BNGO / Bionano Genomics, Inc. - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

Bionano Reports Second Quarter 2025 Results and Highlights Recent Business Progress Conference call today, August 14, 2025, at 4:30 PM ET

Bionano Reports Second Quarter 2025 Results and Highlights Recent Business Progress Conference call today, August 14, 2025, at 4:30 PM ET SAN DIEGO, August 14, 2025 (GLOBE NEWSWIRE) — Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2025 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-3

Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated J

ex-101bionanogenomicsinc BIONANO GENOMICS, INC.-9540 Towne Centre Drive-STES 100, 150, 155-6A3 6/18/2025-Opp-052433 1 SIXTH AMENDMENT THIS SIXTH AMENDMENT (the "Amendment") is made and entered into as of\ , by and between IRVINE EASTGATE OFFICE I LLC, a Delaware limited liability company, hereafter called “Landlord,” and BIONANO GENOMICS, INC., a Delaware corporation, hereafter called “Tenant.” RE

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 14, 2025 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 14, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):June 10, 2025

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):June 10, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporat

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):June 10, 2025 Bionano Genomics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):June 10, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fil

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2025 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-

Bionano Reports First Quarter 2025 Results and Highlights Recent Business Progress Conference call today, May 14, 2025, at 4:30 PM ET

Bionano Reports First Quarter 2025 Results and Highlights Recent Business Progress Conference call today, May 14, 2025, at 4:30 PM ET SAN DIEGO, May 14, 2025 (GLOBE NEWSWIRE) — Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2025 Bionano Genomics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fil

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))  ☐ Definitive Proxy St

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:          ☐     Preliminary Proxy Statement  ☐     Confidential, for Use of the Commission Only (as permitted by Rule

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:         ☒     Preliminary Proxy Statement  ☐     Confidential, for Use of the Commission Only (as permitted by Rule 1

As filed with the Securities and Exchange Commission on April 1, 2025

As filed with the Securities and Exchange Commission on April 1, 2025 Registration No.

Filing Fee Table.

Calculation of Filing Fee Table Form S-8 (Form Type) Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1. Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit(2) Maximum Aggregate Offering Price(2) Fee Rate Amount of Registration Fee Equity 2018 Equity Incentive Plan, as a

Bionano Genomics, Inc. 2020 Inducement Plan, as amended.

Exhibit 99.3 BIONANO GENOMICS, INC. 2020 INDUCEMENT PLAN ADOPTED BY THE BOARD OF DIRECTORS: AUGUST 20, 2020 AMENDED BY THE BOARD OF DIRECTORS: OCTOBER 6, 2021 AMENDED BY THE BOARD OF DIRECTORS: NOVEMBER 23, 2022 AMENDED BY THE BOARD OF DIRECTORS: MARCH 7, 2025 1. GENERAL. (a) Eligible Award Recipients. The only persons eligible to receive grants of Awards under this Plan are individuals who satisf

Up to $6,030,000 Common Stock

Filed Pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus Supplement Dated February 21, 2025 To Prospectus Dated May 10, 2023) Up to $6,030,000 Common Stock This prospectus supplement amends and supplements the information in the prospectus dated May 10, 2023 and the prospectus supplement, dated February 21, 2025 (the “ATM Prospectus Supplement” and, togethe

paration Agreement, effective as of February 20, 2025, by and between

Exhibit 10.19 February 20, 2025 Gülsen Kama Ramsey, New Jersey Re: Separation Agreement Dear Gülsen: This letter sets forth the substance of the separation agreement (the “Agreement”) that Bionano Genomics, Inc. (the “Company”) is offering to you to aid in your employment transition. 1.Separation. Your employment termination date will be September 18, 2024 (the “Separation Date”). Following the Se

Bionano Genomics, Inc.

Exhibit 19.1 BIONANO GENOMICS, INC. INSIDER TRADING AND WINDOW PERIOD POLICY I. INTRODUCTION This document sets forth the insider trading and window period policy (the “Policy”) of Bionano Genomics, Inc. (the “Company”).The purpose of this Policy is to clarify the circumstances under which trading in the stock of the Company or another publicly-traded company, including but not limited to a public

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 31, 2025 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 31, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

Bionano Reports Fourth Quarter and Full-Year 2024 Results and Provides Revenue Outlook for 2025 Conference call today, March 31, 2025 at 4:30 PM ET

Bionano Reports Fourth Quarter and Full-Year 2024 Results and Provides Revenue Outlook for 2025 Conference call today, March 31, 2025 at 4:30 PM ET SAN DIEGO, March 31, 2025 (GLOBE NEWSWIRE) – Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM Commission File Number 001-38613

Subsidiaries of the Registrant.

Exhibit 21.1 Subsidiaries of Bionano Genomics, Inc. Bionano Genomics UK, Ltd., a private limited company organized under the laws of the United Kingdom Bionano Genomics (Shanghai) Trading Co., Ltd., a private limited company organized under the laws of the China BioDiscovery, LLC, a California limited liability company Lineagen, Inc., a Delaware corporation doing business as Bionano Laboratories P

Up to $75,000,000

TABLE OF CONTENTS Filed Pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (to Prospectus dated May 10, 2023) Up to $75,000,000   Common Stock We have entered into a sales agreement dated February 21, 2025 (the “Sales Agreement”) with H.C. Wainwright & Co., LLC (“Wainwright”) relating to the issuance and sale of shares of our common stock, par value $0.0001 per share (the

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).

Exhibit 10.1 Execution Version AT THE MARKET OFFERING AGREEMENT February 21, 2025 H.C. Wainwright & Co., LLC 430 Park Avenue, 3rd Floor New York, New York 10022 Ladies and Gentlemen: Bionano Genomics, Inc., a corporation organized under the laws of Delaware (the “Company”), confirms its agreement (this “Agreement”) with H.C. Wainwright & Co., LLC (the “Manager”) as follows: 1. Definitions. The ter

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 21, 2025 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 21, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 4, 2025 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 4, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

Regulation FD Disclosure, Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Material Modification to Rights of Security Holders, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 24, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

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).

Exhibit 3.1 CERTIFICATE OF AMENDMENT TO THE AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF BIONANO GENOMICS, INC. Bionano Genomics, Inc. (the “Company”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the “DGCL”), hereby certifies that: ONE: The name of the Company is Bionano Genomics, Inc. The Company’s Certificate of Incorp

Bionano Announces Effective Date of Reverse Stock Split

Bionano Announces Effective Date of Reverse Stock Split SAN DIEGO, January 22, 2025 (GLOBE NEWSWIRE) – Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):January 15, 2025 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):January 15, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

Up to 50,555,556 Shares of Common Stock

TABLE OF CONTENTS Filed Pursuant to Rule 424(b)(3) Registration No. 333-284124 Prospectus   Up to 50,555,556 Shares of Common Stock In May 2024, we issued and sold pursuant to a Securities Purchase Agreement, dated May 24, 2024, with certain accredited investors (the “Selling Securityholders”) in a private placement, 2,250,000 shares (the “Upfront Shares”) of our common stock, $0.0001 par value pe

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 13, 2025 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 13, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

Bionano Reports Preliminary Fourth Quarter and Full-Year 2024 Results

Bionano Reports Preliminary Fourth Quarter and Full-Year 2024 Results •Preliminary Q4 2024 revenue expected to be between $7.

As filed with the Securities and Exchange Commission on January 8, 2025

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on January 8, 2025 Registration No.

BIONANO GENOMICS, INC. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121

BIONANO GENOMICS, INC. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121 VIA EDGAR January 8, 2025 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Industrial Applications and Services 100 F Street, N.E. Washington, D.C. 20549 Attn: Abby Adams Re: Bionano Genomics, Inc. Registration Statement on Form S-3 File No. 333-284124 Acceleration Request Requested Date:

Bionano Announces $10 Million Registered Direct Offering Priced At-the-Market under Nasdaq Rules

Exhibit 99.1 Bionano Announces $10 Million Registered Direct Offering Priced At-the-Market under Nasdaq Rules SAN DIEGO, January 3, 2025 – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that it has entered into a definitive agreement with certain institutional investors for the purchase and sale of an aggregate of 39,682,540 shares of its common stock (or common stock equivalents) and warra

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).

Exhibit 4.2 PRE-FUNDED COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date: , 2025 Initial Exercise Date: , 2025 THIS PRE-FUNDED COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 3, 2025 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 3, 2025 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

22,900,000 Shares of Common Stock Pre-Funded Warrants to Purchase up to 16,782,540 Shares of Common Stock Purchase Warrants to Purchase up to 39,682,540 Shares of Common Stock Up to 56,465,080 Shares of Common Stock Issuable Upon Exercise of the Pre-

TABLE OF CONTENTS Filed pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus dated May 10, 2023)   22,900,000 Shares of Common Stock   Pre-Funded Warrants to Purchase up to 16,782,540 Shares of Common Stock   Purchase Warrants to Purchase up to 39,682,540 Shares of Common Stock   Up to 56,465,080 Shares of Common Stock Issuable Upon Exercise of the Pre-Funded

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).

Exhibit 4.1 COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date: , 2025 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the Stockholder Approval Date (the “Initial Ex

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).

Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of January 3, 2025, between Bionano Genomics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on the signature pages hereto (each, including its successors and assigns, a “Purchaser” and collectively the “Purchasers”). WHEREAS, subject to the terms and conditions

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 31, 2024 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 31, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

As filed with the Securities and Exchange Commission on January 3, 2025

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on January 3, 2025 Registration No.

Bionano Announces Amendment to Senior Secured Convertible Debentures in Debt Restructuring that Improves Cash Runway

Exhibit 99.1 Bionano Announces Amendment to Senior Secured Convertible Debentures in Debt Restructuring that Improves Cash Runway Provides financial flexibility by reducing near-term debt maturities, deferring principal redemption payment, and reducing near-term cash needs SAN DIEGO, December 31, 2024 (GLOBE NEWSWIRE) – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that it has entered into

Settlement Agreement and First Amendment to Debentures dated December 31, 2024 (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on January 3, 2025).

Exhibit 4.1 SETTLEMENT AGREEMENT AND FIRST AMENDMENT TO SECURITIES PURCHASE AGREEMENT AND DEBENTURES This FIRST AMENDMENT (“Amendment”) is dated as of December 30, 2024, and is entered into by and among BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), each of the parties executing this Amendment as Guarantors (the “Guarantors” and each a “Guarantor”), and each purchaser identified o

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy Stat

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:  ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ D

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))  ☐ Definitive Proxy St

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):November 27, 2024 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported):November 27, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☒ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))  ☐ D

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2024 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number:

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 13, 2024 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 13, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

September 30, 2024

Bionano Reports Third Quarter 2024 Results and Highlights Recent Business Progress •Q3 2024 revenue was $6.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 30, 2024 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 30, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

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).

Exhibit 4.2 SERIES D COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date: , 2024 THIS SERIES D COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the Stockholder Approval Dat

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).

Exhibit 4.1 SERIES C COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date: , 2024 THIS SERIES C COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the Stockholder Approval Dat

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).

Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of October 30, 2024, between Bionano Genomics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on the signature pages hereto (each, including its successors and assigns, a “Purchaser” and collectively the “Purchasers”). WHEREAS, subject to the terms and condition

9,881,113 Shares of Common Stock Series C Warrants to Purchase up to 9,881,113 Shares of Common Stock Series D Warrants to Purchase up to 9,881,113 Shares of Common Stock

TABLE OF CONTENTS Filed pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus dated May 10, 2023)   9,881,113 Shares of Common Stock Series C Warrants to Purchase up to 9,881,113 Shares of Common Stock   Series D Warrants to Purchase up to 9,881,113 Shares of Common Stock   Up to 19,762,226 Shares of Common Stock Issuable Upon Exercise of the Series C Warrants

Bionano Announces $3 Million Registered Direct Offering Priced At- the-Market under Nasdaq Rules

Exhibit 99.1 Bionano Announces $3 Million Registered Direct Offering Priced At- the-Market under Nasdaq Rules SAN DIEGO, Oct. 31, 2024 – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that it has entered into a definitive agreement with certain institutional investors for the purchase and sale of an aggregate of 9,881,113 shares of its common stock and Series C warrants to purchase up to an

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 10, 2024 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 10, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or other jurisdiction of incorporation) (Commission

Bionano Announces Preliminary 3Q 2024 Revenues and Cash

Exhibit 99.1 Bionano Announces Preliminary 3Q 2024 Revenues and Cash SAN DIEGO, October 10, 2024 (GLOBE NEWSWIRE) – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced select preliminary results for the quarter ended September 30, 2024. The Company now expects revenue for the third quarter of 2024 to be between $6.5 and $6.8 million, down from prior guidance of between $7.9 and $8.9 million. Cas

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy State

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 4, 2024 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 4, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy Stat

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:  ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ D

Up to 35,026,272 Shares of Common Stock Issuable Upon Exercise of Warrants

TABLE OF CONTENTS Filed Pursuant to Rule 424(b)(3) Registration No. 333-281138 PROSPECTUS   Up to 35,026,272 Shares of Common Stock Issuable Upon Exercise of Warrants This prospectus relates to the resale from time to time by the selling securityholders identified in this prospectus (the “Selling Securityholders”) of up to 35,026,272 shares of our common stock, par value $0.0001 per share, compris

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☒ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))  ☐ D

BIONANO GENOMICS, INC. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121

BIONANO GENOMICS, INC. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121 VIA EDGAR August 8, 2024 U.S. Securities and Exchange Commission Division of Corporation Finance Office of Industrial Applications and Services 100 F Street, N.E. Washington, D.C. 20549 Attn: Abby Adams Re: Bionano Genomics, Inc. Registration Statement on Form S-3 File No. 333-281138 Acceleration Request Requested Date:

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.

Exhibit 10.8 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY [***], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL.MASTER SERVICES AGREEMENT MASTER SERVICES AGREEMENT This MASTER SERVICES AGREEMENT (the “Agreement”) is entered into effective as of March 2, 2009 (“E

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

Exhibit 10.13 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. Fourth Amendment to License Agreement AMENDMENT dated as of February 9th, 2012, to the License Agreement (“Agreement”) with an Effective Date of J

Option and Sublicense Agreement by and between the Registrant and Pacific Biosciences of California, Inc. dated February 2, 2016.

Exhibit 10.17 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. OPTION AND SUBLICENSE AGREEMENT THIS OPTION AND SUBLICENSE AGREEMENT (“Agreement”) dated as of February 2, 2016 (“Effective Date”), is entered int

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

MANUFACTURING SERVICES AGREEMENT Exhibit 10.9 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. This AGREEMENT is entered into by Paramit Corporation, a California corporation (referred to in this agreement as

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

Exhibit 10.14 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. NON-EXCLUSIVE PATENT LICENSE AGREEMENT This non-exclusive patent license agreement (“Agreement”), by and between Q Biotechnology C.V. (“Licensor”)

June 30, 2024

Bionano Reports Second Quarter 2024 Results and Highlights Recent Business Progress •Q2 2024 revenue was $7.

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

Exhibit 10.12 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. Second Amendment to License Agreement AMENDMENT dated as of February 25, 2010, to the License Agreement (“Agreement”) with an Effective Date of Ja

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2024 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-3

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

Exhibit 10.15 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. AMENDMENT to the NON-EXCLUSIVE PATENT LICENSE AGREEMENT dated 01 May 2014 (the “Amendment”) effective as of 01 January 2018 (the “Effective Date”)

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

Exhibit 10.10 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. LICENSE AGREEMENT BETWEEN PRINCETON UNIVERSITY AND BIONANOMATRIX LLC TABLE OF CONTENTS Page 1. Definitions 1 2. Grant of License 4 2.1 Grant of Li

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 7, 2024 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 7, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

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

Exhibit 10.11 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. First Amendment to License Agreement AMENDMENT dated as of December 17, 2004, to the License Agreement with an Effective Date of January 7th, 2004

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

Exhibit 10.16 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY […***…], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. LICENSE AGREEMENT This Agreement, effective as of November 4, 2013 (the “Effective Date”), is by and between: NEW YORK UNIVERSITY (hereinafter “NY

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Bionano Genomics, Inc.

As filed with the Securities and Exchange Commission on July 31, 2024

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on July 31, 2024 Registration No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 12, 2024 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 12, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

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).

Exhibit 4.3 NEITHER THIS SECURITY NOR THE SECURITIES FOR WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE REGISTR

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).

Exhibit 10.1 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY [**], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of July 4, 2024, between Bionano Genomics, Inc., a Dela

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).

Exhibit 4.1 PRE-FUNDED COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date: , 2024 Initial Exercise Date: , 2024 THIS PRE-FUNDED COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or

Bionano Announces up to $30 Million Registered Direct Offering Priced At-The-Market Under Nasdaq Rules $10 million upfront with up to an additional $20 million upon the exercise in full of clinical milestone-linked Series Warrants

Exhibit 99.1 Bionano Announces up to $30 Million Registered Direct Offering Priced At-The-Market Under Nasdaq Rules $10 million upfront with up to an additional $20 million upon the exercise in full of clinical milestone-linked Series Warrants SAN DIEGO, July 5, 2024 – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that it has entered into definitive agreements with healthcare-focused insti

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).

Exhibit 4.2 NEITHER THIS SECURITY NOR THE SECURITIES FOR WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE REGISTR

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 4, 2024 Bionano Genomics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 4, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fil

11,700,000 Shares of Common Stock Pre-Funded Warrants to Purchase up to 5,813,136 Shares of Common Stock

TABLE OF CONTENTS Filed pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus dated May 10, 2023)   11,700,000 Shares of Common Stock Pre-Funded Warrants to Purchase up to 5,813,136 Shares of Common Stock Pursuant to this prospectus supplement and the accompanying prospectus, we are offering in a registered direct offering to certain purchasers (i) 11,700,000

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 18, 2024 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 18, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

Up to 12,250,000 Shares of Common Stock

TABLE OF CONTENTS Filed Pursuant to Rule 424(b)(3) Registration No. 333-280098 PROSPECTUS   Up to 12,250,000 Shares of Common Stock In May 2024, we issued and sold pursuant to a Securities Purchase Agreement, dated May 24, 2024 (the “Purchase Agreement”), with certain accredited investors (the “Selling Securityholders”) in a private placement, 2,250,000 shares (the “Upfront Shares”) of our common

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 June 17, 2024

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 June 17, 2024 VIA EDGAR United States Securities and Exchange Commission Division of Corporation Finance Office of Industrial Applications and Services 100 F Street, NE Washington, DC 20549 Attention: Jane Park Re: Bionano Genomics, Inc. Registration Statement on Form S-3 Filed June 10, 2024 File No. 333-280098 L

As filed with the Securities and Exchange Commission on June 10, 2024

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on June 10, 2024 Registration No.

Calculation of Filing Fee Tables FORM S-3 (Form Type) Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities*

Exhibit 107 Calculation of Filing Fee Tables FORM S-3 (Form Type) Bionano Genomics, Inc.

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).

Exhibit 4.1 EXHIBIT A NEITHER THIS SECURITY NOR THE SECURITIES INTO WHICH THIS SECURITY IS CONVERTIBLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECT

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).

Exhibit 10.4 PLACEMENT AGENCY AGREEMENT May 24, 2024 Bionano Genomics, Inc. 9540 Towne Centre Drive Suite 100 San Diego, California 92121 Ladies and Gentlemen: This agreement (the “Agreement”) constitutes the agreement between Canaccord Genuity LLC (the “Placement Agent”) and Bionano Genomics, Inc., a Delaware corporation (the “Company”), pursuant to which the Placement Agent shall serve as the ex

Letter Agreement Re: Agreement to Redeem Senior Secured Convertible Notes due 2025, dated May 23, 2024, by and between the Company and High Trail Special Situations LLC (incorporated by reference to Exhibit 10.6 to the Registrant’s Current Report on Form 8-K, filed with the SEC on May 28, 2024)

Exhibit 10.6 HIGH TRAIL CAPITAL LP 80 River Street, Suite 4C Hoboken, NJ 07030 May 23, 2024 Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121 Attn: R. Erik Holmlin Re: Agreement to Redeem Senior Secured Convertible Notes due 2025 To the addressees set forth above: Reference is made to that certain Securities Purchase Agreement (the “Securities Purchase Agreement”), date

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)

Exhibit 10.2 SECURITY AGREEMENT This SECURITY AGREEMENT, dated as of May 24, 2024 (this “Agreement”), is among Bionano Genomics, Inc, a Delaware corporation (the “Company”), the Subsidiaries of the Company party hereto (such subsidiaries, the “Guarantors” and together with the Company, the “Debtors”) and the holders of the Company’s 11.0% Senior Secured Convertible Debentures Due May 24, 2026, in

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)

Exhibit 10.1 Execution Version SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of May 24, 2024, between Bionano Genomics, Inc, a Delaware corporation (the “Company”), each buyer identified on the signature pages hereto (each, including its successors and assigns, a “Buyer” and collectively, the “Buyers”), and JGB Collateral LLC, a Delaware limited li

Subsidiary Guaranty, dated as of May 24, 2024, by BioDiscovery LLC, Lineagen, Inc., Purigen Biosystems, Inc. in favor the Investors

Exhibit 10.3 SUBSIDIARY GUARANTEE SUBSIDIARY GUARANTEE, dated as of May 24, 2024 (this “Guarantee”), made by each of the signatories hereto (together with any other entity that may become a party hereto as provided herein, the “Guarantors”), in favor of the purchasers signatory (together with their permitted assigns, the “Purchasers”) to that certain Securities Purchase Agreement, dated as of the

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)

Exhibit 10.5 Execution Version REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is made and entered into as of May 24, 2024, between Bionano Genomics, Inc., a Delaware corporation (the “Company”), and each of the several purchasers signatory hereto (each such purchaser, a “Purchaser” and, collectively, the “Purchasers”). This Agreement is made pursuant to the Sec

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 23, 2024 Bionano Genomics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 23, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fil

Bionano Announces Private Placement of Senior Secured Notes in Debt Restructuring that Improves Balance Sheet Provides significant financial flexibility by` retiring near-term debt maturities, deferring principal redemption payments, and further redu

Exhibit 99.1 Bionano Announces Private Placement of Senior Secured Notes in Debt Restructuring that Improves Balance Sheet Provides significant financial flexibility by` retiring near-term debt maturities, deferring principal redemption payments, and further reducing near-term cash needs. SAN DIEGO, May 28, 2024 (GLOBE NEWSWIRE) – Bionano Genomics Inc. (“Bionano” or the “Company”) (NASDAQ: BNGO) t

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2024 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-

March 31, 2024

Bionano Reports First Quarter 2024 Results and Highlights Recent Business Progress •Q1 2024 revenue was $8.

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Form S-8 (Form Type) Bionano Genomics, Inc.

As filed with the Securities and Exchange Commission on May 8, 2024

As filed with the Securities and Exchange Commission on May 8, 2024 Registration No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 8, 2024 Bionano Genomics, Inc

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 8, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission File

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant   ☐ Check the appropriate box:  ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant   ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy Sta

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 8, 2024 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 8, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

6,536,682 Shares of Common Stock Pre-Funded Warrants to Purchase up to 2,196,944 Shares of Common Stock Warrants to Purchase up to 8,733,626 Shares of Common Stock

TABLE OF CONTENTS Filed pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus dated May 10, 2023)   6,536,682 Shares of Common Stock   Pre-Funded Warrants to Purchase up to 2,196,944 Shares of Common Stock   Warrants to Purchase up to 8,733,626 Shares of Common Stock Pursuant to this prospectus supplement and the accompanying prospectus, we are offering in a r

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).

Exhibit 10.1 CERTAIN INFORMATION CONTAINED IN THIS EXHIBIT, MARKED BY [**], HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE THE REGISTRANT HAS DETERMINED THAT IT IS BOTH NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of April 4, 2024, between Bionano Genomics, Inc., a Del

Bionano Announces $10 Million Registered Direct Offering Priced At-The-Market Under Nasdaq Rules

Exhibit 99.1 Bionano Announces $10 Million Registered Direct Offering Priced At-The-Market Under Nasdaq Rules SAN DIEGO, April 4, 2024 – Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that it has entered into definitive agreements for the purchase and sale of an aggregate of 8,733,626 shares of its common stock (or common stock equivalents in lieu thereof) and warrants to purchase up to an

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).

Exhibit 4.2 COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date:, 2024 Initial Exercise Date: , 2024 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or after the date set fort

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 4, 2024 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 4, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

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).

Exhibit 4.1 PRE-FUNDED COMMON STOCK PURCHASE WARRANT BIONANO GENOMICS, INC. Warrant Shares: Issue Date:, 2024 Initial Exercise Date: , 2024 THIS PRE-FUNDED COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at any time on or a

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 1, 2024 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 1, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

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).

Exhibit 4.1 DE L AWA RE SEAL BIONANO GENOMICS, INC. CORPORATE AUGUST 16, 2007 This certifies that is the record holder of INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE CUSIP 0975F10 7 SEE REVERSE FOR CERTAIN DEFINITIONS AND LEGENDS COUNTERSIGNED AND REGISTERED: AMERICAN STOCK TRANSFER & TRUST COMPANY, LLC (BROOKLYN, NY) TRANSFER AGENT AND REGISTRAR BY: AUTHORIZED SIGNATURE PRESIDENT & CEO F

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).

Exhibit 4.5 DESCRIPTION OF SECURITIES General The following summary describes Bionano Genomic, Inc.’s (or “we,” “our” or “us”) securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), certain provisions of our amended and restated certificate of incorporation, as amended (“Restated Certificate”), amended and restated and bylaws, as amended (“B

Bionano Genomics, Inc. Incentive Compensation Recoupment Policy

Exhibit 97.1 Bionano Genomics, Inc. Incentive Compensation Recoupment Policy 1.Introduction The Board of Directors (the “Board”) of Bionano Genomics, Inc., a Delaware corporation (the “Company”), has determined that it is in the best interests of the Company and its stockholders to adopt this Incentive Compensation Recoupment Policy (this “Policy”) providing for the Company’s recoupment of Recover

Affiliates whose securities collateralize securities of the registrant

Exhibit 22.1 Bionano Genomics, Inc. Subsidiary Guarantors Bionano Genomics, Inc. (“Bionano”) issued (i) in a registered offering, $45 million aggregate principal amount of senior secured convertible notes due in 2025 and (ii) in a private placement, $35 million aggregate principal amount of senior secured convertible notes due in 2025 (collectively, the “Notes”). The following subsidiaries of Bion

Bionano Reports Fourth Quarter and Full-Year 2023 Results and Provides Revenue Outlook for 2024

Bionano Reports Fourth Quarter and Full-Year 2023 Results and Provides Revenue Outlook for 2024 •Q4 2023 revenue was $10.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM Commission File Number 001-38613

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).

Exhibit 10.1 HIGH TRAIL CAPITAL LP 80 River Street, Suite 4C Hoboken, NJ 07030 February 27, 2024 Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, CA 92121 Attn: R. Erik Holmlin Re: Agreement to Redeem Senior Secured Convertible Notes due 2025 To the addressees set forth above: Reference is made to that certain Securities Purchase Agreement (the “Securities Purchase Agreement”),

Amendment to Initial Registered Note issued to Purchaser dated February 27, 2024 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on February 28, 2024).

Exhibit 10.2 AMENDMENT TO INITIAL REGISTERED NOTE This AMENDMENT TO INITIAL REGISTERED NOTE (this “Amendment”), dated February 27, 2024, is entered into by and among Bionano Genomics, Inc., a Delaware corporation, (the “Company”), and the investor listed on the Schedule of Buyers (the “Buyer”) attached to the Purchase Agreement (defined below). The Company and the Buyer each may be hereinafter ref

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 27, 2024 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 27, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

Bionano Announces Amendment to Debt Financing Arrangement to Extend Cash Runway - Amendment Reduces Bionano’s Outstanding Debt -

Exhibit 99.1 Bionano Announces Amendment to Debt Financing Arrangement to Extend Cash Runway - Amendment Reduces Bionano’s Outstanding Debt - SAN DIEGO, February 28, 2024 - Bionano Genomics, Inc. (“Bionano”) (Nasdaq: BNGO) today announced that is has amended the convertible debt financing the company entered into in October 2023 pursuant to which the company agreed to issue and sell to a certain a

US09075F3055 / Bionano Genomics Inc / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 2)* Name of issuer: Bionano Genomics Inc Title of Class of Securities: Common Stock CUSIP Number: 09075F305 Date of Event Which Requires Filing of this Statement: December 29, 2023 Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 8, 2024 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 8, 2024 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

Bionano Reports Preliminary Fourth Quarter and Full-Year 2023 Results

Exhibit 99.1 Bionano Reports Preliminary Fourth Quarter and Full-Year 2023 Results • Preliminary Q4 2023 revenue expected to be between $10.4 and $10.7 million, which would represent an estimated increase of 27% to 30% over Q4 2022 • Reached installed base of 326 optical genome mapping (OGM) systems as of YE 2023; increase of 36% over the 240 installed systems as of YE 2022 • Preliminary number of

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 24, 2023 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 24, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

September 30, 2023

Bionano Reports Third Quarter 2023 Results and Highlights Recent Business Progress •Q3 2023 revenue was $9.

Up to $35,000,000 of Senior Secured Convertible Notes due 2025 Up to 12,221,738 Shares of Common Stock

TABLE OF CONTENTS Filed Pursuant to Rule 424(b)(3) Registration No. 333-275181 PROSPECTUS   Up to $35,000,000 of Senior Secured Convertible Notes due 2025 Up to 12,221,738 Shares of Common Stock In October 2023, we issued and sold pursuant to a Securities Purchase Agreement, dated October 11, 2023 (the “Purchase Agreement”), with an institutional investor (the “Selling Securityholder”) (i) in a re

November 2023 Q3 2023 Financial Results Webcast & Call © Copyright 2023, Bionano Genomics, Inc. Legal Disclaimer This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words s

November 2023 Q3 2023 Financial Results Webcast & Call © Copyright 2023, Bionano Genomics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2023 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number:

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 8, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

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

Exhibit 10.2 August 13, 2023 Christopher Stewart Re: Transition, Separation, and Consulting Agreement Dear Chris: This letter sets forth the substance of the separation and consulting agreement (the “Agreement”) that Bionano Genomics, Inc. (the “Company”) is offering to you to aid in your employment transition. 1.Separation. If you timely sign and return this Agreement to the Company and comply wi

Amended and Restated Certificate of Incorporation, as amended.

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF BIONANO GENOMICS, INC. Erik Holmlin, Ph.D. hereby certifies that: ONE: The original name of this company was BioNanomatrix, Inc. and the date of filing the original Certificate of Incorporation of this company with the Secretary of State of the State of Delaware was August 16, 2007. TWO: He is the duly elected and acting President an

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

DocuSign Envelope ID: 5E8E3E16-FAC3-425B-BBD7-B46CA6B50B27 Exhibit 10.1 EMPLOYMENT AGREEMENT This EMPLOYMENT AGREEMENT (the “Agreement”) is made and entered into effective as of September 11, 2023 (the “Effective Date” or “Start Date”), by and between BIONANO GENOMICS, INC. (the “Company”) and Gulsen Kama (“Executive”). The Company and Executive are hereinafter collectively referred to as the “Par

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

Execution Version Exhibit 2.1 SECOND AMENDMENT TO AGREEMENT AND PLAN OF MERGER This First Amendment to Agreement and Plan of Merger (this “Amendment”) is made as of July 15, 2023 (the “Effective Date”) by and among Bionano Genomics, Inc., a Delaware corporation (“Parent”), and Soheil Shams, as the Securityholders’ Representative (“Securityholders’ Representative”). Recitals A.Parent, Starship Merg

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 (858) 888-7600

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 (858) 888-7600 November 2, 2023 Via Edgar United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attn: Jessica Ansart Re: Bionano Genomics, Inc. Registration Statement on Form S-3 File No. 333-275181 Ladies and Gentlemen: Pursuant to Rule 461 und

FORM OF WARRANT BIONANO GENOMICS, INC. WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.2 FORM OF WARRANT BIONANO GENOMICS, INC. WARRANT TO PURCHASE COMMON STOCK Warrant No.: BNGOW-1 Number of Shares of Common Stock: 21,660,650 Date of Issuance: [], 2023 (“Issuance Date”) Bionano Genomics, Inc., a corporation organized under the laws of Delaware (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby ackno

Calculation of Filing Fee Table Form S-3 (Form Type) Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities

Exhibit 107 Calculation of Filing Fee Table Form S-3 (Form Type) Bionano Genomics, Inc.

As filed with the Securities and Exchange Commission on October 26, 2023

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on October 26, 2023 Registration No.

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

Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (the “Agreement”), dated as of October 11, 2023, is by and among Bionano Genomics, Inc., a Delaware corporation with offices located at 9540 Towne Centre Drive, Suite 100, San Diego, CA 92121 (the “Company”), and each of the investors listed on the Schedule of Buyers attached hereto (individually, a “Buyer” and collectiv

Bionano Prices $80.0 Million Financing in Convertible Notes and Warrants, Announces Preliminary Q3 2023 Results, and Implements Streamlined Operational Plan

Exhibit 99.1 Bionano Prices $80.0 Million Financing in Convertible Notes and Warrants, Announces Preliminary Q3 2023 Results, and Implements Streamlined Operational Plan • Bionano announced today that it has priced a financing to raise an aggregate of $80.0 million in a registered offering and concurrent private placement of senior secured convertible notes due 2025 and warrants • Preliminary Q3 r

Bionano Announces Pricing of $80.0 Million Registered Offering and Concurrent Private Placement of Senior Secured Convertible Notes and Warrants

Exhibit 99.2 Bionano Announces Pricing of $80.0 Million Registered Offering and Concurrent Private Placement of Senior Secured Convertible Notes and Warrants SAN DIEGO, Oct. 11, 2023 - Bionano Genomics, Inc. (Nasdaq: BNGO) today announced the pricing of (i) $45.0 million aggregate principal amount of senior secured convertible notes due 2025 (the “Registered Notes”) and warrants (the “Registered W

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).

Exhibit 4.2 FORM OF WARRANT BIONANO GENOMICS, INC. WARRANT TO PURCHASE COMMON STOCK Warrant No.: BNGOW-1 Number of Shares of Common Stock: 21,660,650 Date of Issuance: [], 2023 (“Issuance Date”) Bionano Genomics, Inc., a corporation organized under the laws of Delaware (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby ackno

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

Exhibit 4.1 Bionano Genomics, Inc. Form of Senior Secured Convertible Note due 2025 Bionano Genomics, Inc. Senior Secured Convertible Note due 2025 Certificate No. A-[ ● ] Bionano Genomics, Inc., a Delaware corporation (the “Company”), for value received, promises to pay to [***] (the “Initial Holder”), or its registered assigns, the amount equal to the product of (x) the principal sum of $45,000,

Up to $45,000,000 of Senior Secured Convertible Notes due 2025 Warrants to Purchase Up to 21,660,650 Shares of our Common Stock

Filed pursuant to Rule 424(b)(5) Registration No. 333-270459 PROSPECTUS SUPPLEMENT (To Prospectus dated May 10, 2023) Up to $45,000,000 of Senior Secured Convertible Notes due 2025 Warrants to Purchase Up to 21,660,650 Shares of our Common Stock We entered into a Securities Purchase Agreement, dated October 11, 2023 (the “Purchase Agreement”) with High Trail Special Situations LLC (the “Purchaser”

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 9, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 9, 2023 Bionano Genomics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38613 26-1756290 (State or other jurisdiction of incorporation) (Commission

Bionano Announces CFO Transition and Appointment of Gülsen Kama as Chief Financial Officer

Exhibit 99.1 Bionano Announces CFO Transition and Appointment of Gülsen Kama as Chief Financial Officer SAN DIEGO, August 14, 2023 (GLOBE NEWSWIRE) - Bionano Genomics, Inc. (Nasdaq: BNGO) today announced that Gülsen Kama will serve as its next Chief Financial Officer (CFO), effective September 11, 2023. Christopher Stewart, who held the position of CFO since September 2020, will stay on during the

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 11, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 11, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

June 30, 2023

Bionano Reports Second Quarter 2023 Results and Highlights Recent Business Progress •Q2 2023 revenue was $8.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2023 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-3

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 9, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 9, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

Certificate of Elimination of Series A Preferred Stock.

Exhibit 3.2 CERTIFICATE OF ELIMINATION OF SERIES A PREFERRED STOCK OF BIONANO GENOMICS, INC. (Pursuant to Section 151(g) of the General Corporation Law of the State of Delaware) Bionano Genomics, Inc. (the “Company”), a corporation duly organized and existing under the General Corporation Law of the State of Delaware (the “DGCL”), hereby certifies as follows: First: That, pursuant to Section 151 o

Amended and Restated Certificate of Incorporation, as amended.

Exhibit 3.1 CERTIFICATE OF AMENDMENT TO THE AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF BIONANO GENOMICS, INC. Bionano Genomics, Inc. (the “Company”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware (the “DGCL”), hereby certifies that: One: The name of the Company is Bionano Genomics, Inc. The Company’s Certificate of Incorp

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 4, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 4, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 18, 2023 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 18, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 14, 2023 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 14, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or other jurisdiction of incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 30, 2023 Bionano Genomics, In

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 30, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fil

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2023 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-

First Amendment to Agreement and Plan of Merger, dated March 4, 2023, by and between the Company and Soheil Shams, as the Securityholders’ Representative.

EX-21 3 exhibit21bngo-firstamendme.htm EX-21 Exhibit 2.1 CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. Execution Version FIRST AMENDMENT TO AGREEMENT AND PLAN OF MERGER This First Amendment to Agreement and Plan of Merger (this “Amendment”

March 31, 2023

Bionano Reports First Quarter 2023 Results and Highlights Recent Business Progress •Q1 2023 revenue was $7.

Amendment No. 1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC.

Exhibit 10.1 AMENDMENT NO. 1 TO SALES AGREEMENT March 9, 2023 This Amendment No. 1 (“Amendment No. 1”) amends that certain Sales Agreement, dated as of March 23, 2021 (the “Agreement”), by and between Bionano Genomics, Inc. (the “Company”) and Cowen and Company, LLC, as sales agent (the “Agent”). Defined terms used herein and not otherwise defined shall have the meaning assigned to such terms in t

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 9, 2023 Bionano Genomics, Inc

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 9, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission File

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 (858) 888-7600

Bionano Genomics, Inc. 9540 Towne Centre Drive, Suite 100 San Diego, California 92121 (858) 888-7600 May 8, 2023 Via Edgar United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attn: Jane Park Re: Bionano Genomics, Inc. Registration Statement on Form S-3 File No. 333-270459 Ladies and Gentlemen: Pursuant to Rule 461 under the Sec

As filed with the Securities and Exchange Commission on May 8, 2023

As filed with the Securities and Exchange Commission on May 8, 2023 Registration No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☐ Definitive Proxy Stat

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2))  ☐ Definitive Proxy St

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:  ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ☒ Definitive Proxy St

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 24, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 24, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

UPDATE - Bionano Announces Preliminary Q1 2023 Results and Business Updates

Exhibit 99.1 UPDATE - Bionano Announces Preliminary Q1 2023 Results and Business Updates • Preliminary Q1 total revenue expected to be between $7.3 and $7.5 million, which would represent an estimated increase of 28% to 32% over Q1 2022 • Installed base of Saphyr® systems reached 259 as of March 31, 2023, which represents growth of the installed base by 19 systems in the quarter and an increase of

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).

Exhibit 3.2 AMENDMENT TO AMENDED AND RESTATED BYLAWS OF BIONANO GENOMICS, INC. (A DELAWARE CORPORATION) The Amended and Restated Bylaws, as amended (the “Bylaws”) of Bionano Genomics, Inc., a Delaware corporation (the “Company”), are hereby amended as follows effective as of April 13, 2023. 1. Section 8 of Article III of the Bylaws is hereby amended and restated in its entirety to read as follows:

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 13, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 13, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

Certificate of Designation of Preferences, Rights and Limitations of Series A Preferred Stock

Exhibit 3.1 Bionano Genomics, Inc. Certificate of Designation of Preferences, Rights and Limitations of Series A Preferred Stock Pursuant to Section 151 of the General Corporation Law of the State of Delaware Bionano Genomics, Inc., a Delaware corporation (the “Corporation”), hereby certifies that the following recital and resolution were duly adopted by the board of directors of the Corporation (

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934

PRE 14A 1 ny20008379x1pre14a.htm PRE 14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box: ☒ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission Only (as permitted by

Purchase Agreement

Exhibit 10.1 Purchase Agreement This Purchase Agreement (this “Agreement”) is made as of April 13, 2023, by and between the purchaser listed on Exhibit A attached hereto (the “Purchaser”) and Bionano Genomics, Inc., a Delaware corporation (the “Company”). Recitals Whereas, the Company desires to sell to the Purchaser, and the Purchaser desires to purchase from the Company, one (1) share of Series

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 13, 2023 Bionano Genomics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 13, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

Power of Attorney (reference is made to the signature page of the Registration Statement on Form S-3 filed by the Registrant on March 10, 2023).

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on March 10, 2023 Registration No.

Form of Common Stock Warrant Agreement and Warrant Certificate.

EXHIBIT 4.14 BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF COMMON STOCK WARRANT AGREEMENT DATED AS OF [ ], 20 BIONANO GENOMICS, INC. FORM OF COMMON STOCK WARRANT AGREEMENT This COMMON STOCK WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and existing unde

Form of Debt Indenture.

EXHIBIT 4.12 BIONANO GENOMICS, INC., Issuer AND [TRUSTEE], Trustee INDENTURE Dated as of [•], 20 Debt Securities Table Of Contents PAGE ARTICLE 1 DEFINITIONS 1 Section 1.01 Definitions of Terms 1 ARTICLE 2 ISSUE, DESCRIPTION, TERMS, EXECUTION, REGISTRATION AND EXCHANGE OF SECURITIES 5 Section 2.01 Designation and Terms of Securities 5 Section 2.02 Form of Securities and Trustee’s Certificate 8 Sec

Form of Preferred Stock Warrant Agreement and Warrant Certificate.

EXHIBIT 4.15 BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF PREFERRED STOCK WARRANT AGREEMENT DATED AS OF [ ], 20 BIONANO GENOMICS, INC. FORM OF PREFERRED STOCK WARRANT AGREEMENT This PREFERRED STOCK WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and exis

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Form S-3 (Form Type) Bionano Genomics, Inc.

Form of Debt Securities Warrant Agreement and Warrant Certificate.

EXHIBIT 4.16 BIONANO GENOMICS, INC. and , AS WARRANT AGENT FORM OF DEBT SECURITIES WARRANT AGREEMENT DATED AS OF [ ], 20 BIONANO GENOMICS, INC. FORM OF DEBT SECURITIES WARRANT AGREEMENT This DEBT SECURITIES WARRANT AGREEMENT (this “Agreement”), dated as of between BIONANO GENOMICS, INC., a Delaware corporation (the “Company”), and , a [corporation] [national banking association] organized and exis

Amendment No. 1 to Sales Agreement, dated March 9, 2023, by and between the Company and Cowen and Company, LLC (incorporated by reference to Exhibit 1.3 of the Registrant's Registration Statement on Form S-3 (File No. 333-270459), filed March 10, 2023).

Exhibit 1.3 AMENDMENT NO. 1 TO SALES AGREEMENT March 9, 2023 This Amendment No. 1 (“Amendment No. 1”) amends that certain Sales Agreement, dated as of March 23, 2021 (the “Agreement”), by and between Bionano Genomics, Inc. (the “Company”) and Cowen and Company, LLC, as sales agent (the “Agent”). Defined terms used herein and not otherwise defined shall have the meaning assigned to such terms in th

AMENDMENT NO. 1 TO SALES AGREEMENT March 9, 2023

Exhibit 1.3 AMENDMENT NO. 1 TO SALES AGREEMENT March 9, 2023 This Amendment No. 1 (“Amendment No. 1”) amends that certain Sales Agreement, dated as of March 23, 2021 (the “Agreement”), by and between Bionano Genomics, Inc. (the “Company”) and Cowen and Company, LLC, as sales agent (the “Agent”). Defined terms used herein and not otherwise defined shall have the meaning assigned to such terms in th

Subsidiaries of the Registrant.

Exhibit 21.1 Subsidiaries of Bionano Genomics, Inc. Bionano Genomics UK, Ltd., a private limited company organized under the laws of the United Kingdom Bionano Genomics (Shanghai) Trading Co., Ltd., a private limited company organized under the laws of the China BioDiscovery, Inc, a California limited liability company Lineagen, Inc., a Delaware corporation doing business as Bionano Laboratories P

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

Exhibit 10.2C Double-Trigger Form Bionano Genomics, Inc. Stock Option Grant Notice (2018 Equity Incentive Plan) Bionano Genomics, Inc. (the “Company”), pursuant to its 2018 Equity Incentive Plan (the “Plan”), hereby grants to Optionholder an option to purchase the number of shares of the Company’s Common Stock set forth below. This option is subject to all of the terms and conditions as set forth

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

Exhibit 10.2A Standard Form Bionano Genomics, Inc. Stock Option Grant Notice (2018 Equity Incentive Plan) Bionano Genomics, Inc. (the “Company”), pursuant to its 2018 Equity Incentive Plan (the “Plan”), hereby grants to Optionholder an option to purchase the number of shares of the Company’s Common Stock set forth below. This option is subject to all of the terms and conditions as set forth in thi

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

Exhibit 10.14A FIRST AMENDMENT TO LEASE THIS FIRST AMENDMENT TO LEASE (this “Amendment”) is dated as of August 6, 2021, between SFF BBC, LLC, a California limited liability company (“Landlord”), and PURIGEN BIOSYSTEMS, INC., a Delaware corporation (“Tenant”). RECITALS A. Landlord and Tenant are parties to that certain lease dated August 22, 2016 (the “Lease”), pursuant to which Tenant leases from

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

Exhibit 10.14 LEASE 5700 Stoneridge Drive Pleasanton, California Basic Lease Information 279330373 v2 Date: August 22, 2016 Landlord: SFF BBC, LLC, a California limited liability company Tenant: PURIGEN BIOSYSTEMS, INC., a Delaware corporation Building (section 1.1): That certain building located at 5700 Stoneridge Drive, Pleasanton, California Premises (section 1.1): A portion of the first (1st)

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.

Exhibit 10.22 CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. S05-338: CDT AMENDED AND RESTATED EXCLUSIVE LICENSE AGREEMENT 8/3/2021 AMENDED AND RESTATED EXCLUSIVE LICENSE AGREEMENT WITH EQUITY This Amended and Restated Exclusive License Agr

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Form S-8 (Form Type) Bionano Genomics, Inc.

As filed with the Securities and Exchange Commission on March 9, 2023

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on March 9, 2023 Registration No.

Calculation of Filing Fee Table Form S-3 (Form Type) Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities

Exhibit 107 Calculation of Filing Fee Table Form S-3 (Form Type) Bionano Genomics, Inc.

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.

Exhibit 10.22A CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. S05-338 · CDTAmendment11/12/2022 AMENDMENT № 1 TO THE AMENDED AND RESTATED EXCLUSIVE LICENSE AGREEMENT EFFECTIVE THE 16th DAY OF JULY 2021 BETWEEN STANFORD UNIVERSITY AND PURIGEN

As filed with the Securities and Exchange Commission on March 9, 2023

As filed with the Securities and Exchange Commission on March 9, 2023 Registration No.

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

Exhibit 10.2B Non-Employee Director Form Bionano Genomics, Inc. Stock Option Grant Notice (2018 Equity Incentive Plan) Bionano Genomics, Inc. (the “Company”), pursuant to its 2018 Equity Incentive Plan (the “Plan”), hereby grants to Optionholder an option to purchase the number of shares of the Company’s Common Stock set forth below. This option is subject to all of the terms and conditions as set

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM Commission File Number 001-38613

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 9, 2023 Bionano Genomics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 9, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

Description of the Company’s Securities.

Exhibit 4.10 DESCRIPTION OF SECURITIES General The following summary describes Bionano Genomic, Inc.’s (or “we,” “our” or “us”) securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), certain provisions of our certificate of incorporation and bylaws, and certain provisions of Delaware law. Because it is only a summary, it does not contain all

Bionano Genomics Reports Fourth Quarter and Full Year 2022 Results and Provides Revenue Outlook for 2023

Bionano Genomics Reports Fourth Quarter and Full Year 2022 Results and Provides Revenue Outlook for 2023 •Q4 revenue was $8.

BNGO / BioNano Genomics Inc / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SC 13G/A 1 tv0416-bionanogenomicsinc.htm SCHEDULE 13G/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 1)* Name of issuer: Bionano Genomics Inc. Title of Class of Securities: Common Stock CUSIP Number: 09075F107 Date of Event Which Requires Filing of this Statement: December 30, 2022 Check the appropriate box to desi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 2, 2023 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 2, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

Bionano Genomics Reports Preliminary Fourth Quarter and Full-Year 2022 Results - Preliminary Q4 revenue expected to be between $8.1 and $8.4 million; 29% to 33% increase over Q4 2021 - Reached installed base of 240 systems as of YE 2022; 46% increase

Exhibit 99.1 Bionano Genomics Reports Preliminary Fourth Quarter and Full-Year 2022 Results - Preliminary Q4 revenue expected to be between $8.1 and $8.4 million; 29% to 33% increase over Q4 2021 - Reached installed base of 240 systems as of YE 2022; 46% increase over YE 2021 - Achieved or exceeded all stated goals and milestones for the full year 2022 SAN DIEGO, January 5, 2022 (GLOBE NEWSWIRE) ?

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 5, 2023 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 30, 2022 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 30, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 29, 2022 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 29, 2022 Bionano Genomics, Inc (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

+ Investor Call and Webcast November 29, 2022 Creating an End-to-End Solution for OGM & Transforming the Way the World Sees the Genome Legal Disclaimer This presentation contains forward-looking statements. Forward-looking statements describe future

+ Investor Call and Webcast November 29, 2022 Creating an End-to-End Solution for OGM & Transforming the Way the World Sees the Genome Legal Disclaimer This presentation contains forward-looking statements.

Bionano Genomics, Inc. 2020 Inducement Plan, as amended.

EX-10.1 3 brhc10044740ex10-1.htm EXHIBIT 10.1 Exhibit 10.1 Bionano Genomics, Inc. 2020 Inducement Plan Adopted by the Board of Directors: August 20, 2020 Amended by the Board of directors: October 6, 2021 Amended by the Board of directors: November 23, 2022 1. General. (a) Eligible Award Recipients. The only persons eligible to receive grants of Awards under this Plan are individuals who satisfy t

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 23, 2022 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 23, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

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.

Exhibit 2.1 CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL. CONFIDENTIAL Execution Version AGREEMENT AND PLAN OF MERGER by and among BIONANO GENOMICS, INC.; MAZDAN MERGER SUB, INC.; PURIGEN BIOSYSTEMS, INC.; and SHAREHOLDER REPRESENTATIVE SE

Bionano Genomics to Acquire Purigen Biosystems to Enable Further Simplified and Accelerated DNA Isolation for Optical Genome Mapping (OGM) and Address Difficult Sample Types in New Applications with Isotachophoresis (ITP) on the Ionic Purification Sy

Exhibit 99.1 Bionano Genomics to Acquire Purigen Biosystems to Enable Further Simplified and Accelerated DNA Isolation for Optical Genome Mapping (OGM) and Address Difficult Sample Types in New Applications with Isotachophoresis (ITP) on the Ionic Purification System • Acquisition adds isotachophoresis (ITP), a proprietary technology licensed exclusively from Stanford University and developed by P

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 14, 2022 Bionano Genomic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 14, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio

Bionano Genomics Reports Third Quarter 2022 Financial Results and Highlights Recent Business Progress –55% year-over-year revenue growth in Q3 2022 –On track to achieve all 2022 ELEVATE! milestones –Strong balance sheet with $180.2 million in cash, c

Bionano Genomics Reports Third Quarter 2022 Financial Results and Highlights Recent Business Progress –55% year-over-year revenue growth in Q3 2022 –On track to achieve all 2022 ELEVATE! milestones –Strong balance sheet with $180.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 3, 2022 Bionano Genomics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 3, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2022 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number:

Bionano Genomics Reports Second Quarter 2022 Financial Results and Highlights Recent Business Progress –73% year-over-year revenue growth in Q2 2022 –Achieved all 1H 2022 ELEVATE! milestones –Strong balance sheet with $187.3 million in cash, cash equ

Bionano Genomics Reports Second Quarter 2022 Financial Results and Highlights Recent Business Progress ?73% year-over-year revenue growth in Q2 2022 ?Achieved all 1H 2022 ELEVATE! milestones ?Strong balance sheet with $187.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 4, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission F

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2022 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-3

9540 Towne Centre Drive, Suite 100, San Diego, CA 92121 o: 858.888.7600 f: 858.888.7601 bionanogenomics.com

CORRESP 1 filename1.htm Confidential Treatment Requested By Bionano Genomics, Inc. CERTAIN PORTIONS OF THIS LETTER HAVE BEEN OMITTED FROM THE VERSION FILED VIA EDGAR. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE OMITTED PORTIONS. INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS LETTER WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[***]”. July 18, 2022 United S

* * * * *

CORRESP 1 filename1.htm July 8, 2022 United States Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attn: Gary Newberry Tara Harkins Re: Bionano Genomics, Inc. Form 10-K for the Fiscal Year Ended December 31, 2021 Form 8-K filed on October 19, 2021 File No. 001-38613 Ladies and Gentlemen: We are in receipt of the c

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 OR 15(d) of The Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 9, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or other jurisdiction of incorporation) (Commission Fil

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.?) Filed by the Registrant ? Filed by a Party other than the Registrant ?? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ? Defi

Bionano Genomics Reports First Quarter 2022 Financial Results and Highlights Recent Business Progress –80% year-over-year revenue growth in Q1 2022 –Achieved all Q1 2022 ELEVATE! milestones –Strong balance sheet with $216.5 million in cash, cash equi

Bionano Genomics Reports First Quarter 2022 Financial Results and Highlights Recent Business Progress –80% year-over-year revenue growth in Q1 2022 –Achieved all Q1 2022 ELEVATE! milestones –Strong balance sheet with $216.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2022 ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission file number: 001-

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 5, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission File

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.  )

DEF 14A 1 ny20002836x1def14a.htm DEF 14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.  ) Filed by the Registrant ☒ Filed by a Party other than the Registrant  ☐ Check the appropriate box:  ☐ Preliminary Proxy Statement  ☐ Confidential, for Use of the Commission On

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.?) Filed by the Registrant ? Filed by a Party other than the Registrant ?? Check the appropriate box: ?? Preliminary Proxy Statement ?? Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2)) ?? D

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2021 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM Commission File Number 001-38613

Bionano Genomics Reports Fourth Quarter and Full Year 2021 Financial Results and Provides Revenue Outlook for 2022 •Full-year 2021 revenue growth of 111% over 2020 •Achieved publicly announced anticipated milestones for 2021 •Strong balance sheet wit

Bionano Genomics Reports Fourth Quarter and Full Year 2021 Financial Results and Provides Revenue Outlook for 2022 ?Full-year 2021 revenue growth of 111% over 2020 ?Achieved publicly announced anticipated milestones for 2021 ?Strong balance sheet with $250.

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

Exhibit 10.38 COMMERCIAL SINGLE-TENANT LEASE - NET 1. Basic Provisions (?Basic Provisions?). 1.1 Parties: This Lease (?Lease?), dated for reference purposes only, is made by and between TESA BEACH, LLC (?Lessor?) and BioDiscovery, Inc. (?Lessee?), (collectively the ?Parties,? or individually a ?Party?). 1.2 Premises: That certain real property, including all improvements therein or to be provided

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

Exhibit 10.39 FIFTH AMENDMENT THIS FIFTH AMENDMENT (the "Amendment") is made and entered into as of January 12, 2022, by and between IRVINE EASTGATE OFFICE I LLC, a Delaware limited liability company, hereafter called "Landlord," and BIONANO GENOMICS, INC., a Delaware corporation, hereafter called "Tenant." RECITALS A. Landlord (as successor in interest to The Irvine Company LLC) and Tenant are pa

As filed with the Securities and Exchange Commission on March 1, 2022

As filed with the Securities and Exchange Commission on March 1, 2022 Registration No.

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

STANDARD INDUSTRIAL/COMMERCIAL SINGLE?TENANT LEASE ? NET (DO NOT USE THIS FORM FOR MULTI?TENANT BUILDINGS) 1.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 1, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commission Fi

Subsidiaries of the Registrant.

Exhibit 21.1 Subsidiaries of Bionano Genomics, Inc. Bionano Genomics UK, Ltd., a private limited company organized under the laws of the United Kingdom Bionano Genomics (Shanghai) Trading Co., Ltd., a private limited company organized under the laws of the China BioDiscovery, LLC, a California limited liability company Lineagen, Inc., a Delaware corporation

Employment Agreement, dated June 14, 2021, by and between the Company and Richard Shippy

Exhibit 10.36 EMPLOYMENT AGREEMENT This EMPLOYMENT AGREEMENT (the ?Agreement?) is made and entered into effective as of June 14, 2021 (the ?Effective Date?), by and between BIONANO GENOMICS, INC. (the ?Company?) and Richard Shippy (?Executive?). The Company and Executive are hereinafter collectively referred to as the ?Parties?, and individually referred to as a ?Party?. RECITALS The Company desir

2021, by and between the Company and Soheil Shams

Exhibit 10.34 CONFIDENTIAL Execution Version EMPLOYMENT AGREEMENT This EMPLOYMENT AGREEMENT (the ?Agreement?) is made and entered into by and between Bionano Genomics, Inc. (the ?Company?) and Soheil Shams (?Executive?). The Company and Executive are hereinafter collectively referred to as the ?Parties?, and individually referred to as a ?Party?. RECITALS Concurrently with the execution and delive

Filing Fee Table.

EX-FILING FEES 4 brhc10034627ex107.htm EXHIBIT 107 Exhibit 107 Calculation of Filing Fee Table Form S-8 (Form Type) Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price Per Unit(2) Maximum Aggregate Offering Price(2) Fee Rate Amo

tober 8, 2021 and effective October 18, 2021, by and between the Company and Soheil Sham

Exhibit 10.35 CONFIDENTIAL Execution Version STOCK RESTRICTION AGREEMENT This STOCK RESTRICTION AGREEMENT (this ?Agreement?), dated for reference purposes only as October 8, 2021, is made and entered into by and between Bionano Genomics, Inc., a Delaware corporation (?Parent?), and the undersigned stockholder of the Company (the ?Holder?). Each of Parent and the Holder are collectively referred to

Bionano Genomics, Inc. Non-Employee Director Compensation Policy, as amended

Exhibit 10.7 BIONANO GENOMICS, INC. NON-EMPLOYEE DIRECTOR COMPENSATION POLICY Each member of the Board of Directors (the ?Board?) who is not also serving as an employee of or consultant to Bionano Genomics, Inc. (the ?Company?) or any of its subsidiaries (each such member, an ?Eligible Director?) will receive the compensation described in this policy for his or her Board service. An Eligible Direc

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 17, 2022 Bionano Genomics, Inc. (Exact Name of Registrant as Specified in its Charter) Delaware 001-38613 26-1756290 (State or Other Jurisdiction of Incorporation) (Commissio