Generate Biomedicines, Inc.

1. NATURE OF BUSINESS AND BASIS OF PRESENTATION

Nature of Business – Generate Biomedicines, Inc. (the "Company") is a clinical-stage generative biology company pioneering the AI revolution in biotechnology and drug design and development. The Company’s vision is to program biology to generate optimal therapeutics for the greatest impact on human health. Central to its vision is the Generate Platform, designed to be a therapeutic area and protein modality agnostic system integrating computational innovation with scalable biohardware to address therapeutic challenges beyond the reach of traditional technologies. The Company has built its Generate Platform to be a tight and fully-integrated loop (design–build–test–learn) to create proprietary, therapeutically relevant data and differentiated molecular solutions for the biological challenges we aim to address.

Since inception, the Company has devoted substantially all of its resources to drug discovery, the development of the Generate Platform and the advancement of its programs and product candidates, including its ongoing Phase 3 clinical trials for GB-0895 and Phase 1 clinical trials for GB-4362, for which clinical trial sites have been activated and the first patient is expected to be dosed in mid-2026, and GB-5267, for which the first patient is expected to be dosed in the second half of 2026, along with multiple preclinical programs in immunology and oncology. In addition to its research and development efforts, the Company has invested in establishing and protecting its intellectual property portfolio, raising capital and obtaining financing, organizing and staffing the company, and providing general and administrative support for these operations. It does not have any products approved for sale.

Reverse Stock Split– In February 2026, the Company’s board of directors and stockholders approved an amendment to the amended and restated certificate of incorporation to effect a reverse split of shares of the Company’s common stock on aone-for-1.5190 basis (the “Reverse Stock Split”), which was effected on February 20, 2026. The par value and authorized number of shares of common stock was not adjusted as a result of the Reverse Stock Split. All share data and per share data amounts for all periods presented in the unaudited condensed consolidated financial statements and notes thereto have been retrospectively adjusted to reflect the effect of the Reverse Stock Split.

Initial Public Offering (“IPO”)– On March 2, 2026, the Company closed its IPO, pursuant to which it issued and sold an aggregate of 25,000,000 shares of its common stock at a public offering price of $16.00 to the underwriters of the IPO, resulting in net proceeds of approximately $369.3 million after deducting underwriting discounts and commissions and offering expenses payable by the Company, totaling $30.7 million. Following closing of the IPO, all of the Company's then-outstanding convertible preferred stock converted into an aggregate of 69,333,244 shares of common stock, andno shares of convertible preferred stock were thereafter outstanding.

In connection with the closing of its IPO, on March 2, 2026, the Company’s certificate of incorporation was amended and restated to authorize 500,000,000 shares of common stock, par value $0.001 per share and 10,000,000 shares of preferred stock, par value $0.001 per share.

Liquidity and Managements Plan– As of March 31, 2026, the Company had cash, cash equivalents and marketable securities of $516.6 million. The Company has incurred recurring losses since its inception, including a net loss of $61.7 million for thethree months ended March 31, 2026. As of March 31, 2026, the Company had an accumulated deficit of $737.7 million.

As of December 31, 2025, the Company had concluded that there was substantial doubt about its ability to continue as a going concern. Upon closing of the IPO and receipt of the associated cash proceeds, the Company has alleviated the substantial doubt that previously existed, and based on the Company’s current capital resources, which consists of its cash, cash equivalents and marketable securities on hand at March 31, 2026, it expects to have sufficient cash to support current operating plans into the first half of 2028. The Company expects to require additional capital to support its long-term operations.

2. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

There have been no significant changes from the significant accounting policies and estimates disclosed in Note 2 of the “Notes to Consolidated Financial Statements” in the audited consolidated financial statements for the year ended December 31, 2025 and notes thereto, included in the Company’s final prospectus filed pursuant to Rule 424(b)(4) under the Securities Act with the SEC on February 27, 2026, except as noted below.

Basis of Presentation- The accompanying unaudited condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“GAAP”). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”).

Principles of Consolidation – The accompanying unaudited condensed consolidated financial statements reflect the consolidated operations of the Company, including its wholly owned subsidiaries, Generate Biomedicines Securities Corporation, and Generate Golukibart Therapeutics, Inc. (formerly Pioneering Medicines 02, Inc. (“PMCo”)), which was until February 26, 2026, a variable interest entity where the Company was the primary beneficiary. On February 26, 2026, the Company acquired all of the outstanding capital stock of PMCo. All intercompany accounts and transactions have been eliminated.

At the inception of a transaction, the Company identifies each entity involved in such transaction for which control is achieved by the Company through means other than voting rights (each a “variable interest entity” or “VIE”) and determines if the Company is the primary beneficiary of such entity’s operations. A VIE is broadly defined as an entity where either (i) the equity investors as a group, if any, do not have a controlling financial interest, or (ii) the equity investment at risk is insufficient to finance that entity’s activities without additional subordinated financial support. The Company consolidates investments in a VIE when the Company is determined to be the primary beneficiary. ASC Topic 810, Consolidations (“ASC 810”), requires the Company to perform a qualitative approach to determining whether or not a VIE will need to be consolidated. This evaluation is based on the Company’s ability to direct and influence the activities of a VIE that most significantly impact that entity’s economic performance, whether the Company has the power to direct those activities, and if the Company’s obligation to absorb losses or receive benefits from the VIE could potentially be significant to the VIE.

For consolidated entities with ownership interest or economic rights held by third-parties, the Company records net loss attributable to non-controlling interests in its consolidated statements of operations equal to the percentage of common stock ownership interest retained in the respective operations by the non-controlling parties. The Company presents non-controlling interests as a component of shareholders’ equity or mezzanine equity on its consolidated balance sheets based on the redemption rights of the equity interest. The Company records the non-controlling interests’ share of loss based on the percentage of ownership interest retained by the respective non-controlling interest holders.

Use of Estimates – The preparation of the unaudited condensed consolidated financial statements in accordance with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the unaudited condensed consolidated financial statements and the reported amounts of expenses during the reporting period. The Company bases its estimates and assumptions on historical experience, known trends and other market-specific or other relevant factors that it believes to be reasonable under the circumstances. On an ongoing basis, management evaluates its estimates, which include but are not limited to pre-paid and accrued research and development expenses, liquidity projections, stock-based compensation expense and the incremental borrowing rate for operating and finance lease right-of-use assets, and income taxes. Actual results could differ from those estimates. Changes in estimates are recorded in the period in which they become known.

Cash and Cash Equivalents – Cash and cash equivalents are short-term, highly liquid investments with original maturities of three months or less at the date of purchase. Investments qualifying as cash equivalents primarily consist of money market funds and government securities.

Recently Issued Accounting Pronouncements Not Yet Adopted – In November 2024, the FASB issued ASU 2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures(Subtopic 220-40): Disaggregation of Income Statement Expenses. This update requires that at each interim and annual reporting period public entities disclose (1) the amounts of purchases of inventory, employee compensation, depreciation, amortization, and depletion in commonly presented expense captions; (2) certain amounts that are already required to be disclosed under current GAAP in the same disclosure as the other disaggregation requirements; (3) a qualitative description of the amounts remaining in relevant expense captions that are not separately disaggregated quantitatively; (4) the total amount of selling expenses and; (5) in annual reporting periods, the definition of selling expenses. In January 2025, the FASB issued ASU 2025-01, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures(Subtopic 220-40): Clarifying the Effective Date. This update clarifies that ASU 2024-03 is effective for annual reporting periods beginning after December 15, 2026, and interim periods within annual reporting periods beginning after December 15, 2027. Early adoption is permitted. The Company is currently evaluating the impact of adopting this guidance on its financial statements.

In September 2025, the FASB issued ASU 2025-06, Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Targeted Improvements to the Accounting for Internal-Use Software. This update removes all references to prescriptive and sequential software development stages throughout Subtopic 350-40. The update requires an entity to start capitalizing software costs when management has authorized and committed to funding the software project, and it is probable that the project will be completed and the software will be used to perform the function intended. The update further specifies that the disclosures in Subtopic 360-10 are required for all capitalized internal-use software costs. This update is effective for annual reporting periods beginning after December 15, 2027, and interim reporting periods within those annual reporting periods. Early adoption is permitted. The guidance can be applied using a prospective transition approach, a modified transition approach that is based on the status of the project and whether software costs were capitalized before the date of adoption, or a retrospective transition approach. The Company is currently evaluating the impact of adopting this guidance on its financial statements.

3. CASH EQUIVALENTS AND MARKETABLE SECURITIES

The following tables summarize the amortized cost and fair value of the Company’s cash equivalents and marketable securities (in thousands):

The Company didnot record a provision for credit losses on any marketable securities for thethree months ended March 31, 2026 and year ended December 31, 2025. No securities held by the Company were delinquent on contractual payments as of March 31, 2026 and December 31, 2025, nor were any securities placed on non-accrual status for the period then ended. Interest on investments is recognized as interest income in the unaudited condensed consolidated statements of operations and comprehensive loss.

Information pertaining to marketable securities with gross unrealized losses as of March 31, 2026, for which the Company did not recognize a provision for credit losses under the current expected credit loss methodology, aggregated by investment category and length of time that individual securities had been in a continuous loss position, is as follows (in thousands):

As of December 31, 2025, the Company didnot hold any securities with gross unrealized losses.

Maturity information based on fair value of the available-for-sale securities is as follows as of March 31, 2026:

As of December 31, 2025, the Company’s marketable securities all matured withinone year or less.

4. FAIR VALUE MEASUREMENTS

The following table sets forth by level, within the fair value hierarchy, the assets and liabilities carried at fair value on a recurring basis (in thousands):

Valuation of the Warrant to Purchase Convertible Preferred Stock

The fair value of the convertible preferred stock warrant liabilities was determined using the Black-Scholes Option Pricing Model (the "Black-Scholes OPM") with the assumptions as disclosed in Note 8. These assumptions include significant judgments, including the fair value of the underlying convertible preferred stock.

The following table presents a roll-forward of the aggregate fair values of the Company’s liabilities for which fair value is determined by Level 3 inputs (in thousands):

There wereno transfers among Level 1, Level 2, or Level 3 categories in the period presented.

Financial Instruments Not Recorded at Fair Value – The carrying value of accounts receivable, accounts payable and accrued expenses that are reported on the unaudited condensed consolidated balance sheet approximate their fair value because of the relatively short period of time between origination and expected realization or settlement.

5. COLLABORATION AGREEMENTS

Agreement with Novartis Pharma AG (“Novartis”)

On September 19, 2024, the Company entered into a Collaboration and License Agreement with Novartis (the “Novartis Collaboration Agreement”) to discover, develop, manufacture and commercialize protein therapeutics using the Generate Platform. The collaboration covers multiple collaboration targets, conducted under applicable research plans during defined research terms. As consideration for the collaboration, the Company received a $50.0 million upfront payment. Novartis also purchased 1,265,822 shares of our Series C convertible preferred stock for $15.0 million. The Company is eligible to receive up to $1.0 billion across all programs upon the achievement of certain performance-based milestones, inclusive of $130.0 million in development and regulatory milestones and $210.0 millionin commercial milestones associated with each research program. Novartis is also obligated to pay, on a licensed product-by-licensed product and on a country-by-country basis, tiered royalties ranging from a mid-single digit to a low tens percentage on worldwide net sales of any licensed product, subject to specified reductions and offsets.

The Company concluded that the per share purchase price, paid by Novartis, was equal to the per share fair value of Series C convertible preferred stock. As such, there is no impact to the transaction price related to the investment in Series C convertible preferred stock by Novartis.

The Company concluded that the arrangement contemplated by the Novartis Collaboration Agreement represents a contract with a customer within the scope of ASC 606. The Company determined that for each research program, the research services and related research license granted under the Novartis Collaboration Agreement are not distinct and should be a combined performance obligation. The transaction price at inception was $50.0 million, representing the nonrefundable upfront fee. All contingent payments represent variable consideration that are constrained at inception as the achievement of the milestones underlying such contingent payments is based on either the Company or Novartis’s ability to execute under the respective research program plans which is not certain at contract inception. The Company allocated the transaction price to each of the distinct research program performance obligations on a relative stand-alone selling price basis.

The Company recognizes revenue related to each distinct performance obligation over time using the costs incurred input method, such that revenue is recognized based on the Company’s efforts or inputs to the satisfaction of a performance obligation.

The Company allocated the $50.0 million transaction price equally to the performance obligations based on the relative selling price.

The Company recognized $6.5 million and $6.7 million of revenue under the Novartis Collaboration Agreement during thethree months ended March 31, 2026 and 2025, respectively. The remaining transaction price of $16.1 million is expected to be recognized by the Company as revenue through 2027. As of March 31, 2026, all contingent payments were constrained. The Company will re-evaluate the transaction price in each reporting period, as uncertain events are resolved, or as other changes in circumstances occur.

Agreement with Amgen Inc. (“Amgen”)

On December 24, 2021, the Company entered into a Collaboration and License Agreement, as amended by the First Amendment dated October 5, 2022 and the Second Amendment dated December 12, 2023 (as amended from time to time, the “Amgen Collaboration Agreement”), with Amgen to identify biologic proteins and antibodies directed against specified targets. The Amgen Collaboration Agreement initially covered five collaboration targets. In addition, Amgen has the option to nominate up to five additional collaboration targets, at additional cost, the first of which was exercised in December 2023 related to the sixth target. As consideration for the collaboration, the Company received a $50.0 million upfront payment. In connection with the Second Amendment, which added an additional collaboration target, the Company received an additional payment of $5.0 million. The Company is eligible to receive up to $370.0 million for each program upon the achievement of certain milestones, including $160.0 million in development and regulatory milestones and $210.0 million in commercial milestones per program. Amgen is also obligated to pay, on a licensed product-by-licensed product and on a country-by-country basis, tiered royalties ranging from a mid-single digit up to a low tens percentage on worldwide net sales of any licensed product, subject to customary reductions and offsets. Additionally, the Amgen Collaboration Agreement included an investment by Amgen of $25.0 million in equity, at the offering price, if the Company consummated certain future equity offerings. Amgen purchased 2,109,704 shares of the Company's Series C convertible preferred stock for approximately $25.0 million on May 9, 2023.

The per share purchase price that would be paid by Amgen, if the Company were to engage in a future equity offering, is equal to the per share fair value of the Company’s other investors at the time, therefore would not impact the transaction price under the Amgen Collaboration Agreement.

The Company assessed this arrangement in accordance with ASC 606 and concluded that Amgen is a customer. The Company determined that the research activities and the exclusive license granted under the Amgen Collaboration Agreement are not individually distinct and should be combined for each target program, and each target program was considered as a distinct performance obligation. Therefore, the transaction price was allocated to each target program on a relative stand-alone selling price basis.

In connection with the modification in 2023, the Company allocated the transaction price to the performance obligations on a relative selling price basis as follows: (i) $9.2 million to the first target program; (ii) $10.4 million to the second target program; (iii) $9.2 million to the third target program; (iv) $9.0 million to the fourth target program; (v) $9.5 million to the fifth target program and (vi) $7.7 million to the sixth target program.

The Company recognizes revenue related to each performance obligation over time using the costs incurred input method, such that revenue is recognized based on the Company’s efforts or inputs to the satisfaction of a performance obligation.

During the year ended December 31, 2024, a development milestone related to an initial collaboration target was achieved which triggered a $5.0 million milestone payment to the Company. The $5.0 million milestone payment was fully recognized during the year ended December 31, 2024 as this variable consideration was allocated to a distinct performance obligation and the Company had completed its related performance obligation related to the collaboration target. All other milestones and royalties were constrained as of March 31, 2026. The Company will re-evaluate the transaction price in each reporting period, as uncertain events are resolved, or as other changes in circumstances occur.

On July 21, 2025, the Company and Amgen executed an amendment to the Amgen Collaboration Agreement that effectively eliminated the remaining service obligation related to a collaboration target. The Company determined the amendment represented a modification of the arrangement under ASC 606 and that the remaining fixed transaction price at the modification date of $4.3 million should be re-allocated to the remaining performance obligations based on their updated standalone selling prices. Accordingly, the Company recorded a cumulative adjustment to revenue of approximately $1.3 million on the partially satisfied remaining performance obligations, as the remaining services to be performed under each of the performance obligations are not distinct from the services prior to the modification.

The Company recognized $0.7 million and $2.1 million of revenue during thethree months ended March 31, 2026 and 2025, respectively. The remaining transaction price of $2.4 million is expected to be recognized as revenue through 2026.

Agreement with The University of Texas M.D. Anderson Cancer Center ("MD Anderson")

In April 2023, the Company entered into a co-development and commercialization collaboration agreement with MD Anderson to discover and develop protein therapeutics for up to five oncology targets. Under the agreement, the Company and MD Anderson agreed to share research and development expenses as well as profits generated through commercialization of jointly developed products. The arrangement is considered a collaboration agreement under ASC 808 and the Company recognizes costs as incurred and reimbursements as a reduction of research and development expense. As of March 31, 2026, the Company had a net reimbursement payable to MD Anderson of $0.1 million.

Agreement with Roswell Park Comprehensive Cancer Center ("Roswell Park")

In October 2023, the Company entered into a collaboration agreement with Roswell Park to discover and develop chimeric antigen receptors T-cell therapies and armoring technologies for up to three oncology targets. Under the agreement, the Company and Roswell Park agreed to share research and development expenses as well as profits generated through commercialization of jointly developed products. The arrangement is considered a collaboration agreement under ASC 808 and the Company recognizes costs as incurred and reimbursements as a reduction of research and development expense. During the three months ended March 31, 2026 Roswell Park reimbursed the Company $0.1 million, which was recorded as a reduction of research and development expense.

6. PROPERTY AND EQUIPMENT

Property and equipment consisted of the following (in thousands):

The Company leases equipment under agreements which are classified as finance lease liabilities in the accompanying unaudited condensed consolidated balance sheet. The equipment and obligations related to the leases are recorded at the present value of the lease payments. Depreciation is computed on a straight-line basis over the shorter of the estimated useful lives of the assets or remaining lease term. Depreciation expense related to leased equipment totaled $2.2 million and $2.1 million for the three months ended March 31, 2026 and 2025.

Depreciation and amortization expense for the three months ended March 31, 2026 and 2025 was $3.3 million and $3.4 million, respectively, including the depreciation expense related to the leased equipment.

7. ACCRUED EXPENSES AND OTHER CURRENT LIABILITIES

Accrued expenses and other current liabilities consisted of the following (in thousands):

8. NET LOSS PER SHARE

Basic net loss per share is computed by dividing net loss attributable to the Company's common stockholders by the weighted average number of shares of the Company’s common stock outstanding during the period. Diluted net loss per share is computed similarly to basic net loss per share except that it also includes potential shares of common stock only if they are dilutive. When participating securities exist, earnings or losses are allocated between common and participating securities under the two-class method before calculating earnings per share. For the period presented, basic and diluted net loss per share are the same as any potential shares of common stock would be anti-dilutive and the participating securities do not share in losses of the Company.

The following securities are common stock equivalents, but were excluded in the computation of diluted net loss per common stock because to do so would have been anti-dilutive:

9. WARRANT LIABILITY

On July 10, 2020, the Company issued a warrant to purchase up to 150,000 shares of Series A convertible preferred stock with an exercise price of $1.00 per share (the “Warrant”). The Warrant had an original term to maturity of 10 years, expiring on July 10, 2030. On March 2, 2026, the warrant was reclassified to a warrant to purchase 98,749 shares of common stock due to the automatic conversion of convertible preferred stock upon the closing of the IPO. Upon the automatic conversion of the convertible preferred stock (see Note 10), the Company remeasured the warrant liability to its fair market value and reclassified the total carrying value of the warrant liability into additional paid-in capital. In March 2026, the warrant was exercised by the warrant holder under the warrant's cashless (net) exercise provisions, resulting in the issuance of 86,423 shares of common stock to the warrant holder.

The assumptions that the Company used to determine the fair value of the Warrant are as follows:

10. CONVERTIBLE PREFERRED STOCK

Immediately prior to the closing of the IPO, the Company had an aggregate of 105,317,255 shares of redeemable convertible and convertible preferred stock issued and outstanding which automatically converted into 69,333,244 shares of common stock. Subsequent to the closing of the IPO, no shares of convertible preferred stock were issued or outstanding.

As of December 31, 2025, the Company’s convertible preferred stock consisted of the following (in thousands, except share data):

11. COMMON STOCK

As of March 31, 2026, the Company had authorized 500,000,000 shares of common stock.

As of March 31, 2026, the Company had reserved 31,686,348 shares for the exercise of outstanding stock options and the number of shares remaining available for grant under the 2026 Equity Incentive Plan (see Note 12).

12. STOCK-BASED COMPENSATION

2019 Equity Incentive Plan

During 2019, the Company adopted the 2019 Equity Incentive Plan, as amended (the “2019 Plan”). The 2019 Plan provided for the issuance of up to 19,801,227 shares of common stock as of March 31, 2026, to employees, officers, directors, consultants, and advisors in the form of non-qualified and incentive stock options, restricted stock awards, and other stock-based awards. Options typically vest over four years and have a maximum term of 10 years. Concurrent with the IPO in February 2026, all shares available for issuance under the 2019 Plan ceased to be available for issuance as the 2026 Equity Incentive Plan became effective.

2026 Equity Incentive Plan

During the three months ended March 31, 2026, in connection with the Company's IPO, the Company adopted the 2026 Equity Incentive Plan, as amended (the “2026 Plan”). The 2026 Plan initially provided for the issuance of up to 11,852,719 shares of common stock, and will be increased annually at 4% of the outstanding number of shares of common stock outstanding per year, or a lesser amount determined by the board of directors, as well as for forfeitures and cancellations under the 2019 Plan. As of March 31, 2026, there were 7,094,781 shares of common stock available for issuance to employees, officers, directors, consultants, and advisors in the form of non-qualified and incentive stock options, restricted stock awards, and other stock-based awards. Options typically vest over four years and have a maximum term of 10 years.

Stock Option Valuation

The Company typically grants stock options to employees and non-employees at exercise prices deemed by the Board to be equal to the fair value of the common stock at the time of grant.

The Company utilized the Black-Scholes OPM to estimate the fair value of stock options awarded to employees, officers, directors, consultants and advisors. The Black-Scholes OPM requires several key assumptions. The assumptions that the Company used to determine the grant-date fair value of options granted to employees, non-employees and directors were as follows, presented on a weighted-average basis:

As of March 31, 2026, there was $95.3 million of unrecognized compensation expense, related to unvested time-based stock options that will be recognized over a weighted-average remaining term of 3.0 years.

Prior to January 1, 2024, the Company issued stock options covering shares 631,665 of common stock subject to the performance condition of entering into one or more strategic transactions pursuant to which the Company has the right to receive, in the aggregate, at least $200.0 million in specified payments. During the year ended December 31, 2022, the vesting of stock options covering 157,916 shares of stock with this performance condition was accelerated following the signing of the Amgen Collaboration Agreement in recognition of performance that did not otherwise achieve the performance condition. During the year ended December 31, 2025, the vesting of stock options covering 157,916 shares of common stock with this performance condition was accelerated following the signing of the Novartis Collaboration Agreement in recognition of performance that did not otherwise achieve the performance condition. The balance of 315,833 shares of common stock underlying these stock options remains outstanding. No stock-based compensation expense has been recorded on the remaining unvested stock options as the performance conditions are not deemed probable of occurrence.

During the year ended December 31, 2024, the Company issued stock options covering 65,832 shares of common stock subject to the performance condition of entering into one or more strategic transactions pursuant to which the Company has the right to receive, in the aggregate, at least $50.0 million in specified payments. Additionally, the Company issued stock options covering 65,832 shares of common stock subject to the performance condition of entering into one or more strategic transactions pursuant to which the Company has the right to receive, in the aggregate, at least $100.0 million in specified payments. Any unvested shares underlying both stock option grants lapsed and were forfeited as of January 1, 2026. During thethree months ended March 31, 2026, the stock options covering 131,664 shares of common stock expired.

The following table summarizes the option activity under the 2019 Plan and the 2026 Plan:

During the three months ended March 31, 2026, the Company granted stock options to purchase an aggregate of 5,240,236 shares at weighted average grant date fair value per option share of $15.64.

The Company recorded stock-based compensation expense in the following expense categories of its unaudited condensed consolidated statement of operations and comprehensive loss:

13. COMMITMENTS AND CONTINGENCIES

Legal Proceedings – The Company is not currently party to any material legal proceedings. At each reporting date, the Company evaluates whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of the authoritative guidance that addresses accounting for contingencies. The Company expenses as incurred the costs related to such legal proceedings.

14. RELATED-PARTY TRANSACTIONS

In August 2018, the Company entered into a ten-year management service agreement with Flagship Pioneering, Inc. (“Flagship Pioneering”) to provide management services, including accounting, human resources, information technology, legal, and consultation services. The Company also agreed to reimburse Flagship Pioneering for certain expenses, including insurance and benefits, partner and related fees, software licenses, supplies, and administration consulting services incurred on the Company’s behalf. Upon the effectiveness of the Company's Registration Statement on Form S-1 (File No. 333-293204), as amended, filed in connection with the Company's IPO (the "Registration Statement") on February 26, 2026, the Flagship Managerial Agreement was terminated. The Company recorded general and administrative expense totaling $0.1 million and $0.2 million related to these services and the termination of the agreement for thethree months ended March 31, 2026 and 2025, respectively. As of March 31, 2026 and December 31, 2025, the Company owed $0.1 million and $0.1 million, respectively, to Flagship.

In July 2022, the Company entered into a Vivarium Shared Space Operating Agreement, as amended in May 2024, with Cellarity, Inc. (“Cellarity”), an affiliate of Flagship, to use a vivarium space, along with other companies affiliated with Flagship. The Company pays Cellarity a monthly operating fee for using the vivarium and obtaining various services; the shared cost is variable depending on the actual usage. The Company recognized less than $0.1 million and $0.2 million of expense paid to Cellarity during thethree months ended March 31, 2026 and 2025, respectively. As of March 31, 2026 and December 31, 2025, the Company had less than $0.1 million and $0.1 million in accounts payable to Cellarity, respectively.

In August 2021, the Company entered into an agreement (the “Flagship Agreement”), with Flagship Pioneering Innovations VI, LLC (“Flagship”), pursuant to which it (i) irrevocably and unconditionally assigned to Flagship all of the Company’s right, title and interest in and to certain foundational patent rights conceived prior to the Company’s launch, which is defined as the closing of its Series B financing, and its improvements to such patent rights that cannot be practiced without infringing the foregoing patent rights (such patent rights and improvements, the “Foundational IP”), and (ii) obtained an exclusive, worldwide, royalty-bearing, sublicensable, transferable license from Flagship under such Foundational IP to develop, manufacture and commercialize any product or process or component thereof in the licensed field of human therapeutics and vaccines that would, absent the license granted to the Company by Flagship, infringe at least one valid claim of the Foundational IP. Pursuant to the Flagship Agreement, the Company is obligated to use commercially reasonable efforts to diligently exploit licensed products in the licensed field and maintain such efforts during the term of the Flagship Agreement. To satisfy the due diligence requirements, the Company must spend at least $1.0 million each year on its own development and commercialization activities with respect to licensed products during the term of the Flagship Agreement and at least $10.0 million on such activities until August 2026, which may include internal or external research and development costs. The research and development costs are expensed as incurred. The Company's only financial obligation to Flagship is to pay Flagship, on a licensed product-by-licensed product and jurisdiction-by-jurisdiction basis, royalties equal to a low single-digit percentage on net sales of licensed products by the Company or its sublicensees until the expiration of the last valid claim of any Foundational IP covering such licensed product in such jurisdiction. To date, there have been no amounts paid or received by the Company under the Flagship Agreement.

In June 2023, the Company entered into a collaboration agreement with PMCo, a company newly formed and controlled by Flagship Labs VII, LLC and Flagship Pioneering Fund VII, L.P., each of which are affiliated with Flagship Pioneering (the "Prior PMCo Agreement"). This collaboration agreement was terminated on February 26, 2026. See Note 15.

15. VARIABLE INTEREST ENTITIES

Prior PMCo Agreement

On June 22, 2023, the Company entered into the Prior PMCo Agreement with PMCo, an affiliate of Flagship Pioneering, pursuant to which PMCo was granted an exclusive, worldwide, royalty-free, sublicensable license under certain of the Company’s patent rights and know-how to develop, manufacture and commercialize licensed products containing certain antibodies against TSLP and/or IL-4Rα, including GB-0895, in all fields. The Prior PMCo Agreement was terminated on February 26, 2026.

During the period from the effective date until June 2030, neither the Company nor any of its affiliates were permitted to develop or commercialize, nor collaborate with, enable or otherwise authorize, license or grant any right to any third-party to develop or commercialize, any antibody that (i) binds to TSLP, (ii) binds to both TSLP and IL-4Rα (but no other target), or (iii) binds to IL-4Rα (and no other target, including TSLP) in the territory. Subject to the license to PMCo, as between the parties, the Company solely owned and retained all right, title and interest in and to all technology, know-how and materials conceived, discovered, developed or otherwise made by or on behalf of PMCo or any of its affiliates or sublicensees in the course of performing activities under or in connection with the Prior PMCo Agreement, and any patents or patent applications claiming any of the developed know-how.

Under the terms of the Prior PMCo Agreement, the Company and PMCo were to collaborate on research and development activities with respect to the licensed products and will share research and development costs, with the Company bearing 65% and PMCo bearing 35%of all fully-burdened research costs and development expenses, which percentage commitments are subject to adjustment if the Company or PMCo failed to pay or wished to reduce their respective percentage commitments prior to the consummation of a business combination of PMCo or a license transaction ofall commercial rights for all licensed products. In addition, the Company was entitled to 70% and PMCo was entitled to 30% of the proceeds of a business combination of PMCo or an exclusive license transaction with a third-party; provided, however, that the failure by any party to bear their agreed portion of the fully-burdened research costs and development expenses would have resulted in an automaticpro rata adjustment of such party’s interest in any such proceeds and that such failure would not automatically have been deemed to constitute a breach of the Prior PMCo Agreement.

Subject to the terms and conditions of the Prior PMCo Agreement, the Company was obligated to use commercially reasonable efforts to develop licensed products in the licensed field in the territory, including by way of directing PMCo under the Prior PMCo Agreement, and upon receipt of regulatory approval for a licensed product in a country, PMCo would have been obligated to use commercially reasonable efforts to commercialize such licensed product in such country.

Following the first achievement of a specified regulatory milestone, and prior to a business combination of PMCo or a license transaction of all commercial rights for all licensed products, (i) the Company had the right to acquire all of the securities of PMCo for a price equal to a low tens percentage of the fair market value of such securities on terms and conditions to be negotiated between the Company and PMCo, and if the Company does not exercise such right, the Company had the right to initiate a business combination of PMCo or an exclusive license transaction with a third party; and (ii) PMCo had the right to have us acquire all of the securities of PMCo in exchange for royalties equal to a mid-to-high single-digit percentage on net sales of licensed products on a country-by-country and licensed product-by-licensed product basis until the later of (a) the expiration of the last valid claim of any patent right controlled by us or PMCo covering the use or sale of such licensed product in such country, (b) expiration of regulatory exclusivity for such product in such country, and ten years following the first commercial sale of such licensed product in such country (such transactions in (i) and (ii), collectively, the “Subject Transactions”). Concurrently with the Prior PMCo Agreement, the Company, PMCo and Pioneering Medicines 02, LLC (“PM LLC”), the sole stockholder of PMCo, entered into a drag-along agreement (the "Drag-Along Agreement"), pursuant to which PM LLC agreed to, among other things, vote in favor of a Subject Transaction.

The Company consolidated PMCo, which, prior to the termination of the Prior PMCo Agreement and acquisition by Generate of all of the issued and outstanding capital stock of PMCo on February 26, 2026, was deemed to be VIE and of which the Company was the primary beneficiary based on a combination of the decision-making power over the activities that most significantly impact the economic performance of PMCo and an obligation to absorb losses or receive benefits from PMCo. These decisions and significant activities included, but were not limited to, research and development activities under the research plan and the development plan and other operational and strategic matters. The terms of the agreements governing PMCo prohibited the Company from using the assets of PMCo to satisfy the obligations of other entities.

The Prior PMCo Agreement was treated as an asset acquisition as PMCo’s assets transferred do not meet the definition of a business. Prior to the acquisition, PMCo’s majority stockholder was the same as the Company’s majority stockholder and there was common ownership and control, including common members of the Board. As such, the Company accounted for the asset acquisition as a transaction between entities under common control. The Company initially measured and recognized the assets and liabilities transferred at their carrying amounts in the accounts of PMCo at the date of transfer. Accordingly, the Company recognized non-controlling interest (“NCI”) based on the net assets held by PMCo. As a result of PMCo’s preferred stock being redeemable upon a deemed liquidation event and its put right, the NCI in PMCo is presented in mezzanine equity.

The net assets acquired on June 30, 2023, included cash totaling $0.6 million and liabilities totaling $2.1 million, comprised primarily of accounts payable and accrued liabilities.

Non-Controlling Interest Acquisition

On February 4, 2026, the Company entered into a stock purchase agreement (“Stock Purchase Agreement”) with the stockholder of PMCo, PM LLC, pursuant to which the Company agreed to purchase, and PM LLC agreed to sell, all of the issued and outstanding capital stock in PMCo. In consideration for such sale, PMCo, PM LLC and the Company agreed to terminate the Prior PMCo Agreement, and the Company agreed to pay PM LLC a portion of the net sales, if any, arising from the sale of certain products covered by certain patents or containing certain know-how (“Generate Products”) developed under the Prior PMCo Agreement. The closing of the transactions contemplated by the Stock Purchase Agreement and the termination of the Prior PMCo Agreement occurred on February 26, 2026.

The Company is obligated to make net sales payments equal to a high-single digit percentage of net sales of Generate Products, including any Generate Product that contains GB-0895. However, if a Generate Product (i) does not contain GB-0895, (ii) binds to at least one of TSLP or IL-4Rα, and (iii) binds to other proteins in addition to TSLP or IL-4Rα, then the sales payment is reduced based on the composition of the product. Further, if the Company exclusively license its rights to exploit a Generate Product in one or more countries to a third party, and the royalties on net sales of such Generate Product to be paid by such third party are subject to certain specified reductions, then the Company may be allowed to further proportionally reduce the sales payment due to PM LLC, depending on the relative value of the future royalties due to the Company from such third party as compared to the total deal consideration.

Both PM LLC and the Company have the ability to trigger a buy-out of all future net sales payments under the Stock Purchase Agreement in certain instances, which would require the Company to make a single payment to PM LLC that is equivalent to the fair market value of the projected future net sales payments due to PM LLC based upon the projected future net sales of the applicable and then-existing Generate Products (the “Buy-Out Amount”). Both PM LLC and the Company have this right following the Company entering into an exclusive license to the Company's rights to exploit a Generate Product in one or more countries with a third party (or transaction approximating an exclusive license). In addition, in the event the Company is acquired by a qualified acquirer, the Company has the right to trigger a buy-out of all future sales payments under the Stock Purchase Agreement in exchange for the Buy-Out Amount. Following payment of the Buy-Out Amount with respect to a Generate Product in a country, the Company's diligence obligations and the Company's obligations to make net sales payments with respect to the applicable Generate Products in the applicable countries shall immediately terminate, as do the Company's exclusivity restrictions with respect to the protein targeted by such Generate Products in such countries.

The transaction represents the acquisition of a non-controlling interest in a consolidated subsidiary. The Company accounts for the acquisition of the non-controlling interest as an equity transaction with no gain or loss recognized in net income (loss). The consideration payable by the Company is contingent upon the successful commercialization of licensed products. The contingent consideration will be recognized when the contingency is resolved and the consideration is paid or becomes payable.

As a result of the acquisition of the non-controlling interest, the Company will no longer allocate losses to the non-controlling interest. The net loss allocated to the non-controlling interest, was $0.3 million and $2.6 million during thethree months ended March 31, 2026 and 2025, respectively, primarily represented amounts that PMCo had paid to the Company under the cost sharing arrangement.

16. SEGMENT INFORMATION

The Company hasone operating segment. The Company’s operating segment is engaged in the field of generative biology by using machine learning for drug discovery and development through the programming of novel protein therapeutics. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of assessing performance and allocating resources based on net loss attributable to Generate Biomedicines, Inc. stockholders that also is reported on the consolidated statement of operations as consolidated net loss to Generate Biomedicines, Inc. stockholders. This financial metric is used by the chief operating decision maker ("CODM") to make key operating decisions such as the allocation of capital between program expenses, early-stage discovery expenses, and general and administrative expense, including headcount and facilities decisions. The operating segment’s revenue is derived from multiple collaboration agreements from which the segment licenses certain development or product candidates and performs research and development services. The measure of segment assets is reported on the balance sheet as total consolidated assets. All of the Company’s long-lived assets are held in the United States. The following table presents selected financial information about the Company’ssingle operating segment. The significant expense categories and amounts align with the segment-level information that is regularly provided to the CODM for thethree months ended March 31, 2026 and 2025 (amounts in thousands):

(a)

Other segment expenses include change in fair value of convertible preferred stock warrant liability and foreign currency exchange loss.

17. SUBSEQUENT EVENTS

The Company evaluated subsequent events through the date on which these financial statements were issued to ensure that these condensed consolidated financial statements include appropriate disclosure of events both recognized in the financial statements as of March 31, 2026 and events which occurred subsequently but not recognized in the financial statements. No subsequent events have occurred that require disclosure.