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Cover Page - shares	9 Months Ended
Cover Page - shares	Sep. 30, 2019	Oct. 31, 2019
Cover page.
Document Transition Report	false
Entity Registrant Name	NEWLINK GENETICS CORP
Entity Central Index Key	0001126234
Current Fiscal Year End Date	--12-31
Entity Filer Category	Non-accelerated Filer
Document Type	10-Q
Entity Incorporation, State or Country Code	DE
Document Period End Date	Sep. 30, 2019
Entity Address, Address Line One	2503 South Loop Drive
Entity Address, City or Town	Ames
Entity Address, State or Province	IA
Entity Address, Postal Zip Code	50010
City Area Code	515
Local Phone Number	296-5555
Entity Tax Identification Number	42-1491350
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Small Business	true
Entity Emerging Growth Company	false
Title of 12(b) Security	Common Stock
Trading Symbol	NLNK
Security Exchange Name	NASDAQ
Entity Common Stock, Shares Outstanding		37,314,076
Entity File Number	001-35342
Document Quarterly Report	true
Entity Shell Company	false
Entity Interactive Data Current	Yes
Entity Current Reporting Status	Yes

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 98,527	$ 120,738
Prepaid expenses and other current assets	3,311	5,536
Income tax receivable	76	339
Other receivables	740	459
Total current assets	102,654	127,072
Property and equipment, net	2,889	3,727
Right-of-use asset	1,042	0
Income tax receivable	69	140
Total non-current assets	4,000	3,867
Total assets	106,654	130,939
Current liabilities:
Accounts payable	145	555
Accrued expenses	12,125	8,139
Current portion of deferred rent	0	92
Current portion of lease liability	1,712	0
Current portion of notes payable	58	61
Total current liabilities	14,040	8,847
Long-term liabilities:
Royalty obligation payable to Iowa Economic Development Authority	6,000	6,000
Notes payable	0	43
Lease liability	217	0
Deferred rent	0	906
Total long-term liabilities	6,217	6,949
Total liabilities	20,257	15,796
Stockholders' equity:
Blank check preferred stock, $0.01 par value: Authorized shares — 5,000,000 at September 30, 2019 and December 31, 2018; issued and outstanding shares — 0 at September 30, 2019 and December 31, 2018	0	0
Common stock, $0.01 par value: Authorized shares — 75,000,000 at September 30, 2019 and December 31, 2018; issued 37,426,844 and 37,343,547 at September 30, 2019 and December 31, 2018, respectively; and outstanding 37,314,076 and 37,251,220 at September 30, 2019 and December 31, 2018, respectively	373	373
Additional paid-in capital	413,205	407,199
Treasury stock, at cost: 112,768 and 92,327 shares at September 30, 2019 and December 31, 2018, respectively	(1,451)	(1,417)
Accumulated deficit	(325,730)	(291,012)
Total stockholders' equity	86,397	115,143
Total liabilities and stockholders' equity	$ 106,654	$ 130,939

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
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	37,426,844	37,343,547
Common stock, outstanding shares	37,314,076	37,251,220
Treasury stock, shares	112,768	92,327

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Total operating revenues	$ 246	$ 120	$ 503	$ 12,272
Operating expenses:
Research and development	7,024	7,570	17,464	39,972
General and administrative	8,279	7,588	19,484	23,792
Total operating expenses	15,303	15,158	36,948	63,764
Loss from operations	(15,057)	(15,038)	(36,445)	(51,492)
Other income and expense:
Miscellaneous (expense) income, net	(33)	(18)	(38)	16
Interest income	567	664	1,815	1,510
Interest expense	(25)	(2)	(50)	(51)
Other income, net	509	644	1,727	1,475
Net loss before taxes	(14,548)	(14,394)	(34,718)	(50,017)
Income tax benefit	0	6,991	0	6,991
Net loss	$ (14,548)	$ (7,403)	$ (34,718)	$ (43,026)
Basic and diluted loss per share (in dollars per share)	$ (0.39)	$ (0.20)	$ (0.93)	$ (1.16)
Basic and diluted average shares outstanding (in shares)	37,308,523	37,214,363	37,286,930	37,178,542
Grant revenue
Revenues	$ 0	$ 0	$ 0	$ 11,268
License and collaboration revenue
Revenues	$ 246	$ 120	$ 503	$ 1,004

Condensed Consolidated Statement of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Treasury Stock	Accumulated Deficit
Balance at beginning of period at Dec. 31, 2017	$ 151,557	$ 372	$ 389,786	$ (1,142)	$ (237,459)
Balance at beginning of period (shares) at Dec. 31, 2017		37,109,556
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	4,820		4,820
Restricted stock vested (in shares)		84,262
Restricted stock vested	106	$ 1	105
Repurchase of common stock	(261)			(261)
Repurchase of common stock (shares)		(28,720)
Cumulative effect of accounting change	42				42
Net loss	(18,310)				(18,310)
Balance at end of period at Mar. 31, 2018	137,954	$ 373	394,711	(1,403)	(255,727)
Balance at end of period (shares) at Mar. 31, 2018		37,165,098
Balance at beginning of period at Dec. 31, 2017	151,557	$ 372	389,786	(1,142)	(237,459)
Balance at beginning of period (shares) at Dec. 31, 2017		37,109,556
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net loss	(43,026)
Balance at end of period at Sep. 30, 2018	122,195	$ 373	403,674	(1,409)	(280,443)
Balance at end of period (shares) at Sep. 30, 2018		37,216,892
Balance at beginning of period at Mar. 31, 2018	137,954	$ 373	394,711	(1,403)	(255,727)
Balance at beginning of period (shares) at Mar. 31, 2018		37,165,098
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	4,177		4,177
Restricted stock vested (in shares)		1,250
Restricted stock vested	0
Sales of shares under stock purchase plan (shares)		32,111
Sales of shares under stock purchase plan	130		130
Repurchase of common stock	(2)			(2)
Repurchase of common stock (shares)		(359)
Net loss	(17,313)				(17,313)
Balance at end of period at Jun. 30, 2018	124,946	$ 373	399,018	(1,405)	(273,040)
Balance at end of period (shares) at Jun. 30, 2018		37,198,100
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	4,623		4,623
Restricted stock vested (in shares)		19,881
Restricted stock vested	33		33
Repurchase of common stock	(4)			(4)
Repurchase of common stock (shares)		(1,089)
Net loss	(7,403)				(7,403)
Balance at end of period at Sep. 30, 2018	122,195	$ 373	403,674	(1,409)	(280,443)
Balance at end of period (shares) at Sep. 30, 2018		37,216,892
Balance at beginning of period at Dec. 31, 2018	$ 115,143	$ 373	407,199	(1,417)	(291,012)
Balance at beginning of period (shares) at Dec. 31, 2018	37,251,220	37,251,220
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	$ 1,944		1,944
Restricted stock vested (in shares)		44,329
Restricted stock vested	0
Repurchase of common stock	(32)			(32)
Repurchase of common stock (shares)		(19,447)
Net loss	(10,036)				(10,036)
Balance at end of period at Mar. 31, 2019	107,019	$ 373	409,143	(1,449)	(301,048)
Balance at end of period (shares) at Mar. 31, 2019		37,276,102
Balance at beginning of period at Dec. 31, 2018	$ 115,143	$ 373	407,199	(1,417)	(291,012)
Balance at beginning of period (shares) at Dec. 31, 2018	37,251,220	37,251,220
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net loss	$ (34,718)
Balance at end of period at Sep. 30, 2019	$ 86,397	$ 373	413,205	(1,451)	(325,730)
Balance at end of period (shares) at Sep. 30, 2019	37,314,076	37,314,076
Balance at beginning of period at Mar. 31, 2019	$ 107,019	$ 373	409,143	(1,449)	(301,048)
Balance at beginning of period (shares) at Mar. 31, 2019		37,276,102
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	1,773		1,773
Restricted stock vested (in shares)		1,250
Restricted stock vested	0
Sales of shares under stock purchase plan (shares)		23,967
Sales of shares under stock purchase plan	30		30
Repurchase of common stock	(1)			(1)
Repurchase of common stock (shares)		(359)
Net loss	(10,134)				(10,134)
Balance at end of period at Jun. 30, 2019	98,687	$ 373	410,946	(1,450)	(311,182)
Balance at end of period (shares) at Jun. 30, 2019		37,300,960
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	2,259		2,259
Restricted stock vested (in shares)		13,751
Restricted stock vested	0
Repurchase of common stock	(1)			(1)
Repurchase of common stock (shares)		(635)
Net loss	(14,548)				(14,548)
Balance at end of period at Sep. 30, 2019	$ 86,397	$ 373	$ 413,205	$ (1,451)	$ (325,730)
Balance at end of period (shares) at Sep. 30, 2019	37,314,076	37,314,076

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Cash Flows From Operating Activities
Net loss	$ (34,718)	$ (43,026)
Adjustments to reconcile net loss to net cash used in operating activities:
Share-based compensation	5,976	13,620
Depreciation and amortization	432	901
Impairment of fixed assets	351	0
Gain on sale of fixed assets	40	(16)
Amortization of right-of-use asset and change in operating lease liability	(111)	0
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	2,225	842
Other receivables	(281)	9,982
Accounts payable and accrued expenses	3,576	(11,749)
Income taxes receivable	334	(7,042)
Unearned revenue	0	(56)
Deferred rent	0	(78)
Net cash used in operating activities	(22,176)	(36,622)
Cash Flows From Investing Activities
Purchase of equipment	0	(7)
Proceeds on sale of equipment	15	118
Net cash provided by investing activities	15	111
Cash Flows From Financing Activities
Issuance of common stock, net of offering costs	30	269
Repurchase of common stock	(34)	(267)
Principal payments on notes payable	(46)	(138)
Net cash used in financing activities	(50)	(136)
Net decrease in cash and cash equivalents	(22,211)	(36,647)
Cash and cash equivalents at beginning of period	120,738	158,708
Cash and cash equivalents at end of period	98,527	122,061
Supplemental disclosure of cash flows information:
Cash paid for interest	3	6
Cash paid for taxes, net	14	0
Cash refunds received for taxes, net	$ 348	$ 4

Description of Business	9 Months Ended
Description of Business	Sep. 30, 2019
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 to develop treatments for patients with cancer and other diseases. NewLink initiated operations in April 2000. NewLink and its subsidiaries (the Company) have historically devoted substantially all of their efforts toward research and development. The Company has never earned revenue from commercial sales of its drugs. The accompanying condensed consolidated financial statements as of September 30, 2019 and for the three and nine months ended September 30, 2019 have been prepared assuming the Company will continue as a going concern. The Company’s cash and cash equivalents as of September 30, 2019 are expected to be adequate to satisfy the Company’s liquidity requirements through 2021. If available liquidity becomes insufficient to meet the Company’s operating obligations as they come due, the Company’s plans include selling additional shares of common stock, 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. Proposed Merger with Lumos Pharma On September 30, 2019, the Company, Cyclone Merger Sub, Inc., a wholly-owned subsidiary of the Company (Merger Sub), and Lumos Pharma, Inc., a privately-held Delaware corporation (Lumos), entered into an Agreement and Plan of Merger and Reorganization (the Merger Agreement), pursuant to which, among other things, subject to the satisfaction or waiver of the conditions set forth in the Merger Agreement, Merger Sub will merge with and into Lumos, with Lumos surviving as a wholly-owned subsidiary of NewLink (the Merger). Following the Merger, NewLink will change its name to “Lumos Pharma, Inc.” and Lumos will change its name to a name mutually agreed upon by the Company and Lumos. At the effective time of the Merger (Effective Time), each share of Lumos capital stock outstanding immediately prior to the Effective Time (excluding shares of Lumos capital stock held as treasury stock or held or owned by Lumos or Merger Sub prior to the Effective Time and shares held by Lumos stockholders who have exercised and perfected appraisal rights in accordance with Delaware law) shall be automatically converted solely into the right to receive a number of shares of NewLink’s common stock equal to the amount determined pursuant to a charter amendment to Lumos’ certificate of incorporation that will be filed prior to the Effective Time, at exchange ratios applicable to each type of Lumos capital stock. Pursuant to such conversion, immediately following the Merger, former Lumos stockholders will own approximately 50% of the aggregate number of shares of Company common stock issued and outstanding following the consummation of the Merger (the Post-Closing Shares), and the stockholders of the Company as of immediately prior to the Merger are expected to own approximately 50% of the aggregate number of Post-Closing Shares. Outstanding options to purchase Lumos common stock will be assumed by NewLink and converted into options to purchase a number of shares of NewLink’s common stock at the exchange ratio applicable to exchanging shares of Lumos common stock for NewLink’s common stock. The Merger Agreement includes customary representations, warranties and covenants made by the Company and Lumos, including covenants relating to the Company's and Lumos' conduct of their respective businesses between the date of signing the Merger Agreement and the closing of the Merger. Consummation of the Merger is subject to certain closing conditions, including, among other things, approval by the stockholders of the Company and Lumos. Lumos stockholders approved the Merger in September 2019. The Merger Agreement contains certain termination rights for both the Company and Lumos, and further provides that, upon termination of the Merger Agreement under specified circumstances, the Company or Lumos, as applicable, may be required to pay the other party a termination fee of $2.0 million. The Merger Agreement contemplates that the Company will also seek approval from its stockholders to effect a reverse stock split, with the split ratio to be mutually agreed to by the Company and Lumos immediately prior to the Effective Time. The Merger is expected to close in the first quarter of 2020.

Basis of Presentation	9 Months Ended
Basis of Presentation	Sep. 30, 2019
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, 2018, included in the Company’s Annual Report on Form 10-K. 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, 2019
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 was $58,000 and $104,000 as of September 30, 2019 and December 31, 2018, 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 $7.6 million and $7.0 million as of September 30, 2019 and December 31, 2018, respectively. 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. Recently Adopted Accounting Pronouncements In February 2016, the FASB issued ASU No. 2016-02 (Topic 842), Leases, to improve financial reporting for leasing transactions. The Company adopted the standard on January 1, 2019 using the modified retrospective method, as required, applying the new standard to all leases existing as of the date of initial application. The Company has elected that the date of the initial application, January 1, 2019, will be the effective date. Consequently, financial information will not be updated and the disclosures required under the new standard will not be provided for dates and periods before January 1, 2019. The Company elected the "package of practical expedients", which permits the Company not to reassess under the new standard its prior conclusions about lease identification, lease classification and initial direct costs. The Company did not elect to apply the use-of-hindsight or the practical expedient pertaining to land easements; as the latter is not applicable to the Company. Upon adoption of the standard, the Company recorded a lease liability of $8.5 million and a right of use asset of $7.5 million associated with these leases. Included in the right-of-use asset are lease incentives that were previously recorded as deferred rent liability of $1.0 million as of December 31, 2018 on the consolidated balance sheet. There was no material impact to the consolidated statement of operations. Refer to Note 7 within for additional discussion around the lease liability and right of use asset as of September 30, 2019.

Revenues	9 Months Ended
Revenues	Sep. 30, 2019
Revenue from Contract with Customer [Abstract]
Revenues	Revenues Revenue Recognition Revenues are recognized under Topic 606 when control of the promised goods or services is transferred to the Company's customers, in an amount that reflects the consideration the Company expects to be entitled to in exchange for those goods or services. Prior to transferring the government contracts over to Merck Sharp & Dohme Corp. (Merck) in June 2018, the Company received payments from government entities under its grants and contracts with the Department of Defense and the United States Department of Health and Human Services (HHS). These agreements provided 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 were recognized over time and measured using the input method. The Company used labor costs and subcontractor fees as inputs to measure progress towards satisfying its performance obligations under these agreements. Under this method, the Company recognized revenue generally in the period during which the related costs were incurred, in an amount that reflected the consideration the Company expected to be entitled to in exchange for those goods or services transferred to the government entities due to the government entities' control over the research and development activities. The grants and contracts with government entities were fully transferred to Merck as of June 2018. Accordingly, during the nine months ended September 30, 2019, the Company recognized no grant revenue. The Company had $520,000 and $309,000 of receivables relating to the government contracts on the balance sheet as of September 30, 2019 and December 31, 2018, respectively. The Company had $24,000 and $54,000 of accrued expenses for subcontractor fees incurred under the government contracts as of September 30, 2019 and December 31, 2018, respectively.

License and Research Collaboration Agreements	9 Months Ended
License and Research Collaboration Agreements	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
License and Research Collaboration Agreement	License and Research Collaboration Agreement Merck Sharp & Dohme Corp. In November 2014, the Company entered into a licensing and collaboration agreement (the Merck Agreement) with Merck to develop, manufacture and commercialize rVSV-ZEBOV-GP, an Ebola vaccine the Company licensed from the Public Health Agency of Canada (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 is expected to 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 Merck Agreement was amended on December 5, 2017 in connection with our entry into an amended and restated PHAC license on December 5, 2017. The amended Merck Agreement absolves our subsidiary, BioProtection Systems Corporation (BPS), from any future obligation to negotiate or amend the terms of the PHAC license, converts the scope of Merck's sublicense under PHAC’s intellectual property rights to be non-exclusive in the Ebola Sudan field of use, and requires Merck to reimburse us in certain circumstances where we may be obligated to pay royalties to PHAC as a result of Merck’s product sales but Merck would not otherwise be obligated to pay a royalty to us. On April 26, 2018, the Company entered into an agreement with Merck, the U.S. BioMedical Advanced Research and Development Authority (BARDA), and the Defense Threat Reduction Agency (DTRA) to transfer the government grants from BARDA and DTRA to Merck. The transfer was completed in June 2018 and Merck has replaced the Company as the prime contractor on all such grants. For the three and nine months ended September 30, 2019, the Company recognized revenues under the amended Merck Agreement of $246,000 and $503,000, respectively, for work the Company performed as a subcontractor of Merck under the government contracts that were transferred to Merck. For the three and nine months ended September 30, 2018, the Company recognized license and collaboration revenue under the amended Merck Agreement of $120,000 and $949,000, respectively, for the reimbursement of costs not covered under government contracts.

Common Stock Equity Incentive Plan

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [Abstract]

Common Stock Equity Incentive Plan

2009 Equity Incentive Plan

In April 2000, the stockholders approved the Company's 2000 Equity Incentive Plan (the 2000 Plan), in July 2009, the stockholders approved the Company's 2009 Equity Incentive Plan (the 2009 Plan), and in May 2019, the stockholders approved to amend and extend the Company's 2009 Equity Incentive Plan (the 2019 Plan). Following the approval of the 2019 Plan, no additional stock awards will be granted under the 2009 Plan. Shares that remained available for issuance pursuant to the exercise of options or issuance or settlement of stock awards under the 2009 Plan became available for issuance pursuant to the 2019 Plan and all shares that would have otherwise returned to the 2009 Plan became available for issuance pursuant to the 2019 Plan. Under the provisions of the 2019 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 2019 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, 2019, there were 12,400,653 shares of common stock authorized for the 2019 Plan and 5,271,904 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						714,285
January 1, 2012						823,649
January 1, 2013						839,407
January 1, 2014						1,062,920
January 1, 2015						1,119,233
January 1, 2016						1,152,565
January 1, 2017						1,166,546
January 1, 2018						1,484,382
January 1, 2019						1,490,048

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 2019 were made pursuant to an “evergreen provision,” in accordance with which, on January 1 of each year, from 2013 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.

On May 9, 2019, the Company’s stockholders approved an amendment to the 2009 Plan which, among other modifications, included decreasing the automatic annual “evergreen provision” from 4% to 3%, in accordance with which, on January 1 of each year, from 2020 to (and including) 2029, a number of shares of common stock in an amount equal to 3% 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 (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, 2019, 268,902 shares remain available for issuance under the Directors' Plan.

2010 Employee Stock Purchase Plan

Under the terms of the Company’s 2010 Employee Stock Purchase Plan (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, 2019, 29,542 shares remained available for issuance under the 2010 Purchase Plan.

Share-based Compensation

Share-based compensation expense for the three months ended September 30, 2019 and 2018 was $2.3 million and $4.6 million, respectively. Share-based compensation expense for the nine months ended September 30, 2019 and 2018 was $6.0 million and $13.6 million, respectively. 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, 2019, the total compensation cost related to nonvested option awards not yet recognized was $4.7 million and the weighted-average period over which it is expected to be recognized is 2.7 years.

Stock Options and Performance Stock Options

The following table summarizes the stock option activity, including options with market and performance conditions and options granted and forfeited in conjunction with the option exchange program, for the nine months ended September 30, 2019:


	Number of options	Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	7,978,030	$	11.86	4.5
Options granted	3,753,274	1.77
Options exercised	—	—
Options forfeited	(4,696,520)	11.43
Options expired	(1,318,698)	5.93
Outstanding at end of period	5,716,086	$	6.96	4.0
Options exercisable at end of period	3,165,770	$	11.09	0.9

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, 2019:


Risk-free interest rate						1.8% to 2.7%
Expected dividend yield						—%
Expected volatility						77.0% to 86.3%
Expected term (in years)						4 to 7.7
Weighted-average grant-date fair value per share						$1.89

No options were exercised during the nine months ended September 30, 2019. The fair value of awards vested during the nine months ended September 30, 2019 was $2.7 million.

During the nine months ended September 30, 2019, the Company’s Board of Directors approved and granted 650,000 shares of equity awards to certain executives with either market or performance conditions. The equity awards had a weighted-average grant date fair value per share of $1.24. The equity awards vest upon the achievement of certain performance conditions. Certain performance conditions relating to the equity awards granted in 2017 were met during the three and nine months ended September 30, 2019 and 79,849 shares vested. None of the targets for 2019 equity awards have been met.

Restricted Stock and Performance Restricted Stock

Restricted stock is common stock that is subject to restrictions, including risks of forfeiture, determined by the planning 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, 2019 and changes during the nine months ended September 30, 2019 are as follows:


	Number of restricted stock shares	Weighted average grant date fair value
Unvested at beginning of period	68,585	$	37.75
Granted	—	—
Vested	(59,330)	38.22
Forfeited/cancelled	—	—
Unvested at end of period	9,255	$	34.73

As of September 30, 2019, the total remaining unrecognized compensation cost related to restricted stock was approximately $124,963 and is expected to be recognized over a weighted-average period of 0.3 years.

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.

Option Exchange Program

On June 20, 2019, the Company commenced an option exchange program (Option Exchange) for its officers and employees to exchange eligible stock options to purchase up to an aggregate of 5,849,059 shares of the Company's common stock that had been granted to eligible holders, for a lesser number of new stock options with a lower exercise price. Stock options granted prior to December 31, 2018 with an exercise price equal to or greater than $2.97 and held by eligible holders in continuous service through the termination of the Option Exchange were eligible for exchange in the Option Exchange.

The eligible shares were exercisable for a reduced number of shares based on the following exchange ratios:


Exercise Price Range per Share	Number of Outstanding Eligible Options	Exchange Ratio (Surrendered Stock Options to New Stock Options)
$2.97-$10.99	2,725,812	2 to 1
$11.00-$24.99	720,373	3 to 1
$25.00-And Up	468,671	4 to 1

Upon the expiration of the Option Exchange on July 31, 2019, 45 eligible employees and 5 eligible directors had tendered an aggregate of 3,914,856 options, representing 67% of the total eligible options, for 1,720,341 new options to purchase shares of common stock (New Awards). Each New Award was granted on July 31, 2019, pursuant to the Company's 2009 Plan, with an exercise price per share of $1.77 per share, the closing price on the grant date of the New Awards. Each New Award has a maximum term of seven years. The New Awards will vest in equal annual amounts over either two or three years, depending on whether the tendered eligible option was vested as of the exchange date.

As a result of this transaction the Company will recognize additional stock-based compensation expense of $1.0 million over the vesting schedule of the New Awards.

Leases

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Leases

The Company has certain facility leases with non-cancellable terms ranging between one and three years, with certain renewal options.

The Company records lease liabilities based on the present value of lease payments over the lease term using an incremental borrowing rate to discount its lease liabilities, as the rate implicit in the lease is typically not readily determinable. To compute the present value of the lease liability, the Company used a weighted-average discount rate of 5%. Certain lease agreements include renewal options that are under the Company's control. The Company includes optional renewal periods in the lease term only when it is reasonably certain that the Company will exercise its option. Prior to September 30, 2019, the Company had asserted it would renew the lease terms through expiry of the lease renewal option periods. At September 30, 2019, as part of the Company's efforts to reduce costs and conserve resources, the Company concluded it would not be seeking renewal of the leased facilities in Ames, Iowa and upon termination of the lease agreements, it would identify a new space for the Company. As a result of this decision, the Company remeasured the right-of-use assets and lease liabilities using the shorter term. The weighted-average remaining lease term as of September 30, 2019 is 1.0 year.

The Company does not separate lease components from non-lease components. Variable lease payments include payments to lessors for taxes, maintenance, insurance and other operating costs as well as payments that are adjusted based on an index or rate. The Company's lease agreements do not contain any residual value guarantees or restrictive covenants.

Future minimum lease payments under the non-cancellable operating leases (with initial or remaining lease terms in excess of one year) as of September 30, 2019 are as follows (in thousands), excluding option renewals:


For the Year Ended December 31:
2019	$	255
2020	599
2021	133
2022	0
2023	0
Thereafter	0
Total future minimum lease payments	987
Less: Imputed interest	(9)
Unamortized lease incentive	951
Total	$	1,929

The following table summarizes the aggregate undiscounted non-cancelable future minimum lease payments for operating leases under the prior lease standard as of December 31, 2018 (in thousands), including option renewals:


For the Year Ended December 31:
2019	$	1,105
2020	1,004
2021	923
2022	906
2023	909
Thereafter	6,570
Total	$	11,417

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2019
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes For the three and nine months ended September 30, 2019 and 2018, the Company has recorded no and $7.0 million income tax benefit (expense). The income tax amount for the three and nine months ended September 30, 2019 and 2018 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to a full valuation allowance recorded against anticipated net operating loss carryforwards. The Company has an income tax receivable as of September 30, 2019 for $140,000 of which $71,000 is recorded within short term receivables and $69,000 is recorded in long-term. The full amount was recorded as an income tax benefit in 2017 and is for the receipt of alternative minimum tax (AMT) credit carryovers. The Tax Cuts and Jobs Act of 2017 (the Tax Act), provides that the AMT credit carryovers are partially refundable beginning in 2018 as an offset to a tax liability. The Company expects the amount to be fully refunded by 2021. 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, 2019 and December 31, 2018, 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, 2019 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 Share of Common Stock

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

Net Loss per Share of Common Stock

Basic loss per share is based upon the weighted-average number of shares of common stock 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 share of common stock (in thousands, except share and per share data):


	Three Months Ended September 30,						Nine Months Ended September 30,
	2019		2018		2019		2018
Loss attributable to common stockholders	(14,548)		$	(7,403)	$	(34,718)	$	(43,026)

Basic and diluted weighted-average shares outstanding	37,308,523		37,214,363		37,286,930		37,178,542



Basic and diluted loss per share	$	(0.39)	$	(0.20)	$	(0.93)	$	(1.16)

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, 2019, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 5,716,086 and 9,255, respectively. As of September 30, 2018, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 8,371,005 and 89,053, respectively.

Restructuring and Severance Charges

9 Months Ended

Sep. 30, 2019

Restructuring and Related Activities [Abstract]

Restructuring and Severance 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, is recognized ratably over the future service period. The Company also records costs incurred with contract terminations associated with restructuring activities.

On September 30, 2019, the Company adopted a restructuring plan to reduce its headcount by approximately 60%, which consisted primarily of clinical and research and development staff, and made several changes to senior leadership in order to conserve resources.

In addition to the restructuring, Charles J. Link, Jr, M.D. retired from the Company and the Board of Directors, effective August 3, 2019 and Nicholas Vahanian retired from his position as the President and member of the Board of Directors, effective September 27, 2019, and will remain an employee of the Company through a transition period ending November 11, 2019.

In conjunction with the restructuring and departure of Company executives, the Company recorded restructuring and severance charges of $4.5 million during the three and nine months ended September 30, 2019 of which $2.9 million is included within general and administrative expenses and $1.6 million is included within research and development expenses. As a result of the restructuring, the Company also recorded an impairment charge of $351,000 relating to 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.

In July 2018, the Company reduced its headcount by approximately 30% as compared to June 30, 2018 and made several changes to senior leadership effective July 26, 2018 in order to conserve resources to advance its clinical development programs. Restructuring charges of $1.3 million were recorded during the three and nine months ended September 30, 2018.

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


	Employee Severance Cost		Total
Balance as of December 31, 2018	$	649	$	649
Expensed	4,489		4,489
Cash Payments	554		554
Balance as of September 30, 2019	$	4,584	$	4,584

Commitments and Contingencies	9 Months Ended
Commitments and Contingencies	Sep. 30, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	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 (the Court), captioned Abramson v. NewLink Genetics Corp., et al., Case 1:16-cv-3545 (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 asserting 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, (collectively, the Defendants). The amended complaint alleges the Defendants made material false and/or misleading statements that caused losses to the Company’s investors. The Defendants filed a motion to dismiss the amended complaint on July 14, 2017. On March 29, 2018, the Court dismissed the amended complaint for failure to state a claim, without prejudice, and gave the lead plaintiffs until May 4, 2018 to file any amended complaint attempting to remedy the defects in their claims. On May 4, 2018, the lead plaintiffs filed a second amended complaint asserting claims under the federal securities laws against the Defendants. Like the first amended complaint, the second amended complaint alleges that the Defendants made material false and/or misleading statements or omissions relating to the Phase 2 and 3 trials and efficacy of the product candidate algenpantucel-L that caused losses to the Company’s investors. The lead plaintiffs do not quantify any alleged damages in the second amended complaint but, in addition to attorneys’ fees and costs, they sought 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 Defendants filed a motion to dismiss the second amended complaint on July 31, 2018. On February 13, 2019, the Court dismissed the second amended complaint for failure to state a claim, with prejudice, and closed the case. On March 14, 2019, lead plaintiffs filed a notice of appeal. The briefing on lead plaintiffs' appeal was completed in early July 2019 and oral argument before the Second Circuit Court of Appeals was held on October 21, 2019. The Company intends to continue defending the Securities Action 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 (collectively, the Morrow Defendants), captioned Morrow v. Link., et al., Case 1:17-cv-03039 (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 2 and 3 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 finally resolved. Under the terms of the stay, the plaintiff in the Ely Action has until March 15, 2019 (30 days after dismissal of the Securities Action with prejudice) to file an amended derivative complaint or rest upon the current derivative complaint. By further agreement of the parties, dated March 15, 2019, the Ely Action will continue to be stayed pending the outcome of the appeal in the Securities Action. If the Securities Action continues to be dismissed in its entirety following its appeal plaintiff in the Ely Action has agreed to withdraw or dismiss the action, with prejudice. The Company disputes the claims in the Ely Action and intends to defend against them vigorously.

Significant Accounting Policies (Policies)	9 Months Ended
Significant Accounting Policies (Policies)	Sep. 30, 2019
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 RiskCash 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 was $58,000 and $104,000 as of September 30, 2019 and December 31, 2018, 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 EquipmentProperty and equipment are capitalized as the Company believes they have alternative future uses and are stated at cost, less accumulated depreciation of $7.6 million and $7.0 million as of September 30, 2019 and December 31, 2018, respectively. 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.
Recent Accounting Pronouncements	Recently Adopted Accounting Pronouncements In February 2016, the FASB issued ASU No. 2016-02 (Topic 842), Leases, to improve financial reporting for leasing transactions. The Company adopted the standard on January 1, 2019 using the modified retrospective method, as required, applying the new standard to all leases existing as of the date of initial application. The Company has elected that the date of the initial application, January 1, 2019, will be the effective date. Consequently, financial information will not be updated and the disclosures required under the new standard will not be provided for dates and periods before January 1, 2019. The Company elected the "package of practical expedients", which permits the Company not to reassess under the new standard its prior conclusions about lease identification, lease classification and initial direct costs. The Company did not elect to apply the use-of-hindsight or the practical expedient pertaining to land easements; as the latter is not applicable to the Company. Upon adoption of the standard, the Company recorded a lease liability of $8.5 million and a right of use asset of $7.5 million associated with these leases. Included in the right-of-use asset are lease incentives that were previously recorded as deferred rent liability of $1.0 million as of December 31, 2018 on the consolidated balance sheet. There was no material impact to the consolidated statement of operations. Refer to Note 7 within for additional discussion around the lease liability and right of use asset as of September 30, 2019.
Revenue Recognition	Revenue Recognition Revenues are recognized under Topic 606 when control of the promised goods or services is transferred to the Company's customers, in an amount that reflects the consideration the Company expects to be entitled to in exchange for those goods or services. Prior to transferring the government contracts over to Merck Sharp & Dohme Corp. (Merck) in June 2018, the Company received payments from government entities under its grants and contracts with the Department of Defense and the United States Department of Health and Human Services (HHS). These agreements provided 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 were recognized over time and measured using the input method. The Company used labor costs and subcontractor fees as inputs to measure progress towards satisfying its performance obligations under these agreements. Under this method, the Company recognized revenue generally in the period during which the related costs were incurred, in an amount that reflected the consideration the Company expected to be entitled to in exchange for those goods or services transferred to the government entities due to the government entities' control over the research and development activities.

Common Stock Equity Incentive Plan (Tables)

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [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						714,285
January 1, 2012						823,649
January 1, 2013						839,407
January 1, 2014						1,062,920
January 1, 2015						1,119,233
January 1, 2016						1,152,565
January 1, 2017						1,166,546
January 1, 2018						1,484,382
January 1, 2019						1,490,048

Stock Option Activity


	Number of options	Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	7,978,030	$	11.86	4.5
Options granted	3,753,274	1.77
Options exercised	—	—
Options forfeited	(4,696,520)	11.43
Options expired	(1,318,698)	5.93
Outstanding at end of period	5,716,086	$	6.96	4.0
Options exercisable at end of period	3,165,770	$	11.09	0.9

Assumptions Used in Black-Scholes Pricing Model for New Grants


Risk-free interest rate						1.8% to 2.7%
Expected dividend yield						—%
Expected volatility						77.0% to 86.3%
Expected term (in years)						4 to 7.7
Weighted-average grant-date fair value per share						$1.89

Restricted Stock Activity


	Number of restricted stock shares	Weighted average grant date fair value
Unvested at beginning of period	68,585	$	37.75
Granted	—	—
Vested	(59,330)	38.22
Forfeited/cancelled	—	—
Unvested at end of period	9,255	$	34.73

Option Exchange Eligible For Exchange

The eligible shares were exercisable for a reduced number of shares based on the following exchange ratios:


Exercise Price Range per Share	Number of Outstanding Eligible Options	Exchange Ratio (Surrendered Stock Options to New Stock Options)
$2.97-$10.99	2,725,812	2 to 1
$11.00-$24.99	720,373	3 to 1
$25.00-And Up	468,671	4 to 1

Leases (Tables)

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Maturity of Operating Lease Liabilities


For the Year Ended December 31:
2019	$	255
2020	599
2021	133
2022	0
2023	0
Thereafter	0
Total future minimum lease payments	987
Less: Imputed interest	(9)
Unamortized lease incentive	951
Total	$	1,929

Schedule of Future Minimum Rental Payments for Operating Leases


For the Year Ended December 31:
2019	$	1,105
2020	1,004
2021	923
2022	906
2023	909
Thereafter	6,570
Total	$	11,417

Net Loss per Share of Common Stock (Tables)

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

Basic and Diluted Net Loss per Common Share

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


	Three Months Ended September 30,						Nine Months Ended September 30,
	2019		2018		2019		2018
Loss attributable to common stockholders	(14,548)		$	(7,403)	$	(34,718)	$	(43,026)

Basic and diluted weighted-average shares outstanding	37,308,523		37,214,363		37,286,930		37,178,542



Basic and diluted loss per share	$	(0.39)	$	(0.20)	$	(0.93)	$	(1.16)

Restructuring and Severance Charges (Tables)

9 Months Ended

Sep. 30, 2019

Restructuring and Related Activities [Abstract]

Restructuring and Related Costs

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


	Employee Severance Cost		Total
Balance as of December 31, 2018	$	649	$	649
Expensed	4,489		4,489
Cash Payments	554		554
Balance as of September 30, 2019	$	4,584	$	4,584

Description of Business (Details) $ in Thousands	Sep. 30, 2019 USD ($)
Financings
Ownership percentage after transaction	50.00%
Covenants termination fee	$ 2,000
Lumos Pharma, Inc.
Financings
Ownership percentage after transaction	50.00%

Significant Accounting Policies (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Accounting Policies [Abstract]
Fair Value Disclosure of notes payable and capital lease obligations	$ 58		$ 104
Accumulated depreciation	7,600		7,000
Property, Plant and Equipment [Line Items]
Total	$ 1,929	$ 8,500
Right-of-use asset		$ 7,500
Deferred rent			$ 1,000
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

Revenues (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Government contract receivable	$ 520	$ 309
Accrued expenses for subcontractor fees	$ 24	$ 54

License and Research Collaboration Agreement (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended		9 Months Ended
	Feb. 28, 2015	Dec. 31, 2014	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
License and collaboration revenue
Deferred Revenue Arrangement [Line Items]
Grant revenue			$ 246	$ 120	$ 503	$ 1,004
License and Collaborative Arrangement \| Merck
Deferred Revenue Arrangement [Line Items]
Upfront cash payments	$ 20,000	$ 30,000
License and Collaborative Arrangement \| Merck \| License and collaboration revenue
Deferred Revenue Arrangement [Line Items]
Grant revenue			$ 246	$ 120	$ 503	$ 949

Common Stock Equity Incentive Plan (Narrative) (Details) - USD ($)														2 Months Ended	3 Months Ended		9 Months Ended
	May 09, 2019	May 08, 2019	Jan. 01, 2019	Jan. 01, 2018	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	May 09, 2013	Jan. 01, 2013	Jan. 01, 2012	Jan. 07, 2011	May 15, 2010	Sep. 30, 2019	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Nov. 10, 2011
Share-based Compensation Arrangement by Share-based Payment Award
Share-based compensation expense														$ 1,000,000.0	$ 2,300,000	$ 4,600,000	$ 6,000,000.0	$ 13,600,000
Granted (in shares)																	0
Options exercisable at end of period (in shares)																	59,330
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized														12,400,653	12,400,653		12,400,653
Number of shares remained available for issuance														5,271,904	5,271,904		5,271,904
Increase in number of shares authorized			1,490,048	1,484,382	1,166,546	1,152,565	1,119,233	1,062,920		839,407	823,649	714,285	1,238,095
Evergreen increase (percent)	3.00%	4.00%															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														268,902	268,902		268,902
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														29,542	29,542		29,542
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														$ 4,700,000	$ 4,700,000		$ 4,700,000
Weighted average vesting period for non-vested option awards, in years																	2 years 8 months 12 days
Intrinsic value of options exercised																	$ 0
Fair value of awards vested																	$ 2,700,000
Performance Stock
Share-based Compensation Arrangement by Share-based Payment Award
Granted (in shares)																	650,000
Weighted average grant-date fair value per share (in dollars per share)																	$ 1.24
Options exercisable at end of period (in shares)																	79,849
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award
Weighted average vesting period for non-vested option awards, in years																	3 months 18 days
Weighted average grant-date fair value per share (in dollars per share)																	$ 0
Unrecognized compensation cost														$ 124,963	$ 124,963		$ 124,963

Common Stock Equity Incentive Plan (Authorized Increases of Common Stock) (Details) - shares	Jan. 01, 2019	Jan. 01, 2018	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	Jan. 01, 2013	Jan. 01, 2012	Jan. 07, 2011	May 15, 2010
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Authorized Shares Added	1,490,048	1,484,382	1,166,546	1,152,565	1,119,233	1,062,920	839,407	823,649	714,285	1,238,095

Common Stock Equity Incentive Plan (Stock Option Activity) (Details) - $ / shares		9 Months Ended	12 Months Ended
	Jul. 31, 2019	Sep. 30, 2019	Dec. 31, 2018
Number of options
Options granted (in shares)	1,720,341
Weighted average exercise price
Granted, weighted average exercise price (in dollars per share)	$ 1.77
Stock Option
Number of options
Outstanding at beginning of period (in shares)		7,978,030
Options granted (in shares)		3,753,274
Options exercised (in shares)		0
Options forfeited (in shares)		(4,696,520)
Options expired (in shares)		(1,318,698)
Outstanding at end of period (in shares)		5,716,086	7,978,030
Weighted average exercise price
Outstanding, weighted average exercise price at beginning of period (in dollars per share)		$ 11.86
Granted, weighted average exercise price (in dollars per share)		1.77
Exercised, weighted average exercise price (in dollars per share)		0
Forfeited, weighted average exercise price (in dollars per share)		11.43
Expired, weighted average exercise price (in dollars per share)		5.93
Outstanding, weighted average exercise price at end of period (in dollars per share)		$ 6.96	$ 11.86
Options exercisable at end of period (in shares)		3,165,770
Exercisable, weighted average exercise price (in dollars per share)		$ 11.09
Outstanding, weighted average remaining contractual term, in years		4 years	4 years 6 months
Exercisable, weighted average remaining contractual term, in years		10 months 24 days

Common Stock Equity Incentive Plan (Range of Assumptions Used) (Details) - Stock Option	9 Months Ended
	Sep. 30, 2019 $ / shares
Share-based Compensation Arrangement by Share-based Payment Award
Risk-free interest rate, minimum (percent)	1.80%
Risk free interest rate, maximum (percent)	2.70%
Expected dividend rate (percent)	0.00%
Volatility rate, minimum (percent)	77.00%
Volatility rate, maximum (percent)	86.30%
Weighted average grant-date fair value per share (in dollars per share)	$ 1.89
Minimum
Share-based Compensation Arrangement by Share-based Payment Award
Expected term (in years)	4 years
Maximum
Share-based Compensation Arrangement by Share-based Payment Award
Expected term (in years)	7 years 8 months 12 days

Common Stock Equity Incentive Plan (Restricted Stock Activity) (Details)	9 Months Ended
	Sep. 30, 2019 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Non-Option Equity Instruments, Outstanding [Roll Forward]
Granted (in shares) \| shares	0
Vested (in shares) \| shares	(59,330)
Forfeited / cancelled (in shares) \| shares	0
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award, Non-Option Equity Instruments, Outstanding [Roll Forward]
Unvested at beginning of period (in shares) \| shares	68,585
Unvested at end of period (in shares) \| shares	9,255
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	$ 37.75
Weighted average grant-date fair value per share (in dollars per share) \| $ / shares	0
Vested, weighted average grant date fair value (in dollars per share) \| $ / shares	38.22
Forfeited/cancelled, weighted average grant date fair value (in dollars per share) \| $ / shares	0
Weighted average grant date fair value at end of period (in dollars per share) \| $ / shares	$ 34.73

Common Stock Equity Incentive Plan (Option Exchange Program) (Details) $ in Thousands		2 Months Ended	3 Months Ended		9 Months Ended
	Jul. 31, 2019 $ / shares shares	Sep. 30, 2019 USD ($) $ / shares shares	Sep. 30, 2019 USD ($) $ / shares shares	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($) $ / shares shares	Sep. 30, 2018 USD ($)	Jul. 31, 2019	Jul. 31, 2019 employee	Jul. 31, 2019 director	Jun. 20, 2019 shares	Dec. 31, 2018 $ / shares
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Option exchange shares authorized (in shares) \| shares										5,849,059
Number of participants								45	5
Option Exchange, number of options converted (in shares) \| shares	3,914,856
Percent of eligible options converted							67.00%
Options granted (in shares) \| shares	1,720,341
Granted, weighted average exercise price (in dollars per share)	$ 1.77
Maximum term	7 years
Share-based compensation expense \| $		$ 1,000	$ 2,300	$ 4,600	$ 6,000	$ 13,600
$2.97-$10.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Number of Outstanding Eligible Options (in shares) \| shares		2,725,812	2,725,812		2,725,812
Exchange ratio		2	2		2
$11.00-$24.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Number of Outstanding Eligible Options (in shares) \| shares		720,373	720,373		720,373
Exchange ratio		3	3		3
$25.00-And Up
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Number of Outstanding Eligible Options (in shares) \| shares		468,671	468,671		468,671
Exchange ratio		4	4		4
Minimum
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Option Exchange, lower exercise price range (in usd per share)											2.97
Award vesting period	2 years
Minimum \| $2.97-$10.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Option Exchange, lower exercise price range (in usd per share)		2.97	2.97		2.97
Minimum \| $11.00-$24.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Option Exchange, lower exercise price range (in usd per share)		11.00	11.00		11.00
Minimum \| $25.00-And Up
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Option Exchange, lower exercise price range (in usd per share)		25.00	25.00		25.00
Maximum
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Award vesting period	3 years
Maximum \| $2.97-$10.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Exercise Price Range per share, upper limit (in usd per share)		10.99	10.99		10.99
Maximum \| $11.00-$24.99
Share-based Payment Arrangement, Option, Exercise Price Range [Line Items]
Exercise Price Range per share, upper limit (in usd per share)		24.99	24.99		24.99

Leases (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Lessee, Lease, Description [Line Items]
Operating lease weighted average discount rate	5.00%
Operating lease weighted average remaining lease term	1 year
Operating Lease Liabilities Payments Due
2019	$ 255
2020	599
2021	133
2022	0
2023	0
Thereafter	0
Total	987
Less: imputed interest	(9)
Unamortized lease incentive	951
Total	$ 1,929	$ 8,500
Operating Leases Future Minimum Payments Due
2019			$ 1,105
2020			1,004
2021			923
2022			906
2023			909
Thereafter			6,570
Total			$ 11,417
Minimum
Lessee, Lease, Description [Line Items]
Term of operating lease contract	1 year
Maximum
Lessee, Lease, Description [Line Items]
Term of operating lease contract	3 years

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Income Tax Disclosure [Abstract]
Income tax benefit	$ 0	$ 6,991	$ 0	$ 6,991
Income tax receivable	140		140
Current income tax receivable	71		71
Noncurrent income tax receivable	69		69
Uncertain tax positions	$ 653		$ 653

Net Loss per Share of Common Stock (Net Loss Per Share Computation) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended						9 Months Ended
	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Sep. 30, 2019	Sep. 30, 2018
Earnings Per Share [Abstract]
Loss attributable to common stockholders	$ (14,548)	$ (10,134)	$ (10,036)	$ (7,403)	$ (17,313)	$ (18,310)	$ (34,718)	$ (43,026)
Basic and diluted weighted-average shares (in shares)	37,308,523			37,214,363			37,286,930	37,178,542
Basic and diluted loss per share (in dollars per share)	$ (0.39)			$ (0.20)			$ (0.93)	$ (1.16)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Net Loss per Share of Common Stock (Antidilutive Securities) (Details) - shares	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Stock Option
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	5,716,086	8,371,005
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	9,255	89,053

Restructuring and Severance Charges (Details) - USD ($) $ in Thousands		1 Months Ended	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Jul. 31, 2018	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Restructuring Charges
Percentage reduction in force	60.00%	30.00%
Impairment of fixed assets			$ 351		$ 351
Restructuring Reserve [Roll Forward]
Balance at beginning of period					649
Expensed			4,500	$ 1,300	4,489	$ 1,300
Cash Payments					554
Balance at end of period	$ 4,584		4,584		4,584
Employee Severance Cost
Restructuring Reserve [Roll Forward]
Balance at beginning of period					649
Expensed					4,489
Cash Payments					554
Balance at end of period	$ 4,584		4,584		4,584
Research and Development Expense
Restructuring Reserve [Roll Forward]
Expensed			1,600		1,600
General and Administrative Expense
Restructuring Reserve [Roll Forward]
Expensed			$ 2,900		$ 2,900