Bionano Genomics, Inc. 10-K

ITEM 9A. CONTROLS AND PROCEDURES Evaluation of Disclosure Controls and Procedures We maintain “disclosure controls and procedures,” as defined in Rules 13a-15(e) and Rule 15d-15(e) of the Exchange Act of 1934, as amended (the “Exchange Act”). Disclosure controls and procedures are controls and other procedures designed to ensure that the information required to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and our principal financial officer, or persons performing similar functions, as appropriate to allow timely decisions regarding required disclosure. As of December 31, 2023, our management, with the participation of our principal executive officer and principal financial officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act). Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on this assessment, our management, including our principal executive officer and principal financial officer, has concluded that our disclosure controls and procedures were effective as of December 31, 2023 . Management’s Annual Report on Internal Control over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting as such term as defined in Exchange Act Rule 13a-15(f). Internal control over financial reporting is a process designed by, or under the supervision and with the participation of our management, including our principal executive and financial officers, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with accounting principles generally accepted in the United States of America. As of December 31, 2023, under the supervision and with the participation of our management, including our principal executive officer and principal financial officer, we conducted an evaluation of the effectiveness of our internal control over financial reporting based on the framework in Internal Control-Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Based on this assessment, our management concluded that, as of December 31, 2023, our internal control over financial reporting was effective based on those criteria. Changes in Internal Control over Financial Reporting Except as described below, there were no changes to our internal control over financial reporting (as defined in Rules 13a-15(f) and 15-d-15(f) under the Exchange Act) that occurred during the quarter ended December 31, 2023 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. In November 2022, we acquired Purigen Biosystems Inc.. We have completed our integration of internal controls of the acquired business into our overall system of internal control over financial reporting as of December 31, 2023. ITEM 9B. OTHER INFORMATION During the three months ended December 31, 2023, no director or officer of the Company adopted , terminated or modified a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” as defined in Item 408(a) of Regulation S-K of the Exchange Act. ITEM 9C. DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS Not applicable. PART III 125 Table of Contents ITEM 10. DIRECTORS, EXECUTIVE OFFICERS, AND CORPORATE GOVERNANCE The information required by this item will be set forth under the captions “Proposal 1 – Election of Directors,” “Information Regarding the Board of Directors and Corporate Governance,” “Information Regarding Committees of the Board of Directors,” “Executive Officers,” and “Delinquent Section 16(a) Reports,” if any, in our definitive proxy statement to be filed with the SEC in connection with our 2024 Annual Meeting of Stockholders, or the Proxy Statement, which is expected to be filed not later than 120 days after the end of our fiscal year ended December 31, 2023, and is incorporated in this Annual Report by reference. We have adopted a code of business conduct and ethics, or the Ethics Code, that applies to all our employees, officers and directors. This includes our principal executive officer, principal financial officer and principal accounting officer or controller, or persons performing similar functions. The full text of the Ethics Code is available on our website at www.bionanogenomics.com. If we ever were to amend or waive any provision of our Ethics Code that applies to the Company’s principal executive officer, principal financial officer, principal accounting officer or controller, or any person performing similar functions, we intend to satisfy our disclosure obligations, if any, with respect to any such waiver or amendment by posting such information on our website set forth above rather than by filing a Current Report on Form 8-K. Information contained in, or that can be accessed through, our website is not incorporated by reference herein, and you should not consider information on our website to be part of this Annual Report. ITEM 11. EXECUTIVE COMPENSATION The information required by this item will be set forth under the caption “Executive and Director Compensation” and “Item 402(v) Pay Versus Performance Disclosure” in the Proxy Statement and is incorporated in this Annual Report by reference. ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS The information required by this item will be set forth under the captions “Security Ownership of Certain Beneficial Owners and Management” and “Equity Compensation Plan Information” in the Proxy Statement and is incorporated in this Annual Report by reference. ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE The information required by this item will be set forth under the captions “Transactions With Related Persons and Indemnification” and “Information Regarding the Board of Directors and Corporate Governance” in the Proxy Statement and is incorporated in this Annual Report by reference. ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES The information required by this item will be set forth under the captions “Principal Accountant Fees and Services” and “Pre-Approval Policies and Procedures” in the Proxy Statement and is incorporated in this Annual Report by reference. PART IV ITEM 15. EXHIBIT AND FINANCIAL STATEMENT SCHEDULES List the following documents filed as a part of the report: (1) Financial statements The response to this portion of Item 15 is set forth under Item 8 above. The following consolidated financial statements of Bionano Genomics, Inc are included in Item 8 of this report: • Reports of Independent Registered Public Accounting Firm • Consolidated Balance Sheets — December 31, 2023 and 2022 • Consolidated Statements of Operations — Years ended December 31, 2023 and 2022 • Consolidated Statements of Comprehensive Loss — Years ended December 31, 2023 and 2022 • Consolidated Statements of Stockholders’ Equity (Deficit) – Years ended December 31, 2023 and 2022 • Consolidated Statements of Cash Flows — Years ended December 31, 2023 and 2022 • Notes to Consolidated Financial Statements (2) Financial statement schedule. All schedules have been omitted because they are not required or because the required information is given in the financial statements or notes thereto set forth under Item 8 above. 126 Table of Contents (3) Exhibits A list of exhibits filed with this Annual Report or incorporated herein by reference can be found in the Exhibit Index below. Exhibit Index Exhibit Number Description 2.1^€ (1) Agreement and Plan of Merger, dated October 8, 2021, by and among the Company, Starship Merger Sub I, Inc., Starship Merger Sub II, LLC, BioDiscovery, Inc. and Soheil Shams. 2.2^€ (2) Agreement and Plan of Merger, dated November 23, 2022, by and among the Company, Mazdan Merger Sub, Inc., Purigen Biosystems, Inc. and Shareholder Representative Services LLC. 2.3^€ (3) First Amendment to Agreement and Plan of Merger, dated March 4, 2023, by and between the Company and Soheil Shams, as the Securityholders’ Representative. 2.4^€ (4) Second Amendment to Agreement and Plan of Merger, dated July 15, 2023, by and among the Company, Starship Merger Sub I, Inc., Starship Merger Sub II, LLC, BioDiscovery, Inc. and Soheil Shams 3.1^€ (5) Certificate of Elimination of Series A Preferred Stock. 3.1 (3) Amended and Restated Certificate of Incorporation, as amended. 3.2 (4) Amended and Restated Bylaws. 3.4 (17) Amendment to Amended and Restated Bylaws . 4.1 (5) Form of Common Stock Certificate. 4.2 (5) Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust. 4.3 (8) Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering. 4.4 (9) Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering. 4.5 Description of the Company’s Securities. 4.6 (18) Form of Note, representing the Company’s Senior Secured Convertible Notes due 2025. 4.7 (19) Form of Warrant to Purchase Common Stock issued to Purchaser in October 2023 Offering. 4.8 (62) Amendmen t to Initial Registered Note issued to Purchaser dated February 27, 2024 10.1+ (10) Bionano Genomics, Inc. 2018 Equity Incentive Plan, as amended (the “2018 Plan”). 10.1A+ Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan. 10.1B+ Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan. 10.1C+ Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan. 10.1D+ (5) Forms of international grant notice, stock option agreement and notice of exercise under the 2018 Plan. 10.1E+ (11) Forms of restricted stock unit grant notice and restricted stock unit award agreement under the Bionano Genomics, Inc. 2018 Equity Incentive Plan. 10.2+ (12) Bionano Genomics, Inc. 2018 Employee Stock Purchase Plan. 10.3+ (2) Bionano Genomics, Inc. 2020 Inducement Plan, as amended. 10.3A+ (13) Form of Stock Option Grant Notice and Stock Option Agreement under the Bionano Genomics, Inc. 2020 Inducement Plan. 10.4+ (14) Bionano Genomics, Inc. Non-Employee Director Compensation Policy, as amended 10.5+ (5) Form of Indemnification Agreement by and between the Registrant and each director and executive officer. 10.6+ (5) Employment Agreement by and between the Registrant and R. Erik Holmlin, Ph.D., dated November 7, 2017, as amended. 10.7+ (15) Employment Agreement, effective as of September 1, 2020, by and between Christopher Stewart and the Company. 10.8+ (15) Employment Agreement, effective as of August 31, 2020, by and between Alka Chaubey and the Company. 10.90+ (5) Employment Agreement by and between the Registrant and Mark Oldakowski, dated November 7, 2017. 10.10 (5) Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012. 10.10A (5) First Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated September 10, 2013. 10.10B (5) Second Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated July 1, 2015. 10.10C (3) Third Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated December 19, 2019. 10.10D (3) Fourth Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated February 15, 2021. 10.10E (14) Fifth Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated January 12, 2022. 10.11 (14) Standard Industrial/Commercial Single-Tenant Lease, made effective as of November 23, 2021, by and between the Company and 6777 Nancy Ridge LLC. 127 Table of Contents Exhibit Number Description 10.12 (14) Commercial Single-Tenant Lease – Net, dated February 28, 2016, by and between Tesa Beach LLC and BioDiscovery, Inc. 10.13 Lease, dated August 22, 2016, by and between SFF BBC, LLC and Purigen Biosystems, Inc. 10.13A First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016 10.14 (16) Sales Agreement, dated March 23, 2021, by and between the Company and Cowen and Company, LLC. 10.14A (3) Amendment No. 1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC. 10.15# (5) License Agreement by and between Princeton University and the Registrant, dated January 7, 2004. 10.15A# (5) First Amendment to the License Agreement by and between Princeton University and the Registrant, dated December 17, 2004. 10.15B# (5) Second Amendment to the License Agreement by and between Princeton University and the Registrant, dated February 25, 2010. 10.15C# (5) Third Amendment to the License Agreement by and between Princeton University and the Registrant, dated October 17, 2011. 10.15D# (5) Fourth Amendment License Agreement by and between Princeton University and the Registrant, dated February 9, 2012. 10.16# (5) Master Services Agreement by and between the Registrant and Skorpios Technologies, Inc. (f/k/a Novati Technologies, Inc. and f/k/a SVTC Technologies, LLC), dated March 2, 2009, as amended. 10.17# (5) License Agreement by and between the Registrant and New York University dated November 4, 2013. 10.18# (5) License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014. 10.18A# (5) Amendment to Non-Exclusive Patent License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014. 10.19# (5) Manufacturing Services Agreement by and between the Registrant and Paramit Corporation, dated February 18, 2015. 10.20# (5) Option and Sublicense Agreement by and between the Registrant and Pacific Biosciences of California, Inc. dated February 2, 2016. 10.21^€ Amended and Restated Exclusive License Agreement with Equity, dated July 16, 2021, by and between The Board of Trustees of the Leland Stanford Junior University and Purigen Biosystems, Inc. 10.21A^€ Amendment No. 1 to the Amended and Restated Exclusive License Agreement Effective the 16th Day of July 2021 Between Stanford University and Purigen Biosystems, Inc., dated November 14, 2022, by and between The Board of Trustees of the Leland Stanford Junior University and Purigen Biosystems, Inc. 10.22 Employment Agreement, effective as of September 11, 2023, by and between Gülsen Kama and the Company. 10.23 Transition, Separation and Consulting Agreement dated as of August 11, 2023, by and between Christopher Stewart and the Company. 10.24^ (18) Securities Purchase Agreement, dated October 11, 2023, by and among the Company and the Purchaser named therein. 10.25^ (63) Letter Agreement between the Company and the Purchaser named therein, dated February 27, 2024. 21.1 Subsidiaries of the Registrant. 22.1 Affiliates whose securities collateralize securities of the registrant 23.1 Consent of BDO USA , P. C. , independent registered public accounting firm . 24.1 Power of Attorney (included on signature page). 31.1 Certification of Principal Executive Officer pursuant to Rules 13a-14(a) and 15d-14(a) promulgated under the Securities Exchange Act of 1934, as amended. 31.2 Certification of Principal Financial Officer pursuant to Rules 13a-14(a) and 15d-14(a) promulgated under the Securities Exchange Act of 1934, as amended. 32.1* Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 32.2* Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 97.1* Bionano Genomics, Inc. Incentive Compensation Recoupment Policy 101.INS Inline XBRL Instance Document—the instance document does not appear in the Interactive Data File as its XBRL tags are embedded within the Inline XBRL document. 101.SCH Inline XBRL Taxonomy Extension Schema Document. 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document. 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document. 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document. 128 Table of Contents Exhibit Number Description 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document. 104 Cover Page Interactive Data File (formatted in Inline XBRL and contained in Exhibit 101) (1) Incorporated by reference to Exhibit 2.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 19, 2021. (2) Incorporated by reference to Exhibit 2.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on November 28, 2022. (3) Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023. (4) Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023 (5) Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2023. (6) Incorporated by reference to Exhibit 3.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021 (7) Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018. (8) Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on April 14, 2023. (9) Incorporated by reference to Exhibit 3.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021 (10) Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018. (11) Incorporated by reference to Exhibit 3.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on April 14, 2023. (12) Incorporated by reference to Exhibit 4.13 of the Registrant’s Registration Statement on Form S-1 (File No. 333-233828), as amended. (13) Incorporated by reference to Exhibit 4.16 of the Registrant’s Registration Statement on Form S-1 (File No. 333-237074), as amended, filed with the SEC on March 24, 2020. (14) Incorporated by reference to Exhibit 4.10 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (15) Incorporated by reference to Exhibit 4.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023. (16) Incorporated by reference to Exhibit 4.2 of the Registrant’s Registration Statement on Form S-3 (File No. 333-275181). (17) Incorporated by reference to Exhibit 10.2 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (18) Incorporated by reference to Exhibit 10.3 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (19) Incorporated by reference to Exhibit 99.1 of the Registrant’s Registration Statement on Form S-8 (File No. 333-245764), filed with the SEC on August 14, 2020. (20) Incorporated by reference to Exhibit 10.2A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (21) Incorporated by reference to Exhibit 10.2B of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (22) Incorporated by reference to Exhibit 10.2C of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (23) Incorporated by reference to Exhibit 10.5 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (24) Incorporated by reference to Exhibit 99.5 of the Registrant’s Registration Statement on Form S-8 (File No. 333-227073), filed with the SEC on August 28, 2018. (25) Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on November 28, 2022. (26) Incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2020. (27) Incorporated by reference to Exhibit 10.7 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022. (28) Incorporated by reference to Exhibit 10.7 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (29) Incorporated by reference to Exhibit 10.10 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (30) Incorporated by reference to Exhibit 10.6 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020. 129 Table of Contents Exhibit Number Description (31) Incorporated by reference to Exhibit 10.7 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020. (32) Incorporated by reference to Exhibit 10.14 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (33) Incorporated by reference to Exhibit 10.20 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (34) Incorporated by reference to Exhibit 10.21 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (35) Incorporated by reference to Exhibit 10.22 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (36) Incorporated by reference to Exhibit 10.22 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021 (37) Incorporated by reference to Exhibit 10.23 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021 (38) Incorporated by reference to Exhibit 10.39 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022. (39) Incorporated by reference to Exhibit 10.33 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022. (40) Incorporated by reference to Exhibit 10.38 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022. (41) Incorporated by reference to Exhibit 10.14 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (42) Incorporated by reference to Exhibit 10.14A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (43) Incorporated by reference to Exhibit 1.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on March 24, 2021. (44) Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023 (45) Incorporated by reference to Exhibit 10.25 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (46) Incorporated by reference to Exhibit 10.26 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (47) Incorporated by reference to Exhibit 10.27 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (48) Incorporated by reference to Exhibit 10.28 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (49) Incorporated by reference to Exhibit 10.29 to the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (50) Incorporated by reference to Exhibit 10.23 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (51) Incorporated by reference to Exhibit 10.34 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (52) Incorporated by reference to Exhibit 10.32 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (53) Incorporated by reference to Exhibit 10.33 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (54) Incorporated by reference to Exhibit 10.24 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (55) Incorporated by reference to Exhibit 10.35 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018. (56) Incorporated by reference to Exhibit 10.22 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (57) Incorporated by reference to Exhibit 10.22A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (58) Incorporated by reference to Exhibit 10.1 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023. (59) Incorporated by reference to Exhibit 10.2 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023. (60) Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023. 130 Table of Contents Exhibit Number Description (61) Incorporated by reference to Exhibit 21.1 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023. (62) Incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024 (63) Incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024 ^ Certain exhibits and schedules have been omitted pursuant to Item 601(a)(5) of Regulation S-K. The Registrant hereby undertakes to furnish supplementally a copy of any omitted exhibit or schedule upon request by the SEC. + Indicates management contract or compensatory plan. # Confidential treatment has been granted with respect to certain portions of this exhibit. Omitted portions have been filed separately with the SEC. € Pursuant to Item 601(b)(10) of Regulation S-K, certain portions of this exhibit have been omitted (indicated by “[***]”) because the Company has determined that the information is not material and is the type that the Company treats as private or confidential. * This certification is furnished herewith and deemed not filed for purpose of section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act (whether made before or after the date of this Annual Report on Form 10-K), irrespective of any general incorporation language contained in such filing. ITEM 16. FORM 10-K SUMMARY None. SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended, the Registrant has duly caused this Annual Report to be signed on its behalf by the undersigned, thereunto duly authorized . Bionano Genomics, Inc. Date: March 5, 2024 By: /s/ R. Erik Holmlin, Ph.D. R. Erik Holmlin, Ph.D. President and Chief Executive Officer POWER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints each of R. Erik Holmlin, Ph.D. and Gülsen Kama as his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign this Annual Report on Form 10-K of Bionano Genomics, Inc., and any or all amendments thereto, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorney-in-fact and agent full power and authority to do and perform each and every act and thing requisite or necessary to be done in and about the premises hereby ratifying and confirming all that said attorney-in-fact and agent, or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof. Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, this Annual Report has been signed below by the following persons on behalf of the Registrant in the capacities and on the dates indicated. 131 Table of Contents Signature Title Date /s/ R. Erik Holmlin, Ph.D. Chief Executive Officer and Director (Principal Executive Officer) March 5, 2024 R. Erik Holmlin, Ph.D. /s/ Gülsen Kama Chief Financial Officer (Principal Financial and Accounting Officer) March 5, 2024 Gülsen Kama /s/ David L. Barker, Ph.D. Director March 5, 2024 David L. Barker, Ph.D. /s/ Albert A. Luderer, Ph.D. Director March 5, 2024 Albert A. Luderer, Ph.D. /s/ Yvonne Linney, Ph.D. Director March 5, 2024 Yvonne Linney, Ph.D. /s/ Hannah Mamuszka Director March 5, 2024 Hannah Mamuszka /s/ Aleksandar Rajkovic, M.D., Ph.D Director March 5, 2024 Aleksandar Rajkovic, M.D., Ph.D. /s/ Christopher Twomey Director March 5, 2024 Christopher Twomey /s/ Kristiina Vuori, M.D., Ph.D. Director March 5, 2024 Kristiina Vuori, M.D., Ph.D. /s/ Vincent Wong, J.D., M.B.A. Director March 5, 2024 Vincent Wong, J.D., M.B.A. 132