the JRC. In accordance with the Company’s continuing performance obligation, $642,000 of the $150.0 million upfront payment remains deferred as of September 30, 2016 and will be recognized in future periods. 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. For the three and nine months ended September 30, 2016, the Company recognized license and collaboration revenues of $203,000 and $764,000, respectively, for the reimbursement of costs not covered under government contracts. For the nine months ended September 30, 2015, the Company recognized license and collaboration revenue under the Merck Agreement of $20.0 million associated with the one-time non-refundable milestone payment. For the three and nine months ended September 30, 2015, the Company recognized revenues of $36,000 and $170,000, respectively, associated with the remaining deliverables. In accordance with the Company’s continuing performance obligations, $51,000 of the $30.0 million upfront payment remains deferred as of September 30, 2016 and will be recognized in future periods. The upfront payment provides no general right of return for any non-contingent deliverable, and no portion of any revenue recognized is refundable.

Common Stock Equity Incentive Plan (Notes)

9 Months Ended

Sep. 30, 2016

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, 2016, there were 9,071,674 shares of common stock authorized for the 2009 Plan and 910,275 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

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 2016 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, 2016, zero 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, 2016, 193,504 shares remained available for issuance under the 2010 Purchase Plan.

Share-based Compensation

Share-based compensation expense for the three and nine months ended September 30, 2016 and 2015 was $3.9 million and $13.1 million, $3.3 million, and $12.4 million, respectively, and is allocated between research and development and general and administrative expenses within the condensed consolidated statements of operations.

As of September 30, 2016, the total compensation cost related to nonvested option awards not yet recognized was $29.1 million and the weighted-average period over which it is expected to be recognized is 2.6 years.

Stock Options

The following table summarizes the stock option activity for the nine months ended September 30, 2016:



	Number of options		Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	5,646,480		$	15.11
Options granted	1,345,258		19.04
Options exercised	(184,790	)	7.15
Options forfeited	(327,328	)	31.97
Options expired	(28,633	)	21.47
Outstanding at end of period	6,453,331		$	15.27	6.0
Options exercisable at end of period	4,457,868		$	11.11	4.7

The following table summarizes the range of assumptions used to estimate the fair value of stock options granted during the nine months ended September 30, 2016:



Risk-free interest rate		1.2%-2.0%
Expected dividend yield		—%
Expected volatility		67.1%-69.8%
Expected term (in years)		5.9-7.4
Weighted-average grant-date fair value per share		$11.91

The intrinsic value of options exercised during the nine months ended September 30, 2016 was $908,919. The fair value of awards vested during the nine months ended September 30, 2016 was $11.8 million.

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.

On January 4, 2016, the Company's Board of Directors approved grants of restricted stock unit awards to certain of the named executive officers for extraordinary performance in 2015. These are recognized as grants made in 2016. During the nine months ended September 30, 2016 and 2015, there were 115,566 and 131,610 shares of restricted stock granted, respectively, which vest over a four year period, with 25% vesting on each of the first, second, third and fourth anniversaries of the date the award was granted. The restricted stock grants as of September 30, 2016 and 2015 had a weighted average fair value per share of $34.73 and $43.66, respectively. Compensation expense is recognized for the issuance of restricted stock by amortizing over the requisite service period, or the vesting period, the aggregate fair value of the restricted stock awarded.

Additionally, during the three months ended March 31, 2016, the Company’s Board of Directors approved and granted 78,268 shares of performance restricted stock units. The performance restricted stock units had a weighted average fair value per share of $34.73. As a result of failure to meet certain criteria required for the vesting of the performance restricted stock units, 58,702 of the shares granted were forfeited during the second quarter of 2016. The remaining performance restricted stock units will vest upon the receipt of a milestone payment from Genentech under the Genentech Agreement upon the advancement of GDC-0919 into Phase 2 development. No compensation expense was recognized for these performance restricted stock units during the nine months ended September 30, 2016.

A summary of the Company's unvested restricted stock, including performance restricted stock, at September 30, 2016 and changes during the nine months ended September 30, 2016 are as follows:



	Number of restricted stock shares		Weighted average grant date fair value
Unvested at beginning of period	228,972			$	34.94
Granted	193,834			34.73
Vested	(56,025	)		37.22
Forfeited/cancelled	(59,702	)		34.58
Unvested restricted stock at end of period	307,079			$	34.46

As of September 30, 2016, the total remaining unrecognized compensation cost related to issuances of restricted stock was approximately $7.7 million and is expected to be recognized over a weighted-average period of 2.6 years. As of September 30, 2016, there remains approximately $680,000 of unrecognized compensation cost related to the issuance of performance restricted stock. The fair value of restricted stock, including performance restricted stock, granted during the nine months ended September 30, 2016 was $6.7 million. The fair value of awards vested during the nine months ended September 30, 2016 was $1.7 million.

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.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Income Taxes (Notes)	9 Months Ended
Income Taxes (Notes)	Sep. 30, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes 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. For the three and nine months ended September 30, 2015, the Company recorded an income tax benefit of $160,000 and $0, respectively. The 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 potential to carry back losses to 2014 and the net loss generated by NewLink's foreign subsidiary. Income tax expense for the three and nine months ended September 30, 2015 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to changes in the valuation allowance for deferred taxes, 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, 2016 and December 31, 2015, respectively, due to the uncertainty of future recoverability. The Company has a reserve for uncertain tax positions related to state tax matters of $653,000 as of September 30, 2016 recorded within Accrued Expenses in the condensed consolidated balance sheet.

Net Loss per Common Share (Notes)

9 Months Ended

Sep. 30, 2016

Earnings Per Share [Abstract]

Earnings Per Share [Text Block]

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,
	2016			2015			2016			2015
Loss attributable to common stockholders	$	(15,540	)	$	(15,906	)	$	(71,649	)	$	(18,807	)

Basic and diluted weighted-average shares outstanding	28,983,561			28,734,768			28,911,042			28,518,503

Basic and diluted loss per share	$	(0.54	)	$	(0.55	)	$	(2.48	)	$	(0.66	)

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. For the three and nine months ended September 30, 2016, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 6,453,331 and 307,079, respectively. For the three and nine months ended September 30, 2015, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 5,551,219 and 239,249, respectively.

Restructuring Charges (Notes)

9 Months Ended

Sep. 30, 2016

Restructuring and Related Activities [Abstract]

Restructuring and Related Activities Disclosure [Text Block]

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 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 recorded an impairment charge for 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.

During the three months ended September 30, 2016, the Company did not record any additional restructuring charges. During the nine months ended September 30, 2016 the restructuring resulted in charges of $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. There were no restructuring charges recorded in prior periods.

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		Contract Termination Cost		Total
Balance as of December 31, 2015	—		$	—	$	—
Expensed	1,800,000		6,500,000		8,300,000
Cash Payments	1,528,000		85,000		1,613,000
Balance as of September 30, 2016	$	272,000	$	6,415,000	$	6,687,000

Commitments and Contingencies (Notes)	9 Months Ended
Commitments and Contingencies (Notes)	Sep. 30, 2016
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, against the Company, the Company’s Chief Executive Officer Charles J. Link, Jr., the Company’s Chief Financial Officer John B. Henneman III, and the Company’s former Chief Financial Officer Gordon H. Link, Jr., captioned Abramson v. NewLink Genetics Corp., et al., Case 1:16-cv-3545, or the Action. On August 16, 2016, the Court appointed Michael and Kelly Nguyen as lead plaintiffs and approved their selection of Kahn, Swick & Foti, LLC as lead counsel in the Action. On August 26, 2016, the Court issued an order providing that (i) the lead plaintiffs shall file an amended complaint on or before October 31, 2016, (ii) the defendants shall submit a letter to the Court regarding a potential motion responsive to the amended complaint on November 15, 2016, and (iii) the lead plaintiffs shall submit a letter to the Court opposing the defendants’ letter on November 22, 2016. On October 31, 2016, the lead plaintiffs filed an amended complaint which asserts claims under the federal securities laws against the Company, Charles J. Link, Jr., and the Company’s Chief Medical Officer and President Nicholas Vahanian, or collectively, the Defendants (no claims are asserted in the amended complaint against Messrs. Henneman or Gordon Link). 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. The Company disputes the claims in the Action and intends to defend against them vigorously.

Subsequent Events (Notes)	9 Months Ended
Subsequent Events (Notes)	Sep. 30, 2016
Subsequent Events [Abstract]
Subsequent Events [Text Block]	Subsequent Events The Company announced on October 4, 2016 that the Biomedical Advanced Research and Development Authority, or BARDA, of the United States Department of Health and Human Services issued a $24.8 million contract to a subsidiary of NewLink to support the advanced development of the investigational rVSV∆G-ZEBOV GP (Ebola Zaire) vaccine candidate, designated V920. The new contract with BARDA includes an additional $51.2 million of contract options that may be exercised by BARDA. The funding provided by this contract will support manufacturing facility readiness, manufacturing process qualification activities and additional clinical trials to support regulatory approval of the V920 vaccine.

Significant Accounting Policies (Policies)	9 Months Ended
Significant Accounting Policies (Policies)	Sep. 30, 2016
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 and Concentrations of Credit Risk	Financial Instruments and Concentrations of Credit Risk Cash and cash equivalents, certificates of deposit, 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 $578,000 and $939,000 as of September 30, 2016 and December 31, 2015, respectively, which approximate fair value using Level 2 inputs. 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, Plant and Equipment, Policy	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 $5.2 million and $6.5 million as of September 30, 2016 and December 31, 2015, 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 $14.0 million and $4.1 million of receivables from the government contracts recorded in other receivables and $9.7 million and $3.6 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, 2016 and December 31, 2015, respectively. The Company had $18.3 million and $1.1 million of accrued expenses for subcontractor fees incurred under the government contracts as of September 30, 2016 and December 31, 2015, respectively.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In February 2016, the Financial Accounting Standards Board, or the FASB, issued ASU No. 2016-02, Leases, to improve financial reporting for leasing transactions. The new standard requires lessees to recognize on the balance sheet a right of use asset and related lease liability for all leases with terms greater than twelve months. The ASU also requires disclosures about the amount, timing, and uncertainty of cash flows arising from leases. The effective date for public entities is fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted for all entities. The Company is currently evaluating any impact this standard may have on its consolidated financial statements and related disclosures. In March 2016, the FASB issued ASU No, 2016-09, Compensation—Stock Compensation: Improvements to Employee Share-Based Payment Accounting. The ASU includes multiple provisions intended to simplify various aspects of the accounting for share-based payments. While aimed at reducing the cost and complexity of the accounting for share-based payments, the amendments are expected to significantly impact net income, earnings per share, and the statement of cash flows. The effective date for public entities is for fiscal years beginning after December 15, 2016. Early adoption is permitted in any interim period provided that the entire ASU is adopted. The Company is currently evaluating any impact this standard may have on its consolidated financial statements and related disclosures. In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows, Classification of Certain Cash Receipts and Cash Payments, which addresses eight specific cash flow issues with the objective of reducing the existing diversity in practice. The guidance will be effective for the fiscal year beginning after December 15, 2017, including interim periods within that year. The Company does not expect the adoption of this standard to have an impact on its condensed consolidated financial statements.

Common Stock Equity Incentive Plan (Tables)

9 Months Ended

Sep. 30, 2016

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

Stock Option Activity

The following table summarizes the stock option activity for the nine months ended September 30, 2016:



	Number of options		Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	5,646,480		$	15.11
Options granted	1,345,258		19.04
Options exercised	(184,790	)	7.15
Options forfeited	(327,328	)	31.97
Options expired	(28,633	)	21.47
Outstanding at end of period	6,453,331		$	15.27	6.0
Options exercisable at end of period	4,457,868		$	11.11	4.7

Assumptions Used in Black-Scholes Pricing Model for New Grants

The following table summarizes the range of assumptions used to estimate the fair value of stock options granted during the nine months ended September 30, 2016:



Risk-free interest rate		1.2%-2.0%
Expected dividend yield		—%
Expected volatility		67.1%-69.8%
Expected term (in years)		5.9-7.4
Weighted-average grant-date fair value per share		$11.91

Restricted Stock Activity

A summary of the Company's unvested restricted stock, including performance restricted stock, at September 30, 2016 and changes during the nine months ended September 30, 2016 are as follows:



	Number of restricted stock shares		Weighted average grant date fair value
Unvested at beginning of period	228,972			$	34.94
Granted	193,834			34.73
Vested	(56,025	)		37.22
Forfeited/cancelled	(59,702	)		34.58
Unvested restricted stock at end of period	307,079			$	34.46

Net Loss per Common Share (Tables)

9 Months Ended

Sep. 30, 2016

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,
	2016			2015			2016			2015
Loss attributable to common stockholders	$	(15,540	)	$	(15,906	)	$	(71,649	)	$	(18,807	)

Basic and diluted weighted-average shares outstanding	28,983,561			28,734,768			28,911,042			28,518,503

Basic and diluted loss per share	$	(0.54	)	$	(0.55	)	$	(2.48	)	$	(0.66	)

Restructuring Charges (Tables)

9 Months Ended

Sep. 30, 2016

Restructuring and Related Activities [Abstract]

Restructuring and Related Costs [Table Text Block]

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		Contract Termination Cost		Total
Balance as of December 31, 2015	—		$	—	$	—
Expensed	1,800,000		6,500,000		8,300,000
Cash Payments	1,528,000		85,000		1,613,000
Balance as of September 30, 2016	$	272,000	$	6,415,000	$	6,687,000

Description of Business (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Description of Business (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2014	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015	Feb. 04, 2013	Nov. 16, 2011
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Net loss	$ (15,500)		$ (71,649)	$ (18,807)
Financings
Genentech Upfront Payments		$ 150,000
Merck Upfront Payments		$ 30,000
Merck One-Time Milestones				$ 20,000
Initial Public Offering
Financings
FInancing proceeds							$ 37,600
Follow-on Offering
Financings
FInancing proceeds						$ 49,000
ATM Offering
Financings
FInancing proceeds					$ 58,700

Significant Accounting Policies Accounting Policies (Details) - USD ($)	Sep. 30, 2016	Dec. 31, 2015
Accounting Policies [Abstract]
Fair Value Disclosure of notes payable and capital lease obligations	$ 578,000	$ 939,000
Accumulated Depreciation, Property, Plant, and Equipment	5,200,000	6,500,000
Unbilled Contracts Receivable	9,700,000	3,600,000
Government Contract Receivable	14,000,000	4,100,000
Accrued Expenses for subcontractor fees incurred under government contracts	$ 18,300,000	$ 1,100,000

Long-Term Debt (Details)	9 Months Ended
Long-Term Debt (Details)	Sep. 30, 2016 USD ($)
Debt Instrument
Extinguishment of Debt, Amount	$ 397,000
Amount \| City of Ames Forgivable Loan 2010
Debt Instrument
Original Available Balance	$ 400,000
Jobs by March 10, 2016	150
Lease square feet	20,000

License and Research Collaboration Agreements (Details) - USD ($)	3 Months Ended			9 Months Ended		12 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2014	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2014
Deferred Revenue Arrangement [Line Items]
Genentech Upfront Payments			$ 150,000,000
Merck One-Time Milestones					$ 20,000,000
Merck Upfront Payments			$ 30,000,000
Genentech [Member]
Deferred Revenue Arrangement [Line Items]
Genentech Potential Milestones	$ 1,000,000,000			$ 1,000,000,000
Genentech Revenue Recognized	687,000	$ 808,000		2,200,000	14,400,000
Genentech Upfront Payments						$ 150,000,000
Deferred Revenue	642,000			642,000
Reimbursement for direct labor				1,600,000	2,000,000
Alliance manager				502,000	335,000
Participation in JRC				101,000	118,000
Genentech Revenue Allocated to License and Manufacturing Technology Transfer					11,900,000
Merck [Member]
Deferred Revenue Arrangement [Line Items]
Deferred Revenue	51,000			51,000
Merck One-Time Milestones					20,000,000
Merck Upfront Payments						$ 30,000,000
Merck Revenue Recognized	$ 203,000	$ 36,000		$ 764,000	$ 170,000

Common Stock Equity Incentive Plan (Details)	3 Months Ended		9 Months Ended		12 Months Ended
Common Stock Equity Incentive Plan (Details)	Sep. 30, 2016 USD ($) $ / shares shares	Sep. 30, 2015 USD ($)	Sep. 30, 2016 USD ($) $ / shares shares	Sep. 30, 2015 USD ($) $ / shares shares	Dec. 31, 2015 $ / shares shares	Dec. 31, 2014 shares	Dec. 31, 2013 shares	Dec. 31, 2011 shares	Dec. 31, 2010 shares
Share-based Compensation Arrangement by Share-based Payment Award
Share-based Compensation Expense \| $	$ 3,900,000	$ 3,300,000	$ 13,100,000	$ 12,400,000
Stock Option Activity
Options exercised			240,815
Restricted Stock Activity
Restricted stock granted			115,566
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Evergreen Increase Percentage					4.00%
Number of Shares Authorized	9,071,674		9,071,674
Number of Shares Available for Grant	910,275		910,275
Increase in Number of Shares Authorized			1,152,565		1,119,255	1,066,340	838,375	714,286,000	1,238,095
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 Available for Grant	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 Available for Grant	193,504		193,504
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 \| $	$ 29,100,000		$ 29,100,000
Weighted-average period over which nonvested stock option compensation expenses is expected to be recognized			2.6
Assumptions Used in Black Scholes Pricing Model for New Grants
Risk-free interest rate, minimum			1.20%
Risk free interest rate, maximum			2.00%
Expected dividend rate			0.00%
Volatility rate, minimum			67.10%
Volatility rate, maximum			69.80%
Weighted average grant-date fair value per share \| $ / shares			$ 11.91
Stock Option Activity
Outstanding at beginning of period			5,646,480
Outstanding, weighted average exercise price at beginning of period \| $ / shares			$ 15.11
Options granted			1,345,258
Granted, weighted average exercise price \| $ / shares			$ 19.04
Options exercised			184,790
Exercised, weighted average exercise price \| $ / shares			$ 7.15
Options forfeited			327,328
Forfeitured, weighted average exercise price \| $ / shares			$ 31.97
Options expired			28,633
Expired, weighted average exercise price \| $ / shares			$ 21.47
Outstanding at end of period	6,453,331		6,453,331		5,646,480
Outstanding, weighted average exercise price at end of period \| $ / shares	$ 15.27		$ 15.27		$ 15.11
Options exercisable at end of period	4,457,868		4,457,868
Outstanding, weighted average remaining contractual term, in years			6 years
Exercisable, weighted average exercise price \| $ / shares	$ 11.11		$ 11.11
Exercisable, weighted average remaining contractual term, in years			4 years 8 months 12 days
Intrinsic Value of Options Exercised \| $			$ 908,919
Fair Value of Awards Vested \| $			$ 11,800,000
Performance Shares
Stock Option Activity
Options forfeited			58,702
Restricted Stock Activity
Weighted average grant date fair value per share \| $ / shares			$ 34.73
Restricted stock granted			78,268
Unrecognized compensation cost \| $	$ 680,000		$ 680,000
Fair value of restricted stock awards vested \| $			$ 1,700,000
Restricted Stock
Restricted Stock Activity
Award Vesting Percentage			25.00%
Weighted average grant date fair value per share \| $ / shares			$ 34.73	$ 43.66
Restricted stock unvested at beginning of period	307,079		228,972
Weighted average grant date fair value at beginning of period \| $ / shares	$ 34.46		$ 34.94
Restricted stock granted			193,834	131,610
Granted, weighted average grant date fair value \| $ / shares			$ 34.73
Restricted stock vested			56,025
Vested, weighted average grant date fair value \| $ / shares			$ 37.22
Restricted stock forfeited / cancelled			59,702
Forfeited/cancelled, weighted average grant date fair value \| $ / shares			$ 34.58
Restricted stock unvested at end of period					228,972
Weighted average grant date fair value at end of period \| $ / shares					$ 34.94
Weighted average vesting period for non-vested option awards, in years			2 years 7 months 6 days
Unrecognized compensation cost \| $	$ 7,700,000		$ 7,700,000
Grant date fair value of restricted stock awards granted \| $			$ 6,700,000
Minimum \| Stock Option
Assumptions Used in Black Scholes Pricing Model for New Grants
Expected Term			5 years 10 months 24 days
Maximum \| Stock Option
Assumptions Used in Black Scholes Pricing Model for New Grants
Expected Term			7 years 4 months 27 days

Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended
Income Taxes (Details) - USD ($)	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Operating Loss Carryforwards [Line Items]
Liability for Uncertain Tax Positions, Current	$ 653,000		$ 653,000
Income tax benefit (expense)	$ 1,308,000	$ (160,000)	$ 5,021,000	$ 0

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, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Earnings Per Share [Abstract]
Net loss	$ (15,540)	$ (15,906)	$ (71,649)	$ (18,807)
Basic and diluted average shares outstanding	28,983,561	28,734,768	28,911,042	28,518,503
Basic and diluted loss per share	$ (0.54)	$ (0.55)	$ (2.48)	$ (0.66)

Net Loss per Common Share (Antidilutive Securities) (Details) - shares	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Stock Option
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	6,453,331	5,551,219
Restricted Stock Units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	307,079	239,249

Restructuring Charges (Details)	9 Months Ended
Restructuring Charges (Details)	Sep. 30, 2016 USD ($)
Restructuring Charges
Restructuring Charges	$ 12,300,000
General and administrative restructuring expense	500,000
Research and development restructuring expense	11,800,000
Property, Plant and Equipment Impairment Charge	4,000,000
Employee Severance
Restructuring Charges
Balance as of December 31, 2015	0
Expensed	1,800,000
Cash Payments	1,528,000
Balance as of September 30, 2016	272,000
Contract Termination
Restructuring Charges
Balance as of December 31, 2015	0
Expensed	6,500,000
Cash Payments	85,000
Balance as of September 30, 2016	6,415,000
Restructuring Charges
Restructuring Charges
Balance as of December 31, 2015	0
Expensed	8,300,000
Cash Payments	1,613,000
Balance as of September 30, 2016	$ 6,687,000

Subsequent Events (Details) - Subsequent Event [Member] $ in Millions	3 Months Ended
	Dec. 31, 2016 USD ($)
Subsequent Event [Line Items]
BARDA V920 Contract Award	$ 24.8
BARDA V920 Additional Award Option	$ 51.2