Codexis (CDXS) 10-Q 6 Nov 19 2019 Q3 Quarterly report Financial data

Cover Page

Cover Page - shares	9 Months Ended
	Sep. 30, 2019	Oct. 31, 2019
Cover page.
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2019
Document Transition Report	false
Entity File Number	001-34705
Entity Registrant Name	Codexis, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	71-0872999
Entity Address, Address Line One	200 Penobscot Drive,
Entity Address, City or Town	Redwood City,
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94063
City Area Code	650
Local Phone Number	421-8100
Title of 12(b) Security	Common Stock, par value $0.0001 per share
Trading Symbol	CDXS
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		58,518,105
Entity Central Index Key	0001200375
Amendment Flag	false
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Current Fiscal Year End Date	--12-31

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 92,143	$ 53,039
Accounts receivable, net of allowances of $34 at September 30, 2019 and December 31, 2018	12,327	11,551
Unbilled receivables, current	2,317	1,916
Inventories	397	589
Prepaid expenses and other current assets	1,553	1,068
Contract assets	1,193	35
Total current assets	109,930	68,198
Restricted cash	1,731	1,446
Marketable Securities, Noncurrent	0	588
Right-of-use assets - Operating leases, net	24,542	0
Right-of-use assets - Finance leases, net	321	0
Property and equipment, net	6,241	4,759
Goodwill	3,241	3,241
Other non-current assets	190	1,051
Total assets	146,196	79,283
Current liabilities:
Accounts payable	1,743	3,050
Accrued compensation	4,695	5,272
Other accrued liabilities	6,182	4,855
Current portion of lease obligations - Operating leases	893	0
Current portion of lease obligations - Finance leases	122	0
Deferred revenue	1,288	4,936
Total current liabilities	14,923	18,113
Deferred revenue, net of current portion	1,988	3,352
Long-term lease obligations - Operating leases	25,554	0
Long-term lease obligations - Finance leases	0	61
Lease incentive obligation, net of current portion	0	35
Other long-term liabilities	1,223	1,416
Total liabilities	43,688	22,977
Commitments and Contingencies (Note 11)
Stockholders' equity:
Preferred stock, $0.0001 par value per share; 5,000 shares authorized; none issued and outstanding	0	0
Common stock, $0.0001 par value per share; 100,000 shares authorized; 58,386 shares and 54,065 shares issued and outstanding at September 30, 2019 and December 31, 2018, respectively	6	5
Additional paid-in capital	444,276	386,775
Accumulated deficit	(341,774)	(330,474)
Total stockholders' equity	102,508	56,306
Total liabilities and stockholders' equity	$ 146,196	$ 79,283

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Accounts receivable, allowances	$ 34	$ 34
Preferred stock, par value (usd per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (shares)	5,000,000	5,000,000
Preferred stock, shares issued (shares)	0	0
Preferred stock, shares outstanding (shares)	0	0
Common stock, par value (usd per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (shares)	100,000,000	100,000,000
Common stock, shares, issued (shares)	58,386,000	54,065,000
Common stock, shares outstanding (shares)	58,386,000	54,065,000

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Total revenues	$ 21,906	$ 16,946	$ 49,808	$ 44,526
Costs and operating expenses:
Cost of product revenue	5,067	3,791	12,230	10,228
Research and development	8,711	7,917	25,000	22,464
Selling, general and administrative	7,869	7,344	24,180	22,485
Total costs and operating expenses	21,647	19,052	61,410	55,177
Income (loss) from operations	259	(2,106)	(11,602)	(10,651)
Interest income	480	199	929	444
Other expenses, net	(403)	(80)	(615)	(221)
Income (loss) before income taxes	336	(1,987)	(11,288)	(10,428)
Provision for (benefit from) income taxes	(7)	1	12	(11)
Net Income (loss)	$ 343	$ (1,988)	$ (11,300)	$ (10,417)
Net income (loss) per share, basic (usd per share)	$ 0.01	$ (0.04)	$ (0.20)	$ (0.20)
Net income (loss) per share, diluted (usd per share)	$ 0.01	$ (0.04)	$ (0.20)	$ (0.20)
Weighted average common stock shares used in computing net income (loss) per share, basic (shares)	58,287	53,597	55,818	51,609
Weighted average common stock shares used in computing net income (loss) per share, diluted (shares)	61,412	53,597	55,818	51,609
Product Sales [Member]
Revenues:
Total revenues	$ 10,351	$ 8,405	$ 24,588	$ 18,291
Research and Development Revenue [Member]
Revenues:
Total revenues	$ 11,555	$ 8,541	$ 25,220	$ 26,235

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Accumulated Deficit [Member]
Beginning balance (shares) at Dec. 31, 2017		48,365,000
Increase (Decrease) in Stockholders' Equity Common Shares
Exercise of stock options (shares)	729,596	730,000
Release of stock awards (shares)		824,000
Taxes paid related to net share settlement of equity awards (in shares)		(297,000)
Issuance of common stock, net of issuance costs (in shares)		4,313,000
Ending balance (shares) at Sep. 30, 2018		53,935,000
Beginning balance at Dec. 31, 2017	$ 24,547	$ 5	$ 340,079	$ (472)	$ (315,065)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options	4,319		4,319
Employee stock-based compensation	6,183		6,183
Non-employee stock-based compensation	24		24
Taxes paid related to net share settlement of equity awards	(3,140)		(3,140)
Issuance of common stock, net of issuance costs	37,317		37,317
Issuance of common stock, issuance costs	(179)
Net income (loss)	(10,417)				(10,417)
Ending balance at Sep. 30, 2018	54,773	$ 5	384,782	0	(330,014)
Beginning balance (shares) at Jun. 30, 2018		53,508,000
Increase (Decrease) in Stockholders' Equity Common Shares
Exercise of stock options (shares)		427,000
Ending balance (shares) at Sep. 30, 2018		53,935,000
Beginning balance at Jun. 30, 2018	52,530	$ 5	380,551	0	(328,026)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options	2,461		2,461
Employee stock-based compensation	1,770		1,770
Net income (loss)	(1,988)				(1,988)
Ending balance at Sep. 30, 2018	$ 54,773	$ 5	384,782	0	(330,014)
Beginning balance (shares) at Dec. 31, 2018		54,065,000
Increase (Decrease) in Stockholders' Equity Common Shares
Exercise of stock options (shares)	970,256	970,000
Release of stock awards (shares)		449,000
Taxes paid related to net share settlement of equity awards (in shares)		(147,000)
Issuance of common stock, net of issuance costs (in shares)		3,049,000
Ending balance (shares) at Sep. 30, 2019		58,386,000
Beginning balance at Dec. 31, 2018	$ 56,306	$ 5	386,775	0	(330,474)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options	4,621		4,621
Employee stock-based compensation	5,783		5,783
Taxes paid related to net share settlement of equity awards	(2,850)		(2,850)
Issuance of common stock, net of issuance costs	49,871	1	49,870
Issuance of common stock, issuance costs	(129)
Short swing profit settlement	77		77
Net income (loss)	(11,300)				(11,300)
Ending balance at Sep. 30, 2019	102,508	$ 6	444,276	0	(341,774)
Beginning balance (shares) at Jun. 30, 2019		57,940,000
Increase (Decrease) in Stockholders' Equity Common Shares
Exercise of stock options (shares)		441,000
Release of stock awards (shares)		8,000
Taxes paid related to net share settlement of equity awards (in shares)		(3,000)
Ending balance (shares) at Sep. 30, 2019		58,386,000
Beginning balance at Jun. 30, 2019	98,684	$ 6	440,795	0	(342,117)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Exercise of stock options	1,778		1,778
Employee stock-based compensation	1,732		1,732
Taxes paid related to net share settlement of equity awards	(51)		(51)
Issuance of common stock, issuance costs	(55)		(55)
Short swing profit settlement	77		77
Net income (loss)	343				343
Ending balance at Sep. 30, 2019	$ 102,508	$ 6	$ 444,276	$ 0	$ (341,774)

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Stockholders' Equity (parenthetical) $ in Thousands	Jan. 01, 2018USD ($)
Accounting Standards Update 2014-09 [Member]
Cumulative effect of change on equity or net assets	$ 4,100
Accounting Standards Update 2016-01 [Member]
Cumulative effect of change on equity or net assets	$ 500

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Operating activities:
Net loss	$ (11,300)	$ (10,417)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	1,118	812
Amortization expense - right-of-use assets - operating and finance leases	2,231	0
Gain on disposal of property and equipment	(2)	0
Stock-based compensation	5,783	6,207
Loss on investment in equity securities	526	20
Changes in operating assets and liabilities:
Accounts receivable, net	(776)	3,556
Unbilled receivables	385	0
Inventories	192	206
Prepaid expenses and other current assets	(485)	(1,188)
Contract assets	(1,158)	(1,868)
Other non-current assets	74	188
Accounts payable	(1,294)	(1,686)
Accrued compensation	(577)	409
Other accrued liabilities	2,687	1,332
Other long-term liabilities	(1,291)	(710)
Deferred revenue	(5,012)	(10,235)
Net cash used in operating activities	(8,899)	(13,374)
Investing activities:
Purchase of property and equipment	(3,315)	(2,074)
Proceeds from disposal of property and equipment	2	1
Proceeds from the sale of investment securities	62	0
Net cash used in investing activities	(3,251)	(2,073)
Financing activities:
Proceeds from exercises of stock options	4,621	4,319
Proceeds from issuance of common stock in connection with public offering, net of underwriting discounts and commission	0	37,497
Costs incurred in connection with public offering	0	(180)
Proceeds from issuance of common stock in connection with private placement	50,000	0
Costs incurred in connection with private placement	(129)	0
Payments of lease obligations - Finance leases	(180)	(178)
Recovery of short swing profit	77	0
Taxes paid related to net share settlement of equity awards	(2,850)	(3,140)
Net cash provided by financing activities	51,539	38,318
Net increase in cash, cash equivalents and restricted cash	39,389	22,871
Cash, cash equivalents and restricted cash at the beginning of the period	54,485	32,776
Cash, cash equivalents and restricted cash at the end of the period	93,874	55,647
Supplemental disclosure of cash flow information
Interest paid	16	61
Income taxes paid	5	5
Purchase of property and equipment recorded in accounts payable and accrued expenses	536	420
Cash and cash equivalents	92,143	54,225
Total cash, cash equivalents and restricted cash at the end of the period	$ 54,485	$ 32,776

Description of Business

Description of Business	9 Months Ended
	Sep. 30, 2019
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Description of Business	Description of Business In these notes to the unaudited condensed consolidated financial statements, the "Company," "we," "us," and "our" refers to Codexis, Inc. and its subsidiaries on a consolidated basis. We discover, develop and sell proteins that deliver value to our clients in a growing set of industries. We view proteins as a vast untapped source of value-creating materials, and we are using our proven technologies, which we have been continuously improving since our inception in 2002, to commercialize an increasing number of novel proteins, both as proprietary Codexis products and in partnership with our customers. We are a pioneer in the harnessing of computational technologies to drive biology advancements. Since 2002, we have made substantial investments in the development of our CodeEvolver ® protein engineering technology platform, the primary source of our competitive advantage. Our technology platform is powered by proprietary, artificial intelligence-based, computational algorithms that rapidly mine our large and continuously growing library of protein variants’ performance attributes. These computational outputs enable increasingly reliable predictions for next generation protein variants to be engineered, enabling delivery of targeted performance enhancements in a time-efficient manner. In addition to its computational prowess, our CodeEvolver ® protein engineering technology platform integrates additional modular competencies, including robotic high-throughput screening and genomic sequencing, organic chemistry and process development which are all coordinated to create our novel protein innovations. Our approach to develop commercially viable biocatalytic manufacturing processes begins by conceptually designing the most cost-effective and practical process for a targeted product. We then develop optimized protein catalysts to enable that process design, using our CodeEvolver ® protein engineering platform technology. Engineered protein catalyst candidates - many thousands for each protein engineering project - are then rapidly screened and validated in high throughput screening under relevant manufacturing operating conditions. This approach results in an optimized protein catalyst enabling cost-efficient processes that typically are relatively simple to run in conventional manufacturing equipment. This also allows for the efficient technical transfer of our process to our manufacturing partners. The successful embodiment of our CodeEvolver ® protein engineering technology platform in commercial manufacturing processes requires well-integrated expertise in a number of technical disciplines. In addition to those directly involved in practicing our CodeEvolver ® protein engineering platform technology, such as molecular biology, enzymology, microbiology, cellular engineering, metabolic engineering, bioinformatics, biochemistry and high throughput analytical chemistry, our process development projects also involve integrated expertise in organic chemistry, chemical process development, chemical engineering, fermentation process development and fermentation engineering. Our integrated, multi-disciplinary approach to biocatalyst and process development is a critical success factor for our company. We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, which remains our primary business focus. Our customers, which include several large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop protein catalysts for use in the fine chemicals market. The fine chemicals market consists of several large market verticals, including food and food ingredients, animal feed, flavors, fragrances and agricultural chemicals. We have also begun using the CodeEvolver ® protein engineering technology platform to develop early stage, novel biotherapeutic product candidates, both for our customers and for our own business, most notably our lead program for the potential treatment of phenylketonuria ("PKU") in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we entered into a Global Development, Option and License Agreement (the "Nestlé Agreement") with Nestec Ltd. ("Nestlé Health Science") to advance CDX-6114, our enzyme biotherapeutic product candidate for the potential treatment of PKU. In February 2019, Nestlé Health Science exercised its option to obtain an exclusive license to develop and commercialize CDX-6114. In April 2018, we entered into a strategic agreement (the "Porton Agreement") with Porton Pharma Solutions, Ltd. ("Porton") to license key elements of our CodeEvolver ® protein engineering technology platform to Porton’s global custom intermediate and active pharmaceutical ingredients ("API") development and manufacturing business. This gives us access to a wide variety of small and medium-sized pharmaceutical customers. We are also using our technology to develop enzymes for customers using next generation sequencing ("NGS") and polymerase chain reaction ("PCR/qPCR") for in vitro molecular diagnostic and genomic research applications. Our first enzyme for this application is a DNA ligase which we began marketing to customers in 2018. In May 2019, we entered into a Platform Technology Transfer and License Agreement (the “Novartis CodeEvolver ® Agreement”) with Novartis Pharma AG (“Novartis”). The Novartis CodeEvolver ® Agreement allows Novartis to use Codexis’ proprietary CodeEvolver ® protein engineering platform technology in the field of human healthcare. Below are brief descriptions of our business segments (See Note 13, "Segment, Geographical and Other Revenue Information"): Performance Enzymes We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, and to date this continues to be our largest market served. Our customers, which include many large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop customized enzymes for use in other industrial markets. These markets consist of several large industrial verticals, including food and food ingredients, animal feed, flavors, fragrances, and agricultural chemicals. We also use our technology to develop enzymes for customers using NGS and PCR/qPCR for in vitro molecular diagnostic and molecular biology research applications. Novel Biotherapeutics We are also targeting new opportunities in the pharmaceutical industry to discover, improve, and/or develop biotherapeutic drug candidates. We believe that our CodeEvolver ® protein engineering platform technology can be used to discover novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. Similarly, we believe that we can deploy our platform technology to improve specific characteristics of a customer’s pre-existing biotherapeutic drug candidate, such as its activity, stability or immunogenicity. Most notable is our lead program for the potential treatment of PKU in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we announced a strategic collaboration with Nestlé Health Science to advance CDX-6114, our own novel orally administrable enzyme therapeutic candidate for the potential treatment of PKU. In July 2018, we announced that we had dosed the first subjects in a first-in-human Phase 1a dose-escalation trial with CDX-6114, which was conducted in Australia. In November 2018, we announced top-line results from the Phase 1a study in healthy volunteers with CDX-6114. In December 2018, Nestlé Health Science became obligated to pay us an additional $1.0 million within 60 days after the achievement of a milestone relating to formulation of CDX-6114. In January 2019, we received notice from the U.S. Food and Drug Administration (the “FDA”) that it had completed its review of our investigational new drug application (“IND”) for CDX-6114 and concluded that we may proceed with the proposed Phase 1b multiple ascending dose study in healthy volunteers in the United States. In February 2019, Nestlé Health Science exercised its option to obtain an exclusive, worldwide, royalty-bearing, sub-licensable license for the global development and commercialization of CDX-6114 for the management of PKU. As a result of the option exercise, we earned a milestone and recognized $3.0 million in revenues in the first quarter of 2019. Upon exercising its option, Nestlé Health Science has assumed all responsibilities for future clinical development and commercialization of CDX-6114, with the exception of the completion of an extension study, CDX-6114-004, which was substantially completed in the third quarter of 2019. We have also developed a pipeline of other biotherapeutic drug candidates, which are in preclinical development, and in which we expect to continue to make additional investments with the aim of advancing additional product candidates targeting other therapeutic areas. Recent Financing Activities In June 2019, we entered into a Securities Purchase Agreement with an affiliate of Casdin Capital, LLC (“Casdin”) pursuant to which we issued and sold to Casdin 3,048,780 shares of our common stock at a purchase price of $16.40 per share (the “Private Offering”). After deducting issuance costs of $0.1 million from the Private Offering, our net proceeds were $49.9 million . See Note 10, "Capital Stock" to our unaudited condensed consolidated financial statements for further details.

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2019
Accounting Policies [Abstract]
Basis of Presentation and Summary of Significant Accounting Policies	Basis of Presentation and Summary of Significant Accounting Policies Basis of Presentation and Principles of Consolidation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America ("GAAP") and the applicable rules and regulations of the Securities and Exchange Commission ("SEC") for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December 31, 2018 . The condensed consolidated balance sheet at December 31, 2018 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The significant accounting policies used in preparation of the unaudited condensed consolidated financial statements for the three and nine months ended September 30, 2019 are consistent with those discussed in Note 2 to the audited consolidated financial statements in the Company’s 2018 Annual Report on Form 10-K and are updated below as necessary. The unaudited condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of September 30, 2019 , results of our operations for the three and nine months ended September 30, 2019 and 2018 , changes in stockholders' equity for the three and nine months ended September 30, 2019 and 2018 , and cash flows for the nine months ended September 30, 2019 and 2018 . The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Accounting Standard Update ("ASU") 2016-02, "Leases (Topic 842)" ("ASC 842) establishes a right-of-use ("ROU") model that requires a lessee to record a right-of-use asset and a lease obligation on the balance sheet for all leases with terms longer than 12 months. See "Recently Adopted Accounting Pronouncements" for details regarding the adoption of ASU 2016-02 effective January 1, 2019. The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly owned subsidiaries in the United States, India and the Netherlands. All significant intercompany balances and transactions have been eliminated in consolidation. Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the unaudited condensed consolidated financial statements, and the reported amounts of revenue and expenses during the reporting period. We regularly assess these estimates which primarily affect revenue recognition, accounts receivable, inventories, the valuation of marketable securities, goodwill arising out of business acquisitions, accrued liabilities, stock awards, and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the unaudited condensed consolidated financial statements. Segment Reporting We report two business segments, Performance Enzymes and Novel Biotherapeutics, which are based on our operating segments. Operating segments are defined as components of an enterprise about which separate financial information is available that is evaluated regularly by the chief operating decision maker ("CODM"), or decision making group, in deciding how to allocate resources, and in assessing performance. Our CODM is our Chief Executive Officer. Our business segments are primarily based on our organizational structure and our operating results as used by our CODM in assessing performance and allocating resources for our company. We do not allocate or evaluate assets by segment. The Novel Biotherapeutics segment focuses on new opportunities in the pharmaceutical industry to dis cover or improve novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. The Performance Enzymes segment consists of protein catalyst products and services with focus on pharmaceutical, food, molecular diagnostics, and other industrial markets. Leases We determine if an arrangement is a lease at inception. Operating leases are included in right-of-use ("ROU") lease assets, current portion of lease obligations, and long-term lease obligations on our balance sheets. ROU lease assets represent our right to use an underlying asset for the lease term and lease obligations represent our obligation to make lease payments arising from the lease. Operating ROU lease assets and obligations are recognized at the commencement date based on the present value of the future minimum lease payments over the lease term. As our leases do not provide an implicit rate, we use our incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The lease terms may include options to extend or terminate the lease when it is reasonably certain that the option will be exercised. Lease expense is recognized on a straight-line basis over the lease term. We elected to apply the short-term lease measurement and recognition exemption in which ROU assets and lease obligations are not recognized for short-term leases. Recent Accounting Pronouncements Recently adopted accounting pronouncements In February 2016, the FASB issued ASU 2016-02, "Leases (Topic 842)" (“ASC 842”), which is intended to improve financial reporting of leasing transactions by requiring lessees to recognize leases on balance sheets and disclose key information about leasing arrangements. Topic 842 was subsequently amended by ASU No. 2018-01, "Land Easement Practical Expedient for Transition to Topic 842"; ASU 2018-10, "Codification Improvements to ASC 842, Leases"; and ASU 2018-11, "Leases (Topic 842): Targeted Improvements." The new standard establishes a right-of-use ("ROU") model that requires lessees to record a ROU asset and lease obligations on the balance sheet for all leases with terms longer than 12 months. Leases are classified as either finance or operating, with classification affecting the pattern and classification of expense recognition in the condensed consolidated statement of operations. We adopted the new standard on January 1, 2019 using a modified retrospective approach and effective date method. We also elected the "package of practical expedients," which permit us not to reassess under the new standard its prior conclusions about lease identification, lease classification and initial direct costs. We did not elect the use-of-hindsight or the practical expedient pertaining to land easements; the latter is not applicable to us. Upon adoption, for operating leases, we recognized $26.6 million of ROU assets and $27.6 million of lease obligations, which represents the present value of the lease payments discounted using our incremental borrowing rate ("IBR") of 6.6% . For finance leases, we recognized $0.5 million of ROU assets and $0.3 million of lease obligations which represents the present value of the lease payments discounted using weighted-average implicit rate of 5.0% . These amounts were recorded in our unaudited condensed consolidated balance sheet in the first quarter of 2019. In February 2018, the FASB issued ASU No. 2018-02, “Income Statement - Reporting Comprehensive Income (Topic 220) - Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income”. This standard allows a reclassification from accumulated other comprehensive income to retained earnings for stranded tax effects resulting from the Tax Cuts and Jobs Act and requires certain disclosures about stranded tax effects and will be effective for us beginning January 1, 2019 and should be applied either in the period of adoption or retrospectively. We adopted ASU 2018-02 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. In June 2018, the FASB issued ASU 2018-07, "Compensation-Stock Compensation (Topic 718): Improvements to Non-employee Share-Based Payment Accounting," which expands the scope of Topic 718, Compensation—Stock Compensation (which currently only includes share-based payments to employees) to include share-based payments issued to non-employees for goods or services. Consequently, the accounting for share-based payments to non-employees and employees will be substantially aligned. The ASU supersedes Subtopic 505-50, Equity—Equity-Based Payments to Non-Employees. The new standard is effective for fiscal years beginning after December 15, 2018, with early adoption permitted. We adopted ASU 2018-07 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. In July 2018, the FASB issued ASU 2018-09, "Codification Improvements”, which represent changes to clarify, correct errors in, or make minor improvements to the Codification, eliminating inconsistencies and providing clarifications in current guidance. The amendments in this ASU include those made to: Subtopic 220-10, Income Statement-Reporting Comprehensive Income-Overall; Subtopic 470-50, Debt-Modifications and Extinguishments; Subtopic 480-10, Distinguishing Liabilities from Equity-Overall; Subtopic 718-740, Compensation-Stock Compensation-Income Taxes; Subtopic 805-740, Business Combinations-Income Taxes; Subtopic 815-10, Derivatives and Hedging-Overall; Subtopic 820-10, Fair Value Measurement-Overall; Subtopic 940-405, Financial Services-Brokers and Dealers-Liabilities; and Subtopic 962-325, Plan Accounting-Defined Contribution Pension Plans-Investments-Other. The transition and effective date guidance is based on the facts and circumstances of each amendment. Some of the amendments do not require transition guidance and will be effective upon issuance. However, many of the amendments do have transition guidance with effective dates for annual periods beginning after December 15, 2018, for public business entities. We adopted subtopics under ASU 2018-09 that are applicable to our company which included subtopics 718-740 and 820-10 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. Recently issued accounting pronouncements not yet adopted From time to time, new accounting pronouncements are issued by the FASB or other standards setting bodies that are adopted by us as of the specified effective date. Unless otherwise discussed, we believe that the impact of recently issued standards that are not yet effective will not have a material impact on our unaudited condensed consolidated financial statements upon adoption. In June 2016, the FASB issued ASU 2016-13, "Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments," which amends the FASB's guidance on the impairment of financial instruments. The standard adds a new impairment model (known as the "current expected credit loss model") that is based on expected losses rather than incurred losses. ASU 2016-13 is effective for annual reporting periods ending after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. We are currently evaluating the impact of adopting ASU 2016-13 on our financial statements and related disclosures. In January 2017, the FASB issued ASU No. 2017-04, "Intangibles - Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment." The amendments eliminate Step 2 from the goodwill impairment test. The annual, or interim, goodwill impairment test is performed by comparing the fair value of a reporting unit with its carrying amount. An impairment charge should be recognized for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. In addition, income tax effects from any tax deductible goodwill on the carrying amount of the reporting unit should be considered when measuring the goodwill impairment loss, if applicable. The amendments also eliminate the requirements for any reporting unit with a zero or negative carrying amount to perform a qualitative assessment and, if it fails that qualitative test, to perform Step 2 of the goodwill impairment test. An entity still has the option to perform the qualitative assessment for a reporting unit to determine if the quantitative impairment test is necessary. The new standard is effective for fiscal years beginning after December 15, 2019, with early adoption permitted. We are currently evaluating the impact of adoption of ASU 2017-04 on our financial statements and related disclosures. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". The primary focus of ASU 2018-13 is to improve the effectiveness of the disclosure requirements for fair value measurements. The changes affect all companies that are required to include fair value measurement disclosures. In general, the amendments in ASU 2018-13 are effective for all entities for fiscal years and interim periods within those fiscal years, beginning after December 15, 2019. Early adoption is permitted. We are currently evaluating the impact of adoption of ASU 2018-13 on our financial statements and related disclosures. In November 2018, the FASB issued ASU 2018-18, "Collaborative Arrangements (Topic 808): Clarifying the Interaction Between Topic 808 and Topic 606." ASU 2018-18 provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. The ASU also provides more comparability in the presentation of revenue for certain transactions between collaborative arrangement participants. In general, for public companies, the amendments in this standard are effective for fiscal years beginning after December 15, 2019, and interim periods within those fiscal years. Early adoption is permitted. We are currently evaluating the impact of adoption of ASU 2018-18 on our financial statements.

Revenue Recognition

Revenue Recognition	9 Months Ended
	Sep. 30, 2019
Revenue from Contract with Customer [Abstract]
Revenue Recognition	Revenue Recognition Disaggregation of Revenue The following table provides information about disaggregated revenue from contracts with customers, the nature of the products and services and geographic regions, and includes a reconciliation of the disaggregated revenue with reportable segments. The geographic regions that are tracked are the Americas (United States, Canada, Latin America), EMEA (Europe, Middle East, Africa), and APAC (Australia, New Zealand, Southeast Asia, China). Three months ended September 30, 2019 Three months ended September 30, 2018 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 10,351 $ — $ 10,351 $ 8,405 $ — $ 8,405 Research and development revenue 10,073 1,482 11,555 3,720 4,821 8,541 Total revenues $ 20,424 $ 1,482 $ 21,906 $ 12,125 $ 4,821 $ 16,946 Primary geographical markets: Americas $ 2,706 $ — $ 2,706 $ 4,315 $ — $ 4,315 EMEA 10,723 1,482 12,205 1,453 4,821 6,274 APAC 6,995 — 6,995 6,357 — 6,357 Total revenues $ 20,424 $ 1,482 $ 21,906 $ 12,125 $ 4,821 $ 16,946 Nine months ended September 30, 2019 Nine months ended September 30, 2018 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 24,588 $ — $ 24,588 $ 18,291 $ — $ 18,291 Research and development revenue 16,512 8,708 25,220 15,728 10,507 26,235 Total revenues $ 41,100 $ 8,708 $ 49,808 $ 34,019 $ 10,507 $ 44,526 Primary geographical markets: Americas $ 9,620 $ — $ 9,620 $ 13,968 $ — $ 13,968 EMEA 15,964 8,708 24,672 4,568 10,507 15,075 APAC 15,516 — 15,516 15,483 — 15,483 Total revenues $ 41,100 $ 8,708 $ 49,808 $ 34,019 $ 10,507 $ 44,526 Contract Balances The following table presents changes in the contract assets, unbilled receivables, contract costs, and contract liabilities (in thousands): January 1, 2019 balance Additions Deductions (1) September 30, 2019 balance Contract Assets $ 35 7,142 (5,984 ) $ 1,193 Unbilled receivables, current $ 1,916 4,189 (3,788 ) $ 2,317 Unbilled receivables, non-current (2) $ 786 — (786 ) $ — Contract Costs (2) $ 42 — (41 ) $ 1 Contract Liabilities: Deferred Revenue $ 8,288 6,486 (11,498 ) $ 3,276 (1) The asset or liability balances are presented as a net position per contract and accordingly the deductions column includes the netting effect of presenting each contract on a net position basis as either a net liability or asset. (2) Included in non-current assets in our unaudited condensed consolidated balance sheets. We had no asset impairment charges related to contract assets in the three and nine months ended September 30, 2019 . During the three and nine months ended September 30, 2019 , we recognized the following revenues (in thousands): Revenue recognized in the period from: Three months ended September 30, 2019 Nine months ended September 30, 2019 Amounts included in contract liabilities at the beginning of the period: Performance obligations satisfied $ 5,092 $ 4,948 Changes in the period: Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods 2,641 2,460 Performance obligations satisfied from new activities in the period - contract revenue 14,173 42,400 Total revenue $ 21,906 $ 49,808 Performance Obligations The following table includes estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied or partially unsatisfied at the end of the reporting period. The estimated revenue does not include contracts with original durations of one year or less, amounts of variable consideration attributable to royalties, or contract renewals that are unexercised as of September 30, 2019 . The balances in the table below are partially based on judgments involved in estimating future orders from customers subject to the exercise of material rights pursuant to respective contracts. (in thousands) Remainder of 2019 2020 2021 and Thereafter Total Product Revenue $ — $ 365 $ 1,623 $ 1,988 Research and development revenue 1,288 — — 1,288 Total $ 1,288 $ 365 $ 1,623 $ 3,276

Net Income (loss) per Share

Net Income (loss) per Share	9 Months Ended
	Sep. 30, 2019
Earnings Per Share [Abstract]
Net Income (loss) per Share	Net Income (loss) per Share Basic net income (loss) per share is computed by dividing the net income (loss) by the weighted-average number of shares of common stock outstanding, less restricted stock awards ("RSAs") subject to forfeiture. Diluted net income (loss) per share is computed by dividing net income (loss) by the weighted average number of shares of common stock outstanding, less RSAs subject to forfeiture, plus all additional common stock shares that would have been outstanding, assuming dilutive potential common stock shares had been issued for other dilutive securities. For periods of net loss, diluted and basic net loss per share are identical since potential common stock shares are excluded from the calculation, as their effect was anti-dilutive. The following table sets forth the computation of basic and diluted net income (loss) per share during the three and nine months ended September 30, 2019 and 2018 (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Numerator: Net income (loss) $ 343 $ (1,988 ) $ (11,300 ) $ (10,417 ) Denominator: Weighted average common stock shares used in computing net income (loss) per share, basic 58,287 53,597 55,818 51,609 Effect of dilutive shares 3,125 — — — Weighted average common stock shares used in computing net income (loss) per share, diluted 61,412 53,597 55,818 51,609 Net income (loss) per share, basic $ 0.01 $ (0.04 ) $ (0.20 ) $ (0.20 ) Net income (loss) per share, diluted $ 0.01 $ (0.04 ) $ (0.20 ) $ (0.20 ) Anti-Dilutive Securities The following shares were not considered in the computation of diluted net income (loss) per share because their effect was anti-dilutive (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan 1,019 7,607 5,623 7,607

Collaborative Arrangements

Collaborative Arrangements	9 Months Ended
	Sep. 30, 2019
Research and Development [Abstract]
Collaborative Arrangements	Collaborative Arrangements GSK Platform Technology Transfer, Collaboration and License Agreement In July 2014, we entered into a CodeEvolver ® protein engineering platform technology transfer collaboration and license agreement (the "GSK CodeEvolver ® Agreement") with GlaxoSmithKline ("GSK"). Pursuant to the terms of the agreement, we granted GSK a non-exclusive license to use the CodeEvolver ® protein engineering platform technology to develop novel enzymes for use in the manufacture of GSK's pharmaceutical and health care products. We received an upfront fee upon the execution of the agreement in July 2014 and milestone payments in each of the years from 2014 through April 2016. We completed the transfer of the CodeEvolver ® protein engineering platform technology to GSK in April 2016 and all revenues relating to the technology transfer have been recognized as of April 2016. We have the potential to receive additional cumulative contingent payments that range from $5.75 million to $38.5 million per project based on GSK’s successful application of the licensed technology. We are also eligible to receive royalties based on net sales, if any, of a limited set of products developed by GSK using our CodeEvolver ® protein engineering platform technology. In September 2019, we received notification from GSK that a milestone relating to the advancement of an enzyme developed by GSK using our CodeEvolver ® protein engineering platform technology has been achieved, triggering a $2.0 million milestone payment to Codexis from GSK. We recognized revenue of $2.0 million for the milestone payment for the three and nine months ended September 30, 2019 , respectively, compared to zero for the three and nine months ended September 30, 2018 , respectively, as research and development revenue. Merck Platform Technology Transfer and License Agreement In August 2015, we entered into a CodeEvolver ® platform technology transfer collaboration and license agreement (the "Merck CodeEvolver ® Agreement") with Merck, Sharp & Dohme ("Merck") which allows Merck to use the CodeEvolver ® protein engineering technology platform in the field of human and animal healthcare. We received an upfront license fee upon execution of the Merck CodeEvolver ® Agreement, and milestone payments in September 2015 and in September 2016, when we completed the transfer of the engineering platform technology. Additionally, we recognized research and development revenues of $1.0 million and $3.0 million for the three and nine months ended September 30, 2019 , respectively, compared to $1.1 million and $3.0 million for the three and nine months ended September 30, 2018 , respectively, for various research projects under our collaborative arrangement. We have the potential to receive payments of up to a maximum of $15.0 million for each commercial active pharmaceutical ingredient ("API") that is manufactured by Merck using one or more novel enzymes developed by Merck using the CodeEvolver ® protein engineering technology platform. These potential API payments are based on the quantity of API developed and manufactured by Merck and will be recognized as usage-based royalties. We recognized zero usage-based royalties in both the three and nine months ended September 30, 2019 . In January 2019, we entered into an amendment to the Merck CodeEvolver ® Agreement whereby we installed certain CodeEvolver ® protein engineering technology upgrades into Merck’s platform license. Pursuant to the agreement, we will maintain those upgrades for a multi-year term. We recognized research and development revenues of $0.1 million and $1.0 million for the three and nine months ended September 30, 2019 , respectively, under the amendment. Merck Sitagliptin Catalyst Supply Agreement In February 2012, we entered into a five -year Sitagliptin Catalyst Supply Agreement ("Sitagliptin Catalyst Supply Agreement") with Merck whereby Merck may obtain commercial scale substance for use in the manufacture of Januvia ® , its product based on the active ingredient sitagliptin. In December 2015, Merck exercised its option under the terms of the Sitagliptin Catalyst Supply Agreement to extend the agreement for an additional five years through February 2022. Effective as of January 2016, we and Merck amended the Sitagliptin Catalyst Supply Agreement to prospectively provide for variable pricing based on the cumulative volume of sitagliptin catalyst purchased by Merck and to allow Merck to purchase a percentage of its requirements for sitagliptin catalyst from a specified third-party supplier. Merck received a distinct, functional license to manufacture a portion of its demand beginning January 1, 2018, which we recognized as research and development revenue. Under this agreement, we recognized no research and development revenue for the three and nine months ended September 30, 2019 , compared to zero and $1.3 million for the three and nine months ended September 30, 2018 , respectively. We have determined that the variable pricing, which provides a discount based on the cumulative volume of sitagliptin catalyst purchased by Merck, provides Merck material rights and we are recognizing product revenues using the alternative method. Under the alternative approach, we estimate the total expected consideration and allocate it proportionately with the expected sales. The Sitagliptin Catalyst Supply Agreement requires Merck to pay an annual fee for the rights to the sitagliptin technology each year for the term of the Sitagliptin Catalyst Supply Agreement. Amounts of annual license fees are based on contractually agreed prices and are on a declining scale over the term of the contract. We had a deferred revenue balance from Merck of zero at September 30, 2019 and $3.6 million at December 31, 2018 . In addition, pursuant to the terms of the Sitagliptin Catalyst Supply Agreement, we recognized $3.6 million and $11.4 million for the three and nine months ended September 30, 2019 , respectively, compared to $3.4 million and $10.7 million for the three and nine months ended September 30, 2018 , respectively, in product revenue under this agreement. Enzyme Supply Agreement In November 2016, we entered into a supply agreement whereby our customer may purchase quantities of one of our proprietary enzymes for use in its commercial manufacture of a product. Pursuant to the supply agreement, we received an upfront payment of $0.8 million in December 2016, which we accordingly recorded as deferred revenue. Such upfront payment will be recognized over the period of the supply agreement as the customer purchases our proprietary enzyme. We additionally have determined that the volume discounts under the supply agreement provides the customer material rights and we are recognizing revenues using the alternative method. As of September 30, 2019 and December 31, 2018 , we had deferred revenue from the supply agreement of $2.0 million . Research and Development Agreement In March 2017, we entered into a multi-year research and development services agreement with Tate & Lyle Ingredients Americas LLC ("Tate & Lyle") to develop enzymes for use in the manufacture of Tate & Lyle’s zero-calorie TASTEVA ® M Stevia sweetener. Under the agreement, we received an upfront payment of $3.0 million , which was recognized ratably over the maximum term of the services period of 21 months. Beginning January 1, 2018, we recognized revenue using a single measure of progress that depicted our performance in transferring the services. During the second quarter of 2018, Tate & Lyle opted to obtain additional development services that we completed by June 30, 2018 and we earned milestone payments upon completion of the services. We recognized revenue of zero and $50 thousand for the three and nine months ended September 30, 2019 , respectively, compared to $1.3 million and $7.1 million for the three and nine months ended September 30, 2018 , respectively, for research and development services under the research and development agreement. Global Development, Option and License Agreement and Strategic Collaboration Agreement In October 2017, we entered into a Global Development, Option and License Agreement (the "Nestlé Agreement") with Nestec Ltd. ("Nestlé Health Science") and, solely for the purpose of the integration and the dispute resolution clauses of the Nestlé Agreement, Nestlé Health Science S.A., to advance CDX-6114, our enzyme biotherapeutic product candidate for the potential treatment of PKU. We received an upfront cash payment of $14.0 million upon the execution of the Nestlé Agreement, a $4.0 million milestone payment after dosing the first subjects in a first-in-human Phase 1a dose-escalation trial with CDX-6114, and a $1.0 million milestone payment upon achievement of a milestone relating to formulation of CDX-6114. The $4.0 million milestone payment that was triggered by the initiation of the trial was received in September 2018 and the $1.0 million milestone payment that was triggered by the achievement of a formulation relating to CDX-6114 was received in February 2019. The upfront payment and the variable consideration relating to the progress payment of $4.0 million and milestone payment of $1.0 million are being recognized over time as the development work is being performed. Revenue is being recognized using a single measure of progress that depicts our performance in transferring control of the services, which is based on the ratio of level of effort incurred to date compared to the total estimated level of effort required to complete all performance obligations under the agreement. We recognized development fees of $0.1 million and $1.8 million for the three and nine months ended September 30, 2019 , respectively, compared to $3.7 million and $8.1 million for the three and nine months ended September 30, 2018 , respectively, as research and development revenue. We had deferred revenue related to the development fees attributed to the milestone payment and upfront fees of $50 thousand at September 30, 2019 and $1.9 million at December 31, 2018 . In January 2019, we received notice from the FDA that it had completed its review of our IND for CDX-6114 and concluded that we may proceed with the proposed Phase 1b multiple ascending dose study in healthy volunteers in the United States. In February 2019, Nestlé Health Science exercised its option to obtain an exclusive, worldwide, royalty-bearing, sub-licensable license for the global development and commercialization of CDX-6114 for the management of PKU. The option payment of $3.0 million was recognized in the first quarter of 2019 as research and development fees. Upon exercising its option, Nestlé Health Science has assumed all responsibilities for future clinical development and commercialization of CDX-6114, with the exception of the completion of an extension study, CDX-6114-004, which was substantially completed in the second quarter of 2019. Other potential payments from Nestlé Health Science to us under the Nestlé Agreement include (i) development and approval milestones of up to $85.0 million , (ii) sales-based milestones of up to $250.0 million in the aggregate, which aggregate amount is achievable if net sales exceed $1.0 billion in a single year, and (iii) tiered royalties, at percentages ranging from the middle single digits to low double-digits, of net sales of product. In addition to the Nestlé Agreement, we and Nestlé Health Science concurrently entered into a Strategic Collaboration Agreement (the "Strategic Collaboration Agreement") pursuant to which we and Nestlé Health Science will collaborate to leverage the CodeEvolver ® protein engineering technology platform to develop novel enzymes for Nestlé Health Science’s established Consumer Care and Medical Nutrition business areas. Under the Strategic Collaboration Agreement, we received an upfront payment of $1.2 million in 2017 and an incremental $0.6 million payment in September 2018 for additional services. We recognized research and development fees of $1.4 million and $3.9 million for the three and nine months ended September 30, 2019 , respectively, compared to $1.2 million and $2.4 million for the three and nine months ended September 30, 2018 , respectively. We had deferred revenue of $25 thousand and $0.8 million at September 30, 2019 and December 31, 2018 , respectively. Strategic Collaboration Agreement In April 2018, we entered into the Porton Agreement with Porton to license key elements of Codexis’ biocatalyst technology for use in Porton’s global custom intermediate and API development and manufacturing business. Under the Porton Agreement, we are eligible to receive annual collaboration fees and research and development revenues. We received an initial collaboration fee of $0.5 million within 30 days of the effective date and $1.5 million upon the first anniversary of the effective date of the agreement. We completed the technical transfer in the fourth quarter of 2018. Revenue relating to the functional license provided to Porton was recognized at a point in time when control of the license transferred to the customer. Commercial Agreement In April 2019, we entered into a multi-year commercial agreement with Tate & Lyle under which Tate & Lyle has received an exclusive license to use a suite of Codexis novel performance enzymes in the manufacture of Tate & Lyle’s zero-calorie stevia sweetener, TASTEVA ® M, and other stevia products. Under the agreement, we will supply Tate & Lyle with its requirements for these enzymes over a multiple year period and receive royalties on stevia products. Platform Technology Transfer and License Agreement In May 2019, we entered into a Platform Technology Transfer and License Agreement (the “Novartis CodeEvolver ® Agreement”) with Novartis Pharma AG (“Novartis”). The Agreement allows Novartis to use Codexis’ proprietary CodeEvolver ® protein engineering platform technology in the field of human healthcare. Under the Novartis CodeEvolver ® Agreement, we will transfer Codexis' proprietary CodeEvolver ® protein engineering platform technology to Novartis over approximately 20 months starting with the date on which we commence the technology transfer (the “Technology Transfer Period”). As a part of this technology transfer, our company will provide to Novartis Codexis’ proprietary enzymes, proprietary protein engineering protocols and methods, and proprietary software algorithms. In addition, teams of Codexis and Novartis scientists will participate in technology training sessions and collaborative research projects at Codexis’ laboratories in Redwood City, California and at a designated Novartis laboratory in Basel, Switzerland. Upon completion of technology transfer, Novartis will have the CodeEvolver ® protein engineering platform technology installed at its designated laboratory. Pursuant to the agreement, we received an upfront payment of $5 million shortly after the effective date of the Novartis CodeEvolver ® Agreement. We are entitled to receive an additional $4 million subject to satisfactory completion of the second technology transfer milestone and an additional $5 million upon satisfactory completion of the third technology transfer milestone. In consideration for the continued disclosure and license of improvements to the Codexis technology and materials during a multi-year period that begins on the conclusion of the Technology Transfer Period (“Improvements Term”), Novartis will pay Codexis annual payments which amount to an additional $8 million . Codexis also has the potential to receive quantity-dependent, usage payments for each API that is manufactured by Novartis using one or more enzymes that have been developed or are in development using the CodeEvolver ® protein engineering platform technology during the period that begins on the conclusion of the Technology Transfer Period and ends on the expiration date of the last to expire licensed patent. These product-related usage payments, if any, will be paid by Novartis to Codexis for each quarter that Novartis manufactures API using a CodeEvolver ® -developed enzyme. The usage payments will be based on the total volume of API produced using the CodeEvolver ® -developed enzyme. These usage payments can begin in the clinical stage, and will extend throughout the commercial life of each API. Revenue for the combined initial license and technology transfer, which is expected to occur over twenty months, is being recognized using a single measure of progress that depicts our performance in transferring control of the services, which is based on the ratio of level of effort incurred to date compared to the total estimated level of effort required to complete the performance obligation relating to the combined initial license and technology transfer. Revenue allocated to future improvements will be recognized during the Improvement Term. We recognized $3.8 million in revenue for the three and nine months ended September 30, 2019 from the Novartis CodeEvolver ® Agreement. As of September 30, 2019 , we had deferred revenue of $1.2 million from the Novartis CodeEvolver ® Agreement.

Cash Equivalents and Marketable

Cash Equivalents and Marketable Securities	9 Months Ended
	Sep. 30, 2019
Cash Equivalents and Marketable Securities [Abstract]
Cash Equivalents and Marketable Securities	Cash Equivalents and Marketable Securities Cash equivalents and marketable securities at September 30, 2019 and at December 31, 2018 consisted of the following (in thousands): September 30, 2019 Adjusted Cost Gross Unrealized (3) Gross Unrealized (3) Estimated Money market funds (1) $ 73,450 $ — $ — $ 73,450 December 31, 2018 Adjusted Cost Gross Unrealized (3) Gross Unrealized (3) Estimated Money market funds (1) $ 31,225 $ — $ — $ 31,225 Common shares of CO 2 Solutions (2) 563 25 — 588 Total $ 31,788 $ 25 $ — $ 31,813 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified in equity securities on our unaudited condensed consolidated balance sheets. (3) As a result of adopting ASU 2016-01, " Financial Instruments-Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities ", in 2018 and thereafter gross unrealized gains and gross unrealized losses related to our investment in CO 2 Solutions were recognized in other expense, in our unaudited condensed consolidated statements of operations. As of September 30, 2019 , the total cash and cash equivalents balance of $92.1 million was comprised of money market funds of $73.5 million and cash of $18.6 million held with major financial institutions worldwide. As of December 31, 2018 , the total cash and cash equivalents balance of $53.0 million was comprised of money market funds of $31.2 million and cash of $21.8 million held with major financial institutions worldwide. In December 2009, we purchased 10,000,000 common shares of CO 2 Solutions, a company based in Quebec, Canada, whose shares were publicly traded in Canada on the TSX Venture Exchange until September 17, 2019 and are currently listed on NEX board, which is a separate board of TSX Venture Exchange. Our purchase represented approximately 16.6% of CO 2 Solutions’ total common shares outstanding at the time of investment and was made in a private placement subject to a four -month statutory resale restriction. This restriction expired on April 15, 2010. Our investment in CO 2 Solutions is recorded at its fair value. See Note 7, “Fair Value Measurements.” Through September 30, 2019 , we concluded that we did not have the ability to exercise significant influence over CO 2 Solutions’ operating and financial policies. In the quarter ended September 30, 2019, we sold 1.3 million common shares of our investment in CO 2 Solutions and received proceeds of $0.1 million . At September 30, 2019, we reviewed our investment in the common shares of CO 2 Solutions. Concurrent with CO 2 Solutions' announcement to file under the Bankruptcy and Insolvency Act (Canada) and a suspension in trading of its equity securities, there was no observable market pricing available at September 30, 2019. We assessed that the fair value of the investment and concluded to write down the investment to zero . Previously, we had assessed the fair value of the investment using readily quantifiable market data. We recognized a $0.4 million and a $0.5 million loss, respectively in the three and nine months ended September 30, 2019 . The loss was included in other expenses, net in the unaudited condensed consolidated statement of operations. We recognized a loss of $25 thousand and $20 thousand , respectively, in the three and nine months ended September 30, 2018 .The loss was included in other expenses, net in the unaudited condensed consolidated statement of operations. On January 1, 2018, we adopted ASU 2016-01. Upon adoption, we reclassified the $0.5 million net unrealized loss on our investment from accumulated other comprehensive loss to our opening accumulated deficit.

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2019
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The following tables present the financial instruments that were measured at fair value on a recurring basis at September 30, 2019 and December 31, 2018 by level within the fair value hierarchy (in thousands): September 30, 2019 Level 1 Level 2 Level 3 Total Money market funds $ 73,450 $ — $ — $ 73,450 December 31, 2018 Level 1 Level 2 Level 3 Total Money market funds $ 31,225 $ — $ — $ 31,225 Common shares of CO 2 Solutions 588 — — 588 Total $ 31,856 $ — $ — $ 31,813 We determine the fair value of Level 1 assets using quoted prices in active markets for identical assets. At December 31, 2018, we estimated the fair value of our investment in 10,000,000 common shares of CO 2 Solutions using the market value of common shares as determined by trading on the TSX Venture Exchange, and we classified our investment in CO 2 Solutions within the fair value hierarchy as Level 1 at December 31, 2018 using the quoted prices in an active market to determine their fair value. In the quarter ended September 30, 2019, we reviewed our investment in the common shares of CO 2 Solutions. Concurrent with CO 2 Solutions' announcement to file under the Bankruptcy and Insolvency Act (Canada) and a suspension in trading of its equity securities, there was no observable market pricing available at September 30, 2019. We assessed the fair value of the investment and concluded to write down the investment to zero . We recognized a $0.4 million and a $0.5 million loss, respectively in the three and nine months ended September 30, 2019 in other expenses, net in the unaudited condensed consolidated statement of operations. For information see Note 6. "Cash Equivalents and Marketable Securities".

Balance Sheets Details

Balance Sheets Details	9 Months Ended
	Sep. 30, 2019
Balance Sheets Details [Abstract]
Balance Sheets Details	Balance Sheets Details Inventories Inventories consisted of the following (in thousands): September 30, 2019 December 31, 2018 Raw materials $ 7 $ 165 Work-in-process 52 47 Finished goods 338 377 Inventories $ 397 $ 589 Property and Equipment, net Property and equipment, net consisted of the following (in thousands): September 30, 2019 December 31, 2018 Laboratory equipment $ 23,266 $ 21,328 Leasehold improvements 10,899 10,359 Computer equipment and software 3,806 3,954 Office equipment and furniture 1,461 1,272 Construction in progress 488 939 Property and equipment 39,920 37,852 Less: accumulated depreciation and amortization (33,679 ) (33,093 ) Property and equipment, net $ 6,241 $ 4,759 Goodwill Goodwill had a carrying value of approximately $3.2 million as of September 30, 2019 and December 31, 2018 . Other Accrued Liabilities Other accrued liabilities consisted of the following (in thousands): September 30, 2019 December 31, 2018 Accrued purchases $ 3,894 $ 1,492 Accrued professional and outside service fees 1,833 2,020 Deferred rent — 343 Lease incentive obligation — 425 Other 455 575 Total $ 6,182 $ 4,855

Stock-Based Compensation

Stock-Based Compensation	9 Months Ended
	Sep. 30, 2019
Share-based Payment Arrangement [Abstract]
Stock-Based Compensation	Stock-Based Compensation Equity Incentive Plans In June 2019, our board of directors (the "Board") and stockholders approved the 2019 Incentive Award Plan (the "2019 Plan"). The 2019 Plan supersedes and replaces in its entirety our 2010 Equity Incentive Plan (the “2010 Plan”) which was effective in March 2010, and no further awards will be granted under the 2010 Plan; however, the terms and conditions of the 2010 Plan will continue to govern any outstanding awards thereunder. The number of shares of our common stock available for issuance under the 2019 Plan is equal to the sum of (i) 7,897,144 shares, and (ii) any shares subject to awards granted under the 2010 Plan that were outstanding as of April 22, 2019 and thereafter terminate, expire, lapse or are forfeited; provided that no more than 14,000,000 shares may be issued upon the exercise of incentive stock options (“ISOs”). In June 2019, 8.1 million shares authorized for issuance under the 2019 Plan were registered under the Securities Act of 1933, as amended (the “Securities Act”). The 2019 Plan provides for the grant of stock options, including incentive stock options and non-qualified stock options, stock appreciation rights, restricted stock, restricted stock units, other stock or cash based awards and dividend equivalents to eligible employees and consultants of the Company or any parent or subsidiary, as well as members of the Board. The 2010 Plan provided for the grant of incentive stock options, non-statutory stock options, restricted stock units ("RSUs"), restricted stock awards ("RSAs"), performance-contingent restricted stock units ("PSUs"), performance based options ("PBOs"), stock appreciation rights, and stock purchase rights to our employees, non-employee directors and consultants. Stock Options The option exercise price for incentive stock options is at least 100% of the fair value of our common stock on the date of grant and the option exercise price for non-statutory stock options is at least 85% of the fair value of our common stock on the date of grant, as determined by the Board. If, at the time of a grant, the optionee directly or by attribution owns stock possessing more than 10% of the total combined voting power of all of our outstanding capital stock, the exercise price for these options must be at least 110% of the fair value of the underlying common stock. Stock options granted to employees generally have a maximum term of 10 years and vest over a four year period from the date of grant, of which 25% vest at the end of one year, and 75% vest monthly over the remaining three years. We may grant options with different vesting terms from time to time. Unless an employee's termination of service is due to disability or death, upon termination of service, any unexercised vested options will be forfeited at the end of three months or the expiration of the option, whichever is earlier. Restricted Stock Units (RSUs) We also grant employees RSUs, which generally vest over either a three year period with one-third of the shares subject to the RSUs vesting on each yearly anniversary of the vesting commencement date or over a four year period with 25% of the shares subject to the RSU vesting on each yearly anniversary of the vesting commencement date, in each case contingent upon such employee’s continued service on such vesting date. RSUs are generally subject to forfeiture if employment terminates prior to the release of vesting restrictions. We may grant RSUs with different vesting terms from time to time. Performance-contingent Restricted Stock Units (PSUs) and Performance Based Options (PBOs) The compensation committee of the Board approved, solely in respect of non-executive employees, and delegated to our Chief Executive Officer the authority to approve grants of PSUs. The compensation committee of the Board also approved grants of PBOs and PSUs to our executives. The PSUs and PBOs vest based upon both the successful achievement of certain corporate operating milestones in specified timelines and continued employment through the applicable vesting date. When the performance goals are deemed to be probable of achievement for these types of awards, recognition of stock-based compensation expense commences. Once the number of shares eligible to vest is determined, those shares vest in two equal installments with 50% vesting upon achievement and the remaining 50% vesting on the first anniversary of achievement, in each case, subject to the recipient’s continued service through the applicable vesting date. If the performance goals are achieved at the threshold level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to half the number of PSUs granted and one-quarter the number of shares underlying the PBOs granted. If the performance goals are achieved at the target level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to the number of PSUs granted and half of the shares underlying the PBOs granted. If the performance goals are achieved at the superior level, the number of shares eligible to vest in respect of the PSUs would be equal to two times the number of PSUs granted and equal to the number of PBOs granted. The number of shares issuable upon achievement of the performance goals at the levels between the threshold and target levels for the PSUs and PBOs or between the target level and superior levels for the PSUs would be determined using linear interpolation. Achievement below the threshold level would result in no shares being eligible to vest in respect of the PSUs and PBOs. In the first quarter of 2019, we awarded PSUs ("2019 PSUs") and PBOs ("2019 PBOs"), each of which commence vesting based upon the achievement of various weighted performance goals, including revenue growth, strategic advancement of biotherapeutics, cash balance and strategic plan development. As of September 30, 2019 , we estimated that the 2019 PSUs and 2019 PBOs performance goals would be achieved at 113% of the target level, and recognized expenses accordingly. In 2018, we awarded PSUs ("2018 PSUs") and PBOs ("2018 PBOs"), each of which commenced vesting based upon the achievement of various weighted performance goals, including core business revenue growth, cash balance, new licensing collaborations, new research and development service revenue arrangements, technology advancement and novel therapeutic enzymes advancement. In the first quarter of 2019, we determined that the 2018 PSUs and 2018 PBOs performance goals had been achieved at 118% of the target level, and recognized expenses accordingly. Accordingly, one-half of the shares underlying the 2018 PSUs and PBOs vested in the first quarter of 2019 and one-half of the shares underlying the 2018 PSUs and PBOs will vest in the first quarter of 2020, in each case subject to the recipient’s continued service on each vesting date. In 2017, we awarded PSUs ("2017 PSUs") and PBOs ("2017 PBOs"), each of which commenced vesting based upon the achievement of various weighted performance goals, including revenue growth, fundraising, service revenue, new platform license revenue, and strategic advancement of biotherapeutics pipeline. In the first quarter of 2018, we determined that the 2017 PSU and PBO performance goals had been achieved at 134.2% of the target level, and recognized expenses accordingly. Accordingly, one-half of the shares underlying the 2017 PSUs and PBOs vested in the first quarter of 2018 and one-half of the shares underlying the 2017 PSUs and PBOs vested in the first quarter of 2019, in each case subject to the recipient’s continued service on each vesting date. Stock-Based Compensation Expense Stock-based compensation expense is included in the unaudited condensed consolidated statements of operations as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Research and development $ 458 $ 552 $ 1,249 $ 1,555 Selling, general and administrative 1,274 1,218 4,534 4,652 Total $ 1,732 $ 1,770 $ 5,783 $ 6,207 The following table presents total stock-based compensation expense by security type included in the unaudited condensed consolidated statements of operations for the three and nine months ended September 30, 2019 and 2018 (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Stock options $ 545 $ 472 $ 1,680 $ 1,482 RSUs and RSAs 461 416 1,308 1,293 PSUs 368 407 1,075 1,251 PBOs 358 475 1,720 2,181 Total $ 1,732 $ 1,770 $ 5,783 $ 6,207 As of September 30, 2019 , unrecognized stock-based compensation expense, net of expected forfeitures, was $4.4 million related to unvested employee stock options, $1.8 million related to unvested RSUs and RSAs, $0.8 million related to unvested PSUs, and $1.8 million related to unvested PBOs based on current estimates of the level of achievement. Stock-based compensation expense for these awards will be recognized through the year of 2023.

Capital Stock

Capital Stock	9 Months Ended
	Sep. 30, 2019
Equity [Abstract]
Capital Stock	Capital Stock Exercise of Options For the nine months ended September 30, 2019 and September 30, 2018 , 970,256 and 729,596 shares, respectively, were issued upon option exercises at a weighted-average exercise price of $4.76 and $5.92 per share, respectively, with net cash proceeds of $4.6 million and $4.3 million , respectively. Private Offering In June 2019, we entered into a Securities Purchase Agreement with an affiliate of Casdin pursuant to which we issued and sold to Casdin 3,048,780 shares of our common stock ("Shares") at a purchase price of $16.40 per share. After deducting issuance costs of $0.1 million from the Private Offering, our net proceeds were $49.9 million . In June 2019, we also entered into a Registration Rights Agreement (the “Registration Rights Agreement”) with Casdin. Pursuant to the Registration Rights Agreement, we agreed, subject to certain conditions, to prepare and file a registration statement with the Securities and Exchange Commission (the “SEC”) within 180 days after the closing of the Private Offering, if we are a “well known seasoned issuer” at such time (210 days if we are not then a “well known seasoned issuer”) for purposes of registering the resale of the Shares and any shares of common stock issued as a dividend or other distribution with respect to the Shares. We further agreed, among other things, to indemnify the selling holders under the registration statement from certain losses, claims, damages and liabilities and to pay all fees and expenses (excluding underwriting discounts and selling commissions) incident to the performance of, or compliance with, our obligations under the Registration Rights Agreement. The Private Offering was exempt from registration pursuant to the exemption for transactions by an issuer not involving any public offering under Section 4(a)(2) the Securities Act, and Regulation D under the Securities Act.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases Our headquarters are located in Redwood City, California, where we occupy approximately 107,200 square feet of office and laboratory space in four buildings within the same business park of Metropolitan Life Insurance Company ("MetLife"). Our lease (“Lease”) with MetLife includes approximately 28,200 square feet of space located at 200 and 220 Penobscot Drive, Redwood City, California (the “Penobscot Space”), approximately 37,900 square feet of space located at 400 Penobscot Drive, Redwood City, California (the “Building 2 Space”), approximately 11,200 square feet of space located at 501 Chesapeake Drive, Redwood City, California (the “501 Chesapeake Space”), and approximately 29,900 square feet of space located at 101 Saginaw Drive, Redwood City, California (the “Saginaw Space”). We entered into the initial lease with MetLife for a portion of this space in 2004 and the lease has been amended multiple times since then to adjust space and amend the terms of the Lease. The lease amendment ("Seventh Amendment") in October 2016 waived our existing asset retirement obligation for one of our buildings and extended the lease term to January 2022. The various terms for the spaces under the lease have expiration dates that range from January 2020 through January 2022. Beginning in February 2014, we have subleased certain office and laboratory space to different subtenants with separate options to extend the subleases. These subleases will expire on November 30, 2019 and January 31, 2020. In February 2019, we entered into the eighth amendment to the Lease ("Eighth Amendment") with MetLife to extend the lease terms for the Penobscot Space, the Building 2 Space and the Chesapeake Space for another 88 months . The lease on the Saginaw Space will expire in January 2020. The lease terms for the Penobscot Space and Building 2 Space have an expiration date of May 2027. The lease term for the 501 Chesapeake Space has an expiration date of May 2029. We incurred $3.6 million of capital improvement costs related to the facilities leased from MetLife through December 31, 2012. During 2011 and 2012, we requested and received $3.1 million of reimbursements from the landlord for the tenant improvement and HVAC allowances for the completed construction. The reimbursements were recorded once cash was received and are amortized on a straight line basis over the term of the lease as a reduction in rent expense. The remaining lease incentive obligations were zero and $0.5 million at September 30, 2019 and December 31, 2018 , respectively. Prior to adoption of ASC 842, lease incentive obligation were reflected as liabilities on the unaudited condensed consolidated balance sheets. Upon adoption of ASC 842, lease incentive obligations were cleared to zero to create our right-of-use assets related to operating lease, reflected on the unaudited condensed consolidated balance sheets. Rent expense for the Redwood City properties is recognized on a straight-line basis over the term of the lease. We are required to restore certain areas of the Redwood City facilities that we are renting to their original form. We are expensing the asset retirement obligation over the terms of the respective leases. We review the estimated obligation each reporting period and make adjustments if our estimates change. We recorded asset retirement obligations of $0.2 million as of September 30, 2019 and December 31, 2018 , respectively, which are included in other liabilities on the unaudited condensed consolidated balance sheets. Accretion expense related to our asset retirement obligations was no minal in the three and nine months ended September 30, 2019 and 2018 . Pursuant to the terms of the amended lease agreement, we exercised our right to deliver a letter of credit in lieu of a security deposit. The letter of credit is collateralized by deposit balances held at a bank in the amount of $1.1 million and $0.7 million as of September 30, 2019 and December 31, 2018 , respectively. These deposits are recorded as restricted cash on the unaudited condensed consolidated balance sheets. Rent expense was $1.1 million and $3.4 million during the three and nine months ended September 30, 2019 , respectively, partially offset by sublease income of $0.2 million and $0.7 million , respectively. Rent expense was $0.8 million and $2.4 million during the three and nine months ended September 30, 2018 , respectively, partially offset by sublease income of $0.3 million and $0.9 million , respectively. Finance Leases In December 2016, we entered into a three -year financing lease agreement with a third-party supplier for the purchase of laboratory equipment that was partially financed through a finance lease of approximately $0.4 million . The lease became effective upon delivery of the equipment, which occurred in February 2017, and the term of the lease is three years from the effective date. This financing agreement was accounted for as a finance lease due to the bargain purchase option at the end of the lease. In April 2017, we entered into a three -year financing lease agreement with a third-party supplier for the purchase of information technology equipment for approximately $0.3 million . The effective date of the lease was May 19, 2017 and the term of the lease is three years . This financing agreement was accounted for as a finance lease due to the bargain purchase option at the end of the lease. Adoption of ASC 842 On January 1, 2019, we adopted ASC 842, using a modified retrospective approach and effective date method per adoption of ASU 2018-11. We completed the full analysis by January 2019 and we evaluated the right-of-use (ROU) assets and lease obligations using the incremental borrowing rate (IBR) at December 31, 2018 because the implicit rate is not readily determinable in the lease agreement. Upon adoption of ASC 842, all existing leases were classified as either operating leases or finance leases. All existing leases that were classified as capital leases in accordance with Topic 840 were classified as finance leases. We recorded $26.6 million of ROU assets and $27.6 million of lease obligations for operating leases, and $0.5 million of ROU assets and $0.3 million of lease obligations for finance leases in the balance sheet in the first quarter of 2019. Practical Expedients, Elections, and Exemptions We used a practical expedient available under ASC 842-10-65-1(f) that permits us not to reassess whether any expired or existing contracts are or contain leases; not to reassess the lease classification for any expired or existing leases (for example, all existing leases that were classified as operating leases in accordance with ASC 840 will be classified as operating leases, and all existing leases that were classified as capital leases in accordance with ASC 840 will be classified as finance leases); and not to reassess initial direct costs for any existing leases. On January 1, 2019, we also made an accounting policy election (by class of underlying asset to which the right of use relates) to apply accounting principles to leases that meet ASC 842’s definition of a short-term lease (i.e., the short-term lease exemption). We elected not to apply the recognition requirements of Topic 842 and instead we recognize the lease payments as lease cost on a straight-line basis over the lease term. A short-term lease is defined as a lease that, at the commencement date, has a lease term of 12 months or less and does not include an option to purchase the underlying asset that the lessee is reasonably certain to exercise. The following table shows the reconciliation of right-of-use assets and lease obligations, with balances reflecting the adoption of ASC 842, related to both operating leases and finance leases and gives effect to the modified retrospective adoption and effective date method under the lease guidance on January 1, 2019 (in thousands): Operating leases Finance Leases Right-of-use assets, balance at December 31, 2018 $ — $ — Changes in the period: Right-of-use assets created upon adoption of ASC 842 26,617 493 Right-of-use assets, balance at January 1, 2019 $ 26,617 $ 493 Lease obligations, balance at December 31, 2018 $ — $ — Changes in the period: Lease obligations created upon adoption of ASC 842 27,562 302 Lease obligations, balance at January 1, 2019 $ 27,562 $ 302 Lease related expenses under non-cancellable finance and operating leases and under non-cancellable subleases as follows (in thousands except discount rate and lease term): Three months ended September 30, 2019 Nine months ended September 30, 2019 Lease costs Finance lease cost: Amortization of right-of-use assets $ 54 $ 163 Interest on lease obligations 2 8 Operating lease cost 1,139 3,417 Sublease income (262 ) (727 ) Total lease cost $ 933 $ 2,861 Other information Weighted-average remaining lease term (in years): Finance leases 0.5 Operating leases 7.9 Weighted-average discount rate: Finance leases 5.0 % Operating leases 6.6 % Cash paid for amounts included in the measurement of lease obligations Operating cash flows from operating leases $ (2,456 ) Operating cash flows from finance leases $ (9 ) Financing cash flows from finance leases $ (180 ) As of September 30, 2019 , under ASC 842, maturity analysis of annual undiscounted cash flows of the non-cancellable finance and operating leases are as follows (in thousands): Years ending December 31, Finance Leases Operating Leases 2019 (remaining 3 months) $ 63 $ 824 2020 61 2,816 2021 — 4,197 2022 — 4,285 2023 — 4,589 2024 and thereafter — 18,220 Total minimum lease payments (1) $ 124 $ 34,931 Less: imputed interest (2 ) (8,484 ) Lease Obligations $ 122 $ 26,447 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.3 million to be received under non-cancellable subleases at September 30, 2019 . As of December 31, 2018, under ASC 840, maturity analysis of annual undiscounted cash flows of the non-cancellable capital and operating leases as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2019 $ 252 $ 3,280 2020 61 712 2021 — 490 2022 — 41 2023 — — Total minimum lease payments (1) 313 $ 4,523 Less: amount representing interest (10 ) Present value of capital lease obligations 303 Less: current portion (242 ) Long-term portion of capital leases $ 61 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases. Other Commitments We enter into supply and service arrangements in the normal course of business. Supply arrangements are primarily for fixed-price manufacture and supply. Service agreements are primarily for the development of manufacturing processes and certain studies. Commitments under service agreements are subject to cancellation at our discretion which may require payment of certain cancellation fees. The timing of completion of service arrangements is subject to variability in estimates of the time required to complete the work. The following table provides quantitative data regarding our other commitments. Future minimum payments reflect amounts that we expect to pay including potential obligations under services agreements subject to risk of cancellation by us (in thousands): Other Commitment Agreement Type Agreement Date Future Minimum Payment Development and manufacturing services agreements September 2019 $ 1,645 Manufacture and supply agreement with expected future payment date of December 2022 April 2016 1,242 Service agreement for clinical trial December 2017 80 Total other commitments $ 2,967 Credit Facility Effective June 30, 2017, we entered into a credit facility (the "Credit Facility") consisting of term loans ("Term Debt") totaling up to $10.0 million , and advances ("Advances") under a revolving line of credit ("Revolving Line of Credit") totaling up to $5.0 million with an accounts receivable borrowing base of 80% of eligible accounts receivable. At September 30, 2019 , we have not drawn from the Credit Facility. In January 2019, we entered into a Fifth Amendment to the Credit Facility to allow for Codexis to obtain a letter of credit of up to $1.1 million to secure its obligations under the Lease with MetLife. In July 2019, we entered into a Sixth Amendment to the Credit Facility to increase permitted indebtedness to $0.7 million for financing insurance premiums in the ordinary course of business. In September 2019, we entered into a Seventh Amendment to the Credit Facility whereby the draw period on the term debt was extended to September 30, 2020. We may draw on the Term Debt at any time prior to September 30, 2020, subject to customary conditions for funding including, among others, that no event of default exists. We may draw on the Revolving Line of Credit at any time prior to the maturity date. On October 1, 2023 , any loans for Term Debt mature and the Revolving Line of Credit terminates. Term Debt bears interest through maturity at a variable rate based on the London Interbank Offered Rate plus 3.60% . Advances under the Revolving Line of Credit bear interest at a variable annual rate equal to the greater of (i) 1.00% above the prime rate and (ii) 5.00% . The Credit Facility allows for interest-only payments on Term Debt through November 1, 2020 . Monthly payments of principal and interest on the Term Debt are required following the applicable amortization date. We may elect to prepay in full the Term Debt and Advances under the Revolving Line of Credit at any time. Our obligations under the Credit Facility are secured by a lien on substantially all of our personal property other than our intellectual property. The Credit Facility includes a number of customary covenants and restrictions which require us to comply with certain financial covenants including achieving consolidated product revenues levels at minimum levels as set forth in the Credit Facility unless we maintain certain minimum cash levels with the lender in an amount equal to or greater than six times the sum of the average six -month trailing operating cash flow net outlay plus the average monthly principal due and payable in the immediately succeeding three -month period. The Credit Facility places various restrictions on our transferring collateral, incurring additional indebtedness, engaging in mergers or acquisitions, paying dividends or making other distributions, making investments, creating liens, and selling assets and permitted assets to be held at foreign subsidiaries above specified caps, in each case subject to certain exceptions. A failure to comply with these covenants could permit the lender to exercise remedies against us and the collateral securing the Credit Facility, including foreclosure of our properties securing the Credit Facility and our cash. At September 30, 2019 , we were in compliance with the covenants for the Credit Facility. Legal Proceedings We are not currently a party to any material pending litigation or other material legal proceedings. Indemnifications We are required to recognize a liability for the fair value of any obligations we assume upon the issuance of a guarantee. We have certain agreements with licensors, licensees, and collaborators that contain indemnification provisions. In such provisions, we typically agree to indemnify the licensor, licensee and collaborator against certain types of third-party claims. The maximum amount of the indemnifications is not limited. We accrue for known indemnification issues when a loss is probable and can be reasonably estimated. There were no accruals for expenses related to indemnification issues for any periods presented.

Related Party Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2019
Related Party Transaction, Due from (to) Related Party [Abstract]
Related Party Transactions	Related Party Transactions AstraZeneca PLC Pam P. Cheng, a member of our board of directors, joined AstraZeneca PLC as Executive Vice President, Operations and Information Technology in June 2015. We sell biocatalyst products to AstraZeneca PLC and its controlled purchasing agents and contract manufacturers. We recognized $0.2 million and $0.6 million in revenue in the three and nine months ended September 30, 2019 , respectively, compared to de minimis and $0.4 million in the three and nine months ended September 30, 2018 , respectively, from transactions with AstraZeneca PLC and its controlled purchasing agents and contract manufacturers. At September 30, 2019 and December 31, 2018 , we had zero and $0.2 million of accounts receivable from AstraZeneca, PLC, and its controlled purchasing agents and contract manufacturers, respectively. Settlement of Short Swing Profit Claim In August 2019, we recorded approximately $77 thousand related to the short swing profit settlement remitted by a shareholder of our company under Section 16(b) of the Securities Exchange Act of 1934, as amended. We recognized the proceeds as an increase to additional paid-in capital in the accompanying unaudited condensed consolidated balance sheet as of September 30, 2019 and unaudited condensed consolidated statements of stockholders’ equity as well as in cash provided by financing activities in the unaudited condensed consolidated statements of cash flows for the quarter ended September 30, 2019.

Segment, Geographical and Other

Segment, Geographical and Other Revenue Information	9 Months Ended
	Sep. 30, 2019
Segment Reporting [Abstract]
Segment, Geographical and Other Revenue Information	Segment, Geographical and Other Revenue Information Segment Information As discussed in Note 2, "Basis of Presentation and Summary of Significant Accounting Policies," beginning in 2018, we identified our biotherapeutics business as a standalone business segment. Our two reportable business segments as of January 1, 2018, consisted of Performance Enzymes and Novel Biotherapeutics. We report corporate-related expenses such as legal, accounting, information technology, and other costs that are not otherwise included in our reportable business segments as "Corporate costs." All items not included in income (loss) from operations are excluded from the business segments. We manage our assets on a total company basis, not by business segment, as the majority of our operating assets are shared or commingled. Our CODM does not review asset information by business segment in assessing performance or allocating resources, and accordingly, we do not report asset information by business segment. Performance Enzymes We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, and to date this continues to be our largest market served. Our customers, which include many large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop customized enzymes for use in other industrial markets. These markets consist of several large industrial verticals, including food and food ingredients, animal feed, flavors, fragrances, and agricultural chemicals. We also use our technology to develop enzymes for customers using NGS and PCR/qPCR for in vitro molecular diagnostic and molecular biology research applications. Novel Biotherapeutics We are also targeting new opportunities in the pharmaceutical industry to discover, improve, and/or develop biotherapeutic drug candidates. We believe that our CodeEvolver ® protein engineering platform technology can be used to discover novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. Similarly, we believe that we can deploy our platform technology to improve specific characteristics of a customer’s pre-existing biotherapeutic drug candidate, such as its activity, stability or immunogenicity. Most notable is our lead program for the potential treatment of PKU in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we announced a strategic collaboration with Nestlé Health Science to advance CDX-6114, our own novel orally administrable enzyme therapeutic candidate for the potential treatment of PKU. In July 2018, we announced that we had dosed the first subjects in a first-in-human Phase 1a dose-escalation trial with CDX-6114, which was conducted in Australia. In November 2018, we announced top-line results from the Phase 1a study in healthy volunteers with CDX-6114. In December 2018, Nestlé Health Science became obligated to pay us an additional $1.0 million within 60 days after the achievement of a milestone relating to formulation of CDX-6114. In January 2019, we received notice from the U.S. Food and Drug Administration (the “FDA”) that it had completed its review of our investigational new drug application (“IND”) for CDX-6114 and concluded that we may proceed with the proposed Phase 1b multiple ascending dose study in healthy volunteers in the United States. In February 2019, Nestlé Health Science exercised its option to obtain an exclusive license for the global development and commercialization of CDX-6114 for the management of PKU. The option payment of $3 million was recognized as revenue in the first quarter of 2019 as research and development fees. Upon exercising its option, Nestlé Health Science has assumed all responsibilities for future clinical development and commercialization of CDX-6114, with the exception of the completion of an extension study, CDX-6114-004, which was substantially completed in the second quarter of 2019. For the three and nine months ended September 30, 2019 and 2018 , all revenues related to the Novel Biotherapeutics segment were generated from our collaborations with Nestlé Health Science. We have also developed a pipeline of other biotherapeutic drug candidates, which are in preclinical development, and in which we expect to continue to make additional investments with the aim of advancing additional product candidates targeting other therapeutic areas. Our CODM regularly reviews our segments and the approach provided by management for performance evaluation and resource allocation. Operating expenses that directly support the segment activity are allocated based on segment headcount, revenue contribution or activity of the business units within the segments, based on the corporate activity type provided to the segment. The expense allocation excludes certain corporate costs that are separately managed from the segments. This provides the CODM with more meaningful segment profitability reporting to support operating decisions and allocate resources. The following table provides financial information by our reportable business segments along with a reconciliation to consolidated loss before income taxes (in thousands): Three months ended September 30, 2019 Three months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 10,351 $ — $ 10,351 $ 8,405 $ — $ 8,405 Research and development revenue 10,073 1,482 11,555 3,720 4,821 8,541 Total revenues 20,424 1,482 21,906 12,125 4,821 16,946 Costs and operating expenses: Cost of product revenue 5,067 — 5,067 3,791 — 3,791 Research and development (1) 5,313 3,080 8,393 4,758 2,920 7,678 Selling, general and administrative (1) 2,037 690 2,727 1,870 165 2,035 Total segment costs and operating expenses 12,417 3,770 16,187 10,419 3,085 13,504 Income (loss) from operations $ 8,007 $ (2,288 ) $ 5,719 $ 1,706 $ 1,736 $ 3,442 Corporate costs (2) (4,912 ) (5,120 ) Depreciation and amortization (471 ) (309 ) Income (loss) before income taxes $ 336 $ (1,987 ) (1) Research and development expenses and Selling, general and administrative expenses exclude depreciation and amortization of finance leases. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. Nine months ended September 30, 2019 Nine months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 24,588 $ — $ 24,588 $ 18,291 $ — $ 18,291 Research and development revenue 16,512 8,708 25,220 15,728 10,507 26,235 Total revenues 41,100 8,708 49,808 34,019 10,507 44,526 Costs and operating expenses: Cost of product revenue 12,230 — 12,230 10,228 — 10,228 Research and development (1) 14,889 9,252 24,141 14,548 7,294 21,842 Selling, general and administrative (1) 6,499 1,768 8,267 5,695 615 6,310 Total segment costs and operating expenses 33,618 11,020 44,638 30,471 7,909 38,380 Income (loss) from operations $ 7,482 $ (2,312 ) $ 5,170 $ 3,548 $ 2,598 $ 6,146 Corporate costs (2) (15,185 ) (15,762 ) Depreciation and amortization (1,273 ) (812 ) Loss before income taxes $ (11,288 ) $ (10,428 ) (1) Research and development expenses and Selling, general and administrative expenses exclude depreciation and amortization of finance leases. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. The following table provides stock-based compensation expense included in income (loss) from operations by segment (in thousands): Three months ended September 30, 2019 Three months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 736 $ 225 $ 961 $ 354 $ 97 $ 451 Nine months ended September 30, 2019 Nine months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 1,973 $ 563 $ 2,536 $ 2,005 $ 243 $ 2,248 Significant Customers Customers that each contributed 10% or more of our total revenues were as follows: Percentage of Total Revenues for the Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Customer A 21% 27% 31% 33% Customer B * 28% 17% 24% Customer C * 10% * 17% Customer D 29% 15% 15% 11% Customers that each contributed 10% or more of our total accounts receivable had the following balances as of the periods presented: Percentage of Accounts Receivables as of September 30, 2019 December 31, 2018 Customer A 20% 37% Customer B * 17% Customer D * 11% Customer E 14% * Customer F 15% * Customer G * 16% Customer H 16% * * Less than 10% of the period presented Geographical Information Geographic revenues are identified by the location of the customer and consist of the following (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Revenues Americas $ 2,706 $ 4,315 $ 9,620 $ 13,968 EMEA 12,205 6,274 24,672 15,075 APAC 6,995 6,357 15,516 15,483 Total revenues $ 21,906 $ 16,946 $ 49,808 $ 44,526 Identifiable long-lived assets by location and goodwill by reporting unit were as follows: Long-lived assets: September 30, 2019 December 31, 2018 United States $ 31,104 $ 4,759 As of September 30, 2019 and December 31, 2018 Performance Enzymes Novel Biotherapeutics Total Goodwill $ 2,463 $ 778 $ 3,241

Basis of Presentation and Sum_2

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2019
Accounting Policies [Abstract]
Basis of Presentation and Principles of Consolidation	Basis of Presentation and Principles of Consolidation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America ("GAAP") and the applicable rules and regulations of the Securities and Exchange Commission ("SEC") for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December 31, 2018 . The condensed consolidated balance sheet at December 31, 2018 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The significant accounting policies used in preparation of the unaudited condensed consolidated financial statements for the three and nine months ended September 30, 2019 are consistent with those discussed in Note 2 to the audited consolidated financial statements in the Company’s 2018 Annual Report on Form 10-K and are updated below as necessary. The unaudited condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of September 30, 2019 , results of our operations for the three and nine months ended September 30, 2019 and 2018 , changes in stockholders' equity for the three and nine months ended September 30, 2019 and 2018 , and cash flows for the nine months ended September 30, 2019 and 2018 . The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Accounting Standard Update ("ASU") 2016-02, "Leases (Topic 842)" ("ASC 842) establishes a right-of-use ("ROU") model that requires a lessee to record a right-of-use asset and a lease obligation on the balance sheet for all leases with terms longer than 12 months. See "Recently Adopted Accounting Pronouncements" for details regarding the adoption of ASU 2016-02 effective January 1, 2019. The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly owned subsidiaries in the United States, India and the Netherlands. All significant intercompany balances and transactions have been eliminated in consolidation.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the unaudited condensed consolidated financial statements, and the reported amounts of revenue and expenses during the reporting period. We regularly assess these estimates which primarily affect revenue recognition, accounts receivable, inventories, the valuation of marketable securities, goodwill arising out of business acquisitions, accrued liabilities, stock awards, and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the unaudited condensed consolidated financial statements.
Segment Reporting	Segment Reporting We report two business segments, Performance Enzymes and Novel Biotherapeutics, which are based on our operating segments. Operating segments are defined as components of an enterprise about which separate financial information is available that is evaluated regularly by the chief operating decision maker ("CODM"), or decision making group, in deciding how to allocate resources, and in assessing performance. Our CODM is our Chief Executive Officer. Our business segments are primarily based on our organizational structure and our operating results as used by our CODM in assessing performance and allocating resources for our company. We do not allocate or evaluate assets by segment. The Novel Biotherapeutics segment focuses on new opportunities in the pharmaceutical industry to dis cover or improve novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. The Performance Enzymes segment consists of protein catalyst products and services with focus on pharmaceutical, food, molecular diagnostics, and other industrial markets.
Leases	Leases We determine if an arrangement is a lease at inception. Operating leases are included in right-of-use ("ROU") lease assets, current portion of lease obligations, and long-term lease obligations on our balance sheets. ROU lease assets represent our right to use an underlying asset for the lease term and lease obligations represent our obligation to make lease payments arising from the lease. Operating ROU lease assets and obligations are recognized at the commencement date based on the present value of the future minimum lease payments over the lease term. As our leases do not provide an implicit rate, we use our incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The lease terms may include options to extend or terminate the lease when it is reasonably certain that the option will be exercised. Lease expense is recognized on a straight-line basis over the lease term. We elected to apply the short-term lease measurement and recognition exemption in which ROU assets and lease obligations are not recognized for short-term leases.
Recently Adopted and Issued Accounting Pronouncements	Recent Accounting Pronouncements Recently adopted accounting pronouncements In February 2016, the FASB issued ASU 2016-02, "Leases (Topic 842)" (“ASC 842”), which is intended to improve financial reporting of leasing transactions by requiring lessees to recognize leases on balance sheets and disclose key information about leasing arrangements. Topic 842 was subsequently amended by ASU No. 2018-01, "Land Easement Practical Expedient for Transition to Topic 842"; ASU 2018-10, "Codification Improvements to ASC 842, Leases"; and ASU 2018-11, "Leases (Topic 842): Targeted Improvements." The new standard establishes a right-of-use ("ROU") model that requires lessees to record a ROU asset and lease obligations on the balance sheet for all leases with terms longer than 12 months. Leases are classified as either finance or operating, with classification affecting the pattern and classification of expense recognition in the condensed consolidated statement of operations. We adopted the new standard on January 1, 2019 using a modified retrospective approach and effective date method. We also elected the "package of practical expedients," which permit us not to reassess under the new standard its prior conclusions about lease identification, lease classification and initial direct costs. We did not elect the use-of-hindsight or the practical expedient pertaining to land easements; the latter is not applicable to us. Upon adoption, for operating leases, we recognized $26.6 million of ROU assets and $27.6 million of lease obligations, which represents the present value of the lease payments discounted using our incremental borrowing rate ("IBR") of 6.6% . For finance leases, we recognized $0.5 million of ROU assets and $0.3 million of lease obligations which represents the present value of the lease payments discounted using weighted-average implicit rate of 5.0% . These amounts were recorded in our unaudited condensed consolidated balance sheet in the first quarter of 2019. In February 2018, the FASB issued ASU No. 2018-02, “Income Statement - Reporting Comprehensive Income (Topic 220) - Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income”. This standard allows a reclassification from accumulated other comprehensive income to retained earnings for stranded tax effects resulting from the Tax Cuts and Jobs Act and requires certain disclosures about stranded tax effects and will be effective for us beginning January 1, 2019 and should be applied either in the period of adoption or retrospectively. We adopted ASU 2018-02 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. In June 2018, the FASB issued ASU 2018-07, "Compensation-Stock Compensation (Topic 718): Improvements to Non-employee Share-Based Payment Accounting," which expands the scope of Topic 718, Compensation—Stock Compensation (which currently only includes share-based payments to employees) to include share-based payments issued to non-employees for goods or services. Consequently, the accounting for share-based payments to non-employees and employees will be substantially aligned. The ASU supersedes Subtopic 505-50, Equity—Equity-Based Payments to Non-Employees. The new standard is effective for fiscal years beginning after December 15, 2018, with early adoption permitted. We adopted ASU 2018-07 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. In July 2018, the FASB issued ASU 2018-09, "Codification Improvements”, which represent changes to clarify, correct errors in, or make minor improvements to the Codification, eliminating inconsistencies and providing clarifications in current guidance. The amendments in this ASU include those made to: Subtopic 220-10, Income Statement-Reporting Comprehensive Income-Overall; Subtopic 470-50, Debt-Modifications and Extinguishments; Subtopic 480-10, Distinguishing Liabilities from Equity-Overall; Subtopic 718-740, Compensation-Stock Compensation-Income Taxes; Subtopic 805-740, Business Combinations-Income Taxes; Subtopic 815-10, Derivatives and Hedging-Overall; Subtopic 820-10, Fair Value Measurement-Overall; Subtopic 940-405, Financial Services-Brokers and Dealers-Liabilities; and Subtopic 962-325, Plan Accounting-Defined Contribution Pension Plans-Investments-Other. The transition and effective date guidance is based on the facts and circumstances of each amendment. Some of the amendments do not require transition guidance and will be effective upon issuance. However, many of the amendments do have transition guidance with effective dates for annual periods beginning after December 15, 2018, for public business entities. We adopted subtopics under ASU 2018-09 that are applicable to our company which included subtopics 718-740 and 820-10 in the first quarter of 2019, and the adoption had no impact on our unaudited condensed consolidated financial statements. Recently issued accounting pronouncements not yet adopted From time to time, new accounting pronouncements are issued by the FASB or other standards setting bodies that are adopted by us as of the specified effective date. Unless otherwise discussed, we believe that the impact of recently issued standards that are not yet effective will not have a material impact on our unaudited condensed consolidated financial statements upon adoption. In June 2016, the FASB issued ASU 2016-13, "Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments," which amends the FASB's guidance on the impairment of financial instruments. The standard adds a new impairment model (known as the "current expected credit loss model") that is based on expected losses rather than incurred losses. ASU 2016-13 is effective for annual reporting periods ending after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. We are currently evaluating the impact of adopting ASU 2016-13 on our financial statements and related disclosures. In January 2017, the FASB issued ASU No. 2017-04, "Intangibles - Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment." The amendments eliminate Step 2 from the goodwill impairment test. The annual, or interim, goodwill impairment test is performed by comparing the fair value of a reporting unit with its carrying amount. An impairment charge should be recognized for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. In addition, income tax effects from any tax deductible goodwill on the carrying amount of the reporting unit should be considered when measuring the goodwill impairment loss, if applicable. The amendments also eliminate the requirements for any reporting unit with a zero or negative carrying amount to perform a qualitative assessment and, if it fails that qualitative test, to perform Step 2 of the goodwill impairment test. An entity still has the option to perform the qualitative assessment for a reporting unit to determine if the quantitative impairment test is necessary. The new standard is effective for fiscal years beginning after December 15, 2019, with early adoption permitted. We are currently evaluating the impact of adoption of ASU 2017-04 on our financial statements and related disclosures. In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". The primary focus of ASU 2018-13 is to improve the effectiveness of the disclosure requirements for fair value measurements. The changes affect all companies that are required to include fair value measurement disclosures. In general, the amendments in ASU 2018-13 are effective for all entities for fiscal years and interim periods within those fiscal years, beginning after December 15, 2019. Early adoption is permitted. We are currently evaluating the impact of adoption of ASU 2018-13 on our financial statements and related disclosures. In November 2018, the FASB issued ASU 2018-18, "Collaborative Arrangements (Topic 808): Clarifying the Interaction Between Topic 808 and Topic 606." ASU 2018-18 provides guidance on how to assess whether certain transactions between collaborative arrangement participants should be accounted for within the revenue recognition standard. The ASU also provides more comparability in the presentation of revenue for certain transactions between collaborative arrangement participants. In general, for public companies, the amendments in this standard are effective for fiscal years beginning after December 15, 2019, and interim periods within those fiscal years. Early adoption is permitted. We are currently evaluating the impact of adoption of ASU 2018-18 on our financial statements.

Revenue Recognition (Tables)

Revenue Recognition (Tables)	9 Months Ended
	Sep. 30, 2019
Revenue from Contract with Customer [Abstract]
Disaggregation of revenue	The following table provides information about disaggregated revenue from contracts with customers, the nature of the products and services and geographic regions, and includes a reconciliation of the disaggregated revenue with reportable segments. The geographic regions that are tracked are the Americas (United States, Canada, Latin America), EMEA (Europe, Middle East, Africa), and APAC (Australia, New Zealand, Southeast Asia, China). Three months ended September 30, 2019 Three months ended September 30, 2018 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 10,351 $ — $ 10,351 $ 8,405 $ — $ 8,405 Research and development revenue 10,073 1,482 11,555 3,720 4,821 8,541 Total revenues $ 20,424 $ 1,482 $ 21,906 $ 12,125 $ 4,821 $ 16,946 Primary geographical markets: Americas $ 2,706 $ — $ 2,706 $ 4,315 $ — $ 4,315 EMEA 10,723 1,482 12,205 1,453 4,821 6,274 APAC 6,995 — 6,995 6,357 — 6,357 Total revenues $ 20,424 $ 1,482 $ 21,906 $ 12,125 $ 4,821 $ 16,946 Nine months ended September 30, 2019 Nine months ended September 30, 2018 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 24,588 $ — $ 24,588 $ 18,291 $ — $ 18,291 Research and development revenue 16,512 8,708 25,220 15,728 10,507 26,235 Total revenues $ 41,100 $ 8,708 $ 49,808 $ 34,019 $ 10,507 $ 44,526 Primary geographical markets: Americas $ 9,620 $ — $ 9,620 $ 13,968 $ — $ 13,968 EMEA 15,964 8,708 24,672 4,568 10,507 15,075 APAC 15,516 — 15,516 15,483 — 15,483 Total revenues $ 41,100 $ 8,708 $ 49,808 $ 34,019 $ 10,507 $ 44,526
Contract with customer	During the three and nine months ended September 30, 2019 , we recognized the following revenues (in thousands): Revenue recognized in the period from: Three months ended September 30, 2019 Nine months ended September 30, 2019 Amounts included in contract liabilities at the beginning of the period: Performance obligations satisfied $ 5,092 $ 4,948 Changes in the period: Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods 2,641 2,460 Performance obligations satisfied from new activities in the period - contract revenue 14,173 42,400 Total revenue $ 21,906 $ 49,808 The following table presents changes in the contract assets, unbilled receivables, contract costs, and contract liabilities (in thousands): January 1, 2019 balance Additions Deductions (1) September 30, 2019 balance Contract Assets $ 35 7,142 (5,984 ) $ 1,193 Unbilled receivables, current $ 1,916 4,189 (3,788 ) $ 2,317 Unbilled receivables, non-current (2) $ 786 — (786 ) $ — Contract Costs (2) $ 42 — (41 ) $ 1 Contract Liabilities: Deferred Revenue $ 8,288 6,486 (11,498 ) $ 3,276 (1) The asset or liability balances are presented as a net position per contract and accordingly the deductions column includes the netting effect of presenting each contract on a net position basis as either a net liability or asset. (2) Included in non-current assets in our unaudited condensed consolidated balance sheets.
Performance obligation, expected timing of satisfaction	The following table includes estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied or partially unsatisfied at the end of the reporting period. The estimated revenue does not include contracts with original durations of one year or less, amounts of variable consideration attributable to royalties, or contract renewals that are unexercised as of September 30, 2019 . The balances in the table below are partially based on judgments involved in estimating future orders from customers subject to the exercise of material rights pursuant to respective contracts. (in thousands) Remainder of 2019 2020 2021 and Thereafter Total Product Revenue $ — $ 365 $ 1,623 $ 1,988 Research and development revenue 1,288 — — 1,288 Total $ 1,288 $ 365 $ 1,623 $ 3,276

Net Income (loss) per Share (Ta

Net Income (loss) per Share (Tables)	9 Months Ended
	Sep. 30, 2019
Earnings Per Share [Abstract]
Schedule of earnings (loss) per share, basic and diluted	The following table sets forth the computation of basic and diluted net income (loss) per share during the three and nine months ended September 30, 2019 and 2018 (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Numerator: Net income (loss) $ 343 $ (1,988 ) $ (11,300 ) $ (10,417 ) Denominator: Weighted average common stock shares used in computing net income (loss) per share, basic 58,287 53,597 55,818 51,609 Effect of dilutive shares 3,125 — — — Weighted average common stock shares used in computing net income (loss) per share, diluted 61,412 53,597 55,818 51,609 Net income (loss) per share, basic $ 0.01 $ (0.04 ) $ (0.20 ) $ (0.20 ) Net income (loss) per share, diluted $ 0.01 $ (0.04 ) $ (0.20 ) $ (0.20 )
Securities not included in the net loss per common share calculations	The following shares were not considered in the computation of diluted net income (loss) per share because their effect was anti-dilutive (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan 1,019 7,607 5,623 7,607

Cash Equivalents and Marketab_2

Cash Equivalents and Marketable Securities (Tables)	9 Months Ended
	Sep. 30, 2019
Cash Equivalents and Marketable Securities [Abstract]
Schedule of cash equivalents and marketable securities	Cash equivalents and marketable securities at September 30, 2019 and at December 31, 2018 consisted of the following (in thousands): September 30, 2019 Adjusted Cost Gross Unrealized (3) Gross Unrealized (3) Estimated Money market funds (1) $ 73,450 $ — $ — $ 73,450 December 31, 2018 Adjusted Cost Gross Unrealized (3) Gross Unrealized (3) Estimated Money market funds (1) $ 31,225 $ — $ — $ 31,225 Common shares of CO 2 Solutions (2) 563 25 — 588 Total $ 31,788 $ 25 $ — $ 31,813 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified in equity securities on our unaudited condensed consolidated balance sheets. (3) As a result of adopting ASU 2016-01, " Financial Instruments-Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities ", in 2018 and thereafter gross unrealized gains and gross unrealized losses related to our investment in CO 2 Solutions were recognized in other expense, in our unaudited condensed consolidated statements of operations.

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2019
Fair Value Disclosures [Abstract]
Summary of financial instruments measured at fair value on a recurring basis	The following tables present the financial instruments that were measured at fair value on a recurring basis at September 30, 2019 and December 31, 2018 by level within the fair value hierarchy (in thousands): September 30, 2019 Level 1 Level 2 Level 3 Total Money market funds $ 73,450 $ — $ — $ 73,450 December 31, 2018 Level 1 Level 2 Level 3 Total Money market funds $ 31,225 $ — $ — $ 31,225 Common shares of CO 2 Solutions 588 — — 588 Total $ 31,856 $ — $ — $ 31,813

Balance Sheets Details (Tables)

Balance Sheets Details (Tables)	9 Months Ended
	Sep. 30, 2019
Balance Sheets Details [Abstract]
Schedule of inventory components	Inventories consisted of the following (in thousands): September 30, 2019 December 31, 2018 Raw materials $ 7 $ 165 Work-in-process 52 47 Finished goods 338 377 Inventories $ 397 $ 589
Schedule of property and equipment, net	Property and equipment, net consisted of the following (in thousands): September 30, 2019 December 31, 2018 Laboratory equipment $ 23,266 $ 21,328 Leasehold improvements 10,899 10,359 Computer equipment and software 3,806 3,954 Office equipment and furniture 1,461 1,272 Construction in progress 488 939 Property and equipment 39,920 37,852 Less: accumulated depreciation and amortization (33,679 ) (33,093 ) Property and equipment, net $ 6,241 $ 4,759
Schedule of accrued liabilities	Other accrued liabilities consisted of the following (in thousands): September 30, 2019 December 31, 2018 Accrued purchases $ 3,894 $ 1,492 Accrued professional and outside service fees 1,833 2,020 Deferred rent — 343 Lease incentive obligation — 425 Other 455 575 Total $ 6,182 $ 4,855

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2019
Share-based Payment Arrangement [Abstract]
Schedule of stock-based compensation expense	Stock-based compensation expense is included in the unaudited condensed consolidated statements of operations as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Research and development $ 458 $ 552 $ 1,249 $ 1,555 Selling, general and administrative 1,274 1,218 4,534 4,652 Total $ 1,732 $ 1,770 $ 5,783 $ 6,207
Schedule of stock-based compensation expense by security types	The following table presents total stock-based compensation expense by security type included in the unaudited condensed consolidated statements of operations for the three and nine months ended September 30, 2019 and 2018 (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Stock options $ 545 $ 472 $ 1,680 $ 1,482 RSUs and RSAs 461 416 1,308 1,293 PSUs 368 407 1,075 1,251 PBOs 358 475 1,720 2,181 Total $ 1,732 $ 1,770 $ 5,783 $ 6,207

Commitments and Contingencies (

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2019
Commitments and Contingencies Disclosure [Abstract]
Schedule of new accounting pronouncements	The following table shows the reconciliation of right-of-use assets and lease obligations, with balances reflecting the adoption of ASC 842, related to both operating leases and finance leases and gives effect to the modified retrospective adoption and effective date method under the lease guidance on January 1, 2019 (in thousands): Operating leases Finance Leases Right-of-use assets, balance at December 31, 2018 $ — $ — Changes in the period: Right-of-use assets created upon adoption of ASC 842 26,617 493 Right-of-use assets, balance at January 1, 2019 $ 26,617 $ 493 Lease obligations, balance at December 31, 2018 $ — $ — Changes in the period: Lease obligations created upon adoption of ASC 842 27,562 302 Lease obligations, balance at January 1, 2019 $ 27,562 $ 302
Lease cost	Lease related expenses under non-cancellable finance and operating leases and under non-cancellable subleases as follows (in thousands except discount rate and lease term): Three months ended September 30, 2019 Nine months ended September 30, 2019 Lease costs Finance lease cost: Amortization of right-of-use assets $ 54 $ 163 Interest on lease obligations 2 8 Operating lease cost 1,139 3,417 Sublease income (262 ) (727 ) Total lease cost $ 933 $ 2,861 Other information Weighted-average remaining lease term (in years): Finance leases 0.5 Operating leases 7.9 Weighted-average discount rate: Finance leases 5.0 % Operating leases 6.6 % Cash paid for amounts included in the measurement of lease obligations Operating cash flows from operating leases $ (2,456 ) Operating cash flows from finance leases $ (9 ) Financing cash flows from finance leases $ (180 )
Operating lease maturity	As of September 30, 2019 , under ASC 842, maturity analysis of annual undiscounted cash flows of the non-cancellable finance and operating leases are as follows (in thousands): Years ending December 31, Finance Leases Operating Leases 2019 (remaining 3 months) $ 63 $ 824 2020 61 2,816 2021 — 4,197 2022 — 4,285 2023 — 4,589 2024 and thereafter — 18,220 Total minimum lease payments (1) $ 124 $ 34,931 Less: imputed interest (2 ) (8,484 ) Lease Obligations $ 122 $ 26,447 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.3 million to be received under non-cancellable subleases at September 30, 2019 .
Finance lease liability	As of September 30, 2019 , under ASC 842, maturity analysis of annual undiscounted cash flows of the non-cancellable finance and operating leases are as follows (in thousands): Years ending December 31, Finance Leases Operating Leases 2019 (remaining 3 months) $ 63 $ 824 2020 61 2,816 2021 — 4,197 2022 — 4,285 2023 — 4,589 2024 and thereafter — 18,220 Total minimum lease payments (1) $ 124 $ 34,931 Less: imputed interest (2 ) (8,484 ) Lease Obligations $ 122 $ 26,447 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.3 million to be received under non-cancellable subleases at September 30, 2019 .
Schedule of future operating lease payments	As of December 31, 2018, under ASC 840, maturity analysis of annual undiscounted cash flows of the non-cancellable capital and operating leases as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2019 $ 252 $ 3,280 2020 61 712 2021 — 490 2022 — 41 2023 — — Total minimum lease payments (1) 313 $ 4,523 Less: amount representing interest (10 ) Present value of capital lease obligations 303 Less: current portion (242 ) Long-term portion of capital leases $ 61 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases.
Schedule of future capital lease payments	As of December 31, 2018, under ASC 840, maturity analysis of annual undiscounted cash flows of the non-cancellable capital and operating leases as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2019 $ 252 $ 3,280 2020 61 712 2021 — 490 2022 — 41 2023 — — Total minimum lease payments (1) 313 $ 4,523 Less: amount representing interest (10 ) Present value of capital lease obligations 303 Less: current portion (242 ) Long-term portion of capital leases $ 61 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases.
Schedule of supply and service commitments	The following table provides quantitative data regarding our other commitments. Future minimum payments reflect amounts that we expect to pay including potential obligations under services agreements subject to risk of cancellation by us (in thousands): Other Commitment Agreement Type Agreement Date Future Minimum Payment Development and manufacturing services agreements September 2019 $ 1,645 Manufacture and supply agreement with expected future payment date of December 2022 April 2016 1,242 Service agreement for clinical trial December 2017 80 Total other commitments $ 2,967

Segment, Geographical and Oth_2

Segment, Geographical and Other Revenue Information (Tables)	9 Months Ended
	Sep. 30, 2019
Segment Reporting [Abstract]
Schedule of segment reporting	The following table provides financial information by our reportable business segments along with a reconciliation to consolidated loss before income taxes (in thousands): Three months ended September 30, 2019 Three months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 10,351 $ — $ 10,351 $ 8,405 $ — $ 8,405 Research and development revenue 10,073 1,482 11,555 3,720 4,821 8,541 Total revenues 20,424 1,482 21,906 12,125 4,821 16,946 Costs and operating expenses: Cost of product revenue 5,067 — 5,067 3,791 — 3,791 Research and development (1) 5,313 3,080 8,393 4,758 2,920 7,678 Selling, general and administrative (1) 2,037 690 2,727 1,870 165 2,035 Total segment costs and operating expenses 12,417 3,770 16,187 10,419 3,085 13,504 Income (loss) from operations $ 8,007 $ (2,288 ) $ 5,719 $ 1,706 $ 1,736 $ 3,442 Corporate costs (2) (4,912 ) (5,120 ) Depreciation and amortization (471 ) (309 ) Income (loss) before income taxes $ 336 $ (1,987 ) (1) Research and development expenses and Selling, general and administrative expenses exclude depreciation and amortization of finance leases. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. Nine months ended September 30, 2019 Nine months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 24,588 $ — $ 24,588 $ 18,291 $ — $ 18,291 Research and development revenue 16,512 8,708 25,220 15,728 10,507 26,235 Total revenues 41,100 8,708 49,808 34,019 10,507 44,526 Costs and operating expenses: Cost of product revenue 12,230 — 12,230 10,228 — 10,228 Research and development (1) 14,889 9,252 24,141 14,548 7,294 21,842 Selling, general and administrative (1) 6,499 1,768 8,267 5,695 615 6,310 Total segment costs and operating expenses 33,618 11,020 44,638 30,471 7,909 38,380 Income (loss) from operations $ 7,482 $ (2,312 ) $ 5,170 $ 3,548 $ 2,598 $ 6,146 Corporate costs (2) (15,185 ) (15,762 ) Depreciation and amortization (1,273 ) (812 ) Loss before income taxes $ (11,288 ) $ (10,428 ) (1) Research and development expenses and Selling, general and administrative expenses exclude depreciation and amortization of finance leases. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. The following table provides stock-based compensation expense included in income (loss) from operations by segment (in thousands): Three months ended September 30, 2019 Three months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 736 $ 225 $ 961 $ 354 $ 97 $ 451 Nine months ended September 30, 2019 Nine months ended September 30, 2018 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 1,973 $ 563 $ 2,536 $ 2,005 $ 243 $ 2,248
Schedule of customers that contributed 10% or more of total accounts receivable	Customers that each contributed 10% or more of our total revenues were as follows: Percentage of Total Revenues for the Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Customer A 21% 27% 31% 33% Customer B * 28% 17% 24% Customer C * 10% * 17% Customer D 29% 15% 15% 11% Customers that each contributed 10% or more of our total accounts receivable had the following balances as of the periods presented: Percentage of Accounts Receivables as of September 30, 2019 December 31, 2018 Customer A 20% 37% Customer B * 17% Customer D * 11% Customer E 14% * Customer F 15% * Customer G * 16% Customer H 16% * * Less than 10% of the period presented
Schedule of revenues by geographical area	Geographic revenues are identified by the location of the customer and consist of the following (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2019 2018 2019 2018 Revenues Americas $ 2,706 $ 4,315 $ 9,620 $ 13,968 EMEA 12,205 6,274 24,672 15,075 APAC 6,995 6,357 15,516 15,483 Total revenues $ 21,906 $ 16,946 $ 49,808 $ 44,526
Schedule of long-lived assets by geographical area	Identifiable long-lived assets by location and goodwill by reporting unit were as follows: Long-lived assets: September 30, 2019 December 31, 2018 United States $ 31,104 $ 4,759
Schedule of intangible assets and goodwill	As of September 30, 2019 and December 31, 2018 Performance Enzymes Novel Biotherapeutics Total Goodwill $ 2,463 $ 778 $ 3,241

Description of Business - Textu

Description of Business - Textual (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended		3 Months Ended	9 Months Ended
	Jun. 30, 2019	Dec. 31, 2018	Mar. 31, 2019	Sep. 30, 2019	Sep. 30, 2018
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Issuance costs				$ 0	$ 180
Proceeds from issuance of common stock in connection with private placement				$ 50,000	$ 0
Private Placement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Shares issued (in shares)	3,048,780
Price per share (in dollars per share)	$ 16.40
Issuance costs	$ 100
Proceeds from issuance of common stock in connection with private placement	$ 49,900
Nestec Ltd. (Nestle Health Sciences) [Member] | CDX-6114 [Member] | Collaborative Arrangement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone payment amount		$ 1,000
Duration to pay after milestone achievement (in days)		60 days
Event of counterparty exercising alternative option			$ 3,000

Basis of Presentation and Sum_3

Basis of Presentation and Summary of Significant Accounting Policies - Textual (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2019USD ($)segment	Jan. 01, 2019USD ($)	Dec. 31, 2018USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Number of operating segments | segment	2
Right-of-use assets, operating leases, net	$ 24,542		$ 0
Lease Obligations	$ 26,447		0
Weighted-average discount rate, operating leases	6.60%	6.60%
Right-of-use assets - finance leases, net	$ 321	$ 500	0
Finance lease, liability	$ 122	$ 300	$ 0
Weighted-average discount rate, finance leases	5.00%	5.00%
Accounting Standards Update 2016-02 [Member]
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Right-of-use assets, operating leases, net		$ 26,617
Lease Obligations		27,562
Right-of-use assets - finance leases, net		493
Finance lease, liability		$ 302

Revenue Recognition - Addition

Revenue Recognition - Additional Information (Details) - USD ($)	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Revenue from Contract with Customer [Abstract]
Impairment charges related to contract assets	$ 0	$ 0

Revenue Recognition - Disaggre

Revenue Recognition - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Disaggregation of Revenue [Line Items]
Total revenues	$ 21,906	$ 16,946	$ 49,808	$ 44,526
Americas [Member]
Disaggregation of Revenue [Line Items]
Total revenues	2,706	4,315	9,620	13,968
EMEA [Member]
Disaggregation of Revenue [Line Items]
Total revenues	12,205	6,274	24,672	15,075
APAC [Member]
Disaggregation of Revenue [Line Items]
Total revenues	6,995	6,357	15,516	15,483
Product Sales [Member]
Disaggregation of Revenue [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Total revenues	11,555	8,541	25,220	26,235
Performance Enzymes [Member]
Disaggregation of Revenue [Line Items]
Total revenues	20,424	12,125	41,100	34,019
Performance Enzymes [Member] | Americas [Member]
Disaggregation of Revenue [Line Items]
Total revenues	2,706	4,315	9,620	13,968
Performance Enzymes [Member] | EMEA [Member]
Disaggregation of Revenue [Line Items]
Total revenues	10,723	1,453	15,964	4,568
Performance Enzymes [Member] | APAC [Member]
Disaggregation of Revenue [Line Items]
Total revenues	6,995	6,357	15,516	15,483
Performance Enzymes [Member] | Product Sales [Member]
Disaggregation of Revenue [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Performance Enzymes [Member] | Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Total revenues	10,073	3,720	16,512	15,728
Novel Biotherapeutics [Member]
Disaggregation of Revenue [Line Items]
Total revenues	1,482	4,821	8,708	10,507
Novel Biotherapeutics [Member] | EMEA [Member]
Disaggregation of Revenue [Line Items]
Total revenues	1,482	4,821	8,708	10,507
Novel Biotherapeutics [Member] | Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Total revenues	$ 1,482	$ 4,821	$ 8,708	$ 10,507

Revenue Recognition - Contract

Revenue Recognition - Contracts with Customer (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Contract Assets
January 1, 2019 balance		$ 35
Additions		7,142
Deductions		(5,984)
September 30, 2019 balance	$ 1,193	1,193
Unbilled receivables, current
January 1, 2019 balance		1,916
Additions		4,189
Deductions		(3,788)
September 30, 2019 balance	2,317	2,317
Unbilled receivables, non-current
January 1, 2019 balance		786
Additions		0
Deductions		(786)
September 30, 2019 balance	0	0
Contract Costs
January 1, 2019 balance		42
Additions		0
Deductions		(41)
September 30, 2019 balance	1	1
Contract Liabilities: Deferred Revenue
January 1, 2019 balance		8,288
Additions		6,486
Deductions		(11,498)
September 30, 2019 balance	3,276	3,276
Change in Contract with Customer, Liability [Abstract]
Performance obligations satisfied	5,092	4,948
Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods	2,641	2,460
Performance obligations satisfied from new activities in the period - contract revenue	14,173	42,400
Total revenue	$ 21,906	$ 49,808

Revenue Recognition - Performa

Revenue Recognition - Performance Obligation (Details) $ in Thousands	Sep. 30, 2019USD ($)
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-10-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,288
Expected timing of satisfaction, period	3 months
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 365
Expected timing of satisfaction, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,623
Expected timing of satisfaction, period	2 years
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 3,276
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-10-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 0
Expected timing of satisfaction, period	3 months
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 365
Expected timing of satisfaction, period	1 year
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,623
Expected timing of satisfaction, period	2 years
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,988
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-10-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,288
Expected timing of satisfaction, period	3 months
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 0
Expected timing of satisfaction, period	1 year
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 0
Expected timing of satisfaction, period	2 years
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,288

Net Income (loss) per Share - E

Net Income (loss) per Share - Earnings Per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Earnings Per Share [Abstract]
Net income (loss)	$ 343	$ (1,988)	$ (11,300)	$ (10,417)
Denominator:
Weighted average common stock shares used in computing net income (loss) per share, basic (shares)	58,287	53,597	55,818	51,609
Effect of dilutive shares (shares)	3,125	0	0	0
Weighted average common stock shares used in computing net income (loss) per share, diluted (shares)	61,412	53,597	55,818	51,609
Net income (loss) per share, basic (usd per share)	$ 0.01	$ (0.04)	$ (0.20)	$ (0.20)
Net income (loss) per share, diluted (usd per share)	$ 0.01	$ (0.04)	$ (0.20)	$ (0.20)

Net Income (loss) per Share - A

Net Income (loss) per Share - Anti-Dilutive Securities (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded as anti-dilutive (shares)	1,019	7,607	5,623	7,607

Collaborative Arrangements - Te

Collaborative Arrangements - Textual (Details) - USD ($)	1 Months Ended							3 Months Ended		9 Months Ended
	May 31, 2019	Dec. 31, 2018	Apr. 30, 2018	Oct. 31, 2017	Mar. 31, 2017	Aug. 31, 2015	Feb. 29, 2012	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2017	Dec. 31, 2016
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								$ 21,906,000	$ 16,946,000	$ 49,808,000	$ 44,526,000
Contract with customer, liability		$ 8,288,000						3,276,000		3,276,000
Deferred revenue		4,936,000						1,288,000		1,288,000
Research and Development Revenue [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								11,555,000	8,541,000	25,220,000	26,235,000
GSK [Member] | Technology Transfer, Collaboration and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								2,000,000	0	2,000,000	0
Contract with customer, liability								2,000,000		2,000,000
GSK [Member] | Technology Transfer, Collaboration and License Agreement [Member] | Minimum [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
License revenue, contingent receivables										5,750,000
GSK [Member] | Technology Transfer, Collaboration and License Agreement [Member] | Maximum [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
License revenue, contingent receivables										38,500,000
Merck [Member] | Product [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								3,600,000	3,400,000	11,400,000	10,700,000
Merck [Member] | Collaborative Arrangement [Member] | Research and Development Revenue [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								1,000,000	1,100,000	3,000,000	3,000,000
Merck [Member] | Technology Transfer, Collaboration and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
License revenue, contingent receivables						$ 15,000,000
Merck [Member] | Technology Transfer, Collaboration and License Agreement [Member] | Royalty [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								0		0
Merck [Member] | Merck Platform Technology Transfer and License Agreement, Protein Engineering [Member] | Collaborative Arrangement [Member] | Research and Development Revenue [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								100,000		1,000,000
Merck [Member] | Supply Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Optional extension period							5 years
Contract with customer, liability		3,600,000						0		0
Term of collaborative research and development agreement							5 years
Merck [Member] | Supply Agreement [Member] | Research and Development Revenue [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Total revenues								0	0	0	1,300,000
Customer [Member] | Supply Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability		2,000,000						2,000,000		2,000,000			$ 800,000
Fine chemical customer [Member] | Research and Development Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability					$ 3,000,000
Term of collaborative research and development agreement					21 months
Research and development revenue								0	1,300,000	50,000	7,100,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability		1,900,000		$ 14,000,000				50,000		50,000
Research and development revenue								100,000	3,700,000	1,800,000	8,100,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member] | Milestone One [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability				4,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member] | Milestone Two [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability				1,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | CDX-6114 [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Cumulative catch-up adjustment to revenue, change in measure of progress										3,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Collaborative Arrangement [Member] | CDX-6114 [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone revenue		1,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Collaborative Arrangement [Member] | Strategic Collaboration Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability									600,000		600,000	$ 1,200,000
Research and development revenue								1,400,000	$ 1,200,000	3,900,000	$ 2,400,000
Deferred revenue		$ 800,000						25,000		25,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Research and Development Agreement [Member] | Maximum [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone revenue				85,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Sales-Based Milestone [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Target sales for sales milestone				1,000,000,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Sales-Based Milestone [Member] | Maximum [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone revenue				$ 250,000,000
Porton [Member] | Porton Agreement [Member] | Milestone One [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability			$ 500,000
Number of days for payment			30 days
Porton [Member] | Porton Agreement [Member] | Milestone Two [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone revenue			$ 1,500,000
Novartis [Member] | Platform Technology Transfer and License Agreement [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contract with customer, liability	$ 5,000,000							1,200,000		1,200,000
Term of collaborative research and development agreement	20 months
Research and development revenue								$ 3,800,000		$ 3,800,000
Novartis [Member] | Platform Technology Transfer and License Agreement, Milestone One [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contingent receivable	$ 4,000,000
Novartis [Member] | Platform Technology Transfer and License Agreement, Milestone Two [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contingent receivable	5,000,000
Novartis [Member] | Platform Technology Transfer and License Agreement Annual Technology Transfer [Member]
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Contingent annual receivable increase	$ 8,000,000

Cash Equivalents and Marketab_3

Cash Equivalents and Marketable Securities - Components of Cash Equivalents and Marketable Securities (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Sep. 30, 2019	Sep. 30, 2018
Cash Equivalents and Marketable Securities [Line Items]
Cash and cash equivalents	$ 53,039	$ 92,143	$ 54,225
Equity securities	563
Equity securities, gross unrealized gains	25
Equity securities, gross unrealized losses	0
Equity securities, estimated fair value	588
Adjusted Cost	31,788
Estimated Fair Value	31,813
Money Market Funds [Member]
Cash Equivalents and Marketable Securities [Line Items]
Cash and cash equivalents	31,225	73,450
Cash and cash equivalents, fair value	31,225	73,450
Estimated Fair Value	$ 31,200	$ 73,500

Cash Equivalents and Marketab_4

Cash Equivalents and Marketable Securities - Additional Information (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Dec. 31, 2009	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018	Jan. 01, 2018
Cash and Cash Equivalents [Line Items]
Cash and cash equivalents		$ 92,143	$ 54,225	$ 92,143	$ 54,225	$ 53,039
Cash, cash equivalents, and short-term investments						31,813
Percentage of outstanding shares owned at time of investment	16.60%
Statutory resale restriction expiry period	4 months
Proceeds from the sale of investment securities				62	0
Equity securities, estimated fair value						588
Accounting Standards Update 2016-01 [Member]
Cash and Cash Equivalents [Line Items]
Cumulative effect of change on equity or net assets							$ 500
Other Expense [Member]
Cash and Cash Equivalents [Line Items]
Gain (loss) on equity securities			$ (25)		$ (20)
Common Shares of Co Two Solution [Member]
Cash and Cash Equivalents [Line Items]
Number of common shares fair value (in shares)	10,000,000
Number of common shares sold (in shares)		1,300,000
Proceeds from the sale of investment securities		$ 100
Common Shares of Co Two Solution [Member] | Other Expense [Member]
Cash and Cash Equivalents [Line Items]
Gain (loss) on equity securities		(400)		(500)
Money Market Funds [Member]
Cash and Cash Equivalents [Line Items]
Cash and cash equivalents		73,450		73,450		31,225
Cash, cash equivalents, and short-term investments		73,500		73,500		31,200
Cash [Member]
Cash and Cash Equivalents [Line Items]
Cash, cash equivalents, and short-term investments		$ 18,600		$ 18,600		$ 21,800

Fair Value Measurements - Sche

Fair Value Measurements - Schedule of Financial Instruments Measured at Fair Value on Recurring Basis (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Summary of financial instruments measured at fair value on a recurring basis
Common shares of CO2 Solutions					$ 588,000
Total					31,813,000
Other Expense [Member]
Summary of financial instruments measured at fair value on a recurring basis
Gain (loss) on equity securities		$ (25,000)		$ (20,000)
Common Shares of Co Two Solution [Member] | Other Expense [Member]
Summary of financial instruments measured at fair value on a recurring basis
Gain (loss) on equity securities	$ (400,000)		$ (500,000)
Available-for-sale Securities [Member]
Summary of financial instruments measured at fair value on a recurring basis
Common shares of CO2 Solutions					$ 588,000
Investment owned, balance (in shares)					10,000,000
Available-for-sale Securities [Member] | Common Shares of Co Two Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Common shares of CO2 Solutions	0		0
Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Money market funds	73,450,000		73,450,000		$ 31,225,000
Fair Value, Inputs, Level 1 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total					31,856,000
Fair Value, Inputs, Level 1 [Member] | Available-for-sale Securities [Member]
Summary of financial instruments measured at fair value on a recurring basis
Common shares of CO2 Solutions					588,000
Fair Value, Inputs, Level 1 [Member] | Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Money market funds	$ 73,450,000		$ 73,450,000		$ 31,225,000

Balance Sheets Details - Inven

Balance Sheets Details - Inventories (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Schedule of Inventory Components
Raw materials	$ 7	$ 165
Work-in-process	52	47
Finished goods	338	377
Inventories	$ 397	$ 589

Balance Sheets Details - Prope

Balance Sheets Details - Property and Equipment, net (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Property, Plant and Equipment [Line Items]
Property and equipment	$ 39,920	$ 37,852
Less: accumulated depreciation and amortization	(33,679)	(33,093)
Property and equipment, net	6,241	4,759
Laboratory equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	23,266	21,328
Leasehold improvements [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	10,899	10,359
Computer equipment and software [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	3,806	3,954
Office equipment and furniture [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	1,461	1,272
Construction in progress [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	$ 488	$ 939

Balance Sheets Details - Goodw

Balance Sheets Details - Goodwill (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Balance Sheet Details [Abstract]
Goodwill	$ 3,241	$ 3,241

Balance Sheets Details - Accru

Balance Sheets Details - Accrued Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Balance Sheets Details [Abstract]
Accrued purchases	$ 3,894	$ 1,492
Accrued professional and outside service fees	1,833	2,020
Deferred rent		343
Lease incentive obligation		425
Other	455	575
Total	$ 6,182	$ 4,855

Stock-Based Compensation - Tex

Stock-Based Compensation - Textual (Details) $ in Millions	1 Months Ended
	Jun. 30, 2019installment	Mar. 31, 2010	Sep. 30, 2019USD ($)shares	Mar. 31, 2019	Mar. 31, 2018
Incentive Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock	100.00%
Non-Statutory Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock	85.00%
Stock options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Percent of voting interests	10.00%
Purchase price of common stock above minimum threshold	110.00%
Expiration period	10 years
Award vesting period		4 years
Compensation not yet recognized, stock options			$ 4.4
Stock options [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights	25.00%
Stock options [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights	75.00%
Restricted Stock Units (RSUs) [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period		3 years
Award vesting rights		33.33333%
Restricted Stock Units (RSUs) [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period		4 years
Award vesting rights	25.00%
Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of installments | installment	2
Performance awards, threshold level, number of shares, multiplier	0
Performance Shares [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Future vesting rights, percentage	50.00%
Performance Shares [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Future vesting rights, percentage	50.00%
RSAs and RSUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options			1.8
Performance Stock Units (PSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options			0.8
Performance Based Options (PBOs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options			$ 1.8
2019 Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant (in shares) | shares			7,897,144
Maximum number of shares to be issued upon exercise of stock options (in shares) | shares			14,000,000
Number of shares authorized (in shares) | shares			8,100,000
2019 PSU and PBO Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated performance goal achievement rate			113.00%
2018 PSU and PBO Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated performance goal achievement rate				118.00%
2018 PSU and PBO Plan [Member] | Performance Shares [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2018 PSU and PBO Plan [Member] | Performance Shares [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2017 PSU and PBO Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated performance goal achievement rate					134.20%
2017 PSU and PBO Plan [Member] | Performance Shares [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2017 PSU and PBO Plan [Member] | Performance Shares [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2016 PSU Plan [Member] | Performance Shares [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2016 PSU Plan [Member] | Performance Shares [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%

Stock-Based Compensation - Sto

Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Schedule of stock-based compensation expense
Stock-based compensation	$ 1,732	$ 1,770	$ 5,783	$ 6,207
Stock options [Member]
Schedule of stock-based compensation expense
Stock-based compensation	545	472	1,680	1,482
RSAs and RSUs [Member]
Schedule of stock-based compensation expense
Stock-based compensation	461	416	1,308	1,293
Performance Stock Units (PSUs) [Member]
Schedule of stock-based compensation expense
Stock-based compensation	368	407	1,075	1,251
Performance Based Options (PBOs) [Member]
Schedule of stock-based compensation expense
Stock-based compensation	358	475	1,720	2,181
Research and development [Member]
Schedule of stock-based compensation expense
Stock-based compensation	458	552	1,249	1,555
Selling, General and Administrative Expenses [Member]
Schedule of stock-based compensation expense
Stock-based compensation	$ 1,274	$ 1,218	$ 4,534	$ 4,652

Capital Stock - Textual (Detai

Capital Stock - Textual (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	9 Months Ended
	Jun. 30, 2019	Sep. 30, 2019	Sep. 30, 2018
Equity [Abstract]
Stock options exercised (shares)		970,256	729,596
Weighted average exercise price of stock options exercised (usd per share)		$ 4.76	$ 5.92
Proceeds from exercises of stock options		$ 4,621	$ 4,319
Private Placement Common Stock
Issuance costs		0	180
Proceeds from issuance of common stock in connection with private placement		$ 50,000	$ 0
Private Placement [Member]
Private Placement Common Stock
Shares issued (in shares)	3,048,780
Price per share (in dollars per share)	$ 16.40
Issuance costs	$ 100
Proceeds from issuance of common stock in connection with private placement	$ 49,900

Commitments and Contingencies

Commitments and Contingencies - Textual (Details)	Jun. 30, 2017USD ($)	Apr. 30, 2017USD ($)	Feb. 28, 2017USD ($)	Sep. 30, 2019USD ($)ft²building	Sep. 30, 2018USD ($)	Sep. 30, 2019USD ($)ft²building	Sep. 30, 2018USD ($)	Dec. 31, 2012USD ($)	Dec. 31, 2012USD ($)	Jul. 31, 2019USD ($)	Feb. 28, 2019	Jan. 31, 2019USD ($)	Jan. 01, 2019USD ($)	Dec. 31, 2018USD ($)	Sep. 30, 2017multiplier	Dec. 31, 2016
Commitments and Contingencies [Line Items]
Area of real estate property (in sq. ft.) | ft²				107,200		107,200
Number of buildings leased | building				4		4
Incentive from lessor				$ 0		$ 0								$ 500,000
Asset retirement obligations				200,000		200,000								200,000
Accretion expense related to asset retirement obligation				0	$ 0	0	$ 0
Rent expense				1,100,000	800,000	3,400,000	2,400,000
Operating lease, sublease rentals				200,000	$ 300,000	700,000	$ 900,000
Capital lease obligations incurred		$ 300,000	$ 400,000
Term of contract		3 years	3 years													3 years
Right-of-use assets, operating leases, net				24,542,000		24,542,000								0
Operating lease, liability				26,447,000		26,447,000								0
Right-of-use assets - finance leases, net				321,000		321,000							$ 500,000	0
Finance lease, liability				122,000		122,000							300,000	0
Indemnification Agreement [Member]
Commitments and Contingencies [Line Items]
Loss contingency accrual				0		0
Term Loan [Member]
Commitments and Contingencies [Line Items]
Borrowing capacity	$ 10,000,000
Term Loan [Member] | LIBOR [Member]
Commitments and Contingencies [Line Items]
Basis spread on variable rate	3.60%
Revolving Credit Facility [Member]
Commitments and Contingencies [Line Items]
Borrowing capacity	$ 5,000,000
Accounts receivable borrowing base percentage	80.00%
Stated interest rate	5.00%
Minimum cash multiplier | multiplier															6
Revolving Credit Facility [Member] | Prime Rate [Member]
Commitments and Contingencies [Line Items]
Basis spread on variable rate	1.00%
Letter of Credit [Member]
Commitments and Contingencies [Line Items]
Maximum borrowing capacity										$ 700,000		$ 1,100,000
Accounting Standards Update 2016-02 [Member]
Commitments and Contingencies [Line Items]
Right-of-use assets, operating leases, net													26,617,000
Operating lease, liability													27,562,000
Right-of-use assets - finance leases, net													493,000
Finance lease, liability													$ 302,000
Demand Deposits [Member]
Commitments and Contingencies [Line Items]
Non-current restricted cash				$ 1,100,000		$ 1,100,000								$ 700,000
Eighth Lease Amendment [Member]
Commitments and Contingencies [Line Items]
Renewal term											88 months
Payments for capital improvements								$ 3,600,000
Tenant reimbursements									$ 3,100,000
Redwood City, California, Penobscot Space [Member]
Commitments and Contingencies [Line Items]
Area of real estate property (in sq. ft.) | ft²				28,200		28,200
Redwood City, California, Building 2 Space [Member]
Commitments and Contingencies [Line Items]
Area of real estate property (in sq. ft.) | ft²				37,900		37,900
Redwood City, California, 501 Chesapeake Space [Member]
Commitments and Contingencies [Line Items]
Area of real estate property (in sq. ft.) | ft²				11,200		11,200
Redwood City, California, Saginaw Space [Member]
Commitments and Contingencies [Line Items]
Area of real estate property (in sq. ft.) | ft²				29,900		29,900

Commitments and Contingencies_2

Commitments and Contingencies - Reconciliation of Right-of-use Assets and Lease Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Assets
Right-of-use assets, operating leases, net	$ 24,542		$ 0
Right-of-use assets - finance leases, net	321	$ 500	0
Liabilities
Operating lease, liability	26,447		0
Finance lease, liability	$ 122	300	$ 0
Accounting Standards Update 2016-02 [Member]
Assets
Right-of-use assets, operating leases, net		26,617
Right-of-use assets - finance leases, net		493
Liabilities
Operating lease, liability		27,562
Finance lease, liability		$ 302

Commitments and Contingencies_3

Commitments and Contingencies - Lease Cost (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019	Jan. 01, 2019
Finance lease cost:
Amortization of right-of-use assets	$ 54	$ 163
Interest on lease obligations	2	8
Operating lease cost	1,139	3,417
Sublease income	(262)	(727)
Total lease cost	$ 933	$ 2,861
Weighted-average remaining lease term (in years):
Finance leases	15 days	15 days
Operating leases	7 years 10 months 24 days	7 years 10 months 24 days
Weighted-average discount rate:
Finance leases	5.00%	5.00%	5.00%
Operating leases	6.60%	6.60%	6.60%
Cash paid for amounts included in the measurement of lease obligations
Operating cash flows from operating leases		$ (2,456)
Operating cash flows from finance leases		(9)
Financing cash flows from finance leases		$ (180)

Commitments and Contingencies_4

Commitments and Contingencies - Future Minimum Lease Payments (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Finance Leases
2019 (remaining 3 months)	$ 63
2020	61
2021	0
2022	0
2023	0
2024 and thereafter	0
Total minimum lease payments	124
Less: imputed interest	(2)
Lease Obligations	122	$ 300	$ 0
Operating Leases
2019 (remaining 3 months)	824
2020	2,816
2021	4,197
2022	4,285
2023	4,589
2024 and thereafter	18,220
Total minimum lease payments	34,931
Less: imputed interest	(8,484)
Lease Obligations	26,447		$ 0
Sublease, payments to be received	$ 300

Commitments and Contingencies_5

Commitments and Contingencies - Future Minimum Lease Payments Under Topic 840 (Details) $ in Thousands	Dec. 31, 2018USD ($)
Capital Leases
2019	$ 252
2020	61
2021	0
2022	0
2023	0
Total minimum lease payments	313
Less: amount representing interest	(10)
Present value of capital lease obligations	303
Less: current portion	(242)
Long-term portion of capital leases	61
Future minimum sublease rentals	900
Operating Leases
2019	3,280
2020	712
2021	490
2022	41
2023	0
Total minimum lease payments	$ 4,523

Commitments and Contingencies_6

Commitments and Contingencies - Other Commitments (Details) - Supply Commitment [Member] $ in Thousands	Sep. 30, 2019USD ($)
Other Commitments [Line Items]
Future Minimum Payment	$ 2,967
September 2019 [Member]
Other Commitments [Line Items]
Future Minimum Payment	1,645
April 2016 [Member]
Other Commitments [Line Items]
Future Minimum Payment	1,242
December 2017 [Member]
Other Commitments [Line Items]
Future Minimum Payment	$ 80

Related Party Transactions - Te

Related Party Transactions - Textual (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Related Party Transaction, Due from (to) Related Party [Abstract]
Revenue from related parties	$ 200,000	$ 0	$ 600,000	$ 400,000
Accounts receivable from related parties	$ 0		0		$ 200,000
Recovery of short swing profit			$ 77,000	$ 0

Segment, Geographical and Oth_3

Segment, Geographical and Other Revenue Information - Additional Information (Details) $ in Millions	1 Months Ended	3 Months Ended	9 Months Ended
	Dec. 31, 2018USD ($)	Mar. 31, 2019USD ($)	Sep. 30, 2019segment
Segment Reporting Information [Line Items]
Number of operating segments | segment			2
CDX-6114 [Member] | Nestec Ltd. (Nestle Health Sciences) [Member] | Collaborative Arrangement [Member]
Segment Reporting Information [Line Items]
Milestone payment amount	$ 1
Duration to pay after milestone achievement	60 days
Event of counterparty exercising alternative option		$ 3

Segment, Geographical and Oth_4

Segment, Geographical and Other Revenue Information - Segment Reporting (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Segment Reporting Information [Line Items]
Total revenues	$ 21,906	$ 16,946	$ 49,808	$ 44,526
Cost of product revenue	5,067	3,791	12,230	10,228
Research and development	8,711	7,917	25,000	22,464
Selling, general and administrative	7,869	7,344	24,180	22,485
Total costs and operating expenses	21,647	19,052	61,410	55,177
Income (loss) from operations	259	(2,106)	(11,602)	(10,651)
Depreciation and amortization			(1,118)	(812)
Income (loss) before income taxes	336	(1,987)	(11,288)	(10,428)
Stock-based compensation	1,732	1,770	5,783	6,207
Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	20,424	12,125	41,100	34,019
Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Total revenues	1,482	4,821	8,708	10,507
Operating Segments [Member]
Segment Reporting Information [Line Items]
Total revenues	21,906	16,946	49,808	44,526
Cost of product revenue	5,067	3,791	12,230	10,228
Research and development	8,393	7,678	24,141	21,842
Selling, general and administrative	2,727	2,035	8,267	6,310
Total costs and operating expenses	16,187	13,504	44,638	38,380
Income (loss) from operations	5,719	3,442	5,170	6,146
Stock-based compensation	961	451	2,536	2,248
Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	20,424	12,125	41,100	34,019
Cost of product revenue	5,067	3,791	12,230	10,228
Research and development	5,313	4,758	14,889	14,548
Selling, general and administrative	2,037	1,870	6,499	5,695
Total costs and operating expenses	12,417	10,419	33,618	30,471
Income (loss) from operations	8,007	1,706	7,482	3,548
Stock-based compensation	736	354	1,973	2,005
Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Total revenues	1,482	4,821	8,708	10,507
Research and development	3,080	2,920	9,252	7,294
Selling, general and administrative	690	165	1,768	615
Total costs and operating expenses	3,770	3,085	11,020	7,909
Income (loss) from operations	(2,288)	1,736	(2,312)	2,598
Stock-based compensation	225	97	563	243
Corporate [Member]
Segment Reporting Information [Line Items]
Total costs and operating expenses	4,912	5,120	15,185	15,762
Depreciation and amortization	(471)	(309)	(1,273)	(812)
Product Sales [Member]
Segment Reporting Information [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Product Sales [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Product Sales [Member] | Operating Segments [Member]
Segment Reporting Information [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Product Sales [Member] | Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	10,351	8,405	24,588	18,291
Research and Development Revenue [Member]
Segment Reporting Information [Line Items]
Total revenues	11,555	8,541	25,220	26,235
Research and Development Revenue [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	10,073	3,720	16,512	15,728
Research and Development Revenue [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Total revenues	1,482	4,821	8,708	10,507
Research and Development Revenue [Member] | Operating Segments [Member]
Segment Reporting Information [Line Items]
Total revenues	11,555	8,541	25,220	26,235
Research and Development Revenue [Member] | Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Total revenues	10,073	3,720	16,512	15,728
Research and Development Revenue [Member] | Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Total revenues	$ 1,482	$ 4,821	$ 8,708	$ 10,507

Segment, Geographical and Oth_5

Segment, Geographical and Other Revenue Information - Concentration Risk (Details)	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Customer Concentration Risk [Member] | Customer A [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	21.00%	27.00%	31.00%	33.00%
Customer Concentration Risk [Member] | Customer B [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage		28.00%	17.00%	24.00%
Customer Concentration Risk [Member] | Customer C [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage		10.00%		17.00%
Customer Concentration Risk [Member] | Customer D [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	29.00%	15.00%	15.00%	11.00%
Credit Concentration Risk [Member] | Customer A [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			20.00%		37.00%
Credit Concentration Risk [Member] | Customer B [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage					17.00%
Credit Concentration Risk [Member] | Customer D [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage					11.00%
Credit Concentration Risk [Member] | Customer E [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			14.00%
Credit Concentration Risk [Member] | Customer F [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			15.00%
Credit Concentration Risk [Member] | Customer G [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage					16.00%
Credit Concentration Risk [Member] | Customer H [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			16.00%

Segment, Geographical and Oth_6

Segment, Geographical and Other Revenue Information - Revenues by Geographic Area (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Segment Reporting Information [Line Items]
Total revenues	$ 21,906	$ 16,946	$ 49,808	$ 44,526
Americas [Member]
Segment Reporting Information [Line Items]
Total revenues	2,706	4,315	9,620	13,968
EMEA [Member]
Segment Reporting Information [Line Items]
Total revenues	12,205	6,274	24,672	15,075
APAC [Member]
Segment Reporting Information [Line Items]
Total revenues	$ 6,995	$ 6,357	$ 15,516	$ 15,483

Segment, Geographical and Oth_7

Segment, Geographical and Other Revenue Information - Long-Lived Assets by Geographic Area (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
United States [Member]
Schedule of long-lived assets by geographical area
Long-Lived Assets	$ 31,104	$ 4,759

Segment, Geographical and Oth_8

Segment, Geographical and Other Revenue Information - Goodwill (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Segment Reporting Information [Line Items]
Goodwill	$ 3,241	$ 3,241
Operating Segments [Member]
Segment Reporting Information [Line Items]
Goodwill	3,241	3,241
Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Goodwill	2,463	2,463
Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Goodwill	$ 778	$ 778

Uncategorized Items - cdxs20190

Label	Element	Value	[1]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ (4,060,000)
AOCI Attributable to Parent [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	472,000
Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ (4,532,000)
[1]	(1) Cumulative effect of change in accounting principles included: Accounting Standards Update 2014-9 (Topic 606), of $4.1 million and Accounting Standards Update 2016-01 (Subtopic 825-10), of $0.5 million.