{"url_path":"/sec/bngo/10-q/2026/item-6","section_key":"item-6","section_title":"Item 6 EXHIBITS","topic":"sec","document":{"doc_type":"10-Q","doc_date":"2026-05-13","source_url":"https://www.sec.gov/Archives/edgar/data/1411690/0001411690-26-000028-index.html","accession_number":"0001411690-26-000028","cik":"0001411690","ticker":"BNGO","issuer_name":"Bionano Genomics, Inc.","edgar_url":"https://www.sec.gov/Archives/edgar/data/1411690/0001411690-26-000028-index.html","primary_entity_key":"0001411690","primary_entity_name":"Bionano Genomics, Inc."},"word_count":1161,"has_tables":true,"body_markdown":"ITEM 6. EXHIBITS\n\n \n\nExhibit\n\nNumber\n\n \n\nDescription\n\n \n\n \n\n \n\n3.1\n\n \n\n[Amended and Restated Certificate of Incorporation, as amended (incorporated by reference to Exhibit 3.1 to Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 8, 2023).](https://www.sec.gov/Archives/edgar/data/1411690/000141169023000082/bngo-2023x09x30xexx31.htm)\n\n \n\n \n\n \n\n3.2\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000141169025000008/bionano-certificateofamend.htm)\n\n \n\n \n\n \n\n3.3\n\n \n\n[Amended and Restated Bylaws (incorporated by reference to Exhibit 3.2 to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018).](https://www.sec.gov/Archives/edgar/data/1411690/000119312518257763/d607608dex32.htm)\n\n \n\n \n\n \n\n3.4\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036123018454/brhc20051350_ex3-2.htm)\n\n \n\n \n\n \n\n4.1\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000141169024000013/bngo-ex41x20231231.htm)\n\n \n\n \n\n \n\n4.2\n\n \n\n[Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust (incorporated by reference to Exhibit 4.8 to the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, originally filed with the SEC on June 28, 2018).](https://www.sec.gov/Archives/edgar/data/1411690/000119312518217313/d782664dex48.htm)\n\n \n\n \n\n \n\n4.3\n\n \n\n[Form of Warrant to Purchase Common Stock for Service Providers (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on November 21, 2018).](https://www.sec.gov/Archives/edgar/data/1411690/000119312518332353/d635375dex41.htm)\n\n \n\n \n\n \n\n4.4\n\n \n\n[Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering (incorporated by reference to Exhibit 4.13 to the Registrant’s Registration Statement on Form S-1 (File No. 333-233828), as amended, originally filed with the SEC on September 18, 2019).](https://www.sec.gov/Archives/edgar/data/1411690/000114036119016923/nt10004193x3_ex4-13.htm)\n\n \n\n \n\n \n\n4.5\n\n \n\n[Form of Warrant to Purchase Common Stock issued to Investors in April 2020 Public Offering) (incorporated by reference to Exhibit 4.16 to the Registrant’s Registration Statement on Form S-1 (File No. 333-237074), as amended, originally filed with the SEC on March 11, 2020).](https://www.sec.gov/Archives/edgar/data/1411690/000114036120006739/nt10007734x2_ex4-16.htm)\n\n \n\n \n\n \n\n4.6\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036123047688/ef20012228_ex4-2.htm)\n\n \n\n \n\n \n\n4.7\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124018181/ef20026117_ex4-1.htm)\n\n \n\n \n\n \n\n4.8\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124018181/ef20026117_ex4-2.htm)\n\n \n\n \n\n \n\n4.9^+\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124027553/ef20030067_ex4-1.htm)\n\n \n\n \n\n \n\n4.10\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124032559/ny20032138x2_ex4-1.htm)\n\n \n\n \n\n \n\n4.11\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124032559/ny20032138x2_ex4-2.htm)\n\n \n\n \n\n \n\n4.12\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124032559/ny20032138x1_ex4-3.htm)\n\n \n\n \n\n \n\n4.13\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124044715/ny20037830x2_ex4-1.htm)\n\n \n\n \n\n \n\n39\n\n[Table of Contents](#toc_page)\n\n \n\n4.14\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036124044715/ny20037830x2_ex4-2.htm)\n\n \n\n \n\n \n\n4.15\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036125000132/ny20038822x2_ex4-1.htm)\n\n \n\n \n\n \n\n4.16\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036125000296/ny20041129x2_ex4-1.htm)\n\n \n\n \n\n \n\n4.17\n\n \n\n[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).](https://www.sec.gov/Archives/edgar/data/1411690/000114036125000296/ny20041129x2_ex4-2.htm)\n\n \n\n \n\n \n\n4.18\n\n \n\n[Form of Pre-Funded Warrant to Purchase Common Stock issued to Investors in](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[September](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[2025](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[Offering](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[(incorporated by reference to Exhibit 4.](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[1](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[to the Registrant’s Current Report on Form 8-K, filed with the SEC on](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[September 18](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)[, 2025).](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-1.htm)\n\n \n\n \n\n \n\n4.19\n\n \n\n[Form of](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[Warrant to Purchase](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[Series E](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[/F](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[Common Stock issued to Investors in September 2025 Offering (incorporated by reference to Exhibit 4.](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[2](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)[to the Registrant’s Current Report on Form 8-K, filed with the SEC on September 18, 2025).](https://www.sec.gov/Archives/edgar/data/1411690/000114036125035286/ny20052513x7_ex4-2.htm)\n\n \n\n \n\n \n\n31.1\n\n \n\n[Certification of Principal Executive Officer and Principal Financial Officer pursuant to Rules 13a-14(a) and 15d-14(a) promulgated under the Securities Exchange Act of 1934, as amended.](bngo-ex31_1.htm)\n\n \n\n \n\n \n\n32.1*\n\n \n\n[Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.](bngo-ex32_1.htm)\n\n \n\n \n\n \n\n101.INS\n\n \n\nInline XBRL Instance Document—the instance document does not appear in the Interactive Data File as its XBRL tags are embedded within the Inline XBRL Document.\n\n \n\n \n\n \n\n101.SCH\n\n \n\nInline XBRL Taxonomy Extension Schema with Embedded Linkbase Documents.\n\n \n\n \n\n \n\n104\n\n \n\nCover Page Interactive Data File (formatted in Inline XBRL and contained in Exhibit 101)\n\n \n\n* This certification is deemed not filed for purpose of section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.\n\n^ Certain schedules to this agreement have been omitted pursuant to Item 601(a)(5) of Regulation S-K. The Company agrees to furnish a copy of all omitted schedules to the SEC upon its request.\n\n+ Pursuant to Item 601(b)(10)(iv) of Regulation S-K, certain portions of this exhibit have been redacted because they are both not material and is the type that the Registrant treats as private or confidential. The Registrant hereby agrees to furnish supplementally to the SEC, upon its request, an unredacted copy of this exhibit.\n\n40\n\n[Table of Contents](#toc_page)\n\n \n\nSIGNATURES\n\nPursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.\n\n \n\n \n\nBIONANO GENOMICS, INC.\n\n \n\n \n\nDated: May 13, 2026\n\nBy: /s/ Albert A. Luderer, Ph.D.\n\n \n\nAlbert A. Luderer, Ph.D.\n\n \n\nInterim Chief Executive Officer\n\n(Interim Principal Executive Officer and Interim Principal Financial Officer)\n\n \n\n41"}