UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

~~WASHINGTON~~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~~Report (Date of earliest event reported): ~~September 16~~November 13, 2025

Bionano Genomics, Inc.

(Exact Name of Registrant as Specified in its Charter)

Delaware

~~001-38613~~

~~26-1756290~~

001-38613

26-1756290

(State or Other Jurisdiction of Incorporation)

(Commission File Number)

(IRS Employer Identification No.)

(State or Other Jurisdictionof Incorporation)

(CommissionFile Number)

(IRS EmployerIdentification No.)

9540 Towne Centre Drive, Suite 100San Diego, California

92121

(Address of Principal Executive Offices)

(Zip Code)

9540 Towne Centre Drive, Suite 100 San Diego, California	92121
(Address of Principal Executive Offices)	(Zip Code)

Registrant’s telephone number, including area code: (858) 888-7600

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

☐ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

☐ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

☐ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

☐ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Securities registered pursuant to Section 12(b) of the Act:

Title of each class

Trading Symbol(s)

Name of each exchange on which registered

Common Stock, $0.0001 par value per share

BNGO

The Nasdaq Capital Market

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§240.12b-2 of this chapter).

Emerging growth company ☐

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 13(a) of the Exchange Act. ☐

Item 1 2.~~01.~~02 ~~Entry~~Results ~~Into~~of aOperations ~~Material~~and ~~Definitive~~Financial ~~Agreement~~Condition.

~~Securities~~On November 13, ~~Purchase~~2025, ~~Agreement~~Bionano Genomics, Inc. (the “Company”) issued a press release reporting its financial results for the third quarter ended September 30, 2025. The full text of the press release is attached as Exhibit 99.1 to this Current Report on Form 8-K.

OnIn ~~September~~accordance ~~16,~~with ~~2025,~~General ~~Bionano~~Instruction ~~Genomics, Inc~~B.2. ~~(the “Company”) commenced a best efforts public offering (the “Offering”)~~ of anForm ~~aggregate of (i) 4~~8-K,~~925,000 shares~~ (the ~~“Shares”)~~information ofcontained ~~its~~or ~~common~~incorporated ~~stock,~~into ~~par~~this ~~value~~Item $02.~~0001~~02, ~~per~~including ~~share~~Exhibit 99.1, ~~(ii)~~shall ~~pre-funded~~not ~~warrants~~be ~~(the~~deemed “~~Pre-Funded Warrants~~filed”) tofor ~~purchase~~purposes ~~up to an aggregate~~ of ~~75,000~~Section 18 ~~shares~~ of ~~common~~the ~~stock~~Securities ~~(the~~Exchange ~~“Pre-Funded~~Act ~~Warrant~~of ~~Shares”)~~1934, ~~(iii)~~as ~~Series~~amended ~~E warrants~~ (the “~~Series~~Exchange ~~E Warrants~~Act”), toor ~~purchase~~otherwise upsubject to anthe ~~aggregate~~liabilities of ~~5,000,000~~that ~~shares of common stock (the “Series E Warrant Shares”)~~section, ~~and~~nor ~~(iv)~~shall ~~Series~~it Fbe ~~warrants~~deemed ~~(the~~to ~~“Series~~be Fincorporated ~~Warrants,”~~by ~~and~~reference ~~together~~into ~~with~~any ~~the~~filing ~~Series~~under ~~E Warrants,~~ the ~~“Warrants”)~~Securities toAct ~~purchase up to an aggregate~~ of 51933,~~000,000~~ ~~shares~~as ofamended, ~~common stock. Each Share~~ or ~~Pre-Funded~~the ~~Warrant~~Exchange ~~was~~Act, ~~sold~~whether ~~together~~made ~~with~~before ~~one~~or ~~Series~~after Ethe ~~Warrant~~date tohereof, ~~purchase~~except ~~one~~as ~~share~~expressly ofset ~~common~~forth ~~stock~~by ~~and~~specific ~~one~~reference ~~Series~~in Fsuch ~~Warrant~~filing to ~~purchase~~this ~~one~~Current ~~share~~Report ofon ~~common~~Form ~~stock~~8-K.

~~The combined public offering price for each Share and accompanying Warrants was $2~~Item 9.~~00,~~01 ~~and~~Financial ~~the~~Statements ~~combined public offering price for each Pre-Funded Warrant~~ and ~~accompanying Warrants was $1~~Exhibits.9999. The Pre-Funded Warrants have an exercise price of $0.0001 per share, are exercisable immediately upon issuance and will expire when exercised in full. Each Warrant has an exercise price of $2.00 per share and is exercisable immediately upon issuance. The Series E warrants will expire on the five-year anniversary of the date of issuance and the Series F warrants will expire on the eighteen-month anniversary of the date of issuance.

The net proceeds of the Offering, after deducting the fees and expenses of the Placement Agent (as defined below), described in more detail below, and other offering expenses payable by the Company, but excluding the net proceeds, if any, from the exercise of the Warrants, is approximately $9.0 million. The Company intends to use the net proceeds from the Offering for working capital and general corporate purposes. The Offering closed on September 17, 2025.

In connection with the Offering, the Company entered into a securities purchase agreement (the “Purchase Agreement”) with a certain accredited investor (the “Investor”) participating in the Offering. Pursuant to the Purchase Agreement, the Company agreed not to issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of common stock or any securities convertible into or exercisable or exchangeable for shares of common stock or file any registration statement or prospectus, or any amendment or supplement thereto for 30 days after the closing date of the Offering, subject to certain exceptions. In addition, the Company has agreed not to effect or enter into an agreement to effect any issuance of common stock or any securities convertible into or exercisable or exchangeable for shares of common stock involving a variable rate transaction (as defined in the Purchase Agreement) until the one-year anniversary of the closing date of the Offering, subject to certain exceptions.

The Purchase Agreement contains customary representations, warranties and agreements by the Company, customary conditions to closing, indemnification obligations of the Company and the Investor, including for liabilities arising under the Securities Act of 1933, as amended (the “Securities Act”), other obligations of the parties and termination provisions. The representations, warranties and covenants contained in the Purchase Agreement were made only for the purposes of such agreements and as of specific dates, were solely for the benefit of the parties to such agreements and may be subject to limitations agreed upon by the contracting parties.

A holder will not have the right to exercise any portion of the Warrants or Pre-Funded Warrants if the holder (together with its affiliates) would beneficially own in excess of 4.99% or 9.99%, as applicable, of the number of shares of common stock outstanding immediately after giving effect to the exercise, as such percentage ownership is determined in accordance with the terms of the Warrants or the Pre-Funded Warrants, respectively.

Pursuant to an Engagement Letter (the “Engagement Letter”) with H.C. Wainwright & Co., LLC (the “Placement Agent”), the Company agreed to pay the Placement Agent in connection with the Offering (i) a cash fee equal to 6.0% of the aggregate gross proceeds raised in the Offering, (ii) a management fee equal to 0.5% of the aggregate gross proceeds raised in the Offering, (iii) up to $100,000 for fees and expenses of the Placement Agent’s counsel and other out of pocket expenses, (iv) a non-accountable expense allowance of $50,000, (v) up to $5,000 for road show expenses and (vi) up to $15,950 for clearing expenses.

The Shares, the Pre-Funded Warrants, the Pre-Funded Warrant Shares, the Series E Warrants, the Series E Warrant

Shares, the Series F Warrants and the Series F Warrant Shares were offered by the Company pursuant to a Registration Statement on Form S-1 originally filed on September 11, 2025 (including the prospectus forming a part of such Registration Statement), with the Securities and Exchange Commission (the “SEC”) under the Securities Act (File No. 333-290187), and declared effective by the SEC on September 16, 2025.

The foregoing description of the material terms of the Purchase Agreement, the Pre-Funded Warrants, the Series E Warrants and the Series F Warrants is not complete and is qualified in its entirety by reference to the full text of the form of Purchase Agreement, the form of Pre-Funded Warrant, and the form of Series E/F Warrant, copies of which are filed as Exhibits 10.1, 4.1 and 4.2, respectively, to this Current Report on Form 8-K and are incorporated herein by reference.

This Current Report on Form 8-K does not constitute an offer to sell any securities or a solicitation of an offer to buy any securities, nor shall there be any sale of any securities in any state or jurisdiction in which such an offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such state or jurisdiction.

Item 8.01. Other Events.

Press Releases

On September 16, 2025, the Company issued a press release announcing the pricing of the Offering, and on September 17, 2025, the Company issued a press release announcing the closing of the Offering. A copy of each such press release is attached as Exhibit 99.1 and 99.2, respectively, to this Current Report on Form 8-K and are hereby incorporated by reference herein.

Cautionary Note Regarding Forward-looking Statements

This Current Report on Form 8-K contains “forward-looking statements” within the meaning of the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. All statements other than statements of current or historical fact contained in this Current Report on Form 8-K, including statements that express the Company’s intentions, plans, objectives, beliefs, expectations, strategies, predictions or any other statements relating to our future activities or other future events or conditions are forward-looking statements. The words “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “project,” “should,” “target,” “will,” “would” and similar expressions are intended to identify forward-looking statements. These statements are based on current expectations, estimates and projections made by management about the Company’s business, industry and other conditions affecting its financial condition, results of operations or business prospects. These statements are not guarantees of future performance and involve risks, uncertainties and assumptions that are difficult to predict. Therefore, actual outcomes and results may differ materially from what is expressed or forecasted in, or implied by, the forward-looking statements due to numerous risks and uncertainties, including those risks and uncertainties described in the filings the Company makes with the SEC. Any forward-looking statements speak only as of the date on which they are made, and the Company undertakes no obligation to publicly update or revise any forward-looking statements to reflect events or circumstances that may arise after the date of this Current Report on Form 8-K, except as required by applicable law. Investors should evaluate any statements made by the Company in light of these important factors.

Item 9.01. Financial Statements and Exhibits.

(d) Exhibits

Exhibit No.	~~Description~~	Description
4.1	Form of Pre-Funded Warrant
99.1		Press release issued November 13, 2025, reporting financial results for the third quarter ended September 30, 2025
4.2	Form of Series E/F Warrant
104		Inline XBRL for the cover page of this Current Report on Form 8-K
10.1	Form of Securities Purchase Agreement
99.1	Press Release, dated September 16, 2025, announcing the pricing of the Offering.
99.2	Press Release, dated September 17, 2025, announcing the closing of the Offering.
104	Cover Page Interactive Data File (embedded within the Inline XBRL document)

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, ~~as amended,~~ the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

~~Bionano Genomics, Inc.~~

Bionano Genomics, Inc.

Date: September 17, 2025

Date: November 13, 2025

By:

/s/ R. Erik Holmlin, Ph.D.

By:

/s/ R. Erik Holmlin, Ph.D.

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer(Principal Executive and Financial Officer)

President and Chief Executive Officer (Principal Executive and Financial Officer)

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