Bionano Genomics, Inc.

S-11 bngo-20261027.htm S-1

As filed with the Securities and Exchange Commission on October 27, 2026

Registration No. 333-

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM S-1

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

(Exact name of registrant as specified in its charter)

(858) 888-7600

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

Albert A. Luderer, Ph.D.

Interim Chief Executive Officer

(858) 888-7600

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Copies to:

Rakesh Gopalan

David S. Wolpa

Troutman Pepper Locke LLP

301 S. College Street, Suite 3400

Charlotte, NC 28202

(704) 998-4050

Approximate date of commencement of proposed sale to the public: As soon as practicable after the effective date of this registration statement.

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, check the following box: ☒

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ☐

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ☐

If this Form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act.☐

The Registrant hereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until the registrant shall file a further amendment that specifically states that this registration statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the registration statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

EXPLANATORY NOTE

The 1,332,632 shares of our common stock, par value $0.0001 per share (the “common stock”), the offer and sale of which are being registered hereunder consists of shares of common stock issuable upon the exercise of certain currently outstanding warrants (collectively, the “Warrants”) to purchase shares of common stock, initially offered and sold under our previous “shelf” registration statement on Form S-3 (No. 333-270459) (the “Prior Registration Statement”), that was declared effective on May 10, 2023, and which will expire on November 6, 2026, pursuant to Rule 415(a)(5) under the Securities Act of 1933, as amended, comprising up to:

•

661,377 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $15.120 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated January 3, 2025 (the “2025 Purchase Warrants”);

•

164,684 shares of common stock issuable upon exercise of outstanding Series C warrants to purchase shares of common stock, each with an exercise price of $18.234 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated October 30, 2024 (the “Series C Warrants”);

•

145,560 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $61.20 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated April 4, 2024 (the “2024 Purchase Warrants”); and

•

361,011 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $191.13 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated October 11, 2023 (the “2023 Purchase Warrants”).

The 2025 Purchase Warrants became exercisable on June 11, 2025 and will expire on the five-year anniversary of such date. The Series C Warrants became exercisable on January 15, 2025 and will expire on the five-year anniversary of such date. The 2024 Purchase Warrants were exercisable immediately upon issuance on April 8, 2024 and will expire on the five-year anniversary of the date of issuance. The 2023 Purchase Warrants were exercisable immediately upon issuance on October 13, 2023 and will expire on the five-year anniversary of the date of issuance.

We are filing this new registration statement on Form S-1 for the sole purpose of ensuring that an effective registration statement covers the exercise of the outstanding Warrants.

The information contained in this preliminary prospectus is not complete and may be changed. These securities may not be sold until the registration statement filed with the Securities and Exchange Commission is effective. This preliminary prospectus is not an offer to sell these securities and it is not soliciting an offer to buy these securities in any state where the offer or sale is not permitted.

PRELIMINARY PROSPECTUS SUBJECT TO COMPLETION, DATED OCTOBER 27, 2026

Up to 1,332,632 Shares of Common Stock Underlying Outstanding Warrants

This prospectus relates to the issuance of up to an aggregate of 1,332,632 shares of our common stock, par value $0.0001 per share (the “common stock”), that are issuable upon the exercise of certain currently outstanding warrants to purchase shares of common stock outstanding as of the date hereof that were initially offered and sold under our registration statement on Form S-3 (No. 333-270459), which became effective on May 10, 2023 and will expire on November 6, 2026 (collectively, the “Warrants”), comprising up to:

•

661,377 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $15.120 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated January 3, 2025 (the “2025 Purchase Warrants”);

•

164,684 shares of common stock issuable upon exercise of outstanding Series C warrants to purchase shares of common stock, each with an exercise price of $18.234 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated October 30, 2024 (the “Series C Warrants”);

•

145,560 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $61.20 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated April 4, 2024 (the “2024 Purchase Warrants”); and

•

361,011 shares of common stock issuable upon exercise of outstanding warrants to purchase shares of common stock, each with an exercise price of $191.13 per share, that were originally issued pursuant to a prospectus dated May 10, 2023 and a related prospectus supplement dated October 11, 2023 (the “2023 Purchase Warrants”).

The 2025 Purchase Warrants became exercisable on June 11, 2025 and will expire on the five-year anniversary of such date. The Series C Warrants became exercisable on January 15, 2025 and will expire on the five-year anniversary of such date. The 2024 Purchase Warrants were exercisable immediately upon issuance and will expire on the five-year anniversary of the date of issuance. The 2023 Purchase Warrants were exercisable immediately upon issuance and will expire on the five-year anniversary of the date of issuance. See “Description of Securities Being Registered.”

We will receive the proceeds from the exercise of the Warrants but not from any sale of the underlying shares of common stock.

Our common stock is traded on the Nasdaq Capital Market under the symbol “BNGO.” The last reported sale price of our common stock on the Nasdaq Capital Market on October 26, 2026, was $1.16 per share.

We are a “smaller reporting company” under the federal securities laws and, as such, are subject to reduced public company disclosure standards for this prospectus and future filings. See the section titled “Prospectus Summary—Implications of Being a Smaller Reporting Company” for additional information.

Our business and an investment in our common stock involve significant risks. These risks are described under the caption “Risk Factors” beginning on page 4 of this prospectus, as well as those risks described in our most recent Annual Report on Form 10-K and in our other filings with the Securities and Exchange Commission that are incorporated by reference into this prospectus.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

The date of this prospectus is , 2026.