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Collaboration Agreements - Sanofi Performance Obligation (Details) - USD ($) $ in Millions	Jun. 30, 2020	Dec. 31, 2019
Alzheimer's Disease Services
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction [Line Items]
Performance obligation	$ 3.4	$ 3.5

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 137,184	$ 79,449
Short-term marketable securities	412,397	335,907
Prepaid expenses and other current assets	9,828	14,675
Total current assets	559,409	430,031
Long-term marketable securities	7,229	39,886
Property and equipment, net	43,622	46,732
Operating lease right-of-use asset	33,312	33,923
Other non-current assets	3,765	2,659
Total assets	647,337	553,231
Current liabilities:
Accounts payable	1,866	2,590
Accrued compensation	5,531	8,739
Accrued clinical costs	4,179	5,042
Other accruals and other current liabilities	8,424	6,569
Operating lease liability, current	4,330	3,665
Contract liabilities	34,134	18,739
Total current liabilities	58,464	45,344
Contract liabilities, less current portion	19,715	43,753
Operating lease liability, less current portion	66,612	68,865
Other non-current liabilities	379	379
Total liabilities	145,170	158,341
Commitments and contingencies (Note 8)
Stockholders' equity:
Convertible preferred stock, $0.01 par value; 40,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 0 shares issued and outstanding as of June 30, 2020 and December 31, 2019	0	0
Common stock, $0.01 par value; 400,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 105,897,872 shares and 96,189,935 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively	1,385	1,288
Additional paid-in capital	1,041,303	818,803
Accumulated other comprehensive income	551	350
Accumulated deficit	(541,072)	(425,551)
Total stockholders' equity	502,167	394,890
Total liabilities and stockholders’ equity	$ 647,337	$ 553,231

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Common stock, shares outstanding beginning balance (in shares) at Dec. 31, 2018		94,662,435
Beginning balance at Dec. 31, 2018	$ 546,845	$ 1,273	$ 774,158	$ (649)	$ (227,937)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		547,124
Issuances under equity incentive plans	3,477	$ 5	3,472
Vesting of early exercised common stock (in shares)		93,752
Vesting of early exercised common stock	64	$ 2	62
Vesting of restricted stock units (2020) and restricted stock awards and units (2019) (in shares)		353,585
Vesting of restricted stock units (2020) and restricted stock awards and units (2019)	0	$ 3	(3)
Stock-based compensation	20,588		20,588
Net loss	(97,329)				(97,329)
Other comprehensive income (loss)	1,528			1,528
Common stock, shares outstanding ending balance (in shares) at Jun. 30, 2019		95,656,896
Ending balance at Jun. 30, 2019	475,173	$ 1,283	798,277	879	(325,266)
Common stock, shares outstanding beginning balance (in shares) at Mar. 31, 2019		95,257,705
Beginning balance at Mar. 31, 2019	516,648	$ 1,279	781,966	332	(266,929)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		347,621
Issuances under equity incentive plans	2,569	$ 3	2,566
Vesting of early exercised common stock (in shares)		46,878
Vesting of early exercised common stock	32	$ 1	31
Vesting of restricted stock units (2020) and restricted stock awards and units (2019) (in shares)		4,692
Vesting of restricted stock units (2020) and restricted stock awards and units (2019)	0
Stock-based compensation	13,714		13,714
Net loss	(58,337)				(58,337)
Other comprehensive income (loss)	547			547
Common stock, shares outstanding ending balance (in shares) at Jun. 30, 2019		95,656,896
Ending balance at Jun. 30, 2019	$ 475,173	$ 1,283	798,277	879	(325,266)
Common stock, shares outstanding beginning balance (in shares) at Dec. 31, 2019	96,189,935	96,189,935
Beginning balance at Dec. 31, 2019	$ 394,890	$ 1,288	818,803	350	(425,551)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in follow-on offering, net of issuance costs of $632 (in shares)		9,000,000
Issuance of common stock in follow-on offering, net of issuance costs of $632	193,948	$ 90	193,858
Issuances under equity incentive plans (in shares)		589,516
Issuances under equity incentive plans	5,380	$ 6	5,374
Vesting of restricted stock units (2020) and restricted stock awards and units (2019) (in shares)		118,421
Vesting of restricted stock units (2020) and restricted stock awards and units (2019)	0	$ 1	(1)
Stock-based compensation	23,269		23,269
Net loss	(115,521)				(115,521)
Other comprehensive income (loss)	$ 201			201
Common stock, shares outstanding ending balance (in shares) at Jun. 30, 2020	105,897,872	105,897,872
Ending balance at Jun. 30, 2020	$ 502,167	$ 1,385	1,041,303	551	(541,072)
Common stock, shares outstanding beginning balance (in shares) at Mar. 31, 2020		105,541,343
Beginning balance at Mar. 31, 2020	545,311	$ 1,382	1,025,408	835	(482,314)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		329,947
Issuances under equity incentive plans	3,414	$ 3	3,411
Vesting of restricted stock units (2020) and restricted stock awards and units (2019) (in shares)		26,582
Vesting of restricted stock units (2020) and restricted stock awards and units (2019)	0
Stock-based compensation	12,484		12,484
Net loss	(58,758)				(58,758)
Other comprehensive income (loss)	$ (284)			(284)
Common stock, shares outstanding ending balance (in shares) at Jun. 30, 2020	105,897,872	105,897,872
Ending balance at Jun. 30, 2020	$ 502,167	$ 1,385	$ 1,041,303	$ 551	$ (541,072)

Significant Accounting Policies	6 Months Ended
Significant Accounting Policies	Jun. 30, 2020
Accounting Policies [Abstract]
Significant Accounting Policies	Significant Accounting Policies Organization and Description of Business Denali Therapeutics Inc. ("Denali" or the “Company”) is a biopharmaceutical company, incorporated in Delaware, that discovers and develops therapeutics to defeat neurodegenerative diseases. The Company is headquartered in South San Francisco, California. Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and the instructions to Form 10-Q and Article 10 of SEC Regulation S-X for interim financial information. These unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and notes thereto contained in the Annual Report on Form 10-K for the year ended December 31, 2019, as filed with the Securities and Exchange Commission on February 27, 2020 (the "2019 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2019 was derived from the audited annual consolidated financial statements as of the period then ended. Certain information and footnote disclosures typically included in the Company's annual consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements reflect all adjustments that, in the opinion of management, are necessary for a fair statement of the results of the interim periods presented. All such adjustments are of a normal recurring nature except for the impacts of adopting new accounting standards discussed below. These interim financial results are not necessarily indicative of results expected for the full fiscal year or for any subsequent interim period. During the six months ended June 30, 2020, except as discussed below in the sections titled "Marketable Securities" and "Recently Adopted Accounting Pronouncement," there were no material changes to the Company's significant accounting and financial reporting policies from those reflected in the 2019 Annual Report on Form 10-K. For further information with regard to the Company’s Significant Accounting Policies, please refer to Note 1, "Significant Accounting Policies," to the Company’s Consolidated Financial Statements included in the 2019 Annual Report on Form 10-K. Principles of Consolidation These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiary, the functional currency has been determined to be U.S. dollars. Monetary assets and liabilities denominated in foreign currency are remeasured at period-end exchange rates. Non-monetary assets and liabilities denominated in foreign currencies are remeasured at historical rates. Foreign currency transaction gains and losses resulting from remeasurement are recognized in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent liabilities at the date of the condensed consolidated financial statements, as well as the reported amounts of expenses during the reporting period. Actual results could differ from those estimates, and such differences could be material to the Condensed Consolidated Balance Sheets and Statements of Operations and Comprehensive Loss. Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash, cash equivalents, marketable securities and forward foreign currency exchange contracts. Substantially all of the Company’s cash and cash equivalents are deposited in accounts with financial institutions that management believes are of high credit quality. Such deposits have and will continue to exceed federally insured limits. The Company maintains its cash with accredited financial institutions and accordingly, such funds are subject to minimal credit risk. The Company’s investment policy limits investments to certain types of securities issued by the U.S. government, its agencies and institutions with investment-grade credit ratings and places restrictions on maturities and concentration by type and issuer. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash, cash equivalents and marketable securities and issuers of marketable securities to the extent recorded on the Condensed Consolidated Balance Sheets. As of June 30, 2020 and December 31, 2019, the Company had no off-balance sheet concentrations of credit risk. The Company is exposed to counterparty credit risk on all of its derivative financial instruments. The Company has established and maintains strict counterparty credit guidelines and enters into hedges only with financial institutions that are investment grade or better to minimize the Company’s exposure to potential defaults. The Company does not require collateral to be pledged under these agreements. The Company is subject to a number of risks similar to other early-stage biopharmaceutical companies, including, but not limited to, the need to obtain adequate additional funding, possible failure of current or future preclinical testing or clinical trials, its reliance on third parties to conduct its clinical trials, the need to obtain regulatory and marketing approvals for its product candidates, competitors developing new technological innovations, the need to successfully commercialize and gain market acceptance of the Company’s product candidates, its right to develop and commercialize its product candidates pursuant to the terms and conditions of the licenses granted to the Company, protection of proprietary technology, the ability to make milestone, royalty or other payments due under any license or collaboration agreements, and the need to secure and maintain adequate manufacturing arrangements with third parties. If the Company does not successfully commercialize or partner any of its product candidates, it will be unable to generate product revenue or achieve profitability. The COVID-19 pandemic has caused increased risk and uncertainty for the Company. Credit risk associated with investments in securities may increase if any institution with which the Company has an investment is significantly impacted by the COVID-19 pandemic. As of June 30, 2020, the Company has not realized any losses on its cash deposits or investments. Further, COVID-19 may impact the timelines and progress of the Company's preclinical activities and clinical trials, and may impact its ability to raise capital in the near term. Segments The Company has one operating segment. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources. Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of 90 days or less at the date of purchase to be cash and cash equivalents. Cash equivalents are reported at fair value. The Company’s restricted cash consists of the letter of credit for the Company’s headquarters building lease, and is included within other non-current assets on the accompanying Condensed Consolidated Balance Sheets. Marketable Securities The Company generally invests its excess cash in money market funds and investment grade short to intermediate-term fixed income securities. Such investments are included in cash and cash equivalents, short-term marketable securities, or long-term marketable securities on the Condensed Consolidated Balance Sheets, are considered available-for-sale, and reported at fair value with net unrealized gains and losses included as a component of stockholders’ equity. The Company classifies investments in securities with remaining maturities of less than one year, or where its intent is to use the investments to fund current operations or to make them available for current operations, as short-term investments. The Company classifies investments in securities with remaining maturities of over one year as long-term investments. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Realized gains and losses and declines in value determined to be due to credit losses on marketable securities, if any, are included in interest and other income, net. The Company periodically evaluates the need for an allowance for credit losses. This evaluation consists of several qualitative and quantitative factors, including whether it has plans to sell the security, whether it is more likely than not it will be required to sell any marketable securities before recovery of its amortized cost basis, and if the entity has the ability and intent to hold the security to maturity, and the portion of any unrealized loss that is the result of a credit loss. Factors considered in making these evaluations include quoted market prices, recent financial results and operating trends, implied values from any recent transactions or offers of investee securities, credit quality of debt instrument issuers, expected cash flows from securities, other publicly available information that may affect the value of the marketable security, duration and severity of the decline in value, and the Company's strategy and intentions for holding the marketable security. Accounts Receivable Accounts receivable are included within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets. The accounts receivable balance represents amounts receivable from the Company's collaboration partners, net of an allowance for credit losses, if required. Derivatives and Hedging Activities The Company measures its derivative instruments at fair value, and accounts for them as either assets or liabilities included within prepaid assets and other current assets and other accruals and current liabilities, respectively, on the Condensed Consolidated Balance Sheets. Derivatives are adjusted to fair value through interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Leases The Company adopted Accounting Standards Update ("ASU") No. 2016-02, Leases as of January 1, 2019. A determination is made as to whether an arrangement is a lease at inception. A right-of-use (“ROU”) asset and operating lease liability is recognized for identified operating leases in the Condensed Consolidated Balance Sheets. The changes in operating lease ROU assets and operating lease liabilities are presented net within non-cash adjustment to operating lease expense in the Condensed Consolidated Statements of Cash Flows. ROU assets represent the Company’s right to use the underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments due over the lease term, with the ROU assets adjusted for lease incentives received. When determining the present value of lease payments, the Company uses its incremental borrowing rate on the date of lease commencement, or the rate implicit in the lease, if known. The Company does not assume renewals in its determination of the lease term unless the renewals are deemed by management to be reasonably certain at lease inception. Leases with an initial term of 12 months or less are not recorded on the balance sheet, unless they include an option to purchase the underlying asset that the Company is reasonably certain to exercise. The Company recognizes lease expenses on a straight-line basis over the lease term. The Company has leases with lease and non-lease components, which the Company has elected to account for as a single lease component. Revenue Recognition License and Collaboration Revenue The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC 808, Collaborative Arrangements (“ASC 808”) to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For collaboration arrangements within the scope of ASC 808 that contain multiple elements, the Company first determines which elements of the collaboration are deemed to be within the scope of ASC 808 and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of Topic 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808, an appropriate recognition method is determined and applied consistently, generally by analogy to Topic 606. The accounting treatment pursuant to Topic 606 is outlined below. The terms of licensing and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license fees; development, regulatory and commercial milestone payments; payments for manufacturing supply and research and development services; and royalties on net sales of licensed products. Each of these payments results in license, collaboration and other revenue, except for revenues from royalties on net sales of licensed products, which are classified as royalty revenue. The core principle of Topic 606 is to recognize revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received in exchange for those goods or services. In determining the appropriate amount of revenue to be recognized as the Company fulfills its obligations under each of its agreements, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. Amounts received prior to satisfying the revenue recognition criteria are recorded as contract liabilities in the Company’s Condensed Consolidated Balance Sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to the Company having an unconditional right (other than a right that is conditioned only on the passage of time) to receipt are recorded as contract assets in the Company's Condensed Consolidated Balance Sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer. At contract inception, the Company assesses the goods or services promised in a contract with a customer and identifies those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the performance obligation does not provide the customer with a material right. The Company considers the terms of the contract to determine the transaction price. The transaction price is the amount of consideration to which the Company expects to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling prices ("SSP"). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, the Company uses its best estimate of the SSP for the deliverable. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset, which for a service is considered to be as the services are received and used. The Company recognizes revenue over time by measuring the progress toward complete satisfaction of the relevant performance obligation using an appropriate input or output method based on the nature of the service promised to the customer. After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the transaction price is allocated to the performance obligations on the same basis as at contract inception. Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the SSP of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations. Comprehensive Income (Loss) Comprehensive income (loss) is composed of net loss and certain changes in stockholders’ equity that are excluded from net loss, primarily unrealized gains or losses on the Company’s marketable securities. Net Loss per Share Basic net loss per share is calculated by dividing the net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive given the net loss for each period presented. Recently Issued Accounting Pronouncement In December 2019, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2019-12, Income Taxes (Topic 740) Simplifying the Accounting for Income Taxes. ASU No. 2019-12 modifies ASC 740 to simplify several aspects of accounting for income taxes, including eliminating certain exceptions to the guidance in ASC 740 related to the approach for intraperiod tax allocation. The guidance is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years, with early adoption permitted, and is required to be adopted prospectively, with the exception of certain specific amendments. The Company is currently assessing the impact of this ASU on its Condensed Consolidated Financial Statements. Recently Adopted Accounting Pronouncement In June 2016, the FASB issued Accounting Standards Update No. 2016-13, Financial Instruments-Credit Losses: Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires measurement and recognition of expected credit losses for financial assets. In April 2019, the FASB issued clarification to ASU 2016-13 within ASU 2019-04, Codification Improvements to Topic 326, Financial Instruments-Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments. The Company adopted this standard as of January 1, 2020 using a modified retrospective approach. Adoption of the standard did not have a material impact on the Condensed Consolidated Financial Statements.

Commitments and Contingencies

6 Months Ended

Jun. 30, 2020

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Lease Obligations

In May 2018, the Company entered into an amendment to its operating lease for its former corporate headquarters in South San Francisco (the "Headquarters Lease Amendment") to relocate and expand its headquarters to 148,020 rentable square feet in a building in South San Francisco, California (the "New Premises"). The Headquarters Lease Amendment has a contractual term of ten years from the legal commencement date, which was April 1, 2019, when the building was ready for occupancy. For accounting purposes, the lease commencement date was determined to be August 1, 2018, which was the date at which the Company was deemed to have obtained control over the property. The Company has an option to extend the lease term for a period of ten years by giving the landlord written notice of the election to exercise the option at least nine months, but not more than twelve months, prior to the expiration of the Headquarters Lease Amendment lease term. The Company determined that this renewal was not reasonably certain at lease inception.

The Headquarters Lease Amendment provides for monthly base rent amounts escalating over the term of the lease. In addition, the Headquarters Lease Amendment provided a tenant improvement allowance ("TIA") of up to $25.9 million, which was fully utilized, of which $4.4 million will be repaid to the landlord in the form of additional monthly rent. This is recorded as leasehold improvement assets and an offset to the lease ROU asset on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019. The Company is also required to pay the operating expenses for the New Premises, such as taxes and insurance, which are treated as variable lease payments.

Management exercised judgment in applying the requirements of ASC 842, including the determination as to whether certain contracts contain a lease and for the Headquarters Lease Amendment, the discount rate used to determine the measurement of the lease liability. As the implicit rate of the Headquarters Lease Amendment was not known, the Company estimated a 9.0% discount rate, which was management’s estimate of the Company’s incremental borrowing rate. To estimate the incremental borrowing rate, management considered observable debt yields of comparable market instruments, as well as benchmarks within the Headquarters Lease Amendment that may be indicative of the rate implicit in the lease.

Total operating lease costs, including variable and short-term lease costs, were $2.9 million and $5.5 million for the three and six months ended June 30, 2020, respectively, and $2.5 million and $4.8 million for the three and six months ended June 30, 2019, respectively.

Operating lease liabilities are calculated as the net present value of the remaining lease payments over the remaining lease term. In determining the present value of lease payments, the Company uses its incremental borrowing rate based on the information available at the lease commencement date. As of June 30, 2020, the weighted average remaining lease term was 8.8 years and the weighted average discount rate used to determine the operating lease liability was 9.0%. Cash paid for amounts included in the measurement of lease liabilities for the six months ended June 30, 2020 and June 30, 2019 of $4.7 million and $1.9 million, respectively, was included in net cash used in operating activities in the Company's Condensed Consolidated Statements of Cash Flows.

The following table reconciles the undiscounted cash flows for the next five years and total of the remaining years to the operating lease liabilities recorded in the Condensed Consolidated Balance Sheet as of June 30, 2020 (in thousands):


Year Ended December 31:
2020 (six months)	$	5,071
2021	10,391
2022	10,731
2023	11,083
2024	11,447
Thereafter	54,074
Total undiscounted lease payments	102,797
Present value adjustment	(31,855)
Net operating lease liabilities	$	70,942

In October 2018, the Company entered into a sublease agreement ("Sublease Agreement") to sublease approximately 36,835 rentable square feet of space in its New Premises. The Sublease Agreement has a term of five years from the commencement date of April 12, 2019 and provides for the Company to receive monthly base rent amounts escalating over the term of the lease. The Company also passes through a portion of the operating expenses, such as taxes and insurance for the New Premises to the sublessee, which are treated as variable sublease income. Total sublease income, including rent and variable sublease cost reimbursements, was $1.0 million and $1.9 million for the three and six months ended June 30, 2020, respectively, and $0.8 million for the three and six months ended June 30, 2019, respectively.

The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of June 30, 2020 (in thousands):


Year Ended December 31:
2020 (six months)	$	1,431
2021	2,925
2022	3,009
2023	3,096
2024	876
Thereafter	—
Total undiscounted sublease receipts	$	11,337

Indemnification

In the ordinary course of business, the Company may provide indemnifications of varying scope and terms to vendors, lessors, business partners, board members, officers, and other parties with respect to certain matters, including, but not limited to, losses arising out of breach of such agreements, services to be provided by the Company, negligence or willful misconduct of the Company, violations of law by the Company, or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with directors and certain officers and employees that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors, officers or employees. No demands have been made upon the Company to provide indemnification under such agreements, and thus, there are no claims that the Company is aware of that could have a material effect on the Company’s Condensed Consolidated Balance Sheets, Condensed Consolidated Statements of Operations and Comprehensive Loss, or Condensed Consolidated Statements of Cash Flows.

Commitments

Effective September 2017, the Company entered into a Development and Manufacturing Services Agreement as amended (“DMSA”) with Lonza Sales AG (“Lonza”) for the development and manufacture of biologic products. Under the DMSA, the Company will execute purchase orders based on project plans authorizing Lonza to provide development and manufacturing services with respect to certain of the Company's antibody and enzyme products, and will pay for the services provided and batches delivered in accordance with the DMSA and project plan. Unless earlier terminated, the DMSA will expire on September 6, 2022.

As of June 30, 2020 and December 31, 2019, the Company had open non-cancellable purchase orders for biological product development and manufacturing costs totaling $18.0 million and $21.2 million, respectively. The activities under these purchase orders are expected to be completed by May 2027. As of June 30, 2020 and December 31, 2019, the Company had total non-cancellable purchase commitments under the DMSA of $12.1 million and $11.2 million, respectively.

During the three months ended June 30, 2020 and 2019, the Company incurred costs of $3.8 million and $3.1 million, respectively, and made payments of $2.0 million and $3.9 million, respectively, for the development and manufacturing services rendered under the DMSA. During the six months ended June 30, 2020 and 2019, the Company incurred costs of $4.8 million and $6.7 million, respectively, and made payments of $5.2 million and $6.5 million, respectively, for the development and manufacturing services rendered under the DMSA.

Commitments and Contingencies (Tables)

6 Months Ended

Jun. 30, 2020

Commitments and Contingencies Disclosure [Abstract]

Operating Lease Maturity, Payments


Year Ended December 31:
2020 (six months)	$	5,071
2021	10,391
2022	10,731
2023	11,083
2024	11,447
Thereafter	54,074
Total undiscounted lease payments	102,797
Present value adjustment	(31,855)
Net operating lease liabilities	$	70,942

Operating Lease Maturity, Receivable

The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of June 30, 2020 (in thousands):


Year Ended December 31:
2020 (six months)	$	1,431
2021	2,925
2022	3,009
2023	3,096
2024	876
Thereafter	—
Total undiscounted sublease receipts	$	11,337

Stock-Based Awards - Summary of Restricted Stock Activity (Details) - Restricted Stock	6 Months Ended
	Jun. 30, 2020 $ / shares shares
Share Awards & Units
Unvested, beginning balance (in shares) \| shares	882,636
Granted (in shares) \| shares	957,249
Vested and released (in shares) \| shares	(118,421)
Forfeited (in shares) \| shares	(48,412)
Unvested, ending balance (in shares) \| shares	1,673,052
Expected to vest (in shares) \| shares	1,673,052
Weighted-Average Fair Value at Date of Grant per Share
Unvested, beginning balance (usd per share) \| $ / shares	$ 18.67
Granted (usd per share) \| $ / shares	24.62
Vested and released (usd per share) \| $ / shares	19.13
Forfeited (usd per share) \| $ / shares	21.52
Unvested, ending balance (usd per share) \| $ / shares	21.98
Expected to vest (usd per share) \| $ / shares	$ 21.98

Collaboration Agreements (Tables)

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summary of Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2020		2019		2020		2019
Takeda Collaboration Agreement⁽¹⁾	$	5,537	$	740	$	8,555	$	1,422
Sanofi Collaboration Agreement


Alzheimer's Disease Services⁽¹⁾	36		99		88		193
Retained Activities	274		3,358		808		6,787
Total Sanofi Collaboration Revenue	310		3,457		896		6,980
Total Collaboration Revenue	$	5,847	$	4,197	$	9,451	$	8,402

_________________________________________________

(1)Amounts represent revenue recognized during the period that was included in the contract liability balance at the beginning of the period.

Net Loss Per Share - Schedule of Dilutive Securities Not Included in Diluted Per Share Calculations (Details) - shares	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	16,024,847	12,865,704	16,024,847	12,865,704
Options issued and outstanding and ESPP shares issuable
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	14,351,795	12,214,029	14,351,795	12,214,029
Restricted shares subject to future vesting
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	1,673,052	610,003	1,673,052	610,003
Early exercised common stock subject to future vesting
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	0	41,672	0	41,672

Subsequent Event	6 Months Ended
Subsequent Event	Jun. 30, 2020
Subsequent Events [Abstract]
Subsequent Event	Subsequent Event On August 5, 2020, the Company entered into a binding Provisional Collaboration and License Agreement (“Provisional Collaboration Agreement”) with Biogen Inc.’s subsidiaries Biogen MA, Inc. and Biogen International GmbH (collectively “Biogen”), to co-develop and co-commercialize Denali’s small molecule inhibitors of LRRK2 for Parkinson’s disease. In addition to the LRRK2 program, Biogen will also receive an exclusive option to license two preclinical programs from our TV platform, which aims to improve brain uptake of biotherapeutics, including our Antibody Transport Vehicle (“ATV”): Abeta program (ATV enabled anti-amyloid beta program) and a second program utilizing our TV technology. Further, Biogen will have right of first negotiation on two additional TV-enabled therapeutics, currently at a preclinical stage, should we decide to seek a collaboration for such programs. Under the terms of the agreement, Biogen will make an upfront payment to Denali of $560 million. Should the LRRK2 program achieve certain development and commercial milestones, Denali will be eligible to receive milestone payments exceeding $1.1 billion as well as profit sharing and royalties. Biogen and Denali will share responsibility and costs for global development (60 percent Biogen; 40 percent Denali), and will share responsibility and costs as well as profits and losses for commercialization in the U.S. (50 percent Biogen; 50 percent Denali) and China (60 percent Biogen and 40 percent Denali). Outside the U.S. and China, Biogen will be responsible for commercialization and pay Denali tiered royalties. Further, under an associated common stock purchase agreement, Denali will receive proceeds of $465 million for the sale of approximately 13.3 million newly issued shares of Denali common stock at $34.94 per share, representing approximately 11.2 percent of Denali’s outstanding stock. Closing of the transaction is contingent on satisfaction of requirements under applicable antitrust laws, including the HSR Antitrust Improvements Act of 1976, as amended, in the U.S., and other customary closing conditions, and with respect to the collaboration, execution of a definitive collaboration agreement.

Subsequent Event - Narrative (Details) - Subsequent Event - Provisional Collaborative Arrangement $ / shares in Units, shares in Millions, $ in Millions	Aug. 05, 2020 USD ($) program $ / shares shares
Subsequent Event [Line Items]
Funded percentage	40.00%
U.S.
Subsequent Event [Line Items]
Agreed share of commercial profit (loss) percentage	50.00%
China
Subsequent Event [Line Items]
Agreed share of commercial profit (loss) percentage	40.00%
Biogen
Subsequent Event [Line Items]
Funded percentage	60.00%
Biogen \| U.S.
Subsequent Event [Line Items]
Agreed share of commercial profit (loss) percentage	50.00%
Biogen \| China
Subsequent Event [Line Items]
Agreed share of commercial profit (loss) percentage	60.00%
Biogen
Subsequent Event [Line Items]
Number of programs \| program	2
Number of additional programs, if circumstances met \| program	2
Upfront payment, to be received	$ 560
Eligible milestone payments, exceeding	1,100
Biogen \| Share Purchase Agreement
Subsequent Event [Line Items]
Proceeds to be received upon sale	$ 465
Number of common stock, to be issued (in shares) \| shares	13.3
Number of common stock, to be issued, per share (usd per share) \| $ / shares	$ 34.94
Outstanding share capital	11.20%

Collaboration Agreements

6 Months Ended

Jun. 30, 2020

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

Sanofi

In October 2018, the Company entered into a Collaboration and License Agreement ("Sanofi Collaboration Agreement") with Genzyme Corporation, a wholly owned subsidiary of Sanofi S.A. ("Sanofi") pursuant to which certain small molecule CNS and peripheral receptor interacting serine/threonine protein kinase 1 ("RIPK1") inhibitors contributed by Sanofi and by Denali will be developed and commercialized. The Sanofi Collaboration Agreement became effective in November 2018 when the Hart-Scott-Rodino ("HSR") requirements were satisfied at which time Sanofi paid the Company an upfront payment of $125.0 million. Under the Sanofi Collaboration Agreement, Denali is eligible to receive milestone payments from Sanofi up to approximately $1.1 billion upon achievement of certain clinical, regulatory and sales milestone events. Such milestone payments include $215.0 million in clinical milestone payments and $385.0 million in regulatory milestone payments for CNS Products, as defined, that are developed and approved in the United States, by the European Medicines Agency ("EMA") and in Japan for three indications, including Alzheimer's disease. These milestones also include $120.0 million in clinical milestone payments, $175.0 million in regulatory milestone payments and $200.0 million in commercial milestone payments for Peripheral Products, as defined, that are developed and approved in the United States, by the EMA and Japan for three indications.

Denali will share profits and losses equally with Sanofi for CNS Products sold in the United States and China, and receive variable royalties on net sales for CNS Products sold outside of the United States and China and for Peripheral Products sold worldwide.

Denali and Sanofi will jointly develop CNS Products pursuant to a global development plan. The Company will be responsible, at its own cost, for conducting Phase 1 and Phase 2 trials for CNS Products in Alzheimer’s disease and any activities required to support such clinical trials and specific for Alzheimer’s disease. Denali conducted, at Sanofi’s cost, a Phase 1b trial for the initial lead CNS penetrant RIPK1 inhibitor, DNL747, in ALS. In June 2020, Denali announced that clinical activities on DNL747 would be paused and efforts focused on the development of the backup preclinical candidate, DNL788. Sanofi is responsible, at its cost, for all other Phase 1 and Phase 2 trials for CNS Products, including for multiple sclerosis. Sanofi will lead the conduct of all Phase 3 and later stage development trials for CNS Products, with Sanofi and Denali funding 70% and 30% of such costs, respectively. Sanofi will also lead the commercialization activities globally for CNS Products, subject to certain options that Denali has to conduct co-commercialization activities with respect to each CNS Product in the United States and China.

Sanofi will be responsible, at its cost, for conducting activities relating to the development and commercialization of all Peripheral Products. Denali will be entitled to receive tiered royalties in the low- to mid- teen percentages on net sales of Peripheral Products.

The Company identified the following distinct performance obligations associated with the Sanofi Collaboration Agreement upon inception: the CNS program license, the Peripheral program license, the Phase 1 and Phase 2 trials for CNS Products for Alzheimer’s disease ("Alzheimer's Disease Services"), and the Phase 1b trial for DNL747 for ALS and associated activities ("Retained Activities").

The Company believes that the Sanofi Collaboration Agreement is a collaboration arrangement as defined in ASC 808. The Company also believes that Sanofi meets the definition of a customer as defined in ASC 606, Revenue From Contracts With Customers for three of the performance obligations identified at inception, but does not meet the definition of a customer for the Alzheimer's Disease Services. Further, Sanofi does not meet the definition of a customer for all Phase 3 and later stage development trials for CNS Products led by Sanofi for which Denali will fund 30% of total costs. Since ASC 808 does not address recognition and measurement, the Company looked to other accounting literature for guidance where the performance obligation does not fall under ASC 606, and determined that for the Alzheimer's Disease Services, the guidance in ASC 606 should be analogized for the recognition, measurement and reporting of this performance obligation, and for the cost sharing provisions, the Company determined that the guidance in ASC 730, Research and Development should be applied.

The transaction price at inception included upfront fixed consideration of $125.0 million. All potential future milestones and other payments were considered constrained at the inception of the Sanofi Collaboration Agreement since the Company could not conclude it was probable that a significant reversal in the amount recognized would not occur. From inception through June 30, 2020, the transaction price increased by $23.5 million, consisting of $13.5 million related to costs incurred for Retained Activities that were no longer constrained, and $10.0 million related to a milestone triggered in July 2019. The transaction price increased by $0.3 million and $0.8 million for the three and six months ended June 30, 2020, respectively, and $3.4 million and $6.8 million for the three and six months ended June 30, 2019, respectively, related entirely to costs incurred for Retained Activities that were determined to no longer be constrained during these periods.

The respective standalone value for each of the performance obligations was determined by applying the SSP method and the transaction price allocated based on the relative SSP method with revenue recognition timing to be determined either by delivery or the provision of services.

The Company used an adjusted market assessment approach to estimate the selling price for the program licenses, and an expected cost plus margin approach for estimating the Alzheimer’s Disease Services and the Retained Activities. The program licenses and existing know-how were delivered on the effective date of the Sanofi Collaboration Agreement. The Alzheimer’s Disease Services and the Retained Activities are expected to be delivered over time as the services are performed. For the Alzheimer's Disease Services, revenue will be recognized over time using the input method, based on costs incurred to perform the services, since the level of costs incurred over time is thought to best reflect the transfer of services to Sanofi. For the Retained Activities, revenue will be recognized over time using the output method, based on amounts invoiced to Sanofi, since this is believed to directly correlate to the value of the services performed.

A contract liability of $3.4 million and $3.5 million was recorded on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively. This contract liability relates to the portion of the Alzheimer's Disease Services performance obligation yet to be satisfied, with such amounts to be recognized over the estimated period of the services, which is expected to be several years. There was a receivable of $0.3 million and $1.2 million at June 30, 2020 and December 31, 2019, respectively, associated with the Sanofi Collaboration Agreement.

In assessing the Sanofi Collaboration Agreement, management is required to exercise considerable judgment in estimating revenue to be recognized. Management applies judgment in determining the separate performance obligations, in estimating the selling price, in determining when control was transferred to Sanofi for the licenses, and in estimating total future costs when using the input method.

Through June 30, 2020, Denali has received milestone payments of $10.0 million and has not recorded any product sales recorded under the Sanofi Collaboration Agreement.

Takeda

In January 2018, the Company entered into a Collaboration and Option Agreement ("Takeda Collaboration Agreement") with Takeda Pharmaceutical Company Limited ("Takeda"), pursuant to which the Company granted Takeda an option to develop and commercialize, jointly with the Company, certain biologic products that are enabled by Denali's blood-brain barrier ("BBB") delivery technology and intended for the treatment of neurodegenerative disorders. The programs were Denali’s Antibody Transport Vehicle (“ATV”):BACE1/Tau and ATV:TREM2 and PTV:PGRN programs. The Takeda Collaboration Agreement became effective in February 2018, at which time Takeda paid the Company an upfront payment of $40.0 million. Takeda may pay up to an aggregate of $25.0 million with respect to each of the three programs directed to a target and based upon the achievement of certain preclinical milestone events, up to $75.0 million in total, $5.0 million of which was paid upon the Takeda Collaboration Agreement becoming effective. In February 2019, the agreement was amended to replace the ATV:BACE1/Tau program with the ATV:Tau program. The amendment did not have a material impact to the condensed consolidated financial statements.

Under the Takeda Collaboration Agreement and unless otherwise agreed jointly between both parties, Denali will be responsible, at its cost, for conducting activities relating to pre-IND development of biologic products directed to the three identified targets and enabled by its BBB delivery technology targeting TfR during the applicable research period. The period through which the option can be exercised continues for each target until the first biologic product directed to the relevant target is IND-ready or approximately five years after selection of the target, whichever is earlier.

If Takeda exercises its option with respect to a particular target, then Takeda will have the right to develop and commercialize, jointly with the Company, a specified number of biologic products enabled by its BBB delivery technology that were developed during the research period and which are directed to the relevant target. The Company will grant to Takeda a co-exclusive license under the intellectual property the Company controls related to those biologic products.

Takeda is obligated to pay Denali a $5.0 million option fee for each target for which Takeda exercises its option, up to $15.0 million in total.

In addition, if Takeda exercises its option for all three collaboration programs, Takeda may be obligated to pay Denali up to an aggregate of $407.5 million upon achievement of certain clinical milestone events and up to an aggregate of $300.0 million in regulatory milestone events relating to receipt of regulatory approval in the United States, certain European countries and Japan. Takeda may also be obligated to pay Denali up to $75.0 million per biologic product upon achievement of a certain sales-based milestone, or an aggregate of $225.0 million if one biologic product from each program achieves this milestone.

If Takeda exercises its option for a particular target, Denali and Takeda will share equally the development and commercialization costs, and, if applicable, the profits, for each collaboration program.

Pursuant to the terms of the Takeda Collaboration Agreement, the Company entered into a common stock purchase agreement (the "Stock Purchase Agreement") with Takeda on January 3, 2018, pursuant to which Takeda purchased 4,214,559 shares of Denali’s common stock (the "Shares") for an aggregate purchase price of $110.0 million. The sale of the Shares closed on February 23, 2018. The fair market value of the common stock sold to Takeda was $94.4 million, based on the closing stock price of $22.40 on the date of issuance, resulting in a $15.6 million premium paid to the Company above the fair value of the Company's common stock which was credited to contract liability in the Company's Condensed Consolidated Balance Sheets.

The Company believes that the Takeda Collaboration Agreement is a collaboration arrangement as defined in ASC 808. Further, during the research period, the Company believes that the arrangement is a contract with a customer as defined in ASC 606, Revenue From Contracts With Customers. The Takeda Collaboration Agreement and the Stock Purchase Agreement are being accounted for as one arrangement because they were entered into at the same time with interrelated financial terms.

The Company identified performance obligations during the research period consisting of the license, the development options, and joint steering committee ("JSC") participation together with the research services for each collaboration program. The license rights, JSC involvement, option and research services are considered to be a single performance obligation for each program since the research services are highly interrelated with the option and JSC involvement and will significantly modify the license. The performance obligations under each of the three programs are separate since the activities and risks under the programs are distinct.

The Company determined that all other goods or services which are contingent upon Takeda exercising its option for each program were not considered performance obligations at the inception of the Takeda Collaboration Agreement.

The transaction price at inception included fixed consideration consisting of the upfront fee of $40.0 million, the $15.6 million premium on the sale of common stock, and the first preclinical milestone payment of $5.0 million. It also included variable consideration of $26.0 million relating to future milestones that were not constrained. The amount of variable consideration was estimated using the most likely amount method.

The remaining $44.0 million of preclinical milestones were considered constrained at the inception of the Takeda Collaboration Agreement since the Company could not conclude it is probable that a significant reversal in the amount recognized will not occur. Additionally, cost and profit sharing income, and the development and commercial milestones as outlined above, have not been considered given Takeda has not exercised its options for the development and commercial phases for any program. No change in the transaction price has been recorded since inception. This will be reassessed at each reporting period.

The transaction price has been ascribed in its entirety to the three performance obligations identified in the research term of the Takeda Collaboration Agreement.

Revenue is recognized when, or as, the Company satisfies its performance obligations by transferring the promised services to Takeda. Revenue is being recognized over time using the input method, based on costs incurred to perform the research services, since the level of costs incurred over time is thought to best reflect the transfer of services to Takeda. There were no material changes in estimates during the three and six months ended June 30, 2020 or June 30, 2019.

A contract liability of $50.4 million and $59.0 million is recorded on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively. This contract liability relates to the three performance obligations identified, with such amounts to be recognized over the estimated period of the pre-IND research services, which is expected to be several years. There was no receivable as of June 30, 2020 or December 31, 2019, related to the Takeda Collaboration Agreement.

Revenue recognized relating to future milestone payments of $4.9 million and $2.4 million, which the Company concluded is probable that a significant reversal in the amount recognized will not occur, is presented net in the contract liability on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively.

In assessing the Takeda Collaboration Agreement, management is required to exercise considerable judgment in estimating revenue to be recognized. Management applies judgment in determining the separate performance obligations in the research period, estimating variable consideration, and estimating total future costs when using the input method. There is some increase in the judgment required in estimating the timing of future costs due to the COVID-19 pandemic. This is because it is challenging to predict the duration and extent of the impact of the COVID-19 pandemic on the third-party service providers assisting with the Company's ATV:Tau, ATV:TREM2 and PTV:PGRN programs. This may impact the split between current and non-current contract liability on the Condensed Consolidated Balance Sheet in the future.

Through June 30, 2020, Denali has received $15.0 million in preclinical milestone payments from Takeda and has not recorded any product sales under the Takeda Collaboration Agreement.

Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2020		2019		2020		2019
Takeda Collaboration Agreement⁽¹⁾	$	5,537	$	740	$	8,555	$	1,422
Sanofi Collaboration Agreement


Alzheimer's Disease Services⁽¹⁾	36		99		88		193
Retained Activities	274		3,358		808		6,787
Total Sanofi Collaboration Revenue	310		3,457		896		6,980
Total Collaboration Revenue	$	5,847	$	4,197	$	9,451	$	8,402

_________________________________________________

(1)Amounts represent revenue recognized during the period that was included in the contract liability balance at the beginning of the period.

Cash and Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2020

Cash and Cash Equivalents [Abstract]

Schedule of Cash and Cash Equivalents

A reconciliation of cash, cash equivalents, and restricted cash reported within the Condensed Consolidated Balance Sheets to the amount reported within the Condensed Consolidated Statements of Cash Flows is shown in the table below (in thousands):


	June 30,			December 31,			June 30,			December 31,
			2020			2019			2019			2018
Cash and cash equivalents	$	137,184		$	79,449		$	62,936		$	77,123
Restricted cash included within other non-current assets	1,500			1,500			1,500			1,500
Total cash, cash equivalents, and restricted cash	$	138,684		$	80,949		$	64,436		$	78,623

Schedule of Restricted Cash and Cash Equivalents


	June 30,			December 31,			June 30,			December 31,
			2020			2019			2019			2018
Cash and cash equivalents	$	137,184		$	79,449		$	62,936		$	77,123
Restricted cash included within other non-current assets	1,500			1,500			1,500			1,500
Total cash, cash equivalents, and restricted cash	$	138,684		$	80,949		$	64,436		$	78,623

Summary of Available for Sale Securities

The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	June 30, 2020
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries⁽¹⁾	$	332,659	$	553	$	—	$	333,212

Corporate debt securities	49,458		303		—		49,761
Commercial paper	29,424		—		—		29,424
Total short-term marketable securities	411,541		856		—		412,397
Long-term marketable securities:

Corporate debt securities	7,127		102		—		7,229
Total long-term marketable securities	7,127		102		—		7,229
Total	$	418,668	$	958	$	—	$	419,626

__________________________________________________

(1)Immaterial unrealized holding losses on 4 securities.


	December 31, 2019
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries⁽¹⁾	$	249,478	$	594	$	(2)	$	250,070
U.S. government agency securities	1,999		1		—		2,000
Corporate debt securities⁽²⁾	53,396		94		(11)		53,479
Commercial paper	30,358		—		—		30,358
Total short-term marketable securities	335,231		689		(13)		335,907
Long-term marketable securities:
U.S. government treasuries⁽³⁾	13,865		6		(2)		13,869

Corporate debt securities⁽⁴⁾	25,998		34		(15)		26,017
Total long-term marketable securities	39,863		40		(17)		39,886
Total	$	375,094	$	729	$	(30)	$	375,793

__________________________________________________

(1)Unrealized holding losses on 2 securities with an aggregate fair value of $9.3 million.

(2)Unrealized holding losses on 4 securities with an aggregate fair value of $25.9 million.

(3)Unrealized holding losses on 1 security with an aggregate fair value of $10.1 million.

(4)Unrealized holding losses on 3 securities with an aggregate fair value of $17.2 million.

License Agreements	6 Months Ended
License Agreements	Jun. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
License Agreements	License Agreements Genentech In June 2016, the Company entered into an Exclusive License Agreement with Genentech, Inc. (“Genentech”). The agreement gives the Company access to Genentech’s leucine-rich repeat kinase 2 (“LRRK2”) inhibitor small molecule program for Parkinson’s disease. Under the agreement, Genentech granted the Company (i) an exclusive, worldwide, sublicensable license under Genentech’s rights to certain patents and patent applications directed to small molecule compounds which bind to and inhibit LRRK2 and (ii) a non-exclusive, worldwide, sublicensable license to certain related know-how, in each case, to develop and commercialize certain compounds and licensed products incorporating any such compound. The Company may owe Genentech milestone payments upon the achievement of certain development, regulatory, and commercial milestones, up to a maximum of $315.0 million in the aggregate. These milestones include up to $37.5 million in clinical milestone payments, $102.5 million in regulatory milestone payments and $175.0 million in commercial milestone payments. In addition, the Company may owe royalties on net sales of licensed products ranging from low to high single-digit percentages. To date, the Company has paid Genentech $12.5 million in the aggregate, including an upfront fee, a technology transfer fee and a clinical milestone payment, all of which was recorded as research and development expense as incurred. No amounts were recorded in the three and six months ended June 30, 2020 or 2019.

Commitments and Contingencies - Narrative (Details) $ in Millions		3 Months Ended		6 Months Ended
	May 02, 2018 USD ($) ft²	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)	Oct. 31, 2018 ft²
Loss Contingencies [Line Items]
Discount rate (as a percentage)		9.00%		9.00%
Operating lease costs		$ 2.9	$ 2.5	$ 5.5	$ 4.8
Weighted average remaining lease term		8 years 9 months 18 days		8 years 9 months 18 days
Weighted-average discount rate (as a percentage)		9.00%		9.00%
Cash paid for lease liabilities				$ 4.7	1.9
Sublease income		$ 1.0	0.8	1.9	0.8
DMSA
Loss Contingencies [Line Items]
Purchase order executed		18.0		18.0		$ 21.2
Non-refundable purchase commitments		12.1		12.1		$ 11.2
Costs incurred		3.8	3.1	4.8	6.7
Payments for development and manufacturing services		$ 2.0	$ 3.9	$ 5.2	$ 6.5
Maximum
Loss Contingencies [Line Items]
Leasehold improvements	$ 25.9
Headquarters Lease
Loss Contingencies [Line Items]
New premises, area under lease \| ft²	148,020
Lease period	10 years
Lease renewal option term	10 years
Headquarters Lease \| Landlord Funded Tenant Improvements
Loss Contingencies [Line Items]
Tenant improvement allowance repayable in rent	$ 4.4
Headquarters Lease \| Minimum
Loss Contingencies [Line Items]
Lease renewal notice period	9 months
Headquarters Lease \| Maximum
Loss Contingencies [Line Items]
Lease renewal notice period	12 months
New Premises Sublease Agreement
Loss Contingencies [Line Items]
Rentable square feet \| ft²							36,835
Sublease term							5 years

Collaboration Agreements - Sanofi (Details) $ in Thousands	1 Months Ended		3 Months Ended		6 Months Ended		21 Months Ended
Collaboration Agreements - Sanofi (Details) $ in Thousands	Jul. 31, 2019 USD ($)	Nov. 30, 2018 USD ($) indication	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Dec. 31, 2019 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Number of indications \| indication		3
Sales			$ 5,811	$ 4,098	$ 9,363	$ 8,209
Collaborative Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Funded percentage		30.00%
Sanofi \| Collaborative Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Funded percentage		70.00%
Sanofi \| Collaborative Arrangement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront payment		$ 125,000
Milestone payments upon achievement of certain clinical, regulatory and sales milestone events		1,100,000
Increase in transaction price							$ 23,500
Receivable			300		300		300	$ 1,200
Sanofi \| Collaborative Arrangement \| CNS Product
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Clinical milestone payment		215,000
Regulatory milestone payment		385,000
Sanofi \| Collaborative Arrangement \| Peripheral Product
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Clinical milestone payment		120,000
Regulatory milestone payment		175,000
Commercial milestone payments		$ 200,000
Sanofi \| Collaborative Arrangement \| Retained Activities
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Increase in transaction price			$ 300	$ 3,400	$ 800	$ 6,800	13,500
Sanofi \| Collaborative Arrangement \| Milestone Triggered
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales	$ 10,000						10,000
Sanofi \| Collaborative Arrangement \| Product
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales							$ 0

Commitments and Contingencies - Summary of Company's Future Minimum Lease Receivables (Details) $ in Thousands	Jun. 30, 2020 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2020 (six months)	$ 1,431
2021	2,925
2022	3,009
2023	3,096
2024	876
Thereafter	0
Total undiscounted sublease receipts	$ 11,337

Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2020	Aug. 03, 2020
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 2020
Document Transition Report	false
Entity File Number	001-38311
Entity Registrant Name	Denali Therapeutics Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	46-3872213
Entity Address, Address Line One	161 Oyster Point Blvd
Entity Address, City or Town	South San Francisco
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94080
City Area Code	650
Local Phone Number	866-8548
Title of 12(b) Security	Common Stock, par value $0.01 per share
Trading Symbol	DNLI
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 Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding (shares)		105,983,125
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Central Index Key	0001714899
Current Fiscal Year End Date	--12-31

Cash and Marketable Securities - Narrative (Details) - USD ($)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Dec. 31, 2019
Cash and Cash Equivalents [Abstract]
Allowance for credit losses	$ 0		$ 0
Other-than-temporary impairment					$ 0
Unrealized gain on marketable securities	0
Tax benefit (provision)	$ (79,000)	$ 313,000	56,000	$ 313,000
Tax charge in other comprehensive income		$ 300,000	$ 100,000	$ 300,000
Effective maturity (less than)	2 years		2 years

- Definition

Amount of current income tax expense (benefit) and deferred income tax expense (benefit) pertaining to continuing operations.

+ References + Details

Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2020

Fair Value Disclosures [Abstract]

Assets and Liabilities Measured at Fair Value

Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands):


	June 30, 2020
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	111,201	$	—	$	—	$	111,201


Short-term marketable securities:
U.S. government treasuries	333,212		—		—		333,212

Corporate debt securities	—		49,761		—		49,761
Commercial paper	—		29,424		—		29,424
Long-term marketable securities:


Corporate debt securities	—		7,229		—		7,229

Total	$	444,413	$	86,414	$	—	$	530,827
Liabilities:
Foreign currency derivative contracts	$	—	$	108	$	—	$	108
Total	$	—	$	108	$	—	$	108


	December 31, 2019
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	54,163	$	—	$	—	$	54,163
U.S. government treasuries	15,989		—		—		15,989
Short-term marketable securities:
U.S. government treasuries	250,070		—		—		250,070
U.S. government agency securities	—		2,000		—		2,000
Corporate debt securities	—		53,479		—		53,479
Commercial paper	—		30,358		—		30,358
Long-term marketable securities:
U.S. government treasuries	13,869		—		—		13,869
Corporate debt securities	—		26,017		—		26,017
Foreign currency derivative contracts	—		85		—		85
Total	$	334,091	$	111,939	$	—	$	446,030
Liabilities:
Foreign currency derivative contracts	$	—	$	8	$	—	$	8
Total	$	—	$	8	$	—	$	8

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2020	Dec. 31, 2019
Statement of Financial Position [Abstract]
Convertible preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Convertible preferred stock, shares authorized (in shares)	40,000,000	40,000,000
Convertible preferred stock, shares issued (in shares)	0	0
Convertible preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized (in shares)	400,000,000	400,000,000
Common stock, shares issued (in shares)	105,897,872	96,189,935
Common stock, shares outstanding (in shares)	105,897,872	96,189,935

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019
Operating activities
Net loss	$ (115,521)	$ (97,329)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,254	4,046
Stock–based compensation expense	23,269	20,588
Net amortization of discounts on marketable securities	(1,025)	(2,734)
Non-cash adjustment to operating lease expense	(978)	1,740
Other non-cash items	(39)	(313)
Changes in operating assets and liabilities:
Prepaid expenses and other assets	3,794	2,704
Accounts payable	(744)	1,303
Accruals and other current liabilities	(2,215)	(1,887)
Contract liabilities	(8,644)	(1,616)
Net cash used in operating activities	(97,849)	(73,498)
Investing activities
Purchases of marketable securities	(323,607)	(144,029)
Purchases of property and equipment	(1,194)	(12,299)
Maturities and sales of marketable securities	281,057	212,162
Net cash provided by (used in) investing activities	(43,744)	55,834
Financing activities
Proceeds from public offering of common stock, net of issuance costs	193,948	0
Proceeds from exercise of awards under equity incentive plans	5,380	3,477
Net cash provided by financing activities	199,328	3,477
Net increase (decrease) in cash, cash equivalents and restricted cash	57,735	(14,187)
Cash, cash equivalents and restricted cash at beginning of period	80,949	78,623
Cash, cash equivalents and restricted cash at end of period	138,684	64,436
Supplemental disclosures of cash flow information
Tenant improvements provided by the landlord	0	11,341
Property and equipment purchases accrued but not yet paid	$ 2	$ 2,162

License Agreements - Narrative (Details) - Genentech Inc - USD ($)	1 Months Ended	3 Months Ended		6 Months Ended		49 Months Ended
	Jun. 30, 2016	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020
License Agreement \| Research and Development
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront fee paid		$ 0	$ 0	$ 0	$ 0	$ 12,500,000
Clinical
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments upon achievement of specified clinical and regulatory milestones	$ 37,500,000
Regulatory
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments upon achievement of specified clinical and regulatory milestones	102,500,000
Commercial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments upon achievement of specified clinical and regulatory milestones	175,000,000.0
Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments upon achievement of specified clinical and regulatory milestones	$ 315,000,000.0

Stock-Based Awards (Tables)

6 Months Ended

Jun. 30, 2020

Share-based Payment Arrangement [Abstract]

Summary of Stock Option Activity

The following table summarizes option award activity under the Company's 2017 Equity Incentive Plan and the 2015 Stock Incentive Plan:


	Number of Options	Weighted- Average Exercise Price
Balance at December 31, 2019	11,640,734	$	12.96
Granted	3,244,298	24.78
Exercised	(461,968)	7.67
Forfeited	(232,093)	19.08
Balance at June 30, 2020	14,190,971	$	15.74
Vested and expected to vest at June 30, 2020	12,446,239	$	17.85
Exercisable at June 30, 2020	5,318,846	$	13.52

Summary of Assumptions Used for Estimating the Fair Value of Stock Granted

The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions:


	Six Months Ended June 30,
	2020	2019
Expected term (in years)	5.50 - 6.08	5.50 - 6.08
Volatility	65.2% - 67.1%	66.9% - 77.8%
Risk-free interest rate	0.4% - 1.7%	2.0% - 2.6%
Dividend yield	—	—

Restricted Stock Activity

Aggregated information regarding restricted stock for the six months ended June 30, 2020 is summarized below:


	Share Awards & Units	Weighted-Average Fair Value at Date of Grant per Share
Unvested at December 31, 2019	882,636	$	18.67
Granted	957,249	24.62
Vested and released	(118,421)	19.13
Forfeited	(48,412)	21.52
Unvested at June 30, 2020	1,673,052	$	21.98
Expected to vest at June 30, 2020	1,673,052	$	21.98

Summary of Stock-Based Compensation Expense

The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2020		2019		2020		2019
Research and development	$	7,146	$	5,295	$	13,200	$	9,277
General and administrative	5,338		8,419		10,069		11,311
Total	$	12,484	$	13,714	$	23,269	$	20,588

Acquisition - Narrative (Details) - USD ($)			1 Months Ended		3 Months Ended		6 Months Ended		22 Months Ended	47 Months Ended
Acquisition - Narrative (Details) - USD ($)	May 30, 2018	Aug. 24, 2016	Jun. 30, 2019	Aug. 31, 2016	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019	May 31, 2018	Jun. 30, 2020
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and development					$ 53,152,000	$ 51,884,000	$ 104,168,000	$ 89,287,000
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Amount paid									$ 11,500,000
Upfront option fee				$ 500,000
Contingent consideration payment			$ 1,500,000
Contingent consideration recognized	$ 0				0	1,500,000	0	1,500,000
Research and development					$ 300,000	$ 300,000	$ 600,000	$ 500,000		$ 19,800,000
Maximum development plan period for research costs		24 months
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Initial option exercise payments		$ 17,800,000
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option \| Preclinical
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Contingent payments upon the achievement of milestones	27,000,000.0
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option \| Clinical
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Contingent payments upon the achievement of milestones	50,000,000.0
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option \| Regulatory
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Contingent payments upon the achievement of milestones	120,000,000.0
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option \| Commercial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Contingent payments upon the achievement of milestones	250,000,000.0
Collaborative Arrangement with F-Star and Acquisition of F-Star Gamma \| Exercise of buy-out option \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Contingent payments upon the achievement of milestones	$ 447,000,000.0

Net Loss Per Share

6 Months Ended

Jun. 30, 2020

Earnings Per Share [Abstract]

Net Loss Per Share

Since the Company was in a loss position for all periods presented, basic net loss per share is the same as diluted net loss per share for all periods as the inclusion of all potential shares of common stock outstanding would have been anti-dilutive.

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three and Six Months Ended June 30,
	2020	2019
Options issued and outstanding and ESPP shares issuable	14,351,795	12,214,029
Restricted shares subject to future vesting	1,673,052	610,003
Early exercised common stock subject to future vesting	—	41,672
Total	16,024,847	12,865,704

Net Loss Per Share (Tables)

6 Months Ended

Jun. 30, 2020

Earnings Per Share [Abstract]

Schedule of Dilutive Securities Not Included in Diluted Per Share Calculations

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three and Six Months Ended June 30,
	2020	2019
Options issued and outstanding and ESPP shares issuable	14,351,795	12,214,029
Restricted shares subject to future vesting	1,673,052	610,003
Early exercised common stock subject to future vesting	—	41,672
Total	16,024,847	12,865,704

Stock-Based Awards

6 Months Ended

Jun. 30, 2020

Share-based Payment Arrangement [Abstract]

Stock-Based Awards

The Company has issued stock-based awards from various equity incentive and stock purchase plans, as more fully described in Note 11, Stock-Based Awards to the consolidated financial statements in the Company's 2019 Annual Report on Form 10-K.

Stock Option Activity

The following table summarizes option award activity under the Company's 2017 Equity Incentive Plan and the 2015 Stock Incentive Plan:


	Number of Options	Weighted- Average Exercise Price
Balance at December 31, 2019	11,640,734	$	12.96
Granted	3,244,298	24.78
Exercised	(461,968)	7.67
Forfeited	(232,093)	19.08
Balance at June 30, 2020	14,190,971	$	15.74
Vested and expected to vest at June 30, 2020	12,446,239	$	17.85
Exercisable at June 30, 2020	5,318,846	$	13.52

The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions:


	Six Months Ended June 30,
	2020	2019
Expected term (in years)	5.50 - 6.08	5.50 - 6.08
Volatility	65.2% - 67.1%	66.9% - 77.8%
Risk-free interest rate	0.4% - 1.7%	2.0% - 2.6%
Dividend yield	—	—

Restricted Stock Activity

Aggregated information regarding restricted stock for the six months ended June 30, 2020 is summarized below:


	Share Awards & Units	Weighted-Average Fair Value at Date of Grant per Share
Unvested at December 31, 2019	882,636	$	18.67
Granted	957,249	24.62
Vested and released	(118,421)	19.13
Forfeited	(48,412)	21.52
Unvested at June 30, 2020	1,673,052	$	21.98
Expected to vest at June 30, 2020	1,673,052	$	21.98

Stock-Based Compensation Expense

The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2020		2019		2020		2019
Research and development	$	7,146	$	5,295	$	13,200	$	9,277
General and administrative	5,338		8,419		10,069		11,311
Total	$	12,484	$	13,714	$	23,269	$	20,588

Derivative Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2020

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Summary of Forward Foreign Currency Exchange Purchase Contracts Outstanding

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of June 30, 2020 and December 31, 2019, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional⁽¹⁾Amount in Foreign Currency	Maturity
Euros	26	3,535	July 2020 - May 2021
British Pounds	19	2,868	July 2020 - May 2021
Swiss Francs	2	21	July 2020 - Aug 2020
Total at June 30, 2020	47
Euros	23	1,500	Jan 2020 - Nov 2020
British Pounds	15	2,285	Jan 2020 - Jun 2020
Swiss Francs	10	129	Jan 2020 - Aug 2020
Total at December 31, 2019	48

_________________________________________________

⁽¹⁾The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

- Definition

Tabular disclosure of pertinent information about a derivative or group of derivatives on a disaggregated basis, such as for individual instruments, or small groups of similar instruments. May include a combination of the type of instrument, risks being hedged, notional amount, hedge designation, related hedged item, inception date, maturity date, or other relevant item.

+ References

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+ Details

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Collaboration revenue:
Collaboration revenue from customers	$ 5,811	$ 4,098	$ 9,363	$ 8,209
Other collaboration revenue	36	99	88	193
Total collaboration revenue	5,847	4,197	9,451	8,402
Operating expenses:
Research and development	53,152	51,884	104,168	89,287
General and administrative	13,972	15,076	26,527	24,386
Total operating expenses	67,124	66,960	130,695	113,673
Loss from operations	(61,277)	(62,763)	(121,244)	(105,271)
Interest and other income, net	2,598	4,113	5,667	7,629
Loss before income taxes	(58,679)	(58,650)	(115,577)	(97,642)
Income tax benefit (provision)	(79)	313	56	313
Net loss	(58,758)	(58,337)	(115,521)	(97,329)
Other comprehensive income (loss):
Net unrealized gain (loss) on marketable securities, net of tax	(284)	547	201	1,528
Comprehensive loss	$ (59,042)	$ (57,790)	$ (115,320)	$ (95,801)
Net loss per share, basic and diluted (usd per share)	$ (0.56)	$ (0.61)	$ (1.11)	$ (1.02)
Weighted average number of shares outstanding, basic and diluted (in shares)	105,717,912	95,495,497	104,068,815	95,241,412

Significant Accounting Policies (Policies)	6 Months Ended
Significant Accounting Policies (Policies)	Jun. 30, 2020
Accounting Policies [Abstract]
Organization and Description of Business	Organization and Description of Business Denali Therapeutics Inc. ("Denali" or the “Company”) is a biopharmaceutical company, incorporated in Delaware, that discovers and develops therapeutics to defeat neurodegenerative diseases. The Company is headquartered in South San Francisco, California.
Basis of Presentation	Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and the instructions to Form 10-Q and Article 10 of SEC Regulation S-X for interim financial information. These unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and notes thereto contained in the Annual Report on Form 10-K for the year ended December 31, 2019, as filed with the Securities and Exchange Commission on February 27, 2020 (the "2019 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2019 was derived from the audited annual consolidated financial statements as of the period then ended. Certain information and footnote disclosures typically included in the Company's annual consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements reflect all adjustments that, in the opinion of management, are necessary for a fair statement of the results of the interim periods presented. All such adjustments are of a normal recurring nature except for the impacts of adopting new accounting standards discussed below. These interim financial results are not necessarily indicative of results expected for the full fiscal year or for any subsequent interim period.
Principles of Consolidation	Principles of Consolidation These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiary, the functional currency has been determined to be U.S. dollars. Monetary assets and liabilities denominated in foreign currency are remeasured at period-end exchange rates. Non-monetary assets and liabilities denominated in foreign currencies are remeasured at historical rates. Foreign currency transaction gains and losses resulting from remeasurement are recognized in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent liabilities at the date of the condensed consolidated financial statements, as well as the reported amounts of expenses during the reporting period. Actual results could differ from those estimates, and such differences could be material to the Condensed Consolidated Balance Sheets and Statements of Operations and Comprehensive Loss.
Concentration of Credit Risk and Other Risks and Uncertainties	Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash, cash equivalents, marketable securities and forward foreign currency exchange contracts. Substantially all of the Company’s cash and cash equivalents are deposited in accounts with financial institutions that management believes are of high credit quality. Such deposits have and will continue to exceed federally insured limits. The Company maintains its cash with accredited financial institutions and accordingly, such funds are subject to minimal credit risk. The Company’s investment policy limits investments to certain types of securities issued by the U.S. government, its agencies and institutions with investment-grade credit ratings and places restrictions on maturities and concentration by type and issuer. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash, cash equivalents and marketable securities and issuers of marketable securities to the extent recorded on the Condensed Consolidated Balance Sheets. As of June 30, 2020 and December 31, 2019, the Company had no off-balance sheet concentrations of credit risk. The Company is exposed to counterparty credit risk on all of its derivative financial instruments. The Company has established and maintains strict counterparty credit guidelines and enters into hedges only with financial institutions that are investment grade or better to minimize the Company’s exposure to potential defaults. The Company does not require collateral to be pledged under these agreements. The Company is subject to a number of risks similar to other early-stage biopharmaceutical companies, including, but not limited to, the need to obtain adequate additional funding, possible failure of current or future preclinical testing or clinical trials, its reliance on third parties to conduct its clinical trials, the need to obtain regulatory and marketing approvals for its product candidates, competitors developing new technological innovations, the need to successfully commercialize and gain market acceptance of the Company’s product candidates, its right to develop and commercialize its product candidates pursuant to the terms and conditions of the licenses granted to the Company, protection of proprietary technology, the ability to make milestone, royalty or other payments due under any license or collaboration agreements, and the need to secure and maintain adequate manufacturing arrangements with third parties. If the Company does not successfully commercialize or partner any of its product candidates, it will be unable to generate product revenue or achieve profitability. The COVID-19 pandemic has caused increased risk and uncertainty for the Company. Credit risk associated with investments in securities may increase if any institution with which the Company has an investment is significantly impacted by the COVID-19 pandemic. As of June 30, 2020, the Company has not realized any losses on its cash deposits or investments. Further, COVID-19 may impact the timelines and progress of the Company's preclinical activities and clinical trials, and may impact its ability to raise capital in the near term.
Segments	Segments The Company has one operating segment. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources.
Cash, Cash Equivalents and Restricted Cash	Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of 90 days or less at the date of purchase to be cash and cash equivalents. Cash equivalents are reported at fair value. The Company’s restricted cash consists of the letter of credit for the Company’s headquarters building lease, and is included within other non-current assets on the accompanying Condensed Consolidated Balance Sheets.
Marketable Securities	Marketable Securities The Company generally invests its excess cash in money market funds and investment grade short to intermediate-term fixed income securities. Such investments are included in cash and cash equivalents, short-term marketable securities, or long-term marketable securities on the Condensed Consolidated Balance Sheets, are considered available-for-sale, and reported at fair value with net unrealized gains and losses included as a component of stockholders’ equity. The Company classifies investments in securities with remaining maturities of less than one year, or where its intent is to use the investments to fund current operations or to make them available for current operations, as short-term investments. The Company classifies investments in securities with remaining maturities of over one year as long-term investments. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Realized gains and losses and declines in value determined to be due to credit losses on marketable securities, if any, are included in interest and other income, net. The Company periodically evaluates the need for an allowance for credit losses. This evaluation consists of several qualitative and quantitative factors, including whether it has plans to sell the security, whether it is more likely than not it will be required to sell any marketable securities before recovery of its amortized cost basis, and if the entity has the ability and intent to hold the security to maturity, and the portion of any unrealized loss that is the result of a credit loss. Factors considered in making these evaluations include quoted market prices, recent financial results and operating trends, implied values from any recent transactions or offers of investee securities, credit quality of debt instrument issuers, expected cash flows from securities, other publicly available information that may affect the value of the marketable security, duration and severity of the decline in value, and the Company's strategy and intentions for holding the marketable security.
Accounts Receivable	Accounts ReceivableAccounts receivable are included within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets. The accounts receivable balance represents amounts receivable from the Company's collaboration partners, net of an allowance for credit losses, if required.
Derivatives and Hedging Activities	Derivatives and Hedging ActivitiesThe Company measures its derivative instruments at fair value, and accounts for them as either assets or liabilities included within prepaid assets and other current assets and other accruals and current liabilities, respectively, on the Condensed Consolidated Balance Sheets. Derivatives are adjusted to fair value through interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss.
Leases	Leases The Company adopted Accounting Standards Update ("ASU") No. 2016-02, Leases as of January 1, 2019. A determination is made as to whether an arrangement is a lease at inception. A right-of-use (“ROU”) asset and operating lease liability is recognized for identified operating leases in the Condensed Consolidated Balance Sheets. The changes in operating lease ROU assets and operating lease liabilities are presented net within non-cash adjustment to operating lease expense in the Condensed Consolidated Statements of Cash Flows. ROU assets represent the Company’s right to use the underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments due over the lease term, with the ROU assets adjusted for lease incentives received. When determining the present value of lease payments, the Company uses its incremental borrowing rate on the date of lease commencement, or the rate implicit in the lease, if known. The Company does not assume renewals in its determination of the lease term unless the renewals are deemed by management to be reasonably certain at lease inception. Leases with an initial term of 12 months or less are not recorded on the balance sheet, unless they include an option to purchase the underlying asset that the Company is reasonably certain to exercise. The Company recognizes lease expenses on a straight-line basis over the lease term. The Company has leases with lease and non-lease components, which the Company has elected to account for as a single lease component.
Revenue Recognition	Revenue Recognition License and Collaboration Revenue The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC 808, Collaborative Arrangements (“ASC 808”) to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For collaboration arrangements within the scope of ASC 808 that contain multiple elements, the Company first determines which elements of the collaboration are deemed to be within the scope of ASC 808 and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of Topic 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808, an appropriate recognition method is determined and applied consistently, generally by analogy to Topic 606. The accounting treatment pursuant to Topic 606 is outlined below. The terms of licensing and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license fees; development, regulatory and commercial milestone payments; payments for manufacturing supply and research and development services; and royalties on net sales of licensed products. Each of these payments results in license, collaboration and other revenue, except for revenues from royalties on net sales of licensed products, which are classified as royalty revenue. The core principle of Topic 606 is to recognize revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received in exchange for those goods or services. In determining the appropriate amount of revenue to be recognized as the Company fulfills its obligations under each of its agreements, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. Amounts received prior to satisfying the revenue recognition criteria are recorded as contract liabilities in the Company’s Condensed Consolidated Balance Sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to the Company having an unconditional right (other than a right that is conditioned only on the passage of time) to receipt are recorded as contract assets in the Company's Condensed Consolidated Balance Sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer. At contract inception, the Company assesses the goods or services promised in a contract with a customer and identifies those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the performance obligation does not provide the customer with a material right. The Company considers the terms of the contract to determine the transaction price. The transaction price is the amount of consideration to which the Company expects to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling prices ("SSP"). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, the Company uses its best estimate of the SSP for the deliverable. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset, which for a service is considered to be as the services are received and used. The Company recognizes revenue over time by measuring the progress toward complete satisfaction of the relevant performance obligation using an appropriate input or output method based on the nature of the service promised to the customer. After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the transaction price is allocated to the performance obligations on the same basis as at contract inception. Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the SSP of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations.
Comprehensive Income (Loss)	Comprehensive Income (Loss) Comprehensive income (loss) is composed of net loss and certain changes in stockholders’ equity that are excluded from net loss, primarily unrealized gains or losses on the Company’s marketable securities.
Net Loss per Share	Net Loss per Share Basic net loss per share is calculated by dividing the net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive given the net loss for each period presented.
Recently Issued and Recently Adopted Accounting Pronouncements	Recently Issued Accounting Pronouncement In December 2019, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2019-12, Income Taxes (Topic 740) Simplifying the Accounting for Income Taxes. ASU No. 2019-12 modifies ASC 740 to simplify several aspects of accounting for income taxes, including eliminating certain exceptions to the guidance in ASC 740 related to the approach for intraperiod tax allocation. The guidance is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years, with early adoption permitted, and is required to be adopted prospectively, with the exception of certain specific amendments. The Company is currently assessing the impact of this ASU on its Condensed Consolidated Financial Statements. Recently Adopted Accounting Pronouncement In June 2016, the FASB issued Accounting Standards Update No. 2016-13, Financial Instruments-Credit Losses: Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires measurement and recognition of expected credit losses for financial assets. In April 2019, the FASB issued clarification to ASU 2016-13 within ASU 2019-04, Codification Improvements to Topic 326, Financial Instruments-Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments. The Company adopted this standard as of January 1, 2020 using a modified retrospective approach. Adoption of the standard did not have a material impact on the Condensed Consolidated Financial Statements.

Fair Value Measurements - Schedule of Assets and Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019
Assets:
Aggregate Fair Value	$ 419,626	$ 375,793
Foreign currency derivative contracts		85
Total	530,827	446,030
Liabilities:
Foreign currency derivative contracts	108	8
Total	108	8
Money market funds
Assets:
Cash equivalents	111,201	54,163
U.S. government treasuries
Assets:
Cash equivalents		15,989
Short-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value	333,212	250,070
Short-term marketable securities: \| U.S. government agency securities
Assets:
Aggregate Fair Value		2,000
Short-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	49,761	53,479
Short-term marketable securities: \| Commercial paper
Assets:
Aggregate Fair Value	29,424	30,358
Long-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value		13,869
Long-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	7,229	26,017
Level 1
Assets:
Foreign currency derivative contracts		0
Total	444,413	334,091
Liabilities:
Foreign currency derivative contracts	0	0
Total	0	0
Level 1 \| Money market funds
Assets:
Cash equivalents	111,201	54,163
Level 1 \| U.S. government treasuries
Assets:
Cash equivalents		15,989
Level 1 \| Short-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value	333,212	250,070
Level 1 \| Short-term marketable securities: \| U.S. government agency securities
Assets:
Aggregate Fair Value		0
Level 1 \| Short-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	0	0
Level 1 \| Short-term marketable securities: \| Commercial paper
Assets:
Aggregate Fair Value	0	0
Level 1 \| Long-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value		13,869
Level 1 \| Long-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	0	0
Level 2
Assets:
Foreign currency derivative contracts		85
Total	86,414	111,939
Liabilities:
Foreign currency derivative contracts	108	8
Total	108	8
Level 2 \| Money market funds
Assets:
Cash equivalents	0	0
Level 2 \| U.S. government treasuries
Assets:
Cash equivalents		0
Level 2 \| Short-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value	0	0
Level 2 \| Short-term marketable securities: \| U.S. government agency securities
Assets:
Aggregate Fair Value		2,000
Level 2 \| Short-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	49,761	53,479
Level 2 \| Short-term marketable securities: \| Commercial paper
Assets:
Aggregate Fair Value	29,424	30,358
Level 2 \| Long-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value		0
Level 2 \| Long-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	7,229	26,017
Level 3
Assets:
Foreign currency derivative contracts		0
Total	0	0
Liabilities:
Foreign currency derivative contracts	0	0
Total	0	0
Level 3 \| Money market funds
Assets:
Cash equivalents	0	0
Level 3 \| U.S. government treasuries
Assets:
Cash equivalents		0
Level 3 \| Short-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value	0	0
Level 3 \| Short-term marketable securities: \| U.S. government agency securities
Assets:
Aggregate Fair Value		0
Level 3 \| Short-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	0	0
Level 3 \| Short-term marketable securities: \| Commercial paper
Assets:
Aggregate Fair Value	0	0
Level 3 \| Long-term marketable securities: \| U.S. government treasuries
Assets:
Aggregate Fair Value		0
Level 3 \| Long-term marketable securities: \| Corporate debt securities
Assets:
Aggregate Fair Value	$ 0	$ 0

Fair Value Measurements

6 Months Ended

Jun. 30, 2020

Fair Value Disclosures [Abstract]

Fair Value Measurements

Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands):


	June 30, 2020
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	111,201	$	—	$	—	$	111,201


Short-term marketable securities:
U.S. government treasuries	333,212		—		—		333,212

Corporate debt securities	—		49,761		—		49,761
Commercial paper	—		29,424		—		29,424
Long-term marketable securities:


Corporate debt securities	—		7,229		—		7,229

Total	$	444,413	$	86,414	$	—	$	530,827
Liabilities:
Foreign currency derivative contracts	$	—	$	108	$	—	$	108
Total	$	—	$	108	$	—	$	108


	December 31, 2019
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	54,163	$	—	$	—	$	54,163
U.S. government treasuries	15,989		—		—		15,989
Short-term marketable securities:
U.S. government treasuries	250,070		—		—		250,070
U.S. government agency securities	—		2,000		—		2,000
Corporate debt securities	—		53,479		—		53,479
Commercial paper	—		30,358		—		30,358
Long-term marketable securities:
U.S. government treasuries	13,869		—		—		13,869
Corporate debt securities	—		26,017		—		26,017
Foreign currency derivative contracts	—		85		—		85
Total	$	334,091	$	111,939	$	—	$	446,030
Liabilities:
Foreign currency derivative contracts	$	—	$	8	$	—	$	8
Total	$	—	$	8	$	—	$	8

The carrying amounts of prepaid expenses and other current assets, accounts payable and accrued liabilities approximate their fair values due to their short-term maturities.

The Company’s Level 2 securities are valued using third-party pricing sources. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly.

There were no transfers of assets or liabilities between the fair value measurement levels during the three and six months ended June 30, 2020 or 2019.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Derivative Financial Instruments

6 Months Ended

Jun. 30, 2020

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Derivative Financial Instruments

Foreign Currency Exchange Rate Exposure

The Company uses forward foreign currency exchange contracts to hedge certain operational exposures resulting from potential changes in foreign currency exchange rates. Such exposures result from portions of the Company’s forecasted cash flows being denominated in currencies other than the U.S. dollar, primarily the Euro and British Pound. The derivative instruments the Company uses to hedge this exposure are not designated as cash flow hedges, and as a result, changes in their fair value are recorded in interest and other income, net, on the Company's Condensed Consolidated Statements of Operations and Comprehensive Loss.

The fair values of forward foreign currency exchange contracts are estimated using current exchange rates and interest rates and take into consideration the current creditworthiness of the counterparties. Information regarding the specific instruments used by the Company to hedge its exposure to foreign currency exchange rate fluctuations is provided below.

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of June 30, 2020 and December 31, 2019, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional⁽¹⁾Amount in Foreign Currency	Maturity
Euros	26	3,535	July 2020 - May 2021
British Pounds	19	2,868	July 2020 - May 2021
Swiss Francs	2	21	July 2020 - Aug 2020
Total at June 30, 2020	47
Euros	23	1,500	Jan 2020 - Nov 2020
British Pounds	15	2,285	Jan 2020 - Jun 2020
Swiss Francs	10	129	Jan 2020 - Aug 2020
Total at December 31, 2019	48

_________________________________________________

⁽¹⁾The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

Stock-Based Awards - Summary of Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	$ 12,484	$ 13,714	$ 23,269	$ 20,588
Research and Development
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	7,146	5,295	13,200	9,277
General and Administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	$ 5,338	$ 8,419	$ 10,069	$ 11,311

Cash and Marketable Securities - Schedule of Restricted Cash and Cash Equivalents (Details) - USD ($) $ in Thousands	Jun. 30, 2020	Dec. 31, 2019	Jun. 30, 2019	Dec. 31, 2018
Cash and Cash Equivalents [Abstract]
Cash and cash equivalents	$ 137,184	$ 79,449	$ 62,936	$ 77,123
Restricted cash included within other non-current assets	1,500	1,500	1,500	1,500
Total cash, cash equivalents, and restricted cash	$ 138,684	$ 80,949	$ 64,436	$ 78,623

Significant Accounting Policies - Narrative (Details)	6 Months Ended
Significant Accounting Policies - Narrative (Details)	Jun. 30, 2020 Segment
Accounting Policies [Abstract]
Number of operating segments	1

Condensed Consolidated Statements of Stockholders' Equity (Parenthetical) $ in Thousands	6 Months Ended
	Jun. 30, 2020 USD ($)
Common Stock
Common stock issuance costs	$ 632

Commitments and Contingencies - Summary of Company's Future Minimum Lease Commitments (Details) $ in Thousands	Jun. 30, 2020 USD ($)
Operating Lease Liabilities, Payments Due [Abstract]
2020 (six months)	$ 5,071
2021	10,391
2022	10,731
2023	11,083
2024	11,447
Thereafter	54,074
Total undiscounted lease payments	102,797
Present value adjustment	(31,855)
Net operating lease liabilities	$ 70,942

Derivative Financial Instruments - Summary of Forward Foreign Currency Exchange Contracts Outstanding (Details) - Designated as Hedging Instrument € in Thousands, £ in Thousands, SFr in Thousands	Jun. 30, 2020 EUR (€) derivative_instrument	Jun. 30, 2020 GBP (£) derivative_instrument	Jun. 30, 2020 CHF (SFr) derivative_instrument	Dec. 31, 2019 EUR (€) derivative_instrument	Dec. 31, 2019 GBP (£) derivative_instrument	Dec. 31, 2019 CHF (SFr) derivative_instrument
Euros
Derivative [Line Items]
Number of Contracts	26	26	26	23	23	23
Aggregate Notional Amount in Foreign Currency \| €	€ 3,535			€ 1,500
British Pounds
Derivative [Line Items]
Number of Contracts	19	19	19	15	15	15
Aggregate Notional Amount in Foreign Currency \| £		£ 2,868			£ 2,285
Swiss Francs
Derivative [Line Items]
Number of Contracts	2	2	2	10	10	10
Aggregate Notional Amount in Foreign Currency \| SFr			SFr 21			SFr 129
Foreign Exchange Contracts
Derivative [Line Items]
Number of Contracts	47	47	47	48	48	48

Stock-Based Awards - Summary of Stock Option Activity (Details)	6 Months Ended
	Jun. 30, 2020 $ / shares shares
Number of Options
Beginning balance (in shares) \| shares	11,640,734
Granted (in shares) \| shares	3,244,298
Exercised (in shares) \| shares	(461,968)
Forfeited (in shares) \| shares	(232,093)
Ending balance (in shares) \| shares	14,190,971
Vested and expected to vest (in shares) \| shares	12,446,239
Exercisable (in shares) \| shares	5,318,846
Weighted- Average Exercise Price
Beginning balance (usd per share) \| $ / shares	$ 12.96
Granted (usd per share) \| $ / shares	24.78
Exercised (usd per share) \| $ / shares	7.67
Forfeited (usd per share) \| $ / shares	19.08
Ending balance (usd per share) \| $ / shares	15.74
Vested and expected to vest (usd per share) \| $ / shares	17.85
Exercisable (usd per share) \| $ / shares	$ 13.52

Collaboration Agreements - Takeda (Details) $ / shares in Units, $ in Thousands		3 Months Ended		6 Months Ended		12 Months Ended	30 Months Ended
	Feb. 23, 2018 USD ($) program targets $ / shares shares	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Jun. 30, 2020 USD ($)	Jun. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)	Jun. 30, 2020 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales		$ 5,811	$ 4,098	$ 9,363	$ 8,209
Collaborative Arrangement \| Takeda Pharmaceutical Company Limited
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront payment	$ 40,000
Number of programs \| program	3
Preclinical milestone payment received	$ 5,000
Number of targets \| targets	3
Target option period	5 years
Option fee	$ 5,000
Number of performance obligations \| program	3
Variable consideration relating to future milestones	$ 26,000
Remaining preclinical milestones, cost and profit sharing income, and the development and commercial milestones	$ 44,000
Contract liability		50,400		50,400		$ 59,000	$ 50,400
Preclinical milestone payment earned not yet received		$ 0		0		0	0
Revenue recognized				$ 4,900		$ 2,400
Sales							15,000
Collaborative Arrangement \| Takeda Pharmaceutical Company Limited \| Product
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales							$ 0
Collaborative Arrangement \| Takeda Pharmaceutical Company Limited \| Share Purchase Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Number of common stock (in shares) \| shares	4,214,559
Purchase price	$ 110,000
Fair market value of common stock	$ 94,400
Closing stock price (usd per share) \| $ / shares	$ 22.40
Premium on sale of common stock	$ 15,600
Collaborative Arrangement \| Maximum \| Takeda Pharmaceutical Company Limited
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Preclinical milestone payments per program	25,000
Total aggregate payments due upon achievement of certain preclinical milestone events	75,000
Aggregated option exercise fee	15,000
Total aggregate payments due upon achievement of certain clinical and regulatory milestone events	407,500
Regulatory milestone payment	300,000
Milestone payments per biologic product upon achievement of a certain sales-based milestone	75,000
Milestone payments upon achievement of biologic product from each program	$ 225,000

Cash and Marketable Securities

6 Months Ended

Jun. 30, 2020

Cash and Cash Equivalents [Abstract]

Cash and Marketable Securities

Cash, cash equivalents and restricted cash


	June 30,			December 31,			June 30,			December 31,
			2020			2019			2019			2018
Cash and cash equivalents	$	137,184		$	79,449		$	62,936		$	77,123
Restricted cash included within other non-current assets	1,500			1,500			1,500			1,500
Total cash, cash equivalents, and restricted cash	$	138,684		$	80,949		$	64,436		$	78,623

Marketable securities

All marketable securities were considered available-for-sale at June 30, 2020 and December 31, 2019. On a recurring basis, the Company records its marketable securities at fair value using Level 1 or Level 2 inputs as discussed in Note 2, "Fair Value Measurements". The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	June 30, 2020
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries⁽¹⁾	$	332,659	$	553	$	—	$	333,212

Corporate debt securities	49,458		303		—		49,761
Commercial paper	29,424		—		—		29,424
Total short-term marketable securities	411,541		856		—		412,397
Long-term marketable securities:

Corporate debt securities	7,127		102		—		7,229
Total long-term marketable securities	7,127		102		—		7,229
Total	$	418,668	$	958	$	—	$	419,626

__________________________________________________

(1)Immaterial unrealized holding losses on 4 securities.


	December 31, 2019
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries⁽¹⁾	$	249,478	$	594	$	(2)	$	250,070
U.S. government agency securities	1,999		1		—		2,000
Corporate debt securities⁽²⁾	53,396		94		(11)		53,479
Commercial paper	30,358		—		—		30,358
Total short-term marketable securities	335,231		689		(13)		335,907
Long-term marketable securities:
U.S. government treasuries⁽³⁾	13,865		6		(2)		13,869

Corporate debt securities⁽⁴⁾	25,998		34		(15)		26,017
Total long-term marketable securities	39,863		40		(17)		39,886
Total	$	375,094	$	729	$	(30)	$	375,793

__________________________________________________

(1)Unrealized holding losses on 2 securities with an aggregate fair value of $9.3 million.

(2)Unrealized holding losses on 4 securities with an aggregate fair value of $25.9 million.

(3)Unrealized holding losses on 1 security with an aggregate fair value of $10.1 million.

(4)Unrealized holding losses on 3 securities with an aggregate fair value of $17.2 million.

As of December 31, 2019, some of the Company’s marketable securities were in an unrealized loss position, and unrealized losses were immaterial as of June 30, 2020. The Company has not recognized an allowance for credit losses as of June 30, 2020 and there was no other-than-temporary impairment as of December 31, 2019. The Company determined that it had the ability and intent to hold all marketable securities that have been in a continuous loss position until maturity or recovery. Further, these marketable securities were initially, and continue to be, held with investment grade, high credit quality institutions. All marketable securities with unrealized losses as of each balance sheet date have been in a loss position for less than twelve months or the loss is not material.

The Company recorded unrealized gains on marketable securities as other comprehensive income in the six months ended June 30, 2020 and the three and six months ended June 30, 2019. There was no unrealized gain on marketable securities in other comprehensive income for the three months ended June 30, 2020. As a result, the Company recorded a tax benefit of $0.1 million for the six months ended June 30, 2020, and a tax benefit of $0.3 million for the three and six months ended June 30, 2019 on the Condensed Consolidated Statements of Operations and Comprehensive Loss and a corresponding tax charge in other comprehensive income.

All of the Company’s marketable securities have an effective maturity of less than two years.

Collaboration Agreements - Summary of Collaboration Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenue, revenue from contract with customer	$ 5,811	$ 4,098	$ 9,363	$ 8,209
Collaborative revenue, excluding revenue from contract with customer	36	99	88	193
Collaborative Revenue	5,847	4,197	9,451	8,402
Takeda Collaboration Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenue, revenue from contract with customer	5,537	740	8,555	1,422
Sanofi Collaboration Agreement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative Revenue	310	3,457	896	6,980
Sanofi Collaboration Agreement \| Alzheimer's Disease Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenue, excluding revenue from contract with customer	36	99	88	193
Sanofi Collaboration Agreement \| Retained Activities
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenue, revenue from contract with customer	$ 274	$ 3,358	$ 808	$ 6,787

- Definition

Amount, excluding tax collected from customer, of revenue from satisfaction of performance obligation by transferring promised good or service to customer. Tax collected from customer is tax assessed by governmental authority that is both imposed on and concurrent with specific revenue-producing transaction, including, but not limited to, sales, use, value added and excise.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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- Definition

Amount of revenue recognized from goods sold, services rendered, insurance premiums, or other activities that constitute an earning process. Includes, but is not limited to, investment and interest income before deduction of interest expense when recognized as a component of revenue, and sales and trading gain (loss).

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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-Name Accounting Standards Codification
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+ Details

Cash and Marketable Securities - Summary of Available for Sale Securities (Details) $ in Thousands	Jun. 30, 2020 USD ($) security	Dec. 31, 2019 USD ($) security
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 418,668	$ 375,094
Unrealized Holding Gains	958	729
Unrealized Holding Losses	0	(30)
Aggregate Fair Value	419,626	375,793
Short-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	411,541	335,231
Unrealized Holding Gains	856	689
Unrealized Holding Losses	0	(13)
Aggregate Fair Value	412,397	335,907
Short-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	332,659	249,478
Unrealized Holding Gains	553	594
Unrealized Holding Losses	0	(2)
Aggregate Fair Value	$ 333,212	$ 250,070
Number of securities held in unrealized holding loss position \| security	4	2
Aggregate fair value, unrealized holding loss position		$ 9,300
Short-term marketable securities \| U.S. government agency securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost		1,999
Unrealized Holding Gains		1
Unrealized Holding Losses		0
Aggregate Fair Value		2,000
Short-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 49,458	53,396
Unrealized Holding Gains	303	94
Unrealized Holding Losses	0	(11)
Aggregate Fair Value	49,761	$ 53,479
Number of securities held in unrealized holding loss position \| security		4
Aggregate fair value, unrealized holding loss position		$ 25,900
Short-term marketable securities \| Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	29,424	30,358
Unrealized Holding Gains	0	0
Unrealized Holding Losses	0	0
Aggregate Fair Value	29,424	30,358
Long-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	7,127	39,863
Unrealized Holding Gains	102	40
Unrealized Holding Losses	0	(17)
Aggregate Fair Value	7,229	39,886
Long-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost		13,865
Unrealized Holding Gains		6
Unrealized Holding Losses		(2)
Aggregate Fair Value		$ 13,869
Number of securities held in unrealized holding loss position \| security		1
Aggregate fair value, unrealized holding loss position		$ 10,100
Long-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	7,127	25,998
Unrealized Holding Gains	102	34
Unrealized Holding Losses	0	(15)
Aggregate Fair Value	$ 7,229	$ 26,017
Number of securities held in unrealized holding loss position \| security		3
Aggregate fair value, unrealized holding loss position		$ 17,200

Acquisition	6 Months Ended
Acquisition	Jun. 30, 2020
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Acquisition	Acquisition In August 2016, the Company entered into a License and Collaboration Agreement (“F-star Collaboration Agreement”) with F-star Gamma Limited (“F-star Gamma”), F-star Biotechnologische Forschungs-Und Entwicklungsges M.B.H ("F-star GmbH") and F-star Biotechnology Limited ("F-star Ltd") (collectively, “F-star”) to leverage F-star’s modular antibody technology and the Company’s expertise in the development of therapies for neurodegenerative diseases. Under the F-star Collaboration Agreement, the Company made payments to F-star totaling $11.5 million. In connection with the entry into the F-star Collaboration Agreement, the Company also purchased an option for an upfront option fee of $0.5 million (the “buy-out-option”), to acquire all of the outstanding shares of F-star Gamma pursuant to a pre-negotiated buy-out option agreement (the “Option Agreement”). In May 2018, the Company exercised the Option Agreement and entered into a Share Purchase Agreement (the “Purchase Agreement”) with the shareholders of F-star Gamma and Shareholder Representative Services LLC, pursuant to which the Company acquired all of the outstanding shares of F-star Gamma (the “Acquisition”). As a result of the Acquisition, F-star Gamma became a wholly-owned subsidiary of the Company and the Company changed the entity’s name to Denali BBB Holding Limited. In addition, the Company became a direct licensee of certain intellectual property of F-star Ltd by way of the Company’s assumption of F-star Gamma’s license agreement with F-star Ltd, dated August 24, 2016, (the “F-star Gamma License”). The Company made initial exercise payments under the Purchase Agreement and the F-star Gamma License, in the aggregate, of $17.8 million. In addition, the Company is required to make future contingent payments, to F-star Ltd and the former shareholders of F-star Gamma, up to a maximum amount of $447.0 million in the aggregate upon the achievement of certain defined preclinical, clinical, regulatory and commercial milestones. These include up to $27.0 million in preclinical contingent payments, $50.0 million in clinical contingent payments, $120.0 million in regulatory contingent payments and $250.0 million in commercial contingent payments. The amount of the contingent payments will vary based on whether F-star delivers an Fcab (constant Fc-domains with antigen-binding activity) that meets pre-defined criteria and whether the Fcab has been identified solely by the Company or solely by F-star or jointly by the Company and F-star. In June 30, 2019, the Company made a payment of $1.5 million to F-star Ltd upon the achievement of a specified preclinical milestone in the Company's ETV:IDS program. The Company concluded that the assets acquired and liabilities assumed upon the exercise of the Option Agreement did not meet the accounting definition of a business, and as such, the acquisition was accounted for as an asset purchase. As the transaction was accounted for as an asset purchase rather than a business combination, the Company did not recognize any contingent consideration on the acquisition date. To date, the Company has paid consideration of $19.8 million in the aggregate, consisting of up-front and contingent consideration, all of which was recorded as research and development expense as incurred. The Company recognized $1.5 million of contingent consideration as research and development expense for the three and six months ended June 30, 2019. There has been no contingent consideration recognized for the three and six months ended June 30, 2020. Any future contingent consideration is expected to be recognized as incurred in research and development expense on the Condensed Consolidated Statements of Operations and Comprehensive Loss. Under the F-star Collaboration Agreement, the Company is responsible for certain research costs incurred by F-star Ltd in conducting activities under an agreed development plan for each Fcab, for up to 24 months after the target Fcab is accepted. The Company's responsibility for research costs under the first development plan related to an Fcab that targets the transferrin receptor was completed during the year ended December 31, 2018. The responsibility for costs under the second development plan related to an undisclosed Fcab target commenced in February 2019. The Company recognized $0.3 million and $0.6 million in research and development expense related to the funding of F-star Ltd activities under this development plan during the three and six months ended June 30, 2020, respectively, and $0.3 million and $0.5 million for the three and six months ended June 30, 2019, respectively.

Stock-Based Awards - Summary of Assumptions Used for Estimating the Fair Value of Stock Options Granted (Details) - Stock Options	6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Volatility, minimum	65.20%	66.90%
Volatility, maximum	67.10%	77.80%
Risk-free interest rate, minimum	0.40%	2.00%
Risk-free interest rate, maximum	1.70%	2.60%
Dividend yield	0.00%	0.00%
Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	5 years 6 months	5 years 6 months
Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	6 years 29 days	6 years 29 days