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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2018	Aug. 01, 2018
Document and Entity Information [Abstract]
Entity Registrant Name	NEWLINK GENETICS CORP
Entity Central Index Key	0001126234
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		37,214,286

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 137,066	$ 158,708
Prepaid expenses and other current assets	5,243	6,226
Income tax receivable	360	356
Other receivables	817	10,176
Total current assets	143,486	175,466
Property and equipment, net	4,387	5,091
Income tax receivable	140	140
Total non-current assets	4,527	5,231
Total assets	148,013	180,697
Current liabilities:
Accounts payable	7,334	9,256
Accrued expenses	8,527	12,467
Current portion of unearned revenue	0	56
Current portion of deferred rent	87	92
Current portion of notes payable and obligations under capital leases	93	160
Total current liabilities	16,041	22,031
Long-term liabilities:
Royalty obligation payable to Iowa Economic Development Authority	6,000	6,000
Notes payable and obligations under capital leases	74	111
Deferred rent	952	998
Total long-term liabilities	7,026	7,109
Total liabilities	23,067	29,140
Stockholders' equity:
Blank check preferred stock, $0.01 par value: Authorized shares — 5,000,000 at June 30, 2018 and December 31, 2017; issued and outstanding shares — 0 at June 30, 2018 and December 31, 2017	0	0
Common stock, $0.01 par value: Authorized shares — 75,000,000 at June 30, 2018 and December 31, 2017; issued 37,285,745 and 37,168,122 at June 30, 2018 and December 31, 2017, respectively, and outstanding 37,198,100 and 37,109,556 at June 30, 2018 and December 31, 2017, respectively	373	372
Additional paid-in capital	399,018	389,786
Treasury stock, at cost: 87,286 and 58,566 shares at March 31, 2018 and December 31, 2017, respectively	(1,405)	(1,142)
Accumulated deficit	(273,040)	(237,459)
Total stockholders' equity	124,946	151,557
Total liabilities and stockholders' equity	$ 148,013	$ 180,697

Condensed Consolidated Balance Sheets (Parentheticals) - $ / shares	Jun. 30, 2018	Dec. 31, 2017
Stockholders' Equity:
Blank check preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Blank check preferred stock, authorized shares	5,000,000	5,000,000
Blank check preferred stock, issued shares	0	0
Blank check preferred stock, outstanding shares	0	0
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, authorized shares	75,000,000	75,000,000
Common stock, issued shares	37,285,745	37,168,122
Common stock, outstanding shares	37,198,100	37,109,556
Treasury stock, shares	87,645	58,566

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Income Statement [Abstract]
Grant revenue	$ 1,884	$ 10,314	$ 11,268	$ 12,900
Licensing and collaboration revenue	368	56	884	231
Total operating revenues	2,252	10,370	12,152	13,131
Operating expenses:
Research and development	12,088	18,200	32,402	33,925
General and administrative	7,912	8,897	16,204	17,131
Total operating expenses	20,000	27,097	48,606	51,056
Loss from operations	(17,748)	(16,727)	(36,454)	(37,925)
Other income and expense:
Miscellaneous income (expense)	10	(109)	34	(113)
Interest income	461	117	846	202
Interest expense	(36)	(7)	(49)	(113)
Other income (expense), net	435	1	831	(24)
Net loss before taxes	(17,313)	(16,726)	(35,623)	(37,949)
Income tax benefit	0	0	0	310
Net loss	$ (17,313)	$ (16,726)	$ (35,623)	$ (37,639)
Basic and diluted loss per share (in dollars per share)	$ (0.47)	$ (0.57)	$ (0.96)	$ (1.29)
Basic and diluted average shares outstanding (in shares)	37,165,529	29,225,386	37,160,334	29,219,469

Condensed Consolidated Statement of Stockholders' Equity - 6 months ended Jun. 30, 2018 - 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	37,109,556
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Share-based compensation	$ 8,997		8,997
Exercise of stock options and restricted stock vested	106	$ 1	105
Exercise of stock options and restricted stock vested (shares)		85,512
Sales of shares under stock purchase plan	130		130
Sales of shares under stock purchase plan (shares)		32,111
Shares withheld for statutory tax withholding (in shares)		(29,079)
Shares withheld for statutory tax withholding	(263)			(263)
Cumulative effect of accounting change	42				42
Net loss	(35,623)				(35,623)
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	37,198,100

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017
Cash Flows From Operating Activities
Net loss	$ (35,623)	$ (37,639)
Adjustments to reconcile net loss to net cash used in operating activities:
Share-based compensation	8,997	10,568
Depreciation and amortization	637	707
(Gain) Loss on sale of fixed assets	(34)	113
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	519	1,005
Other receivables	9,865	13,268
Accounts payable and accrued expenses	(5,862)	(11,356)
Income taxes receivable	(4)	(312)
Unearned revenue	(56)	(224)
Deferred rent	(51)	(44)
Net cash used in operating activities	(21,612)	(23,914)
Cash Flows From Investing Activities
Purchase of equipment	(7)	(57)
Proceeds on sale of equipment	108	172
Net cash provided by investing activities	101	115
Cash Flows From Financing Activities
Issuance of common stock, net of offering costs	236	453
Repurchase of common stock	(263)	(245)
Payments under capital lease obligations and principal payments on notes payable	(104)	(122)
Net cash provided by (used in) financing activities	(131)	86
Net decrease in cash and cash equivalents	(21,642)	(23,713)
Cash and cash equivalents at beginning of period	158,708	131,490
Cash and cash equivalents at end of period	137,066	107,777
Supplemental disclosure of cash flows information:
Cash paid for interest	5	8
Cash paid for taxes, net	5	2
Noncash financing and investing activities:
Purchased leasehold improvements and equipment in accounts payable	$ 0	$ 14

Description of Business	6 Months Ended
Description of Business	Jun. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Description of Business	Description of Business On June 4, 1999, NewLink Genetics Corporation (NewLink) was incorporated as a Delaware corporation. NewLink was formed for the purpose of developing treatments for patients with cancer and other diseases. NewLink initiated operations in April 2000. NewLink and its subsidiaries (the Company) are devoting substantially all of their efforts toward research and development. The Company has never earned revenue from commercial sales of its drugs. The accompanying condensed consolidated financial statements as of June 30, 2018 and for the three and six 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 inital public offering in 2011, completed a follow-on offering of its common stock raising net proceeds of $49.0 million in 2013, and raised an additional $58.7 million in net proceeds from an at the market (ATM) offering completed in 2015. During 2017, the Company sold 1,940,656 shares of its common stock under an ATM offering, with aggregate net proceeds of $19.3 million after commissions of $398,000 paid to Cantor Fitzgerald & Co. (Cantor) as the placement agent, and other costs of $163,000. In October 2017, the Company sold 5,750,000 of its shares of common stock in a public offering for aggregate net proceeds of $55.2 million after underwriters' discounts, commissions and other expenses of $3.7 million. On March 12, 2018, the Company entered into a new Sales Agreement with Cantor under which the Company may sell up to $60.0 million of its common stock in one or more placements at prevailing market prices in an ATM offering (the 2018 ATM Offering). As of June 30, 2018, no shares have been sold under the 2018 ATM Offering. The Company's cash and cash equivalents as of June 30, 2018 are expected to be adequate to satisfy the Company's liquidity requirements into the second half of 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.

Basis of Presentation	6 Months Ended
Basis of Presentation	Jun. 30, 2018
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, 2017, 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	6 Months Ended
Significant Accounting Policies	Jun. 30, 2018
Accounting Policies [Abstract]
Significant Accounting Policies	Significant Accounting Policies Use of Estimates The preparation of the condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates. Principles of Consolidation The condensed consolidated financial statements include the financial statements of NewLink and its wholly owned subsidiaries. All significant intercompany balances and transactions have been eliminated in consolidation. Financial Instruments and Concentrations of Credit Risk Cash and cash equivalents, receivables, and accounts payable are recorded at cost, which approximates fair value based on the short-term nature of these financial instruments. The carrying value of notes payable and capital lease obligations was $167,000 and $271,000 as of June 30, 2018 and December 31, 2017, respectively, which approximate fair value using Level 2 inputs (computed in accordance with ASC 820). The Company is unable to estimate the fair value of the royalty obligation based on future product sales, as the timing of payments, if any, is uncertain. Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash and cash equivalents. Cash and cash equivalents are held by financial institutions and are federally insured up to certain limits. At times, the Company’s cash and cash equivalents balance exceeds the federally insured limits. To limit the credit risk, the Company invests its excess cash primarily in high-quality securities such as certificates of deposit and money market funds. Property and equipment Property and equipment are capitalized as the Company believes they have alternative future uses and are stated at cost, less accumulated depreciation of $6.9 million and $6.6 million as of June 30, 2018 and December 31, 2017, 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. Recently Issued Accounting Pronouncements not yet adopted 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 does not currently have any material leases and therefore does not anticipate adoption to have a material impact on its consolidated financial statements and related disclosures. Recently Adopted Accounting Pronouncements On May 28, 2014, the FASB issued ASU No. 2014-09 (Topic 606), Revenue from Contracts with Customers. Topic 606 supersedes the revenue recognition requirements in Topic 605 “Revenue Recognition” (Topic 605), and requires entities to recognize revenue when control of the promised goods or services is transferred to customers at an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. The Company adopted Topic 606 as of January 1, 2018 and as a result changed its accounting policy for revenue recognition, as discussed in Note 4.

Revenues

6 Months Ended

Jun. 30, 2018

Revenue from Contract with Customer [Abstract]

Revenues

Adoption of ASC Topic 606, "Revenue from Contracts with Customers"

On January 1, 2018, we adopted Topic 606 using the modified retrospective method by recognizing the cumulative effect of initially applying Topic 606 as an adjustment to the opening balance of equity as of January 1, 2018. Therefore results for reporting periods beginning after January 1, 2018 are presented under Topic 606, while prior period amounts are not adjusted and continue to be reported in accordance with our historic accounting policy under Topic 605. The change in accounting policy from Topic 605 to Topic 606 impacted how the Company recognizes revenue from government grants, and did not impact license and collaboration revenues due to the nature of those services in the period leading up to and after the adoption of Topic 606.

The Company recorded an immaterial net reduction to the opening accumulated deficit within equity as of January 1, 2018 due to the cumulative impact of adopting Topic 606 with respect to grants from government entities which were not completed as of the date of adoption. As a result of applying the modified retrospective method to adopt the new revenue guidance, the following adjustments were made to accounts on the Condensed Consolidated Balance Sheet as of January 1, 2018 (in thousands):


	As Reported December 31, 2017		Adjustments		Adjusted January 1, 2018
Balance Sheet
Assets:
Prepaid expenses and other current assets	$	6,226	$	(464)	$	5,762
Other receivables	$	10,176	$	506	$	10,682
Total assets	$	180,697	$	42	$	180,739
Equity:
Accumulated deficit	$	(237,459)	$	42	$	(237,417)
Total liabilities and stockholders' equity	$	180,697	$	42	$	180,739

The impact of adoption on the Company’s Condensed Consolidated Statement of Operations for the three and six months ended June 30, 2018 was as follows (in thousands):


	Three months ended June 30, 2018										Six months ended June 30, 2018
	As Reported		Adjustments		Balance without Adoption of Topic 606		As Reported		Adjustments		Balance without Adoption of Topic 606
Statement of Operations
Grant revenue	$	1,884	$	4,774	$	6,658	$	11,268	$	346	$	11,614
Licensing and collaboration revenue	$	368	$	129	$	497	$	884	$	146	$	1,030
Research and development	$	12,088	$	4,439	$	16,527	$	32,402	$	450	$	32,852
Net Loss	$	(17,313)	$	464	$	(16,849)	$	(35,623)	$	42	$	(35,581)

The impact of adoption on the Company’s Condensed Consolidated Statement of Cash Flows for the six months ended June 30, 2018 was as follows (in thousands):


	As Reported		Adjustments		Balance without Adoption of Topic 606
Statement of Cash Flows
Net Loss	$	(35,623)	$	42	$	(35,581)
Changes in operating assets and liabilities:
Other receivables	$	9,865	$	(492)	$	9,373
Prepaid expenses and other current assets	$	519	$	450	$	969
Net cash used in operating activities	$	(21,612)	$	—	$	(21,612)

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. 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 or HHS. 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 over time and measured using the input method. The Company uses labor costs and subcontractor fees as inputs to measure progress towards satisfying its performance obligations under these agreements. This is the most faithful depiction of the transfer of goods and services to the government entities due to the government entities’ control over the research and development activities. Under this method, the Company recognizes revenue generally in the period during which the related costs are incurred, in an amount that reflects the consideration the Company expects to be entitled to in exchange for those goods or services. The Company had $406,000 and $9.3 million of receivables relating to the government contracts recorded in other receivables and zero and $465,000 of unbilled expenses relating to the government contracts recorded in prepaid expenses and other current assets on the balance sheet as of June 30, 2018 and December 31, 2017, respectively. The Company had $25,000 and $1.8 million of accrued expenses for subcontractor fees incurred under the government contracts as of June 30, 2018 and December 31, 2017, respectively.

License and Research Collaboration Agreements	6 Months Ended
License and Research Collaboration Agreements	Jun. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Licensing and Research Collaboration Agreements	License and Research Collaboration Agreements Genentech, a Member of the Roche Group In October 2014, the Company entered into an exclusive worldwide collaboration and license agreement with Genentech, or the Genentech Agreement, for the development and commercialization of NLG919, one of the Company's clinical stage IDO pathway inhibitors and for the discovery of next generation IDO/TDO compounds 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. On June 6, 2017, the Company received a formal notice of Genentech’s intent to terminate the Genentech Agreement with respect to NLG919. As part of the partial termination, worldwide rights to NLG919 reverted to us, and Genentech granted to us an exclusive, royalty-bearing license under certain Genentech intellectual property to develop and commercialize NLG919. If NLG919 is commercialized, we will be obligated to pay to Genentech royalties as a low single-digit percentage of net sales of NLG919. Additionally, on May 9, 2018 the Company received formal notice that Genentech would not continue the collaboration with respect to next generation IDO/TDO inhibitors identified through the research program. The Genentech Agreement will terminate in its entirety no later than November 6, 2018. For the three and six months ended June 30, 2018, the Company recognized license and collaboration revenue under the Genentech Agreement of zero and $56,000, respectively, for providing an alliance manager. For the three and six months ended June 30, 2017, the Company recognized license and collaboration revenue under the Genentech Agreement of $56,000 and $223,000, respectively, for providing an alliance manager. All of the deliverables identified within the collaboration and license agreement were completed in their entirety and all of the $150.0 million upfront payment was recognized as of March 31, 2018. Merck Sharp & Dohme Corp. In November 2014, the Company entered into a licensing and collaboration agreement with Merck, or the Merck Agreement, to develop, manufacture and commercialize rVSV-ZEBOV GP, an Ebola vaccine the Company licensed from the Public Health Agency of Canada, or PHAC. Under the terms of the Merck Agreement, the Company granted Merck an exclusive, royalty bearing license to rVSV-ZEBOV GP and related technology. Under the Merck Agreement, the Company received a $30.0 million non-refundable, upfront payment in December 2014, and a one-time $20.0 million non-refundable milestone payment in February 2015 upon the initiation of the pivotal clinical trial using the current rVSV-ZEBOV GP vaccine product as one arm of the trial. In addition, the Company can receive escalating royalties on potential commercial sales by Merck of the current product candidate ranging from single digit to double digits on the rVSV-ZEBOV GP license agreement product sales and escalating royalties on potential commercial sales by Merck of products other than current products within the Company’s patent rights ranging from low to high single digit, on increasing levels of annual net sales worldwide. Merck will lead the development of rVSV-ZEBOV GP and any other rVSV-based viral hemorrhagic fever vaccine product candidates in order to create a marketable product safe for human use. The 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, or 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. The Company completed all deliverables under the Merck Agreement in their entirety during the year ended December 31, 2016. For the three and six months ended June 30, 2018, the Company recognized license and collaboration revenues under the Merck Agreement of $368,000 and $828,000, respectively, for the reimbursement of costs not covered under government contracts. For the three and six months ended June 30, 2017, the company recognized license and collaboration revenue under the Merck Agreement of zero and $8,000, respectively, for the reimbursement of costs not covered under government contracts.

Common Stock Equity Incentive Plan

6 Months Ended

Jun. 30, 2018

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 June 30, 2018, there were 11,722,602 shares of common stock authorized for the 2009 Plan and 1,327,344 shares remained available for issuance.

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


Date Authorized						Authorized Shares Added
May 15, 2010						1,238,095
January 7, 2011						714,286
January 1, 2013						838,375
January 1, 2014						1,066,340
January 1, 2015						1,119,255
January 1, 2016						1,152,565
January 1, 2017						1,166,546
January 1, 2018						1,484,382

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 2013 through 2018 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.

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 June 30, 2018, no shares remained available for issuance under the Directors' Plan.

2010 Employee Stock Purchase Plan

Under the terms of the Company’s 2010 Employee Stock Purchase Plan, or the 2010 Purchase Plan, which became effective on November 10, 2011, 214,285 shares of common stock were reserved for future issuance. On May 9, 2013, an additional 185,715 shares of common stock were added to the shares reserved for future issuance under the 2010 Purchase Plan. As of June 30, 2018, 69,885 shares remained available for issuance under the 2010 Purchase Plan.

Share-based Compensation

Share-based compensation expense for the three months ended June 30, 2018 and 2017 was $4.2 million and $4.6 million, respectively. Share-based compensation expense for the six months ended June 30, 2018 and 2017 was $9.0 million and $10.6 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 June 30, 2018, the total compensation cost related to nonvested option awards not yet recognized was $16.6 million and the weighted-average period over which it is expected to be recognized is 2.1 years.

Stock Options and Performance Stock Options

The following table summarizes the stock option activity, including options with market and performance conditions, for the six months ended June 30, 2018:


	Number of options	Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	7,202,221	$	13.72	5.3
Options granted	1,457,523	7.37
Options exercised	(16,760)	6.31
Options forfeited	(84,801)	14.65
Options expired	(15,193)	28.12
Outstanding at end of period	8,542,990	$	12.62	5.5
Options exercisable at end of period	6,022,833	$	13.05	4.0

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 six months ended June 30, 2018:


Risk-free interest rate						2.6% to 2.9%
Expected dividend yield						—%
Expected volatility						76.2% to 79.2%
Expected term (in years)						4.0 to 7.9
Weighted-average grant-date fair value per share						$5.21

The intrinsic value of options exercised during the six months ended June 30, 2018 was $34,233. The fair value of awards vested during the six months ended June 30, 2018 was $6.1 million.

During the six months ended June 30, 2018, the Company’s Board of Directors approved and granted 466,750 shares of compensation and equity awards to certain executives with either market or performance conditions. The compensation and equity awards had a weighted-average grant date fair value per share of $7.85. The compensation and equity awards will vest upon the achievement of certain performance conditions. During the six months ended June 30, 2018, none of the performance conditions related to these grants were met. Certain performance conditions relating to equity awards granted in 2017 were met during the six months ended June 30, 2018 and 97,000 shares vested.

Restricted Stock and Performance Restricted Stock

Restricted stock is common stock that is subject to restrictions, including risks of forfeiture, determined by the plan committee of the Board of Directors in its sole discretion, for as long as such common stock remains subject to any such restrictions. A holder of restricted stock has all rights of a stockholder with respect to such stock, including the right to vote and

to receive dividends thereon, except as otherwise provided in the award agreement relating to such award. Restricted stock awards are classified as equity within the consolidated balance sheets. The fair value of each restricted stock grant is estimated on the date of grant using the closing price of the Company's common stock on the NASDAQ Stock Market on the date of grant.

A summary of the Company's unvested restricted stock, including restricted stock with performance conditions, at June 30, 2018 and changes during the six months ended June 30, 2018 are as follows:


	Number of restricted stock shares	Weighted average grant date fair value
Unvested at beginning of period	168,221	$	35.82
Granted	—	—
Vested	(68,752)	35.17
Forfeited/cancelled	(5,125)	42.93
Unvested at end of period	94,344	$	35.90

As of June 30, 2018, the total remaining unrecognized compensation cost related to restricted stock was approximately $2.3 million and is expected to be recognized over a weighted-average period of 1.2 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.

Income Taxes	6 Months Ended
Income Taxes	Jun. 30, 2018
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes For the three and six months ended June 30, 2018, the Company recorded no income tax benefit. The income tax benefit for the three and six months ended June 30, 2018 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to the full valuation allowance recorded against net operating losses due to the uncertainty of future recoverability. For the six months ended June 30, 2017, the Company recorded an income tax benefit of $310,000. For the three months ended June 30, 2017, the Company recorded no income tax benefit. Income tax benefit for the three and six months ended June 30, 2017 differs from the amount that would be expected after applying the statutory U.S. federal income tax rate primarily due to the ability to carry back losses to 2015 and the net loss generated by the NewLink's foreign subsidiary. On December 22, 2017, the U.S. government enacted comprehensive tax legislation commonly referred to as the Tax Cuts and Jobs Act, or the Tax Act. The Tax Act repealed the two-year carryback provision for net operating losses arising after 2017, thereby reducing any benefit realized as a result of carryback to zero for the current period. Additionally, the Company has a noncurrent income tax receivable as of June 30, 2018 for $140,000 which was recorded as an income tax benefit in 2017 and is for the receipt of AMT Credit carryovers. The Tax Act provides that 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 June 30, 2018 and December 31, 2017, 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 June 30, 2018 recorded within Accrued Expenses in the condensed consolidated balance sheet, which includes the accrual of interest and penalties. The Company does not expect the amount to change significantly within the next 12 months.

Net Loss per Common Share

6 Months Ended

Jun. 30, 2018

Earnings Per Share [Abstract]

Net Loss per Common Share

Net Loss per Common ShareBasic 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 comm on share (in thousands, except share and per share data):


	Three Months Ended June 30,						Six Months Ended June 30,
	2018		2017		2018		2017
Loss attributable to common stockholders	$	(17,313)	$	(16,726)	$	(35,623)	$	(37,639)
Basic and diluted weighted-average shares outstanding	37,165,529		29,225,386		37,160,334		29,219,469
Basic and diluted loss per share	$	(0.47)	$	(0.57)	$	(0.96)	$	(1.29)

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 June 30, 2018, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 8,542,990 and 94,344, respectively. As of June 30, 2017, anti-dilutive stock options and restricted stock awards excluded from our calculation totaled 7,667,926 and 196,209, respectively.

Restructuring Charges

6 Months Ended

Jun. 30, 2018

Restructuring and Related Activities [Abstract]

Restructuring Charges

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

In July 2018, the Company completed an organizational review of its clinical programs and reduced its headcount by approximately 30% as compared to June 30, 2018 and made several changes to senior leadership in order to conserve resources to further advance its clinical development programs. There were no restructuring charges recorded during the three and six months ended June 30, 2018 relating to this reorganization. Restructuring charges relating to this reorganization are expected to be recorded during the third quarter of 2018.

The Company undertook an organizational realignment in July 2017 to refocus its clinical development efforts and align the Company's resources to focus on the Company's highest value opportunities. The Company's restructuring activities included a reduction of its workforce by approximately 50%, which consisted primarily of clinical and research and development staff, as well as stopping additional research on the Zika virus. The Company recorded total restructuring charges of $1.7 million during the year ended December 31, 2017.

There were no restructuring charges recorded during the three and six months ended June 30, 2018 and 2017.

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


	Employee Severance Cost	Total
Balance as of December 31, 2017	207	207
Expensed	—	—
Cash Payments	207	207
Balance as of June 30, 2018	—	—

Commitments and Contingencies	6 Months Ended
Commitments and Contingencies	Jun. 30, 2018
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies Disclosure	Commitments and Contingencies From time to time, claims are asserted against the Company arising in the ordinary course of business. In the opinion of management, liabilities, if any, arising from existing claims are not expected to have a material effect on the Company's earnings, financial position, or liquidity. On or about May 12, 2016, Trevor Abramson filed a putative securities class action lawsuit in the United States District Court for the Southern District of New York, or the Court, captioned Abramson v. NewLink Genetics Corp., et al., Case 1:16-cv-3545, or the Securities Action. Subsequently, the Court appointed Michael and Kelly Nguyen as lead plaintiffs and approved their selection of Kahn, Swick & Foti, LLC as lead counsel in the Securities Action. On October 31, 2016, the lead plaintiffs filed an amended complaint 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, or collectively, the Defendants. The amended complaint alleges the Defendants made material false and/or misleading statements that caused losses to the Company’s investors. In particular, the lead plaintiffs allege that the Defendants made material misstatements or omissions related to the Phase 2 and 3 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 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 amended complaint on July 14, 2017. The lead plaintiffs filed an opposition to the motion to dismiss on September 12, 2017. The Defendants filed a reply in support of the motion to dismiss on September 26, 2017. Oral argument was held on October 19, 2017, after which the Court reserved decision. 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. 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, or collectively, the Morrow Defendants, captioned Morrow v. Link., et al., Case 1:17-cv-03039, or the Morrow Action. The complaint alleges that the Morrow Defendants caused the Company to issue false statements in its 2016 proxy statement regarding risk management and compensation matters in violation of federal securities law. The complaint also asserts state law claims against the Morrow Defendants for breaches of fiduciary duties, unjust enrichment, abuse of control, insider trading, gross mismanagement, and corporate waste, alleging that the Morrow Defendants made material misstatements or omissions related to the Phase 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 will be provided with any discovery that is provided in the Securities Action, and given an opportunity to participate in any mediation or settlement efforts in the Securities Action. The Company disputes the claims in the Ely Action and intends to defend against them vigorously.

Subsequent Events	6 Months Ended
Subsequent Events	Jun. 30, 2018
Subsequent Events [Abstract]
Subsequent Events	Subsequent EventsIn July 2018, the Company completed an organizational review of its clinical programs and reduced its headcount by approximately 30% as compared to June 30, 2018 and made several changes to senior leadership in order to conserve resources to further advance its clinical development programs.

Significant Accounting Policies (Policies)	6 Months Ended
Significant Accounting Policies (Policies)	Jun. 30, 2018
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	Cash and cash equivalents, receivables, and accounts payable are recorded at cost, which approximates fair value based on the short-term nature of these financial instruments. The carrying value of notes payable and capital lease obligations was $167,000 and $271,000 as of June 30, 2018 and December 31, 2017, respectively, which approximate fair value using Level 2 inputs (computed in accordance with ASC 820). The Company is unable to estimate the fair value of the royalty obligation based on future product sales, as the timing of payments, if any, is uncertain.
Concentration of Credit Risk	Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash and cash equivalents. Cash and cash equivalents are held by financial institutions and are federally insured up to certain limits. At times, the Company’s cash and cash equivalents balance exceeds the federally insured limits. To limit the credit risk, the Company invests its excess cash primarily in high-quality securities such as certificates of deposit and money market funds.
Property and equipment	Property and equipment Property and equipment are capitalized as the Company believes they have alternative future uses and are stated at cost, less accumulated depreciation of $6.9 million and $6.6 million as of June 30, 2018 and December 31, 2017, 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.
Recent Accounting Pronouncements	Recently Issued Accounting Pronouncements not yet adopted 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 does not currently have any material leases and therefore does not anticipate adoption to have a material impact on its consolidated financial statements and related disclosures. Recently Adopted Accounting Pronouncements On May 28, 2014, the FASB issued ASU No. 2014-09 (Topic 606), Revenue from Contracts with Customers. Topic 606 supersedes the revenue recognition requirements in Topic 605 “Revenue Recognition” (Topic 605), and requires entities to recognize revenue when control of the promised goods or services is transferred to customers at an amount that reflects the consideration to which the entity expects to be entitled to in exchange for those goods or services. The Company adopted Topic 606 as of January 1, 2018 and as a result changed its accounting policy for revenue recognition, as discussed in Note 4.
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. 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 or HHS. 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 over time and measured using the input method. The Company uses labor costs and subcontractor fees as inputs to measure progress towards satisfying its performance obligations under these agreements. This is the most faithful depiction of the transfer of goods and services to the government entities due to the government entities’ control over the research and development activities. Under this method, the Company recognizes revenue generally in the period during which the related costs are incurred, in an amount that reflects the consideration the Company expects to be entitled to in exchange for those goods or services.

Revenues (Tables)

6 Months Ended

Jun. 30, 2018

Revenue from Contract with Customer [Abstract]

Schedule of New Accounting Pronouncements

As a result of applying the modified retrospective method to adopt the new revenue guidance, the following adjustments were made to accounts on the Condensed Consolidated Balance Sheet as of January 1, 2018 (in thousands):


	As Reported December 31, 2017		Adjustments		Adjusted January 1, 2018
Balance Sheet
Assets:
Prepaid expenses and other current assets	$	6,226	$	(464)	$	5,762
Other receivables	$	10,176	$	506	$	10,682
Total assets	$	180,697	$	42	$	180,739
Equity:
Accumulated deficit	$	(237,459)	$	42	$	(237,417)
Total liabilities and stockholders' equity	$	180,697	$	42	$	180,739

The impact of adoption on the Company’s Condensed Consolidated Statement of Operations for the three and six months ended June 30, 2018 was as follows (in thousands):


	Three months ended June 30, 2018										Six months ended June 30, 2018
	As Reported		Adjustments		Balance without Adoption of Topic 606		As Reported		Adjustments		Balance without Adoption of Topic 606
Statement of Operations
Grant revenue	$	1,884	$	4,774	$	6,658	$	11,268	$	346	$	11,614
Licensing and collaboration revenue	$	368	$	129	$	497	$	884	$	146	$	1,030
Research and development	$	12,088	$	4,439	$	16,527	$	32,402	$	450	$	32,852
Net Loss	$	(17,313)	$	464	$	(16,849)	$	(35,623)	$	42	$	(35,581)

The impact of adoption on the Company’s Condensed Consolidated Statement of Cash Flows for the six months ended June 30, 2018 was as follows (in thousands):


	As Reported		Adjustments		Balance without Adoption of Topic 606
Statement of Cash Flows
Net Loss	$	(35,623)	$	42	$	(35,581)
Changes in operating assets and liabilities:
Other receivables	$	9,865	$	(492)	$	9,373
Prepaid expenses and other current assets	$	519	$	450	$	969
Net cash used in operating activities	$	(21,612)	$	—	$	(21,612)

Common Stock Equity Incentive Plan (Tables)

6 Months Ended

Jun. 30, 2018

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

Authorized Increases of Common Stock under the 2009 Plan

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


Date Authorized						Authorized Shares Added
May 15, 2010						1,238,095
January 7, 2011						714,286
January 1, 2013						838,375
January 1, 2014						1,066,340
January 1, 2015						1,119,255
January 1, 2016						1,152,565
January 1, 2017						1,166,546
January 1, 2018						1,484,382

Stock Option Activity

The following table summarizes the stock option activity, including options with market and performance conditions, for the six months ended June 30, 2018:


	Number of options	Weighted average exercise price		Weighted average remaining contractual term (years)
Outstanding at beginning of period	7,202,221	$	13.72	5.3
Options granted	1,457,523	7.37
Options exercised	(16,760)	6.31
Options forfeited	(84,801)	14.65
Options expired	(15,193)	28.12
Outstanding at end of period	8,542,990	$	12.62	5.5
Options exercisable at end of period	6,022,833	$	13.05	4.0

Assumptions Used in Black-Scholes Pricing Model for New Grants


Risk-free interest rate						2.6% to 2.9%
Expected dividend yield						—%
Expected volatility						76.2% to 79.2%
Expected term (in years)						4.0 to 7.9
Weighted-average grant-date fair value per share						$5.21

Restricted Stock Activity

A summary of the Company's unvested restricted stock, including restricted stock with performance conditions, at June 30, 2018 and changes during the six months ended June 30, 2018 are as follows:


	Number of restricted stock shares	Weighted average grant date fair value
Unvested at beginning of period	168,221	$	35.82
Granted	—	—
Vested	(68,752)	35.17
Forfeited/cancelled	(5,125)	42.93
Unvested at end of period	94,344	$	35.90

Net Loss per Common Share (Tables)

6 Months Ended

Jun. 30, 2018

Earnings Per Share [Abstract]

Basic and Diluted Net Loss per Common Share

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


	Three Months Ended June 30,						Six Months Ended June 30,
	2018		2017		2018		2017
Loss attributable to common stockholders	$	(17,313)	$	(16,726)	$	(35,623)	$	(37,639)
Basic and diluted weighted-average shares outstanding	37,165,529		29,225,386		37,160,334		29,219,469
Basic and diluted loss per share	$	(0.47)	$	(0.57)	$	(0.96)	$	(1.29)

Restructuring Charges (Tables)

6 Months Ended

Jun. 30, 2018

Restructuring and Related Activities [Abstract]

Restructuring and Related Costs

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


	Employee Severance Cost	Total
Balance as of December 31, 2017	207	207
Expensed	—	—
Cash Payments	207	207
Balance as of June 30, 2018	—	—

Description of Business (Details) - USD ($) $ in Thousands			1 Months Ended	12 Months Ended
Description of Business (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Mar. 12, 2018	Oct. 31, 2017	Dec. 31, 2017	Dec. 31, 2015	Dec. 31, 2013	Dec. 31, 2011
IPO
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Financing proceeds							$ 37,600
Follow-on Offering
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Financing proceeds						$ 49,000
ATM Offering
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Financing proceeds				$ 19,300	$ 58,700
Maximum available under ATM offering		$ 60,000
Number of shares of common stock sold	0			1,940,656
Commissions paid				$ 398
Other costs				$ 163
Public Offering
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Financing proceeds			$ 55,200
Number of shares issued			5,750,000
Fees and commissions			$ 3,700

Significant Accounting Policies (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Accounting Policies [Abstract]
Fair Value Disclosure of notes payable and capital lease obligations	$ 167	$ 271
Accumulated depreciation	$ 6,900	$ 6,600
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 (Narrative) (Details) - USD ($)	Jun. 30, 2018	Dec. 31, 2017
Disaggregation of Revenue [Line Items]
Government contract receivables	$ 406,000	$ 9,300,000
Accrued expenses for subcontractor fees	25,000	1,800,000
Prepaid Expenses and Other Current Assets
Disaggregation of Revenue [Line Items]
Unbilled contracts receivable	$ 0	$ 465,000

Revenues (Effects of New Accounting Pronouncements)(Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Jan. 01, 2018	Dec. 31, 2017
Assets
Prepaid expenses and other current assets	$ 5,243		$ 5,243		$ 5,762	$ 6,226
Other receivables	817		817		10,682	10,176
Total assets	148,013		148,013		180,739	180,697
Stockholders' equity:
Accumulated deficit	(273,040)		(273,040)		(237,417)	(237,459)
Total liabilities and stockholders' equity	148,013		148,013		180,739	180,697
Grant Revenues	1,884	$ 10,314	11,268	$ 12,900
Licensing and collaboration revenue	368	56	884	231
Research and Development	12,088	18,200	32,402	33,925
Net loss	(17,313)	$ (16,726)	(35,623)	(37,639)
Other receivables			9,865	13,268
Prepaid expenses and other current assets			519	1,005
Net cash used in operating activities			(21,612)	$ (23,914)
Balance without Adoption of Topic 606
Assets
Prepaid expenses and other current assets						6,226
Other receivables						10,176
Total assets						180,697
Stockholders' equity:
Accumulated deficit						(237,459)
Total liabilities and stockholders' equity						$ 180,697
Net loss			(35,581)
Other receivables			9,373
Prepaid expenses and other current assets			969
Net cash used in operating activities			(21,612)
Adjustments
Assets
Prepaid expenses and other current assets					(464)
Other receivables					506
Total assets					42
Stockholders' equity:
Accumulated deficit					42
Total liabilities and stockholders' equity					$ 42
Accounting Standards Update 2014-09 \| Balance without Adoption of Topic 606
Stockholders' equity:
Grant Revenues	6,658		11,614
Licensing and collaboration revenue	497		1,030
Research and Development	16,527		32,852
Net loss	(16,849)		(35,581)
Accounting Standards Update 2014-09 \| Adjustments
Stockholders' equity:
Grant Revenues	4,774		346
Licensing and collaboration revenue	129		146
Research and Development	4,439		450
Net loss	$ 464		42
Other receivables			(492)
Prepaid expenses and other current assets			450
Net cash used in operating activities			$ 0

License and Research Collaboration Agreements (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended		6 Months Ended		12 Months Ended
	Feb. 28, 2015	Dec. 31, 2014	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2014
Deferred Revenue Arrangement [Line Items]
Licensing and collaboration revenue			$ 368	$ 56	$ 884	$ 231
License and Collaborative Arrangement \| Genentech
Deferred Revenue Arrangement [Line Items]
Upfront cash payments							$ 150,000
Alliance manager			0	56	56	223
License and Collaborative Arrangement \| Merck
Deferred Revenue Arrangement [Line Items]
Upfront cash payments	$ 20,000	$ 30,000
Licensing and collaboration revenue			$ 368	$ 0	$ 828	$ 8

Common Stock Equity Incentive Plan (Narrative)(Details) - USD ($)										3 Months Ended		6 Months Ended
	Jan. 01, 2018	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	May 09, 2013	Jan. 01, 2013	Jan. 07, 2011	May 10, 2010	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Nov. 10, 2011
Share-based Compensation Arrangement by Share-based Payment Award
Share-based compensation expense										$ 4,200,000	$ 4,600,000	$ 9,000,000.0	$ 10,600,000
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized										11,722,602		11,722,602
Number of shares remained available for issuance										1,327,344		1,327,344
Increase in number of shares authorized	1,484,382	1,166,546	1,152,565	1,119,255	1,066,340		838,375	714,286	1,238,095
Evergreen increase (percent)												4.00%
2010 Non-Employee Directors' Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized														238,095
Number of shares remained available for issuance										0		0
Increase in number of shares authorized						161,905
2010 Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award
Number of shares authorized														214,285
Number of shares remained available for issuance										69,885		69,885
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										$ 16,600,000		$ 16,600,000
Weighted average vesting period for non-vested option awards, in years												2 years 1 month 6 days
Intrinsic value of options exercised												$ 34,233
Fair value of awards vested												$ 6,100,000
Performance Stock
Share-based Compensation Arrangement by Share-based Payment Award
Granted (in shares)												466,750
Weighted average grant-date fair value per share (in dollars per share)												$ 7.85
Options exercisable at end of period (in shares)												97,000
Restricted Stock
Share-based Compensation Arrangement by Share-based Payment Award
Weighted average vesting period for non-vested option awards, in years												1 year 2 months 12 days
Granted (in shares)												0
Weighted average grant-date fair value per share (in dollars per share)												$ 0
Options exercisable at end of period (in shares)												68,752
Unrecognized compensation cost										$ 2,300,000		$ 2,300,000

Common Stock Equity Incentive Plan (Authorized Increases of Common Stock) (Details) - shares	Jan. 01, 2018	Jan. 01, 2017	Jan. 01, 2016	Jan. 01, 2015	Jan. 01, 2014	Jan. 01, 2013	Jan. 07, 2011	May 10, 2010
2009 Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award
Authorized Shares Added	1,484,382	1,166,546	1,152,565	1,119,255	1,066,340	838,375	714,286	1,238,095

Common Stock Equity Incentive Plan (Stock Option Activity) (Details) - Stock Option - $ / shares	6 Months Ended	12 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Number of options
Outstanding at beginning of period (in shares)	7,202,221
Options granted (in shares)	1,457,523
Options exercised (in shares)	(16,760)
Options forfeited (in shares)	(84,801)
Options expired (in shares)	(15,193)
Outstanding at end of period (in shares)	8,542,990	7,202,221
Weighted average exercise price
Outstanding, weighted average exercise price at beginning of period (in dollars per share)	$ 13.72
Granted, weighted average exercise price (in dollars per share)	7.37
Exercised, weighted average exercise price (in dollars per share)	6.31
Forfeitured, weighted average exercise price (in dollars per share)	14.65
Expired, weighted average exercise price (in dollars per share)	28.12
Outstanding, weighted average exercise price at end of period (in dollars per share)	$ 12.62	$ 13.72
Options exercisable at end of period (in shares)	6,022,833
Exercisable, weighted average exercise price (in dollars per share)	$ 13.05
Outstanding, weighted average remaining contractual term, in years	5 years 6 months	5 years 3 months 18 days
Exercisable, weighted average remaining contractual term, in years	4 years

Common Stock Equity Incentive Plan (Range of Assumptions Used) (Details) - Stock Option	6 Months Ended
	Jun. 30, 2018 $ / shares
Share-based Compensation Arrangement by Share-based Payment Award
Risk-free interest rate, minimum (percent)	2.60%
Risk free interest rate, maximum (percent)	2.90%
Expected dividend rate (percent)	0.00%
Volatility rate, minimum (percent)	76.20%
Volatility rate, maximum (percent)	79.20%
Weighted average grant-date fair value per share (in dollars per share)	$ 5.21
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 10 months 24 days

Common Stock Equity Incentive Plan (Restricted Stock Activity) (Details) - Restricted Stock	6 Months Ended
	Jun. 30, 2018 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Non-Option Equity Instruments, Outstanding [Roll Forward]
Unvested at beginning of period (in shares) \| shares	168,221
Granted (in shares) \| shares	0
Vested (in shares) \| shares	(68,752)
Forfeited / cancelled (in shares) \| shares	(5,125)
Unvested at end of period (in shares) \| shares	94,344
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	$ 35.82
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	35.17
Forfeited/cancelled, weighted average grant date fair value (in dollars per share) \| $ / shares	42.93
Weighted average grant date fair value at end of period (in dollars per share) \| $ / shares	$ 35.90

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Income Tax Disclosure [Abstract]
Income tax benefit	$ 0	$ 0	$ 0	$ 310
Income tax benefit from Tax Act			140
Uncertain tax positions	$ 653		$ 653

Net Loss per Common Share (Net Loss Per Share Computation) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Earnings Per Share [Abstract]
Loss attributable to common stockholders	$ (17,313)	$ (16,726)	$ (35,623)	$ (37,639)
Basic and diluted average shares outstanding (in shares)	37,165,529	29,225,386	37,160,334	29,219,469
Basic and diluted loss per share (in dollars per share)	$ (0.47)	$ (0.57)	$ (0.96)	$ (1.29)

Net Loss per Common Share (Antidilutive Securities) (Details) - shares	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017
Stock Option
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	8,542,990	7,667,926
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities (in shares)	94,344	196,209

Restructuring Charges (Details) - USD ($)	1 Months Ended		3 Months Ended		6 Months Ended		12 Months Ended
Restructuring Charges (Details) - USD ($)	Jul. 31, 2018	Jul. 31, 2017	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Restructuring Charges
Percentage reduction in force		50.00%
Restructuring Reserve [Roll Forward]
Balance at beginning of period					$ 207,000
Expensed			$ 0	$ 0	0	$ 0	$ 1,700,000
Cash Payments					207,000
Balance at end of period							207,000
Employee Severance Cost
Restructuring Reserve [Roll Forward]
Balance at beginning of period					207,000
Expensed					0
Cash Payments					$ 207,000
Balance at end of period							$ 207,000
Subsequent event
Restructuring Charges
Percentage reduction in force	30.00%

Subsequent Events (Details)	1 Months Ended
Subsequent Events (Details)	Jul. 31, 2018	Jul. 31, 2017
Subsequent Event [Line Items]
Percentage reduction in force		50.00%
Subsequent event
Subsequent Event [Line Items]
Percentage reduction in force	30.00%