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Item 9A. Controls and Procedures

2025-03-31 compared with 2024-03-05 · 101 added, 181 removed, 116 unchanged (71% of the section changed)

13 unchanged sentences

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.

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, 2024 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

OTHER INFORMATION

5 unchanged sentences

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.

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.bionano.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.

25 unchanged sentences

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.

Amended and Restated Certificate of Incorporation, as amended.

Amended and Restated Bylaws.

Amendment to Amended and Restated Bylaws .

Form of Common Stock Certificate.

Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust.

Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering.

Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering.

Description of the Company’s Securities.

Form of Note, representing the Company’s Senior Secured Convertible Notes due 2025.

Form of Warrant to Purchase Common Stock issued to Purchaser in October 2023 Offering.

Amendmen t to Initial Registered Note issued to Purchaser dated February 27, 2024

Amended and Restated Certificate of Incorporation, as amended (incorporated by reference to Exhibit 3.1 to Registrant's Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023).

Number Description

Certificate of Amendment to the Amended and Restated Certificate of Incorporation, as amended (incorporated by reference to Exhibit 3.1 to Registrant’s Current Report on Form 8-K, filed with the SEC on January 27, 2025).

Amended and Restated Bylaws (incorporated by reference to Exhibit 3.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018).

Amendment to Amended and Restated Bylaws (incorporated by reference to Exhibit 3.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on April 14, 2023).

Form of Common Stock Certificate (incorporated by reference to Exhibit 4.1 to the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, originally filed with the SEC on June 28, 2018).

Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust (incorporated by reference to Exhibit 4.8 to the Registrant’s Registration Statement on Form S-1 (File No.

333-225970), as amended, originally filed with the SEC on June 28, 2018).

Form of Warrant to Purchase Common Stock for Service Providers (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on November 21, 2018) .

Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering (incorporated by reference to Exhibit 4.13 to the Registrant’s Registration Statement on Form S-1 (File No.

333-233828), as amended, originally filed with the SEC on September 18, 2019).

Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering) (incorporated by reference to Exhibit 4.16 to the Registrant’s Registration Statement on Form S-1 (File No.

333-237074), as amended, originally filed with the SEC on March 11, 2020).

Form of Warrant to Purchase Common Stock issued to Purchaser in October 2023 Offering (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023).

Form of Warrant to Purchase Common Stock issued to Investors in April 2024 Registered Direct Offering) (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on April 5, 2024).

Form of Warrant to Purchase Common Stock issued to Investors in April 2024 Registered Direct Offering ) (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on April 5, 2024).

Form of Senior Secured Convertible Debenture Due May 24, 2026 (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024).

Form of Pre-Funded Warrant to Purchase Common Stock issued to Investors in July 2024 Registered Direct Offering (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on July 8, 2024).

Form of Warrant to Purchase Series A Common Stock issued to Investors in July 2024 Registered Direct Offering (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on July 8, 2024).

Form of Warrant to Purchase Series B Common Stock issued to Investors in July 2024 Registered Direct Offering (incorporated by reference to Exhibit 4.3 to the Registrant’s Current Report on Form 8-K, filed with the SEC on July 8, 2024).

Form of Warrant to Purchase Series C Common Stock issued to Investors in October 2024 Registered Direct Offering (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 31, 2024).

Form of Warrant to Purchase Series D Common Stock issued to Investors in October 2024 Registered Direct Offering (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 31, 2024).

S et tlement Agreement and First Amendment to Debentures dated December 31, 2024 (inc orporated by reference to Exhibit 4.1 to the Registrant ’ s Current R eport on Form 8-K, filed wi th the SEC on January 3, 2025).

Form of Warrant to Purchase Common Stock issued to Investors in January 2025 Registered Direct Offering) (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on January 6, 2025).

Form of Pre-Funded Warrant to Purchase Common Stock issued to Investors in January 2025 Registered Direct Offering) (incorporated by reference to Exhibit 4.

2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on January 6, 2025).

Description of the Company’s Securities (incorporated by reference to Exhibit 4.5 to the Registrant's Annual Report on Form 10-K, filed with the SEC on March 5, 2024).

Form of Note, representing the Company’s Senior Secured Convertible Notes due 2025 (incorporated by reference to the Registrant's Current Report on Form 8-K filed with the SEC on October 11, 2023).

Number Description

Amendment to Initial Registered Note issued to Purchaser dated February 27, 2024 (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).

Form of Securities Purchase Agreement, dated April 4, 2024, by and among the Company and the Purchasers named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on April 5, 2024).

Form of Securities Purchase Agreement, dated July 4, 2024, by and among the Company and the Purchasers named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on July 8, 2024).

Form of Securities Purchase Agreement, dated October 30, 2024, by and among the Company and the Purchasers named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 31, 2024).

Form of Securities Purchase Agreement, dated January 3, 2025, by and among the Company and the Purchasers named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on January 6, 2025).

Bionano Genomics, Inc.

2018 Equity Incentive Plan, as amended (the “2018 Plan”).

Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan.

Forms of international grant notice, stock option agreement and notice of exercise under the 2018 Plan.

2018 Equity Incentive Plan, as amended (the “2018 Plan”) (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 13, 2020).

Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan (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).

Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan (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).

Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan (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).

Forms of international grant notice, stock option agreement and notice of exercise under the 2018 Plan (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).

Forms of restricted stock unit grant notice and restricted stock unit award agreement under the Bionano Genomics, Inc.

2018 Equity Incentive Plan.

2018 Equity Incentive Plan (incorporated by reference to Exhibit 10.1 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on August 4, 2021).

Bionano Genomics, Inc.

2018 Employee Stock Purchase Plan.

2018 Employee Stock Purchase Plan (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).

Bionano Genomics, Inc.

2020 Inducement Plan, as amended.

2020 Inducement Plan, as amended (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).

Form of Stock Option Grant Notice and Stock Option Agreement under the Bionano Genomics, Inc.

2020 Inducement Plan.

2020 Inducement Plan (incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2020).

Bionano Genomics, Inc.

Non-Employee Director Compensation Policy, as amended

Form of Indemnification Agreement by and between the Registrant and each director and executive officer.

Non-Employee Director Compensation Policy, as amended (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).

Form of Indemnification Agreement by and between the Registrant and each director and executive officer (incorporated by reference to Exhibit 10.7 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 10, 2020).

Employment Agreement by and between the Registrant and R.

Erik Holmlin, Ph.D., dated November 7, 2017, as amended.

Employment Agreement, effective as of September 1, 2020, by and between Christopher Stewart and the Company.

Employment Agreement, effective as of August 31, 2020, by and between Alka Chaubey and the Company.

Employment Agreement by and between the Registrant and Mark Oldakowski, dated November 7, 2017.

Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012.

First Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated September 10, 2013.

Second Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated July 1, 2015.

Third Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated December 19, 2019.

Fourth Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated February 15, 2021.

Fifth Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated January 12, 2022.

Standard Industrial/Commercial Single-Tenant Lease, made effective as of November 23, 2021, by and between the Company and 6777 Nancy Ridge LLC.

Erik Holmlin, Ph.D., dated November 7, 2017, as amended (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Employment Agreement, effective as of August 31, 2020, by and between Alka Chaubey and the Company (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).

Employment Agreement by and between the Registrant and Mark Oldakowski, dated November 7, 2017 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

First Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated September 10, 2013 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Second Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated July 1, 2015 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Third Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated December 19, 2019 (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).

Number Description

Fourth Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated February 15, 2021 (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).

Fifth Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated January 12, 2022.

(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).

Standard Industrial/Commercial Single-Tenant Lease, made effective as of November 23, 2021, by and between the Company and 6777 Nancy Ridge LLC (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).

Commercial Single-Tenant Lease – Net, dated February 28, 2016, by and between Tesa Beach LLC and BioDiscovery, Inc.

(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).

Lease, dated August 22, 2016, by and between SFF BBC, LLC and Purigen Biosystems, Inc.

First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016

Sales Agreement, dated March 23, 2021, by and between the Company and Cowen and Company, LLC.

Amendment No.

1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC.

License Agreement by and between Princeton University and the Registrant, dated January 7, 2004.

First Amendment to the License Agreement by and between Princeton University and the Registrant, dated December 17, 2004.

Second Amendment to the License Agreement by and between Princeton University and the Registrant, dated February 25, 2010.

Third Amendment to the License Agreement by and between Princeton University and the Registrant, dated October 17, 2011.

Fourth Amendment License Agreement by and between Princeton University and the Registrant, dated February 9, 2012.

(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).

First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016 (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).

At the Market Offering Agreement, dated February 21, 2025, by and between the Company and H.C.

Wainwright, LLC (incorporated by reference to Exhibit 10.1 of the Registrant’s Current Report on Form 8-K filed with the SEC on February 21, 2025).

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.

License Agreement by and between the Registrant and New York University dated November 4, 2013.

License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014.

Amendment to Non-Exclusive Patent License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014.

Manufacturing Services Agreement by and between the Registrant and Paramit Corporation, dated February 18, 2015.

Option and Sublicense Agreement by and between the Registrant and Pacific Biosciences of California, Inc.

dated February 2, 2016.

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.

Employment Agreement, effective as of September 11, 2023, by and between Gülsen Kama and the Company.

Transition, Separation and Consulting Agreement dated as of August 11, 2023, by and between Christopher Stewart and the Company.

Securities Purchase Agreement, dated October 11, 2023, by and among the Company and the Purchaser named therein.

Letter Agreement between the Company and the Purchaser named therein, dated February 27, 2024.

and f/k/a SVTC Technologies, LLC), dated March 2, 2009, as amended (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Manufacturing Services Agreement by and between the Registrant and Paramit Corporation, dated February 18, 2015 (incorporated by reference to Exhibit 10.24 to the Company’s Registration Statement on Form S-1 (File No.

333-225970), as amended).

Securities Purchase Agreement, dated October 11, 2023, by and among the Company and the Purchaser named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023).

Letter Agreement between the Company and the Purchaser named therein, dated February 27, 2024 (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024).

S e paration Agreement, effective as of February 20, 2025, by and between Gülsen Kama and the Company.

Securities Purchase Agreement, dated May 24, 2024, by and among the Company and the Buyers named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024)

Security Agreement, dated as of May 24, 2024, by and among the Company, BioDiscovery, LLC, Lineagen, Inc., Purigen Biosystems, Inc., and JGB Collateral LLC (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024)

Placement Agency Agreement, dated May 24, 2024, by and between the Company and Canaccord Genuity LLC (incorporated by reference to Exhibit 10.4 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024).

Registration Rights Agreement, dated May 24, 2024, by and between the Company and the Investors (incorporated by reference to Exhibit 10.5 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024)

Bionano Genomics, Inc.

I nsider Trading and Window Period Pol icy .

21.1 Subsidiaries of the Registrant.

Affiliates whose securities collateralize securities of the registrant

23.1 Consent of BDO USA , P.

, independent registered public accounting firm .

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.

31.1 Certification of Principal Executive Officer and 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 and Principal Financial Officer pursuant to 18 U.S.C.

Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

Bionano Genomics, Inc.

Incentive Compensation Recoupment Policy

Incentive Compensation Recoupment Policy (incorporated by reference to Exhibit 97.1 to the Registrant's Annual Report on Form 10-K, filed with the SEC on March 5, 2024).

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.

Number Description

101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document.

1 unchanged sentence

101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document.

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).

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.

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.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023

Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 4, 2023.

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

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.

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.

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

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.

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.

Incorporated by reference to Exhibit 4.13 of the Registrant’s Registration Statement on Form S-1 (File No.

333-233828), as amended.

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.

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.

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.

Incorporated by reference to Exhibit 4.2 of the Registrant’s Registration Statement on Form S-3 (File No.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Number Description

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on May 9, 2023

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Number Description

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.

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

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.

1 unchanged sentence

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.

# Portions of this exhibit have been omitted pursuant to Item 601(b)(2)(ii) of Regulation S-K.

The Company agrees to furnish supplementally an unredacted copy of the Exhibits to the SEC upon its request.

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.

The Registrant hereby agrees to furnish supplementally to the SEC, upon its request, an unredacted copy of this exhibit.

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.

9 unchanged sentences

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.

and Mark Adamchak 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.

2 unchanged sentences

Chief Executive Officer and Director

(Principal Executive Officer)

(Principal Executive and Principal Financial Officer)

March 31, 2025

Erik Holmlin, Ph.D.

/s/ Gülsen Kama

Chief Financial Officer

(Principal Financial and Accounting Officer)

/s/ Mark Adamchak

VP, Accounting

(Principal Accounting Officer)

March 31, 2025

Mark Adamchak

Barker, Ph.D.

22 unchanged sentences

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures