As filed with the Securities and Exchange Commission on ~~March~~ September 11, ~~2020~~2025.

Registration No. 333-

UNITED ~~STATESSECURITIES~~STATES ~~AND EXCHANGE COMMISSIONWASHINGTON, D.C. 20549~~

~~FORM S-1REGISTRATION STATEMENTUNDERTHE~~ SECURITIES ~~ACT~~AND OFEXCHANGE ~~1933~~COMMISSION

~~Bionano Genomics~~Washington, ~~Inc~~D.~~(Exact~~C. ~~name~~20549 ~~of registrant as specified in its charter)~~

Delaware	3826	26-1756290
(State or Other Jurisdiction ofIncorporation or Organization)	(Primary Standard IndustrialClassification Code Number)	(I.R.S. EmployerIdentification Number)

FORM S-1

~~Bionano~~REGISTRATION ~~Genomics,~~STATEMENT ~~Inc.9540 Towne Centre Drive, Suite 100San Diego, California 92121(858) 888-7600(Address, including zip code, and telephone number, including area code of registrant’s principal executive offices)~~

R.UNDER Erik Holmlin, Ph.D.President and Chief Executive OfficerBionano Genomics, Inc.9540 Towne Centre Drive, Suite 100San Diego, California 92121(858) 888-7600(Name, address, including zip code, and telephone number, including area code, of agent for service)

THE SECURITIES ACT OF 1933

Bionano Genomics, Inc.

(Exact name of registrant as specified in its charter)

Bionano Genomics, Inc.

9540 Towne Centre Drive, Suite 100

San Diego, California 92121

(858) 888-7600

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

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer

Bionano Genomics, Inc.

9540 Towne Centre Drive, Suite 100

San Diego, California 92121

(858) 888-7600

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

Copies to:

~~Thomas~~Rakesh A.Gopalan ~~Coll,~~David ~~Esq~~S.~~James~~ C.Wolpa ~~Pennington,~~Troutman ~~Esq.Cooley~~Pepper ~~LLP4401~~Locke ~~Eastgate~~LLP ~~MallSan~~301 ~~Diego, California 92121(858) 550-6000 R~~S. ~~Erik~~College ~~Holmlin~~Street, ~~Ph.D.President and Chief Executive OfficerBionano Genomics, Inc.9540 Towne Centre Drive,~~ Suite ~~100San~~3400 ~~Diego~~Charlotte, ~~California~~NC ~~92121~~28202 (~~858~~704) ~~888~~998-~~7600~~4050 ~~Ivan~~Rick KA. ~~Blumenthal,~~WernerAlla ~~Esq.Cliff~~DigilovaHaynes M.and ~~Silverman~~Boone, ~~Esq.Mintz,~~LLP30 ~~Levin,~~Rockefeller ~~Cohn~~Plaza, ~~Ferris,~~26th ~~Glovskyand~~FloorNew ~~Popeo~~York, ~~P.C.Chrysler~~New ~~Center666 Third AvenueNew~~ York, ~~NY 10017~~10112(212) ~~935~~659-~~3000~~7300

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. o☐

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. o☐

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. o☐

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.

Large accelerated filer o☐ Accelerated filer o☐ Non-accelerated filer ☒ Smaller reporting company ☒ 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 7(a)(2)(B) of the Securities Act. o☐

~~CALCULATION~~The OFRegistrant ~~REGISTRATION~~hereby ~~FEE~~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.

Title of each class ofsecurities to be registered	Proposed MaximumAggregate Offering Price(1)		Amount ofRegistration Fee(1)
Common Stock, par value $0.0001 per share(2)(3)	$	15,000,800
Pre-funded warrants to purchase shares of common stock and common stock issuable upon exercise thereof(2)(3)	$	15,000,800
Warrants to purchase Common Stock and shares of Common Stock issuable upon exercise thereof(2)	$	15,000,800
Total	$	30,001,600	$	3,895

(1) Estimated solely for the purpose of calculating the registration fee in accordance with Rule 457(o) under the Securities Act of 1933, as amended (the “Securities Act”).

(2) Pursuant to Rule 416 under the Securities Act, the securities being registered hereunder include such indeterminate number of additional securities as may be issuable to prevent dilution resulting from stock splits, dividends or similar transactions.

(3) The proposed maximum aggregate offering price of the common stock proposed to be sold in the offering will be reduced on a dollar-for-dollar basis based on the aggregate offering price of the pre-funded warrants offered and sold in the offering (plus the aggregate exercise price of the common stock issuable upon exercise of the pre-funded warrants), and as such the proposed aggregate maximum offering price of the common stock and pre-funded warrants (including the common stock issuable upon exercise of the pre-funded warrants), if any, is $15,000,800.

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 which 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 Commission, acting pursuant to said Section 8(a), may determine.

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The information contained in this preliminary prospectus is not complete and may be changed. WeThese securities may not ~~sell~~be ~~these~~sold ~~securities~~ 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 weit ~~are~~is not soliciting ~~offers~~an offer to buy these securities, in any state where the offer or sale ~~of these securities~~ is not permitted.

PRELIMINARY PROSPECTUS SUBJECT TO COMPLETION, DATED ~~MARCH~~SEPTEMBER 11, ~~2020~~2025

~~PROSPECTUS~~Up to 2,032,520 Shares of Common Stock

17Up to 2,~~648~~032,~~000~~520 ~~Shares of Common StockPre~~Pre-Funded Warrants to Purchase ~~Shares of Common StockWarrants to Purchase~~ up to 172,~~648~~032,~~000~~520 Shares of Common Stock

WeUp ~~are offering 17,648,000 shares of our common stock and common warrants~~ to ~~purchase an aggregate of 17~~2,~~648~~032,~~000~~520 ~~shares~~Series E ofWarrants ~~our common stock (and the shares of common stock that are issuable from time~~ to ~~time~~Purchase ~~upon~~up ~~exercise of the warrants). We are also offering~~ to ~~certain purchasers whose purchase of shares of common stock in this offering would otherwise result in the purchaser~~2, ~~together with its affiliates and certain related parties~~032,520 ~~beneficially~~Shares ~~owning more than 4.99% (or, at the election~~ of ~~the~~Common ~~purchaser,~~Stock 9.99%) of our outstanding common stock immediately following the consummation of this offering, the opportunity to purchase, if any such purchaser so chooses, pre-funded warrants, in lieu of shares of common stock that would otherwise result in such purchaser’s beneficial ownership exceeding 4.99% (or, at the election of the purchaser, 9.99%) of our outstanding common stock. Each pre-funded warrant will be exercisable for one share of our common stock. The purchase price of each pre-funded warrant and the accompanying common warrant will be equal to the price at which a share of common stock and accompanying common warrant are sold to the public in this offering, minus $0.001, and the exercise price of each pre-funded warrant will be $0.001 per share. The pre-funded warrants will be immediately exercisable and may be exercised at any time until all of the pre-funded warrants are exercised in full. This offering also relates to the shares of common stock issuable upon exercise of any pre-funded warrants sold in this offering. Each share of common stock and pre-funded warrant is being sold together with a common warrant to purchase one share of our common stock, at an exercise price of $ per share. For each pre-funded warrant we sell, the number of shares of common stock we are offering will be decreased on a one-for-one basis. Because we will issue a common warrant for each share of our common stock and for each pre-funded warrant to purchase one share of our common stock sold in this offering, the number of common warrants sold in this offering will not change as a result of a change in the mix of the shares of our common stock and pre-funded warrants sold. The common warrants will be exercisable immediately and will expire five years from the date of issuance. The shares of common stock and pre-funded warrants, and the accompanying common warrants, can only be purchased together in this offering but will be issued separately and will be immediately separable upon issuance. Our common stock is listed on The Nasdaq Capital Market under the symbol “BNGO”. The last reported sale price of our common stock on The Nasdaq Capital Market on March 9, 2020 was $0.85 per share. The public offering price per share of common stock and accompanying common warrant and any pre-funded warrant and accompanying common warrant, as the case may be, will be determined by us at the time of pricing, may be at a discount to the current market price, and the recent market price used throughout this prospectus may not be indicative of the final offering price. There is no established public trading market for the pre-funded warrants or common warrants, and we do not expect a market to develop. In addition, we do not intend to apply for a listing of the pre-funded warrants or common warrants on any national securities exchange.

~~You~~Up ~~should~~to ~~read this prospectus and any prospectus supplement~~2,032,520 ~~together~~Series F ~~with~~Warrants ~~additional~~to ~~information~~Purchase ~~described~~up ~~under~~to ~~the headings “Incorporation of Certain Information by Reference” and “Where You Can Find More Information~~2,”032,520 ~~carefully~~Shares ~~before you invest in any~~ of ~~our~~Common ~~securities.~~Stock

WeUp ~~are~~to ~~an “emerging growth company” as defined by the Jumpstart Our Business Startups Act of 2012~~6, ~~and as such~~097,560 weShares ~~have~~of ~~elected~~Common toStock ~~comply~~Issuable ~~with~~Upon ~~certain~~Exercise ~~reduced~~of ~~public~~the ~~company reporting requirements for this prospectus and future filings.~~

~~Investing~~Pre-Funded inWarrants, ~~our~~Series E ~~securities~~Warrants ~~involves~~and aSeries F ~~high~~Warrants ~~degree of risk. See “Risk Factors” beginning on page 6 of this prospectus as well as in the documents incorporated by reference.~~

Per Share

Per Pre-Funded Warrant

Per CommonWarrant

Total

Public offering price

Underwriting discounts and commissions(1)

Proceeds to us, before expenses

We are offering up to 2,032,520 shares of common stock, par value $0.0001 per share (“common stock”), together with Series E warrants to purchase up to 2,032,520 shares of common stock (the “Series E Warrants”) and Series F warrants to purchase up to 2,032,520 shares of common stock (the “Series F Warrants”, and together with the Series E Warrants, the “Warrants”) at an assumed combined public offering price of $4.92 per share and accompanying Warrants, which is equal to the closing price per share of our common stock on the Nasdaq Capital Market on September 10, 2025 pursuant to this prospectus. The shares of common stock and Warrants will be separately issued, but must be purchased together in this offering. Each share of common stock is being sold together with one Series E Warrant to purchase one share of common stock and one Series F Warrant to purchase one share of common stock. Each Warrant will have an assumed exercise price of $4.92 per share (representing 100% of the assumed combined price at which a share of common stock and accompanying Warrants are sold to the public in this offering) and will be exercisable beginning on the effective date of stockholder approval of the issuance of the shares upon exercise of the Warrants (“Warrant Stockholder Approval”); provided, however, if the Pricing Conditions (as defined below) are met, the Warrant Stockholder Approval will not be required and the Warrants will be exercisable upon issuance (the “Initial Exercise Date”). The Series E Warrants will expire on the five-year anniversary of the Initial Exercise Date. The Series F Warrants will expire on the 18-month anniversary of the Initial Exercise Date. As used herein, “Pricing Conditions” means that the combined public offering price per share and accompanying Warrants is such that Warrant Stockholder Approval is not required under the rules of The Nasdaq Stock Market LLC (“Nasdaq”) because either (i) the offering is an at-the-market offering under Nasdaq rules and such price equals or exceeds the sum of (a) the applicable “Minimum Price” per share under Nasdaq Rule 5635(d) plus (b) $0.125 per whole share of common stock underlying the Warrants or (ii) the offering is a discounted offering where the pricing and discount (including attributing a value of $0.125 per whole share underlying the Warrants) meet the pricing requirements under Nasdaq’s rules.

~~(1)~~We ~~See~~are also offering up to 2,032,520 pre-funded warrants (the “~~Underwriting~~Pre-Funded Warrants”) to purchase up to an aggregate of 2,032,520 shares of common stock to those purchasers whose purchase of shares of common stock in this offering would result in the purchaser, together with its affiliates and certain related parties, beneficially owning more than 4.99% (or, at the election of the purchaser, 9.99%) of our outstanding common stock following the consummation of this offering in lieu of the shares of our common stock that would result in ownership in excess of 4.99% (or, at the election of the purchaser, 9.99%). Each Pre-Funded Warrant will be exercisable for ~~additional~~one ~~information~~share ~~regarding~~of ~~underwriting~~common ~~compensation~~stock at an exercise price of $0.0001 per share. Each Pre-Funded Warrant is being issued together with the same Warrants described above being issued with each share of common stock. The assumed combined public offering price for each such Pre-Funded Warrant, together with the accompanying Warrants, is $4.9199, which is equal to the closing price of our common stock on the Nasdaq Capital Market on September 10, 2025, less the $0.0001 per share exercise price of each such Pre-Funded Warrant. Each Pre-Funded Warrant will be exercisable upon issuance and will expire when exercised in full. The Pre-Funded Warrants and accompanying Warrants are immediately separable and will be issued separately in this offering, but must be purchased together in this offering. For each Pre-Funded Warrant we sell, the number of shares of common stock we are offering will be decreased on a one-for-one basis. This offering also relates to the shares of common stock issuable upon the exercise of the Warrants and the Pre-Funded Warrants.

~~The~~This ~~delivery~~offering ofwill terminate on October 11, 2025, unless we decide to terminate the ~~shares~~offering of(which ~~common~~we ~~stock~~may ~~and~~do at any ~~pre-funded~~time ~~warrants~~in ~~and~~our ~~common~~discretion) ~~warrants~~prior to ~~purchasers~~that isdate. ~~expected~~We towill behave ~~made~~one onclosing for all the securities purchased in this offering. The combined public offering price per share (or ~~about ,~~Pre-Funded ~~2020~~Warrant) and accompanying Warrants will be fixed for the duration of this offering.

We have engaged H.C. Wainwright & Co., LLC (the “placement agent”) to act as our exclusive placement agent in connection with this offering. The placement agent has agreed to use its reasonable best efforts to arrange for the sale of the securities offered by this prospectus. The placement agent is not purchasing or selling any of the securities we are offering, and the placement agent is not required to arrange the purchase or sale of any specific number or dollar amount of securities. We have agreed to pay to the placement agent the placement agent fees set forth in the table below, which assumes that we sell all of the securities offered by this prospectus. There is no arrangement for funds to be received in escrow, trust or similar arrangement. There is no minimum offering requirement. We will bear all costs associated with the offering. See “Plan of Distribution” on page 18 of this prospectus for more information regarding these arrangements.

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Our common stock is currently listed on the Nasdaq Capital Market under the symbol “BNGO.” On September 10, 2025, the closing price of our common stock on the Nasdaq Capital Market was $4.92 per share. All share, Warrant and Pre-Funded Warrant numbers are based on an assumed combined public offering price of $4.92 per share and accompanying Warrants and $4.9199 per Pre-Funded Warrant and accompanying Warrants. There is no established public trading market for the Pre-Funded Warrants or Warrants that are part of this offering, and we do not expect a market to develop. We do not intend to apply for listing of the Pre-Funded Warrants or Warrants on any securities exchange or other nationally recognized trading system. Without an active trading market, the liquidity of the Pre-Funded Warrants and Warrants will be limited.

Certain information in this prospectus is based on an assumed combined public offering price of $4.92 per share and accompanying Warrants, the last reported sale price of our common stock on the Nasdaq Capital Market on September 10, 2025 (or assumed combined public offering price of $4.9199 per Pre-Funded Warrant and accompanying Warrants). The actual combined public offering price per share and accompanying Warrants and the actual combined public offering price per Pre-Funded Warrant and accompanying Warrants, as the case may be, will be determined between us, the placement agent and investors in this offering based on market conditions at the time of pricing and may be at a discount to the current market price of our common stock. Therefore, the recent market price used throughout this prospectus may not be indicative of the final offering price.

You should read this prospectus, together with additional information described under the headings “Information Incorporated by Reference” and “Where You Can Find More Information,” carefully before you invest in any of our securities.

We are a “smaller reporting company” as defined under the federal securities laws and, as such, have elected to comply with certain reduced public company reporting requirements for this prospectus and may elect to do so in future filings. Investing in our securities involves a high degree of risk. See “Risk Factors” beginning on page 6 of this prospectus for a discussion of information that should be considered in connection with an investment in our securities. See “Prospectus Summary — Implications of Being a Smaller Reporting Company.”

Investing in our securities involves a high degree of risk. See the section titled “Risk Factors” beginning on page 6 of this prospectus and in the documents incorporated by reference into this prospectus for a discussion of risks that should be considered in connection with an investment in our securities.


	Per Share and Accompanying Warrants	Per Pre- Funded Warrant and Accompanying Warrants	Total
Combined public offering price	$	$	$
Placement agent fees⁽¹⁾	$	$	$
Proceeds to us, before expenses⁽²⁾	$	$	$

(1)

We have agreed to pay the placement agent a cash fee equal to 6.0%. We have also agreed to pay the placement agent a management fee of 0.5% of the aggregate gross proceeds raised in this offering and to reimburse the placement agent for certain of its offering related expenses, including reimbursement for non-accountable expenses in an amount up to $50,000, legal fees and expenses and other out-of-pocket expenses in the amount of up to $100,000, road show expenses in the amount of up to $5,000, and for its clearing expenses in the amount up to $15,950. For a description of compensation to be received by the placement agent, see “Plan of Distribution” for more information.

(2)

Because there is no minimum number of securities or amount of proceeds required as a condition to closing in this offering, the actual public offering amount, placement agent fees, and proceeds to us, if any, are not presently determinable and may be substantially less than the total maximum offering amounts set forth above. The amount of the proceeds to us presented in this table does not give effect to any exercise of the Warrants or the Pre-Funded Warrants offered hereby. For more information, see “Plan of Distribution.”

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense.

~~Sole~~Delivery ~~Book-Running~~of ~~ManagerOppenheimer~~the &securities Cooffered hereby to the purchasers is expected to be made on or about , 2025, subject to the satisfaction of customary closing conditions.

~~Lead~~H.C. ~~Manager~~Wainwright ~~Co-Lead~~& ~~Manager Roth Capital Partners Maxim Group LLC~~Co.

The date of this prospectus is , ~~2020~~2025.

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	~~Page~~		Page
Prospectus Summary		1
ABOUT THIS PROSPECTUS			ii
The Offering		4
CAUTIONARY NOTE CONCERNING FORWARD-LOOKING STATEMENTS			iii
Risk Factors		6
PROSPECTUS SUMMARY			1
Special Note Regarding Forward-Looking Statements		8
THE OFFERING			3
Use of Proceeds		9
RISK FACTORS			6
Dividend Policy		10
USE OF PROCEEDS			9
Dilution		11
DIVIDEND POLICY			10
Selected Financial Data		12
DESCRIPTION OF CAPITAL STOCK			11
Principal Stockholders		13
DESCRIPTION OF SECURITIES WE ARE OFFERING			14
Description of Capital Stock		15
PLAN OF DISTRIBUTION			18
Description of Securities We are Offering		17
INFORMATION INCORPORATED BY REFERENCE			21
Underwriting		20
WHERE YOU CAN FIND MORE INFORMATION			22
Legal Matters		26
LEGAL MATTERS			23
Experts		26
EXPERTS			23
Where You Can Find More Information		26
Incorporation of Certain Information by Reference		27
Disclosure of Commission Position on Indemnification for Securities Act Liability		27

We incorporate by reference important information into this prospectus. You may obtain the information incorporated by reference without charge by following the instructions under “Where You Can Find More Information.” You should carefully read this prospectus as well as additional information described under “Incorporation of Certain Information by Reference,” before deciding to invest in our common stock.

Neither we nor the underwriters have authorized anyone to provide you with additional information or information different from that contained in this prospectus filed with the Securities and Exchange Commission. We take no responsibility for, and can provide no assurance as to the reliability of, any other information that others may give you. The underwriters are offering to sell, and seeking offers to buy, our common stock only in jurisdictions where offers and sales are permitted. The information contained in this prospectus is accurate only as of the date of this prospectus, regardless of the time of delivery of this prospectus or any sale of shares of our common stock. Our business, financial condition, results of operations and prospects may have changed since that date.

For investors outside the United States: We and the underwriters have not done anything that would permit this offering or the possession or distribution of this prospectus in any jurisdiction where action for those purposes is required, other than in the United States. Persons outside the United States who come into possession of this prospectus must inform themselves about, and observe any restrictions relating to, the offering of the shares of common stock and the distribution of this prospectus outside of the United States.

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ABOUT THIS PROSPECTUS

We incorporate by reference important information into this prospectus. You may obtain the information incorporated by reference without charge by following the instructions under “Where You Can Find More Information.” You should carefully read this prospectus as well as additional information described under “Information Incorporated by Reference,” before deciding to invest in our securities.

We have not, and the placement agent has not, authorized anyone to provide any information or to make any representations other than those contained in this prospectus or in any free writing prospectuses prepared by or on behalf of us or to which we have referred you. We take no responsibility for and can provide no assurance as to the reliability of, any other information that others may give you. This prospectus is an offer to sell only the securities offered hereby, and only under circumstances and in jurisdictions where it is lawful to do so. The information contained in this prospectus or in any applicable free writing prospectus is current only as of its date, regardless of its time of delivery or any sale of our securities. Our business, financial condition, results of operations and prospects may have changed since that date.

The information incorporated by reference or provided in this prospectus contains statistical data and estimates, including those relating to market size and competitive position of the markets in which we participate, that we obtained from our own internal estimates and research, as well as from industry and general publications and research, surveys and studies conducted by third parties. Industry publications, studies and surveys generally state that they have been obtained from sources believed to be reliable. While we believe our internal company research is reliable and the definitions of our market and industry are appropriate, neither this research nor these definitions have been verified by any independent source.

For investors outside the United States: We have not, and the placement agent has not, done anything that would permit this offering or possession or distribution of this prospectus in any jurisdiction where action for that purpose is required, other than in the United States. Persons outside the United States who come into possession of this prospectus must inform themselves about, and observe any restrictions relating to, the offering of the securities and the distribution of this prospectus outside the United States.

Unless otherwise mentioned or unless the context indicates otherwise, all references in this prospectus to “Bionano,” “the Company,” “we,” “us,” “our” and similar references refer to Bionano Genomics, Inc. and its subsidiaries or, as the context may require, Bionano Genomics, Inc. only. “Bionano Laboratories,” “BioDiscovery” and “Purigen” refer to our wholly owned subsidiaries, Lineagen, Inc. (doing business as Bionano Laboratories), BioDiscovery, LLC and Purigen Biosystems, Inc., respectively.

Our design logo, “Bionano,” and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc. The trademarks, trade names and service marks appearing in this prospectus and the information incorporated by reference into this prospectus are the property of their respective owners. Solely for convenience, trademarks and trade names referred to in this prospectus and the information incorporated by reference into this prospectus, including logos, artwork, and other visual displays, may appear without the ® or TM symbols, but such references are not intended to indicate, in any way, that we will not assert, to the fullest extent under applicable law, our rights or the rights of the applicable licensor to these trademarks and trade names. We do not intend our use or display of other companies’ trademarks, trade names or service marks to imply a relationship with, or endorsement or sponsorship of us by, any other companies or products.

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CAUTIONARY NOTE CONCERNING FORWARD-LOOKING STATEMENTS

Except for historical information, this prospectus contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). Forward-looking statements include statements with respect to our beliefs, plans, objectives, goals, expectations, anticipations, assumptions, estimates, intentions and future performance, and involve known and unknown risks, uncertainties and other factors, which may be beyond our control, and which may cause our actual results, performance or achievements to be materially different from future results, performance or achievements expressed or implied by such forward-looking statements. All statements other than statements of historical fact are statements that could be forward-looking statements. You can identify these forward-looking statements through our use of words such as “may,” “can,” “anticipate,” “assume,” “should,” “indicate,” “would,” “believe,” “contemplate,” “expect,” “seek,” “estimate,” “continue,” “plan,” “point to,” “project,” “predict,” “could,” “intend,” “target,” “will,” “potential” and other similar words and expressions of the future.

There are a number of important factors that could cause the actual results to differ materially from those expressed in any forward-looking statement made by us. These factors include, but are not limited to:

•	our ability to improve our margins, extend our cash runway and reach a potential pathway to profitability;

•	our ability to continue as a going concern within 12 months of the filing of our Quarterly Report on Form 10-Q for the quarter ended June 30, 2025, which requires us to manage costs and obtain significant additional financing to fund our strategic plans and commercialization efforts;

•	our ability to execute on our strategy and achieve our objectives;

•	the impact and utility of our cost savings initiative and our recent financing;

•	our ability to continue to drive OGM (as defined below) adoption by potential customers for routine use in genomic analysis;

•	the impact, or lack thereof, of Category I CPT codes to accelerate or increase the adoption of OGM;

•	continued research, presentations and publications involving OGM and its utility compared to traditional cytogenetics and our technologies;

•	the impact of our Stratys™ system and VIA™ software to increase throughput and simplify analysis of OGM data;

•	our ability to drive adoption of OGM and our technology solutions;

•	our ability to further deploy new products and applications for our technology platforms;

•	our expectations and beliefs regarding future growth of the business and the markets in which we operate;

•	our ability to consummate any strategic alternatives including the risk that if we fail to obtain additional financing we may seek relief under applicable insolvency laws;

•	the size and growth potential of the markets for our products, and our ability to serve those markets;

•	the rate and degree of market acceptance of our products;

•	our ability to manage the growth of our business and integrate acquired businesses;

•	our ability to expand our commercial organization to address effectively existing and new markets that we intend to target;

•	the impact from future regulatory, judicial, and legislative changes or developments in the U.S. and foreign countries;

•	our ability to compete effectively in a competitive industry;

•	the introduction of competitive technologies or improvements in existing technologies and the success of any such technologies;

•	the performance of our third-party contract sales organizations, suppliers and manufacturers;

•	our ability to attract and retain key scientific or management personnel;

iii

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•	the accuracy of our estimates regarding expenses, future revenues, reimbursement rates, capital requirements and needs for additional financing;

•

the impact of adverse geopolitical and macroeconomic developments, such as recent and future bank failures, the ongoing conflicts between Ukraine and Russia and in the Middle East, and related sanctions, regional or global pandemics, inflation, increased cost of goods, supply chain issues, and global financial market conditions; on our business and operations, as well as the business or operations of our suppliers, customers, manufacturers, research partners and other third parties with whom we conduct business and our expectations with respect to the duration of such impacts and the resulting effects on our business;

•	our ability to realize the anticipated benefits and synergies of our prior and any future acquisitions or other strategic transactions;

•	our ability to attract collaborators and strategic partnerships; and

•	other factors discussed in our most recent Annual Report on Form 10-K and any other subsequent filings we make with the SEC.

The foregoing does not represent an exhaustive list of matters that may be covered by the forward-looking statements contained herein or risk factors that we are faced with that may cause our actual results to differ from those anticipated in such forward-looking statements. The events and circumstances reflected in our forward-looking statements may not be achieved or occur and actual results could differ materially from those projected in the forward-looking statements. You should refer to the “Risk Factors” section of this prospectus for a discussion of important factors that may cause our actual results to differ materially from those expressed or implied by our forward-looking statements. You should review the factors and risks and other information we describe in the reports we will file from time to time with the Securities and Exchange Commission (the “SEC”) after the date of this prospectus.

All forward-looking statements are expressly qualified in their entirety by this cautionary note. You are cautioned to not place undue reliance on any forward-looking statements, which speak only as of the date of this prospectus or the date of the document incorporated by reference into this prospectus. You should read this prospectus and the documents that we reference in this prospectus and have filed as exhibits to the registration statement, of which this prospectus is a part, completely and with the understanding that our actual future results may be materially different from what we expect. We have no obligation, and expressly disclaims any obligation, to update, revise or correct any of the forward-looking statements, whether as a result of new information, future events or otherwise. We have expressed our expectations, beliefs and projections in good faith and believe they have a reasonable basis. However, we cannot assure you that our expectations, beliefs or projections will result or be achieved or accomplished.

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PROSPECTUS SUMMARY

~~The~~This ~~following~~ summary highlights information about our company, this offering and information contained in greater detail in other parts of this prospectus or incorporated by reference ~~elsewhere~~into in this prospectus ~~and~~from our filings with the SEC listed in the section titled “Information Incorporated by Reference.” Because it is only a summary, it does not contain all of the information that you should consider before purchasing our securities in ~~making~~this ~~your~~offering, ~~investment~~and ~~decision.~~it ~~Before~~is ~~investing~~qualified in ~~our~~its ~~common~~entirety ~~stock~~by, ~~you~~and should ~~carefully~~be read in conjunction with, the more detailed information appearing elsewhere or incorporated by reference into this prospectus. You should read the entire prospectus, the registration statement of which this prospectus is a part, and the information incorporated by reference into this prospectus in their entirety, including the “Risk Factors” and our financial statements and the related notes ~~and other documents~~ incorporated by reference ininto this prospectus, before purchasing our securities in this offering. Except as ~~well~~otherwise indicated herein or as the ~~information~~context ~~under~~otherwise requires, all references in this prospectus to “Bionano,” “the ~~caption~~Company,” “~~Risk~~we,” ~~Factors~~“us,” ~~herein~~“our” and ~~under~~ similar ~~headings~~references inrefer to Bionano Genomics, Inc. and its subsidiaries or, as the ~~other~~context ~~documents~~may ~~that~~require, ~~are~~Bionano ~~incorporated~~Genomics, byInc. ~~reference~~only. ~~into~~“Bionano ~~this~~Laboratories,” ~~prospectus~~“BioDiscovery” and “Purigen” refer to our wholly owned subsidiaries, Lineagen, Inc. (doing business as Bionano Laboratories), BioDiscovery, LLC and Purigen Biosystems, Inc., respectively.

~~Except~~Corporate asOverview ~~otherwise indicated herein or as the context otherwise requires, references in this prospectus to “Bionano,” “the company,” “we,” “us” and “our” refer to Bionano Genomics, Inc.~~

We are a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. Our mission is to transform the way the world sees the genome through optical genome mapping (“OGM”) solutions, diagnostic services and software. We offer OGM solutions for applications across basic, translational and clinical research, and for other applications including bioprocessing. We offer a platform-agnostic software solution, which integrates next-generation sequencing, microarray and OGM data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. The Company ~~Overview~~also offers nucleic acid extraction and purification solutions using proprietary isotachophoresis ITP technology. Through our Bionano Laboratories business, we also provide OGM-based diagnostic testing services.

We ~~are~~market ~~a genome analysis company providing tools~~ and ~~services~~sell ~~based~~OGM onsystems, ~~our~~including the Saphyr® system ~~to scientists~~ and ~~clinicians conducting genetic research and patient testing. We developed~~ the ~~Saphyr~~Stratys™ system, awhich ~~platform~~deliver ~~for~~OGM data to enable ultra-sensitive and ultra-specific detection of all classes of structural variation ~~detection,~~(“SV”). ~~that~~These ~~enables~~systems ~~researchers~~are ~~and~~used ~~clinicians~~ to ~~accelerate~~identify structural changes in chromosomes, the ~~search~~study ~~for~~of ~~new~~which ~~diagnostics~~is ~~and~~known ~~therapeutic~~as ~~targets~~cytogenetics, and to ~~streamline~~accelerate the ~~evaluation~~search offor ~~changes~~answers in ~~chromosomes,~~genetic ~~which~~disease isand ~~known~~cancer applications as ~~cytogenetics.~~well ~~Our~~as ~~commercial~~in ~~offering~~applications ~~includes~~for ~~the~~cell ~~Saphyr~~and ~~system,~~gene ~~which~~therapy. isThe systems are comprised of an instrument, chip consumables, reagents and software containing a suite of data analysis and visualization tools,. ~~and~~OGM ~~genome~~has ~~analysis~~been ~~services~~shown to ~~provide~~outperform ~~access~~the tocurrent ~~data~~gold ~~generated~~standard bycytogenetic ~~the~~methods ~~Saphyr~~including ~~system~~karyotyping, ~~for~~fluorescence ~~researchers~~in-situ ~~who~~hybridization ~~prefer~~(“FISH”), ~~not~~Southern toblot ~~adopt~~and chromosomal microarray (“CMA”), for the ~~Saphyr~~detection ~~system~~of SVs. OGM has also been shown to identify structural changes in ~~their~~chromosomes ~~labs~~that cannot be identified using current commercially available gene sequencing solutions.

~~Structural~~We ~~variation~~market ~~refers~~and tosell ~~large-scale structural differences in~~ the ~~genomic~~Ionic® ~~DNA~~Purification ofsystem, ~~one~~which ~~individual~~is ~~compared~~able to ~~another.~~deliver ~~Each~~high ~~structural~~quality ~~variation~~DNA ~~involves~~in ~~the~~a ~~rearrangement~~more ornatural, ~~repetition~~native ofform asand ~~few~~with asfewer ~~several~~contaminants ~~hundred~~when compared to asother ~~many~~isolation asand ~~tens~~purification ~~of millions of DNA base pairs~~solutions. ~~Structural~~The ~~variations~~Ionic® ~~may~~Purification besystem ~~inherited~~is orused ~~arise~~to ~~spontaneously~~extract, purify, and ~~many~~concentrate ~~structural~~DNA ~~variations~~or ~~cause~~RNA ~~genetic~~from ~~disorders~~a ~~and~~variety ~~diseases. Until our commercial launch~~ of ~~the~~sample ~~Saphyr system in February 2017~~types, and ~~since,~~is wecomprised ~~believe~~of noan ~~other~~instrument, ~~products~~consumables, ~~existed or exist that could more comprehensively~~ and ~~cost and time-efficiently detect structural variation~~reagents.

~~Our~~We ~~customers~~market ~~include researchers~~ and ~~clinicians~~sell ~~who~~the ~~seek~~VIA™ tosoftware ~~uncover~~which ~~and~~delivers ~~understand~~genomic ~~the~~data ~~biological~~interpretation orsolutions ~~clinical~~tailored ~~impact~~for ofresearch ~~genome~~use ~~variation~~in tocytogenomics ~~improve the diagnosis~~ and ~~treatment~~molecular ofpathology ~~patients~~labs ~~with~~in ~~better~~genetic ~~clinical~~disease ~~tests~~ and ~~new~~cancer ~~medicines~~research ormarkets, towith ~~replace~~an ~~existing~~emphasis ~~cytogenetic~~on ~~tests~~SV. ~~that~~This ~~are~~industry ~~expensive~~leading, ~~slow~~platform ~~and~~agnostic ~~labor-intense,~~software ~~with a modern~~ solution is designed to ~~simplify~~provide ~~workflow~~analysis, ~~and~~visualization, ~~reduce~~interpretation ~~cost~~ and ~~that~~reporting ~~has~~of ~~the~~SVs, ~~potential~~single-nucleotide tovariants ~~significantly~~and ~~increase~~absence ~~diagnostic~~of ~~yields~~heterozygosity across the ~~industry.~~genome ~~Our customers also include researchers~~ in ~~non-human~~one ~~segments,~~consolidated ~~such~~view. asOur ~~agricultural~~software ~~genomics,~~currently ~~seeking~~enables toanalysis ~~advance their understanding~~ of ~~how~~OGM, ~~structural~~next-generation ~~variation~~sequencing ~~impacts~~(“NGS”) ~~industrial applications of plants~~ and ~~animals~~microarray data. We ~~have~~believe ~~established~~the ~~relationships~~integration of OGM with ~~key~~data ~~opinion~~types ~~leaders~~common in ~~genomics~~the ~~research and clinical applications~~industry, ~~including~~such ~~rare~~as ~~diseases~~Variant ~~and~~Call ~~oncology~~Format (“VCF”), and ~~our~~Binary ~~installed~~Alignment ~~base~~Map ~~of over 138 systems made up of Saphyr and its predecessor system~~(“BAM”), ~~includes~~into ~~some of~~ the ~~world’s~~VIA ~~most~~software ~~prominent~~should ~~clinical,~~accelerate ~~translational research, basic research, academic~~ and ~~government~~broaden ~~institutions~~our asposition ~~well~~in asdigital ~~leading~~cytogenetics ~~pharmaceutical~~ and ~~diagnostic~~comprehensive ~~companies.~~genome ~~Examples~~analysis ~~include~~by ~~Children’s~~enabling ~~Hospital~~us ofto ~~Philadelphia,~~simplify ~~Children’s~~the ~~National~~assessment ~~Health~~of ~~System,~~clinically ~~Boston~~relevant ~~Children’s~~variants ~~Hospital,~~in ~~PerkinElmer,~~cytogenomics ~~GeneDx~~applications, ~~Mayo~~potentially ~~Clinic,~~reducing ~~Columbia~~interpretation ~~University,~~time ~~DuPont~~per ~~Pioneer,~~sample ~~Garvan~~and ~~Institute~~expanding ofour ~~Medical~~reach ~~Research,~~into ~~Genentech,~~the ~~McDonnell~~discovery ~~Genome~~and ~~Institute~~translational atresearch ~~Washington~~markets ~~University,~~through ~~National~~the ~~Institutes~~combination of ~~Health,~~OGM ~~Pennsylvania State University, Radboud University Medical Center~~ and ~~Salk Institute for Biological Studies~~NGS.

~~Approximately~~Our ~~7,000~~Bionano ~~research~~Laboratories ~~use~~business ~~only,~~has ordeveloped ~~RUO,~~and ~~high~~provides ~~throughput~~several ~~sequencers~~OGM-based ~~are~~laboratory ~~currently installed worldwide. These sequencers are~~ developed ~~and~~tests ~~sold~~(“LDTs”) ~~almost~~for ~~entirely~~facioscapulohumeral bymuscular ~~Illumina~~dystrophy ~~and~~type ~~are~~1 ~~owned by an estimated 3~~(“FSHD1”),~~000~~ ~~unique~~which ~~customers. Sequencing~~ is ~~very~~a ~~good~~progressive atdisorder ~~detecting~~that ~~genome~~primarily ~~differences~~affects ~~involving~~the ~~just~~muscles aof ~~few~~the ~~base pairs or single-nucleotide variations~~face, ~~which~~shoulder ~~Saphyr~~blades ~~cannot detect~~(scapula), ~~but~~upper ~~sequencing~~arms, ~~including~~and ~~next-generation~~lower ~~sequencing~~legs, orfor ~~NGS,~~detecting ~~cannot~~SVs ~~reliably~~in ~~detect~~individuals ~~the~~with ~~larger~~hematologic ~~structural variations that our Saphyr system can detect. Therefore~~malignancies, ~~Saphyr~~and isfor ~~being~~detecting ~~adopted~~SVs ~~alongside~~in ~~this~~pre- ~~installed~~and ~~base~~post-natal ofsamples, ~~sequencers~~through asits ~~a complement that is designed to give users the ability to see a much wider scope of genome variation than ever before.~~

The Saphyr system, which is for RUO, is also beginning to be adopted by cytogenetics labs that seek to use it in commercial clinical tests of its patients as a laboratory-developed test, or LDT. We estimate that approximately 2,500 cytogenetics labs exist worldwide. These labs currently rely on existing methods such as karyotyping, fluorescence in situ hybridization, or FISH, and microarrays for clinical tests and research that look at chromosomal structure, location and function in cells. Major guidelines for oncology and genetic disease clinical diagnostics

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~~recommend first~~OGM-~~line~~Dx™ ~~structural variation~~ testing byservices. ~~these~~During ~~existing~~2024, ~~methods.~~Bionano ~~The~~Laboratories ~~organizations~~phased ~~issuing~~out ~~these~~the ~~guidelines~~offering ~~include,~~of ~~among~~certain ~~many~~testing ~~others,~~services ~~World~~for ~~Health~~individuals ~~Organization~~demonstrating ~~(WHO),~~clinical ~~National~~presentations ~~Comprehensive~~consistent ~~Cancer~~with ~~Network~~neurodevelopmental disorders (~~NCCN~~“NDDs”), ~~American~~including ~~College~~autism ofspectrum ~~Medical~~disorders ~~Genetics~~ (~~ACMG~~“ASDs”) and ~~American~~other ~~College~~disorders of ~~Obstetricians~~childhood ~~& Gynecologists (ACOG)~~development.

~~More~~Bionano ~~than~~Laboratories 30also ~~medical~~provides ~~institutions~~laboratory ~~are~~services ~~conducting~~to ~~more~~clinicians, ~~than~~scientists, 20pharmaceutical ~~human~~companies, ~~translational~~and ~~research~~others ~~and~~who ~~human~~are ~~clinical~~seeking ~~studies~~to inincorporate ~~2019~~OGM ~~and~~into ~~2020~~their togenomics ~~assess~~research ~~Saphyr’s~~without ~~ability~~the need to ~~detect~~bring ~~structural~~one ~~variations~~of ~~and~~our ~~diagnose~~OGM ~~patients~~systems ~~and,~~ in ~~certain~~house. ~~studies,~~Laboratory toservices ~~compare~~for ~~those~~OGM ~~results~~are toperformed ~~those~~in ~~produced~~our ~~via~~laboratory ~~existing~~facilities ~~cytogenetic~~in ~~methods.~~San WeDiego, ~~expect~~California and at partner laboratories in the ~~findings~~United ~~from~~States ~~these~~and ~~studies~~Europe, ~~whether~~and ~~assessed~~serve ~~internally~~as orsolutions ~~published~~for byresearchers ~~the~~and ~~institution,~~clinicians towho ~~help~~would ~~drive~~like ~~adoption~~to ofuse ~~Saphyr~~OGM ~~beginning~~for various applications in ~~2020~~genomics but have yet to acquire an OGM system.

~~Saphyr~~We ~~and~~believe ~~its predecessor system, which~~ we ~~collectively~~have ~~refer~~transformed ~~to as~~ our ~~system~~business infrom ~~this~~an ~~prospectus,~~instrument ~~have~~company ~~been~~to ~~cited~~a byprovider ~~researchers~~of ~~and~~a ~~clinicians~~full insuite ~~hundreds~~ of ~~publications~~genomic ~~covering~~solutions. ~~structural~~We ~~variations~~expanded ininto ~~areas~~molecular ofgenetic ~~high~~clinical ~~unmet~~testing ~~medical~~services ~~need~~through ~~and~~our ~~research~~August 2020 ~~interest,~~acquisition ~~such~~of asLineagen. ~~rare~~We ~~and~~furthered ~~undiagnosed~~our ~~pediatric~~transformation ~~diseases,~~through ~~muscular~~the ~~diseases,~~expansion ~~developmental~~into ~~delays~~software ~~and disorders~~solutions, ~~prostate~~made ~~cancer~~possible ~~and~~by ~~leukemia.~~our ~~Importantly,~~October 2021 ~~Saphyr~~acquisition ~~can~~of beBioDiscovery ~~used~~and ~~alone~~continued towith ~~provide~~our ~~comprehensive~~November 2022 ~~detection~~acquisition of ~~structural~~Purigen ~~variations~~bringing ~~and~~their ~~enable~~leading ~~diagnostic~~nucleic ~~calls~~acid ~~without~~isolation ~~the~~and ~~need~~purification ~~for~~technology ~~sequencing~~to ~~or cytogenetic technology~~Bionano. ~~Saphyr~~We ~~enables~~believe that these ~~diagnostic~~acquisitions, ~~calls~~along with ~~low~~internal ~~cost~~investments ~~per~~in ~~patient,~~research ~~high~~and ~~speed~~development and ~~industry~~the ~~leading~~build ~~performance.~~out ~~Saphyr’s~~of ~~performance~~our ~~characteristics~~commercial ~~include~~teams, uphave topositioned ~~99%~~us ~~sensitivity,~~well ~~less~~to ~~than~~provide 2%solutions ~~false~~to ~~positive~~our ~~rates~~customers ~~and~~that ~~accurate~~we ~~diagnosis~~believe ~~with~~will ~~allele~~make ~~fraction,~~OGM or the ~~percentage~~standard ofcytogenetic ~~sample~~technique ~~exhibiting~~for ~~the~~structural variant, ~~as low as between 3-5%~~analysis.

~~Recent~~Implications ~~Highlights~~of Being a Smaller Reporting Company

~~Below~~We isare a ~~summary~~“smaller reporting company” as defined in Item 10(f)(1) of ~~selected~~Regulation ~~highlights~~S-K. ~~since~~Smaller reporting companies may take advantage of certain reduced disclosure obligations, including, among other things, providing only two years of audited financial statements. We will remain a smaller reporting company until the last day of any fiscal year for so long as either (1) the market value of our ~~follow~~shares of common stock held by non-onaffiliates does not equal or exceed $250.0 million as of the prior June 30th, or (2) our annual revenues did not equal or exceed $100.0 million during such completed fiscal year and the market value of our shares of common stock held by non-affiliates did not equal or exceed $700.0 million as of the prior June 30th. To the extent we take advantage of any reduced disclosure obligations, it may make comparison of our financial statements with other public ~~offering~~companies indifficult ~~October~~or ~~2019:~~impossible.

• We announced the adoption of our Saphyr system by PerkinElmer Genomics and the University of Iowa, including their development of assays using our optical mapping technology to expand their genetic tests assessing disease-associated chromosomal abnormalities.

• We announced that Novogene added the Saphyr system to their repertoire of genomics data services.

• We announced the adoption of our Saphyr system by Mayo Clinic for applications in neurodegenerative disease.

• We announced the adoption of our Saphyr system by GeneDx, using our system for the clinical detection of genetic variants in muscular dystrophies, developmental and reproductive disorders.

• We announced the publication of a study by Radboud University Medical Center showing 100% concordance of Saphyr with standard of care for the detection of somatic chromosomal abnormalities in leukemia.

• We announced a collaboration with GrandOmics in Wuhan, China to study gene variants that contribute to Coronavirus disease susceptibility.

Corporate Information

We were formed in January 2003 as BioNanomatrix LLC, a Delaware limited liability company. In August 2007, we became BioNanomatrix Inc., a Delaware corporation. In October 2011, we changed our name to BioNano Genomics, Inc., and in July 2018, we changed our name to Bionano Genomics, Inc.

Our principal executive offices are located at 9540 Towne Centre Drive, Suite 100, San Diego, California 92121, and our telephone number is (858) 888-7600. Our website address is www.bionanogenomics.com, and we regularly post copies of our press releases as well as additional information about us on our website. Information contained in, or that can be accessed through, our website is not incorporated by reference into this prospectus, and you should not consider information on our website to be part of this prospectus or in deciding whether to purchase our securities.

Information contained in, or that can be accessed through, our website is not incorporated by reference into this prospectus, and you should not consider information on our website to be part of this prospectus. Our design logo, “Bionano,” and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc.

The trademarks, trade names and service marks appearing in this prospectus are the property of their respective owners. We do not intend our use or display of other companies’ trademarks, trade names or service marks to imply a relationship with, or endorsement or sponsorship of us by, any other companies or products.

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~~Implications~~THE ofOFFERING ~~Being an Emerging Growth Company~~

WeCommon ~~are~~Stock ~~an emerging growth company, as defined in the Jumpstart Our Business Startups Act of 2012, or the JOBS Act. For as long as we continue~~ to be an emerging growth company, we may take advantage of exemptions from various reporting requirements that are applicable to other public companies that are not emerging growth companies, including not being required to comply with the auditor attestation requirements of Section 404 of the Sarbanes-Oxley Act of 2002, or the Sarbanes-Oxley Act, reduced disclosure obligations regarding executive compensation in this prospectus and our periodic reports and proxy statements and exemptions from the requirements of holding nonbinding advisory votes on executive compensation and stockholder approval of any golden parachute payments not previously approved. We can remain an emerging growth company until the earlier of (1) the last day of the fiscal year (a) ending December 31, 2023, which is the end of the fiscal year following the fifth anniversary of the closing of our initial public offering, (b) in which we have total annual gross revenue of at least $1.07 billion, or (c) in which we are deemed to be a large accelerated filer, which means the market value of our common stock that is held by non-affiliates exceeds $700 million as of the prior June 30th, and (2) the date on which we have issued more than $1.0 billion in non-convertible debt during the prior three-year period. Even after we no longer qualify as an emerging growth company, we may still qualify as a “smaller reporting company” which would allow us to take advantage of many of the same exemptions from disclosure requirements, including reduced disclosure obligations regarding executive compensation in our periodic reports and proxy statements. Additionally, even if we no longer qualify as an emerging growth company, as long as we are neither a “large accelerated filer” nor an “accelerated filer,” we would not be required to comply with the auditor attestation requirements of Section 404 of the Sarbanes-Oxley Act. Offered

WeUp ~~cannot~~to ~~predict~~2,032,520 ifshares ~~investors~~based ~~will~~on ~~find~~the sale of our ~~securities~~common ~~less~~stock ~~attractive~~at ~~because~~an weassumed ~~may~~combined ~~rely~~public onoffering ~~these~~price ~~exemptions,~~of ~~which~~$4.92 ~~could~~per ~~result~~share inof acommon ~~less~~stock ~~active~~and ~~trading~~accompanying ~~market~~Warrants, ~~for~~which was the closing price of our ~~securities~~common ~~and~~stock ~~increased~~on ~~volatility~~September 10, in2025, ~~the~~and ~~price~~assuming no sale of ~~our~~any ~~securities~~Pre-Funded Warrants.

~~Under~~Pre-Funded ~~the~~Warrants ~~JOBS Act, emerging growth companies can also delay adopting new or revised accounting standards that have different effective dates for public and private companies until those standards apply~~ to ~~private companies. We have elected to use this extended transition period. As a result of this election, our timeline to comply with these standards will in many cases~~ be delayed as compared to other public companies that are not eligible to take advantage of this election or have not made this election. Therefore, our financial statements may not be comparable to those of companies that comply with the public company effective dates for these standards.Offered

InWe ~~addition,~~are ifalso weoffering ~~cease~~ to becertain anpurchasers ~~emerging~~whose ~~growth~~purchase ~~company,~~of weshares ~~will~~of nocommon ~~longer~~stock bein ~~able~~this tooffering ~~use~~would ~~the~~otherwise ~~extended~~result ~~transition~~in ~~period~~the ~~for~~purchaser, ~~complying~~together with ~~new~~its affiliates and certain related parties, beneficially owning more than 4.99% (or, ~~revised~~at ~~accounting~~the ~~standards~~election of the purchaser, 9.99%) Asof aour ~~result~~outstanding common stock immediately following the consummation of this offering, ~~changes~~the opportunity to purchase, if such purchasers so choose, Pre-Funded Warrants to purchase shares of common stock, in ~~rules~~lieu of ~~U.S.~~shares ~~generally~~of ~~accepted~~common ~~accounting~~stock ~~principles~~that orwould ~~their~~otherwise ~~interpretation~~result in any such purchaser’s beneficial ownership exceeding 4.99% (or, at the ~~adoption~~election of ~~new~~the ~~guidance~~purchaser, or9.99%) of our outstanding common stock. Each Pre-Funded Warrant will be exercisable for one share of our common stock. The purchase price of each Pre-Funded Warrant and accompanying Warrants will equal the ~~application~~price at which the share of ~~existing~~common ~~guidance~~stock and accompanying Warrants are being sold to ~~changes~~the public in ~~our~~this ~~business~~offering, ~~could~~minus ~~significantly~~$0.0001, ~~affect~~and the exercise price of each Pre-Funded Warrant will be $0.0001 per share. The Pre-Funded Warrants will be exercisable immediately and may be exercised at any time until all of the Pre-Funded Warrants are exercised in full. Purchasers of Pre-Funded Warrants will also receive accompanying Warrants as if such purchasers were buying shares of our ~~financial~~common ~~position~~stock in this offering. This prospectus also relates to the offer and ~~results~~sale of ~~operations~~the shares of common stock issuable upon exercise of the Pre-Funded Warrants sold in this offering.

~~Finally,~~For weeach ~~are~~Pre-Funded aWarrant ~~“smaller~~we ~~reporting~~sell, ~~company”~~the ~~(and~~number ~~may~~of ~~continue~~shares toof ~~qualify~~common asstock ~~such even after~~ we noare ~~longer~~offering ~~qualify~~will asbe andecreased ~~emerging~~on ~~growth~~a ~~company)~~one-for-one ~~and~~basis. ~~accordingly~~Because ~~may~~we ~~provide~~will ~~less~~issue ~~public~~accompanying ~~disclosure~~Warrants ~~than~~for ~~larger~~each ~~public~~share ~~companies, including the inclusion~~ of ~~only~~our ~~two~~common ~~years~~stock ofand ~~audited~~for ~~financial~~each ~~statements~~Pre-Funded ~~and~~Warrant ~~only~~to ~~two~~purchase ~~years~~one share of ~~related~~our ~~selected~~common ~~financial~~stock ~~data~~sold ~~and~~in ~~management’s~~this ~~discussion~~offering, ~~and~~the ~~analysis~~number of ~~financial~~Warrants ~~condition~~sold ~~and~~in ~~results~~this ofoffering ~~operations~~will ~~disclosure.~~not Aschange as a result, ~~the~~of ~~information~~a ~~that~~change wein ~~provide~~the tomix ~~our~~of ~~stockholders~~the ~~may~~shares beof ~~different~~our ~~than~~common ~~you~~stock ~~might~~and ~~receive~~Pre-Funded ~~from~~Warrants ~~other~~sold. ~~public~~See ~~reporting~~“Description ~~companies~~of inSecurities ~~which~~– ~~you~~Pre-Funded ~~hold~~Warrants” ~~equity~~for ~~interests~~additional information.

Warrants to be Offered

Each share of our common stock and each Pre-Funded Warrant to purchase one share of our common stock is being sold together with one Series E Warrant to purchase one share of our common stock and one Series F Warrant to purchase one share of our common stock.

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~~THE~~Each ~~OFFERING~~Warrant will have an assumed exercise price of $4.92 per share (representing 100% of the assumed combined price at which a share of common stock and accompanying Warrants are sold to the public in this offering) and will be exercisable beginning on the effective date of Warrant Stockholder Approval; provided, however, that if the Pricing Conditions are met, the Warrants will be exercisable upon issuance. The Series E Warrants will expire on the five-year anniversary of the Initial Exercise Date. The Series F Warrants will expire on the 18-month anniversary of the Initial Exercise Date.

~~Common~~The shares of common stock toand the accompanying Warrants and the Pre-Funded Warrants and the accompanying Warrants, as the case may be, ~~offered~~can only be purchased together in this offering but will be issued separately and will be immediately separable upon issuance. This prospectus also relates to the offer and sale of the shares of common stock issuable upon exercise of the Warrants. See “Description of Securities — Warrants” for additional information.

~~17,648,000~~Common ~~shares,~~Stock ~~assuming~~Outstanding ~~the~~Immediately ~~sale~~Prior ofto ~~our~~this ~~common stock at an assumed public offering price of $0.85 per share, which is the last reported sale price of our common stock on March 9, 2020, and no sale of any pre-funded warrants.~~ Offering(1)

~~Pre-funded~~4,755,265 ~~warrants~~shares ~~offered~~of bycommon usstock.

WeCommon ~~are~~Stock ~~also offering~~ to ~~certain~~be ~~purchasers~~Outstanding ~~whose~~Immediately ~~purchase~~After ~~of shares of common stock in~~ this ~~offering would otherwise result in the purchaser, together with its affiliates and certain related parties, beneficially owning more than 4.99%~~ Offering(~~or, at the election of the purchaser, 9.99%~~1) of our outstanding common stock immediately following the consummation of this offering, the opportunity to purchase, if such purchasers so choose, pre-funded warrants, in lieu of shares of common stock that would otherwise result in any such purchaser’s beneficial ownership exceeding 4.99% (or, at the election of the purchaser, 9.99%) of our outstanding common stock. Each pre-funded warrant will be exercisable for one share of our common stock. The purchase price of each pre-funded warrant and the accompanying common warrant will equal the price at which the share of common stock and the accompanying common warrant are being sold to the public in this offering, minus $0.001, and the exercise price of each pre-funded warrant will be $0.001 per share. The pre-funded warrants will be exercisable immediately and may be exercised at any time until all of the pre-funded warrants are exercised in full. This offering also relates to the shares of common stock issuable upon exercise of any pre-funded warrants sold in this offering. For each pre-funded warrant we sell, the number of shares of common stock we are offering will be decreased on a one-for-one basis. Because we will issue a common warrant for each share of our common stock and for each pre-funded warrant to purchase one share of our common stock sold in this offering, the number of common warrants sold in this offering will not change as a result of a change in the mix of the shares of our common stock and pre-funded warrants sold.

~~Common~~6,787,785 shares of common stock (assuming we sell only shares of common stock and no Pre-Funded Warrants ~~offered~~and byassuming usno exercise of the Warrants offered hereby).

~~Common~~Use ~~warrants to purchase an aggregate~~ of 17,648,000 shares of our common stock. Each share of our common stock and each pre-funded warrant to purchase one share of our common stock is being sold together with a common warrant to purchase one share of our common stock. Each common warrant will have an exercise price of $0.85 per share, will be immediately exercisable and will expire on the fifth anniversary of the original issuance date. The shares of common stock and pre-funded warrants, and the accompanying common warrants, as the case may be, can only be purchased together in this offering but will be issued separately and will be immediately separable upon issuance. This prospectus also relates to the offering of the shares of common stock issuable upon exercise of the common warrants. Proceeds

We estimate that the net proceeds from this offering will be approximately $9.0 million, based on an assumed combined public offering price of $4.92 per share of common stock and accompanying Warrants, which was the closing price of our common stock on the Nasdaq Capital Market on September 10, 2025, after deducting the placement agent fees and estimated offering expenses payable by us, and assuming we sell only shares of common stock and no Pre-Funded Warrants and excluding the proceeds, if any, from the exercise of the Warrants.

We currently intend to use the net proceeds from the offering for working capital and general corporate purposes. See “Use of Proceeds” for additional information.

Risk Factors

An investment in our securities involves a high degree of risk. See “Risk Factors” beginning on page 6 of this prospectus and the other information included and incorporated by reference in this prospectus for a discussion of the risk factors you should carefully consider before deciding to invest in our securities.

National Securities Exchange Listing

Our common stock is listed on the Nasdaq Capital Market under the symbol “BNGO.”

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~~Common~~There ~~stock~~is no established public trading market for the Pre-Funded Warrants or Warrants, and we do not expect a market to bedevelop. ~~outstanding~~In ~~after~~addition, ~~this~~we ~~offering~~do not intend to apply to list the Pre-Funded Warrants or Warrants on Nasdaq or on any other national securities exchange or other nationally recognized trading system. Without an active trading market, the liquidity of the Pre-Funded Warrants and Warrants will be limited.

~~51,922,469~~Best ~~shares~~Efforts (assuming none of the warrants issued in this offering are exercised and assuming the sale of our common stock at an assumed public offering price of $0.85 per share, which is the last reported sale price of our common stock on March 9, 2020, and no sale of any pre-funded warrants). Offering

~~Use~~The placement agent has agreed to use its reasonable best efforts to arrange for the sale of ~~proceeds~~the securities offered by this prospectus. The placement agent is not purchasing or selling any of the securities we are offering, and the placement agent is not required to arrange the purchase or sale of any specific number or dollar amount of securities. See “Plan of Distribution” on page 18 of this prospectus.

We(1) ~~estimate~~The ~~that~~number ~~the~~of ~~net~~shares ~~proceeds~~of ~~from~~our ~~this~~common ~~offering~~stock ~~will~~outstanding beprior ~~approximately~~to ~~$13.6~~this ~~million~~offering ~~based~~and onto anbe ~~assumed~~outstanding ~~offering~~after ~~price~~this ofoffering ~~$0.85~~is ~~per~~based ~~share~~on ~~and accompanying warrant~~4,755,265 ~~which~~shares ~~was the last reported sales price~~ of ~~our~~ common stock onoutstanding ~~The~~as ~~Nasdaq~~of ~~Capital~~September ~~Market on March~~ 9, ~~2020~~2025, and ~~assuming~~excludes noas ~~sale~~ of ~~any~~such ~~pre-funded warrants, after deducting estimated underwriting discounts and commissions and estimated offering expenses payable by us.~~date:

We• ~~intend~~191,532 toshares ~~use~~of tocommon ~~use~~stock ~~$2.9~~issuable ~~million~~upon of the ~~net~~exercise ~~proceeds from this offering to repay a portion~~ of ~~the aggregate principal amount~~ outstanding ~~under~~stock ~~our~~options ~~Loan and Security Agreement~~ with ~~Innovatus~~a ~~Life~~weighted-average ~~Sciences~~exercise ~~Lending~~price Fund I, LP, our senior lender, and the remainder primarily for general corporate purposes, including working capital, sales and marketing activities, general and administrative matters and capital expenditures. See “Use of ~~Proceeds” for additional information~~$251.09 per share;

~~Risk~~• ~~factors~~2,081,088.57 shares of common stock issuable upon the exercise of outstanding warrants with a weighted average exercise price of $54.74 per share;

An• ~~investment~~633,703.70 inshares ~~our securities involves a high degree~~ of ~~risk.~~common ~~See~~stock ~~“Risk~~issuable ~~Factors”~~upon ~~and~~ the ~~other~~exercise ~~information~~of ~~included~~outstanding inconvertible ~~this~~notes ~~prospectus~~with ~~and incorporated by reference herein for~~ a ~~discussion~~conversion price of ~~factors you should carefully consider before deciding to invest in our securities~~$16.20 per share;

~~National~~• ~~Securities~~35,471 ~~Exchange~~shares ~~Listing~~of common stock reserved for future issuance under our 2020 Inducement Plan (“2020 Plan”), plus any additional shares of our common stock that may become available under the 2020 Plan;

~~Our~~• ~~common~~1,013 ~~stock~~shares isof ~~listed~~our oncommon ~~the~~stock ~~Nasdaq~~reserved ~~Capital~~for ~~Market~~issuance under ~~the~~our ~~symbol~~2018 ~~“BNGO.”~~Employee WeStock doPurchase ~~not~~Plan ~~intend~~(“ESPP”); ~~to list the pre-funded warrants or common warrants on any securities exchange or nationally recognized trading system.~~ and

~~The~~• ~~number~~11,838 of shares of our common stock ~~that~~reserved ~~will~~for ~~be outstanding after this offering is based on 34,274,469 shares of common stock outstanding as of December 31, 2019, and assumes the sale and~~ issuance byunder usour of2018 ~~17,648,000~~Equity ~~shares~~Incentive ~~of common stock (and no sale of any pre-funded warrants) in this offering and excludes:~~Plan.

•Unless 1otherwise indicated,~~742,912~~ ~~shares~~all ofinformation ~~common~~contained ~~stock~~in ~~issuable~~this ~~upon~~prospectus ~~the~~assumes (i) no exercise of ~~options~~the outstanding asstock options, convertible notes, or common warrants summarized above, (ii) no vesting or settlement of ~~December~~the 31outstanding restricted stock units summarized above, ~~2019~~(iii) we atissue aonly ~~weighted~~shares ~~average~~of ~~exercise~~common ~~price~~stock and no Pre-Funded Warrants and (iv) no exercise of ~~$5.73~~the ~~per~~Warrants ~~share;~~offered hereby.

• 196,731 shares of common stock reserved for future issuance under our 2018 Equity Incentive Plan as of December 31, 2019;

• 165,402 shares of common stock reserved for future issuance under our 2018 Employee Stock Purchase Plan as of December 31, 2019;

• 24,406,050 shares of common stock issuable upon the exercise of common warrants outstanding as of December 31, 2019 at a weighted-average exercise price of $1.76 per share;

• 163,000 shares of common stock issuable upon the exercise of pre-funded warrants outstanding as of December 31, 2019 at a weighted-average exercise price of $0.001 per share; and

• 17,648,000 shares of common stock issuable upon the exercise of the common warrants issued in this offering.

Unless otherwise indicated, this prospectus reflects and assumes no issuances or exercises of any other outstanding options or warrants after December 31, 2019.

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RISK FACTORS

~~Investing~~An investment in our ~~common~~securities ~~stock~~ involves a high degree of risk. ~~You~~Before ~~should~~purchasing ~~consider~~any ~~carefully~~of ~~the~~our ~~following~~securities ~~risks~~you ~~and~~should ~~uncertainties~~carefully asconsider ~~well~~the asrisk ~~the~~factors ~~risks~~set ~~and~~forth ~~uncertainties~~below ~~described~~and inthose ~~the~~incorporated ~~section~~by ~~entitled~~reference ~~“Risk~~in ~~Factors”~~this ~~contained~~prospectus infrom our Annual Report on Form 10-K for the fiscal year ended December 31, ~~2019~~2024, asand ~~filed~~any ~~with~~subsequent ~~the~~updates ~~Securities~~described ~~and~~in ~~Exchange~~our ~~Commission,~~Quarterly orReports ~~SEC,~~ on ~~March~~ Form 10,-Q ~~2020~~and Current Reports on Form 8-K, as well as inthe ~~our~~risks, ~~subsequent~~uncertainties ~~Quarterly~~ and ~~Annual~~additional ~~Reports~~information ~~filed~~set ~~with~~forth ~~the~~in our SEC, ~~which~~reports ~~descriptions~~on ~~are~~Forms ~~incorporated~~10-K, in10-Q, ~~this~~and ~~prospectus~~8-K byand ~~reference~~ in ~~their~~the ~~entirety,~~other asdocuments ~~well~~incorporated asby reference in ~~any~~this prospectus ~~supplement hereto~~. ~~These~~For ~~risks~~a ~~and~~description ~~uncertainties~~of ~~are~~these ~~not~~reports ~~the only risks~~ and ~~uncertainties~~documents, ~~we face. Additional risks~~ and ~~uncertainties~~information ~~not~~about ~~currently~~where ~~known~~you tocan usfind them, orsee ~~that~~“Where weYou ~~currently~~Can ~~view~~Find asMore ~~immaterial,~~Information” ~~may~~and ~~also~~“Information ~~impair~~Incorporated ~~our~~by ~~business~~Reference.” IfAdditional ~~any~~risks ofnot ~~the~~presently ~~risks~~known or ~~uncertainties~~that ~~described~~we inpresently ~~our~~consider ~~SEC~~to ~~filings~~be orimmaterial ~~any~~could ~~additional~~subsequently ~~risks~~materially and ~~uncertainties~~adversely ~~actually~~affect ~~occur,~~ our ~~business,~~ financial condition, results of operations, ~~and cash flow could be materially and adversely affected. In that case~~business, ~~the trading price of our common stock could decline~~ and ~~you might lose all or part of your investment~~prospects. ~~You should carefully consider the following information about risks, together with the other information contained in this prospectus, before making an investment in our common stock.~~

IfRisks ~~you~~Related ~~purchase~~to ~~shares of common stock in~~ this ~~offering,~~Offering ~~you will experience immediate and substantial dilution in your investment. You will experience further dilution if we issue additional equity or equity-linked securities in the future.~~

~~Since~~We ~~the~~have ~~price~~broad ~~per~~discretion ~~share~~in ~~of our common stock being offered is substantially higher than~~ the ~~net~~use ~~tangible book value per share~~ of ~~our common stock, you will suffer immediate and substantial dilution with respect to~~ the net ~~tangible~~proceeds ~~book~~from ~~value of the common stock you purchase in~~ this offering. ~~Based on the assumed combined public offering price of $0.85 per share of common stock~~ and ~~accompanying~~may ~~warrants~~not ~~being~~use ~~sold~~them ~~in this offering, and our net tangible book value as of December 31, 2019, if you purchase shares of common stock in this offering, you will suffer immediate and substantial dilution of $0~~effectively.52 per share with respect to the net tangible book value of the common stock. See the section entitled “Dilution” for a more detailed discussion of the dilution you will incur if you purchase common stock in this offering.

IfOur wemanagement ~~issue~~will ~~additional~~have ~~shares~~broad discretion in the application of ~~common~~the ~~stock~~net proceeds, orincluding ~~securities~~for ~~convertible~~any ~~into~~of orthe ~~exchangeable~~purposes ordescribed ~~exercisable~~in ~~for~~the ~~shares~~section of ~~common~~this ~~stock,~~prospectus ~~our~~titled ~~stockholders,~~“Use ~~including~~of ~~investors~~Proceeds”. ~~who~~You ~~purchase~~will ~~shares~~be ofrelying ~~common~~on ~~stock~~the ~~and~~judgment ~~accompanying~~of ~~warrants~~our inmanagement ~~this~~with ~~offering,~~regard ~~will~~to ~~experience~~the ~~additional~~use ~~dilution~~of these net proceeds, and ~~any~~you ~~such~~will ~~issuances~~not ~~may~~have ~~result~~the inopportunity, ~~downward~~as ~~pressure~~part onof ~~the~~your ~~price~~investment ofdecision, ~~our~~to ~~common~~assess ~~stock.~~whether Wethe ~~also~~net ~~cannot~~proceeds ~~assure~~are ~~you~~being ~~that~~used weappropriately. ~~will~~The befailure ~~able~~by our management to ~~sell~~apply ~~shares~~these orfunds ~~other~~effectively ~~securities~~could result in ~~any~~financial ~~other~~losses ~~offering~~that atcould have a ~~price~~material ~~per~~adverse ~~share~~effect ~~that~~on isour ~~equal~~business, cause the price of our securities to ordecline ~~greater~~and ~~than~~delay the ~~price~~commercialization ~~per~~of ~~share~~our ~~paid~~products byand ~~investors~~technologies. inPending ~~this~~the ~~offering~~application of these funds, ~~and~~we ~~investors~~may ~~purchasing~~invest ~~shares~~the ornet ~~other~~proceeds ~~securities~~from this offering in ~~the~~a ~~future~~manner ~~could~~that ~~have~~does ~~rights~~not ~~superior~~produce toincome ~~existing~~or ~~stockholders~~that loses value.

~~Future~~There ~~sales~~is ofno ~~substantial~~public ~~amounts~~market offor ~~our~~the ~~common~~Warrants ~~stock,~~ or ~~the~~Pre-Funded ~~possibility~~Warrants ~~that~~being ~~such~~offered ~~sales~~by ~~could~~us ~~occur,~~in ~~could~~this ~~adversely affect the market price of our common stock~~offering.

~~Future~~There ~~sales~~is inno ~~the~~established public trading market offor ~~shares~~the ofWarrants ~~our~~or ~~common~~the ~~stock~~Pre-Funded Warrants, ~~including~~and ~~shares~~we ~~referred~~do tonot inexpect ~~the~~a ~~foregoing~~market ~~risk~~to ~~factor~~develop. orIn ~~shares~~addition, ~~issued~~we ~~upon~~do ~~exercise~~not ofintend ~~our~~to ~~outstanding~~apply ~~stock~~to ~~options,~~list the Warrants or ~~the~~Pre-Funded ~~perception~~Warrants byon the ~~market~~Nasdaq ~~that~~Capital ~~these~~Market ~~sales~~or ~~could~~any ~~occur,~~other ~~could~~national ~~lower~~securities ~~the~~exchange ~~market~~or ~~price~~other ofnationally ~~our~~recognized ~~common~~trading ~~stock~~system. orWithout ~~make~~an itactive ~~difficult~~market, ~~for~~the usliquidity toof ~~raise~~the ~~additional~~Warrants ~~capital~~and Pre-Funded Warrants will be limited.

~~There~~The isWarrants noand ~~public market for the pre~~Pre-~~funded~~Funded ~~warrants~~Warrants orare ~~common~~speculative ~~warrants being offered~~ in ~~this offering~~nature.

~~There~~The isWarrants noand ~~established~~Pre-Funded ~~public~~Warrants ~~trading~~offered ~~market~~hereby ~~for~~do ~~the~~not ~~pre-funded~~confer ~~warrants~~any orrights ~~common~~of ~~warrants~~share ~~being~~of ~~offered~~common instock ~~this~~ownership ~~offering~~on their holders, ~~and~~such weas dovoting ~~not~~rights, ~~expect~~but arather ~~market~~merely represent the right to ~~develop.~~acquire Inshares ~~addition~~of common stock at a fixed price. Specifically, wecommencing doon ~~not~~the ~~intend~~date toof ~~apply~~issuance, toholders ~~list~~of the ~~pre-funded~~Warrants ~~warrants~~may oracquire the shares of common stock issuable upon exercise of such warrants onat ~~any~~an ~~securities~~assumed ~~exchange~~exercise orprice ~~nationally~~of ~~recognized~~$4.92 ~~trading~~per ~~system~~share of common stock, ~~including~~and holders of the ~~Nasdaq~~Pre-Funded ~~Capital~~Warrants ~~Market.~~may ~~Without~~acquire the shares of common stock issuable upon exercise of such warrants at an ~~active~~exercise ~~market~~price of $0.0001 per share of common stock. Moreover, following this offering, the ~~liquidity~~market value of the ~~pre~~Warrants and Pre-~~funded~~Funded ~~warrants~~Warrants is uncertain and there can be no assurance that the market value of the Warrants or Pre-Funded Warrants will equal or exceed their respective public offering prices. There can be no assurance that the market price of the shares of common ~~warrants~~stock will ever equal or exceed the exercise price of the Warrants or Pre-Funded Warrants, and consequently, whether it will ever be ~~limited~~profitable for holders of Warrants to exercise the Warrants or for holders of the Pre-Funded Warrants to exercise the Pre-Funded Warrants.

Holders of ~~pre~~the Pre-~~funded~~Funded ~~warrants~~Warrants orand ~~common~~the ~~warrants~~Warrants ~~purchased~~offered inhereby ~~this offering~~ will have no rights as common stockholders with respect to the shares our common stock underlying the warrants until such holders exercise ~~such~~their warrants and acquire our common stock, except as otherwise provided in the Pre-Funded Warrants and the Warrants.

Until holders of ~~pre-funded~~the ~~warrants~~Warrants orand ~~common~~the ~~warrants~~Pre-Funded Warrants acquire shares of our common stock upon exercise thereof, such holders will have no rights with respect to the shares of our common stock underlying such warrants, except to the extent that holders of ~~pre-funded~~such ~~warrants~~Warrants orand ~~common~~Pre-Funded ~~warrants~~Warrants will have nocertain rights ~~with~~to ~~respect~~participate toin ~~the~~distributions ~~shares~~or ofdividends paid on our common stock ~~underlying~~as ~~such~~set ~~warrants~~forth in the Warrants and the Pre-Funded Warrants. Upon exercise of the ~~pre-funded~~Warrants ~~warrants~~and orthe ~~common~~Pre-Funded ~~warrants~~Warrants, the holders will be entitled to exercise the rights of a common stockholder only as to matters for which the record date occurs after the exercise date.

The Warrants are not exercisable until the Warrant Stockholder Approval; provided, however, that if the Pricing Conditions are met, the Warrants will be exercisable upon issuance.

The Warrants will have an assumed exercise price of $4.92 per share and will be exercisable beginning on the effective date of the Warrant Stockholder Approval; provided, however, that if the Pricing Conditions are met, the

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WeWarrants will ~~have~~be ~~broad~~exercisable ~~discretion~~upon inissuance (the ~~use~~“Initial ofExercise ~~our~~Date”). ~~existing~~The ~~cash~~Series E ~~and~~Warrants ~~cash~~will ~~equivalents,~~expire ~~including~~on the ~~proceeds~~five-year ~~from~~anniversary ~~this~~of ~~offering,~~the ~~and~~Initial ~~may~~Exercise ~~invest~~Date. orThe ~~spend~~Series F ~~our~~Warrants ~~cash~~will inexpire ~~ways~~on ~~with~~the ~~which~~18-month ~~you~~anniversary doof ~~not agree and in ways that may not increase~~ the ~~value~~Initial ofExercise ~~your investment~~Date.

WeWhile ~~will~~we have broad discretion over the use of our cash and cash equivalents, including the proceeds from this offering. You may not agree with our decisions, and our use of cash may not yield any return on your investment. We intend to ~~use~~promptly ~~the~~seek ~~net~~Warrant ~~proceeds~~Stockholder ~~from this offering to expand our commercial capabilities in selling and marketing related to our products~~Approval, tothere ~~fund~~is ~~our~~no ~~ongoing~~guarantee ~~research~~that ~~and~~the ~~development~~Warrant ~~activities,~~Stockholder ~~and~~Approval ~~for~~will ~~general~~ever ~~corporate~~be ~~purposes, including working capital, operating expenses and capital expenditures~~obtained. ~~Our~~If ~~failure to apply the net proceeds from this offering effectively could compromise our ability to pursue our growth strategy and~~ we ~~might~~are ~~not~~unable ~~be able~~ to ~~yield~~obtain athe ~~significant~~Warrant ~~return,~~Stockholder ~~if any~~Approval, onthe ~~our~~Warrants ~~investment~~may ~~of these net proceeds. You will not~~ have ~~the~~no ~~opportunity to influence our decisions on how to use our net proceeds from this offering~~value.

Purchasers who purchase our securities in this offering pursuant to a securities purchase agreement may have rights not available to purchasers who purchase without the benefit of a securities purchase agreement.

In addition to rights and remedies available to all purchasers in this offering under federal securities and state law, the purchasers who enter into a securities purchase agreement will also be able to bring claims of breach of contract against us. The ability to pursue a claim for breach of contract provides those investors with the means to enforce the covenants uniquely available to them under the securities purchase agreement including, but not limited to: (i) timely delivery of securities; (ii) agreement to not enter into variable rate financings for a period of time after closing, subject to certain exceptions; (iii) agreement to not enter into any financings for a period of time after closing, subject to certain exceptions; and (iv) indemnification for breach of contract.

This is a best efforts offering, with no minimum amount of securities is required to be sold, and we may not raise the amount of capital we believe is required for our business plans, including our near-term business plans.

The placement agent has agreed to use its reasonable best efforts to solicit offers to purchase the securities in this offering. The placement agent has no obligation to buy any of the securities from us or to arrange for the purchase or sale of any specific number or dollar amount of the securities. There is no required minimum number of securities that must be sold as a condition to completion of this offering. Because there is no minimum offering amount required as a condition to the closing of this offering, the actual offering amount, placement agent fees and proceeds to us are not presently determinable and may be substantially less than the maximum amounts set forth herein. We may sell fewer than all of the securities offered hereby, which may significantly reduce the amount of proceeds received by us, and investors in this offering will not receive a refund in the event that we do not sell an amount of securities sufficient to support our continued operations, including our near-term continued operations. Thus, we may not raise the amount of capital we believe is required for our operations in the short-term and may need to raise additional funds, which may not be available or available on terms acceptable to us.

If we are not able to comply with the applicable continued listing requirements or standards of the Nasdaq Capital Market, Nasdaq could delist our common stock.

Our ability to publicly or privately sell equity securities and the liquidity of our common stock could be adversely affected if we are delisted from the Nasdaq Capital Market or if we are unable to transfer our listing to another stock market. In order to maintain this listing, we must satisfy minimum financial and other continued listing requirements and standards, including a requirement to maintain a minimum bid price of our common stock of $1.00 per share pursuant to Nasdaq Listing Rule 5550(a)(2) (the “Minimum Bid Price Requirement”).

On multiple occasions in the past, we have failed to comply with the per share minimum required for continued listing on Nasdaq. For example, on May 30, 2023. we received a letter (the “First Notice”) from Nasdaq advising us that for 30 consecutive trading days preceding the date of the First Notice, the bid price of our common stock had closed below the Minimum Bid Price Requirement.

While we implemented a reverse stock split, effective August 4, 2023, that temporarily enabled us to satisfy the Minimum Bid Price Requirement, on July 11, 2024, we received another letter (the “Second Notice”) from Nasdaq advising us that for 30 consecutive trading days preceding the date of the Second Notice, the bid price of our common stock had closed below the Minimum Bid Price Requirement. The Second Notice had no effect on the listing of our common stock, and our common stock continues to trade on Nasdaq under the symbol “BNGO.”

Even though we have implemented another reverse stock split, effective January 24, 2025, and received a letter from Nasdaq on February 10, 2025 that informed us that we had regained compliance with the Minimum Bid Price Requirement, we cannot assure you that we will be able to continue to satisfy the Minimum Bid Price Requirement or each other Nasdaq requirement for continued listing. If we fail to satisfy any Nasdaq requirement for continued listing, Nasdaq staff could provide notice that our common stock may become subject to delisting. Accordingly, there

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~~SPECIAL~~can ~~NOTE~~be ~~REGARDING~~no ~~FORWARD~~guarantee that we will be able to maintain our Nasdaq listing. If our common stock is delisted by Nasdaq, it could lead to a number of negative consequences, including an adverse effect on the price of our common stock, increased volatility in our common stock, reduced liquidity in our common stock, the loss of federal preemption of state securities laws and greater difficulty in obtaining financing. In addition, delisting of our common stock could deter broker-~~LOOKING~~dealers ~~STATEMENTS~~from making a market in or otherwise seeking or generating interest in our common stock, could result in a loss of current or future coverage by certain sell-side analysts and might deter certain institutions and persons from investing in our securities at all. Moreover, any such delisting could trigger a default or event of default under certain agreements that we have in place with third parties. Delisting could also cause a loss of confidence of our customers, collaborators, vendors, suppliers and employees, which could harm our business and future prospects.

~~This~~We ~~prospectus~~do ~~and~~not ~~the~~currently ~~documents~~intend ~~incorporated~~to bypay ~~reference~~dividends ~~herein~~on ~~contain forward-looking statements that reflect~~ our ~~management’s~~common ~~beliefs~~stock, and ~~views~~any ~~with~~return ~~respect~~ to ~~future~~investors ~~events~~is ~~and~~expected ~~are subject~~ to ~~substantial risks and uncertainties within the meaning of Section 27A of the Securities Act~~come, ~~Section~~if ~~21E~~at ~~of the Securities Exchange Act of 1934~~all, asonly ~~amended~~from and the safe harbor provisions for the U.S. Private Securities Litigation Reform Act of 1955. All statements, other than statements of historical fact, contained in this prospectus and the documents incorporated by reference herein, including statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans and objectives of management, are forward-looking statements. In some cases, forward-looking statements can be identified by the use of forward-looking words such as “aim,” “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” ~~“predict,”~~increases ~~“pro forma,” “project,” “seek,” “should,” “target,” “will,” “would” or other similar words or expressions (including their use~~ in the ~~negative),~~price ~~or by discussions~~ of ~~future~~our ~~matters~~common ~~such as the development of products, technology enhancements, possible changes in legislation, and other statements that are not historical~~stock.

We have ~~based~~never ~~these~~declared ~~forward-looking~~or ~~statements~~paid ~~largely~~any cash dividends on our ~~current~~capital ~~expectations~~stock, and ~~projections~~you ~~about~~should ~~future~~not ~~events~~rely ~~and~~on ~~financial~~an ~~trends~~investment ~~that~~in weour ~~believe~~common ~~may~~stock ~~affect~~to ~~our~~provide ~~financial~~dividend ~~condition,~~income. ~~results~~We ofcurrently ~~operations,~~intend ~~business~~to ~~strategy~~retain ~~and~~all ~~financial~~of ~~needs.~~our ~~These~~future ~~forward-looking~~earnings, ~~statements~~if ~~are~~any, ~~subject~~ to ~~known~~finance ~~and~~the ~~unknown~~growth ~~risks,~~and ~~uncertainties~~development ~~and~~of ~~assumptions,~~our ~~including~~business ~~risks~~and ~~described~~do innot ~~“Risk~~anticipate ~~Factors”~~declaring ~~and~~or ~~elsewhere~~paying inany ~~this~~cash ~~prospectus~~dividends ~~and~~for the ~~documents~~foreseeable ~~incorporated~~future. byAs ~~reference~~a ~~herein~~result, ~~regarding~~capital appreciation, ~~among~~if ~~other~~any, ~~things:~~of our common stock will be your sole source of gain for the foreseeable future.

• the size and growth potential of the markets for our products, and our ability to serve those markets;

• the rate and degree of market acceptance of our products;

• ability to expand our sales organization to address effectively existing and new markets that we intend to target;

• impact from future regulatory, judicial, and legislative changes or developments in the U.S. and foreign countries;

• ability to compete effectively in a competitive industry;

• the success of competing technologies that are or may become available;

• the performance of our third-party contract sales organizations, suppliers and manufacturers;

• our ability to attract and retain key scientific or management personnel;

• the accuracy of our estimates regarding expenses, future revenues, reimbursement rates, capital requirements and needs for additional financing;

• our ability to comply with the covenants and satisfy certain conditions of our debt facility;

• our ability to obtain funding for our operations; and

• our ability to attract collaborators and strategic partnerships.

We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements. We operate in a very competitive and rapidly changing environment. It is not possible for our management to predict all risks, nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statements we may make. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make, and accordingly you should not place undue reliance on our forward-looking statements. We have included important factors in the cautionary statements included in this prospectus, particularly in the “Risk Factors” section in this prospectus and the documents incorporated by reference herein, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make.

You should read this prospectus, the documents incorporated by reference herein and the documents that we have filed as exhibits to the registration statement of which this prospectus is a part completely and with the understanding that our actual future results may be materially different from what we expect. We qualify all of the forward-looking statements in this prospectus and the documents incorporated by reference herein by these cautionary statements. Except as required by law, we undertake no obligation to publicly update any forward-looking statements, whether as a result of new information, future events or otherwise.

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USE OF PROCEEDS

We estimate that wethe ~~will receive~~ net proceeds ~~of approximately $13.6 million~~ from the ~~sale~~offering ofwill ~~the~~be ~~securities~~approximately ~~offered~~$9.0 ~~by us in this offering~~million, assuming a combined public offering price ~~of $0.85~~ per share of common stock and accompanying ~~common~~Warrants ~~warrant~~of $4.92, ~~which was~~ the ~~last~~closing ~~reported~~price ~~sale~~per ~~price~~share of our common stock on ~~The~~the Nasdaq Capital Market on ~~March 9~~September 10, ~~2020~~2025, ~~and~~ after deducting ~~estimated~~the ~~underwriting~~placement ~~discounts~~agent ~~and~~fees ~~commissions~~ and estimated offering expenses payable by us, assuming no sale of any Pre-Funded Warrants and ~~excluding~~no exercise of any of the ~~proceeds~~Warrants offered hereunder. However, ifbecause ~~any~~this is a best efforts offering and there is no minimum offering amount required as a condition to the closing of this offering, the actual offering amount, the placement agent fees and net proceeds to us are not presently determinable and may be substantially less than the maximum amounts set forth on the cover page of this prospectus. As a result, we may receive significantly less in net proceeds. We estimate that our net proceeds from the ~~exercise~~sale of 75%, 50%, and 25% of the ~~common~~maximum ~~warrants~~number ~~issued~~of securities offered in this offering would be approximately $6.7 million, $4.3 million, and $2.0 million, respectively, after deducting the estimated placement agent fees and estimated offering expenses payable by us, and assuming no sale of any Pre-Funded Warrants and assuming no exercise of the Warrants.

A $0.2510 increase or decrease in the assumed combined public offering price of $04.8592 per share of common stock and accompanying ~~common~~Warrants ~~warrant~~ would increase or decrease the ~~expected~~ net proceeds offrom ~~the~~this offering ~~to us~~ by approximately $40.1 2 million, assuming that the number of shares of common stock and accompanying Warrants offered by us, as set forth on the cover page of this prospectus, remains the same, and after deducting the estimated ~~underwriting~~placement ~~discounts~~agent ~~and~~fees ~~commissions~~ and estimated offering expenses payable by us. An increase or decrease of ~~1.0~~100,000 ~~million~~ shares ~~from~~of ~~the~~common ~~assumed~~stock ~~number~~and ofaccompanying ~~shares~~Warrants ~~sold~~offered inby ~~this~~us ~~offering~~ would increase or decrease ~~the~~our ~~expected net~~ proceeds ~~of the offering to us~~ by approximately $0.8 5 million, assuming the assumed combined public offering price of $04.8592 per share of common stock and accompanying ~~common~~Warrants ~~warrant~~ remains the same, and after deducting ~~the~~placement ~~estimated~~agent ~~underwriting~~fees ~~discounts~~ and ~~commissions and~~ estimated offering expenses payable by us.

~~The~~These ~~principal~~estimates ~~purposes~~exclude ofthe ~~this~~proceeds, ~~offering~~if ~~are~~any, tofrom ~~obtain~~the ~~additional~~exercise ~~capital~~of tothe ~~support~~Warrants ~~our~~issued ~~operations.~~in Wethis ~~intend to use $2~~offering.9 ~~million~~If all of the ~~net~~Warrants ~~proceeds~~issued ~~from~~in this offering were to ~~repay~~be aexercised ~~portion~~in cash at an assumed exercise price of ~~the~~$4.92 ~~aggregate~~per ~~principal~~share ~~amount~~of ~~outstanding~~common ~~under~~stock, ~~the~~we ~~Innovatus~~would ~~Loan~~receive ~~Agreement~~additional ~~(as~~proceeds ~~defined~~of ~~below)~~approximately ~~and~~$20.0 ~~the~~million. ~~remainder~~We ~~primarily~~cannot ~~for~~predict ~~general~~when ~~corporate~~or ~~purposes,~~if ~~including~~these ~~working~~Warrants ~~capital,~~will ~~sales~~be ~~and~~exercised. ~~marketing~~It ~~activities,~~is ~~general~~possible ~~and~~that ~~administrative~~these ~~matters~~Warrants may expire and ~~capital~~may ~~expenditures~~never be exercised. WeAdditionally, ~~may~~the ~~also~~Warrants ~~use~~contain a ~~portion~~cashless ofexercise ~~our~~provision ~~net~~that ~~proceeds~~permit toexercise ~~co-develop,~~of ~~acquire~~Warrants oron ~~invest~~a incashless ~~products,~~basis ~~technologies~~at orany ~~businesses~~time ~~that~~where ~~are~~there ~~complementary~~is tono ~~our~~effective ~~business.~~registration ~~However,~~statement weunder ~~currently~~the ~~have~~Securities noAct ~~agreements~~covering orthe ~~commitments~~issuance toof ~~complete~~the ~~any~~underlying ~~such transaction~~shares.

AsWe ~~noted~~intend ~~above,~~to ~~we will~~ use ~~a portion of~~ the net proceeds from ~~this~~the offering tofor ~~repay~~working ~~$2.9~~capital ~~million~~and ofgeneral ~~the~~corporate ~~approximately~~purposes. ~~$20~~These ~~million~~expected ~~aggregate~~uses ~~principal~~represent ~~amount~~our ~~outstanding~~intentions ~~under~~based upon our ~~Loan~~current plans and ~~Security~~business ~~Agreement~~conditions, orwhich could change in the ~~Innovatus~~future ~~Loan~~as ~~Agreement,~~our ~~with~~plans ~~Innovatus~~and ~~Life~~business ~~Sciences~~conditions ~~Lending~~evolve. ~~Fund~~The I,amounts ~~LP,~~and atiming ~~Delaware~~of ~~limited~~these ~~partnership,~~expenditures aswill ~~collateral~~depend ~~agent~~on ~~and~~numerous factors, including the ~~Lenders~~development ~~listed~~of onour ~~Schedule~~current 1business initiatives.1 ~~thereto,~~We ~~including~~have ~~East~~no ~~West~~specific ~~Bank~~acquisition contemplated at this time. ~~The~~As ~~total~~of ~~interest~~the ~~rate~~date ~~under~~of this prospectus, we cannot specify with certainty all of the ~~Innovatus~~particular ~~Loan~~uses ~~Agreement~~for isthe 10net proceeds from this offering.~~25%~~ As a result, ~~such~~our ~~that~~management ~~interest~~will ishave ~~payable~~broad discretion in ~~cash~~the atapplication aof ~~rate~~the ofnet ~~7.25%~~proceeds ~~per~~from ~~annum~~this offering, ~~with~~and the ~~remaining~~investors ~~3.0%~~will ~~per~~be ~~annum~~relying ofon the ~~interest~~judgment ~~added~~of ~~back~~our tomanagement regarding the ~~outstanding~~application ~~principal~~of ~~amount~~the net proceeds from this offering. The ~~Innovatus~~amounts ~~Loan~~and ~~Agreement~~timing ~~matures~~of our actual expenditures will depend on ~~March~~numerous 1factors, ~~2024~~including factors described under “Risk Factors” in this prospectus and the documents incorporated by reference herein and therein.

~~The~~Pending ~~foregoing~~application ~~discussion~~of ~~assumes~~the nonet ~~sale~~proceeds ofas ~~pre-funded~~described ~~warrants~~above, ~~which~~we ifintend ~~sold,~~to ~~would~~invest ~~reduce~~ the ~~number~~net ofproceeds ~~shares~~ of ~~common~~this ~~stock that we are~~ offering onin ashort-term, ~~one~~investment-~~for~~grade, interest-~~one~~bearing ~~basis~~securities.

We believe that the net proceeds from this offering, together with our existing cash and cash equivalents, will enable us to fund our operations through at least the next 12 months. We have based this estimate on assumptions that may prove to be wrong, and we could use our available capital resources sooner than we expect.

Our management will have broad discretion in the application of the net proceeds from this offering, and investors will be relying on the judgment of our management regarding the application of those net proceeds. The timing and amount of our actual expenditures will be based on many factors, including cash flows from operations and the anticipated growth of our business. Pending the uses described above, we plan to invest these net proceeds in short-term, interest bearing investments, investment-grade instruments, certificates of deposit or direct or guaranteed obligations of the United States. We also may use a portion of the net proceeds from the offering to fund acquisitions or other business development opportunities. However, we have no current commitments or obligations with respect to any such acquisitions or business development opportunities at this time.

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DIVIDEND POLICY

We dohave ~~not~~never ~~anticipate~~declared ~~declaring~~ or ~~paying,~~paid ~~in the foreseeable future, any~~ cash dividends on our capital stock. We currently intend to retain ~~all~~any ~~available funds and~~ future earnings, iffor ~~any,~~use toin ~~fund~~ the ~~development~~operation ~~and expansion~~ of our business, and we do not ~~anticipate~~intend ~~paying~~to declare or pay any cash dividends in the foreseeable future. Any future determination ~~regarding~~to ~~the~~pay ~~declaration~~dividends ~~and~~on ~~payment~~our ofcapital ~~dividends,~~stock ifwould ~~any, will~~ be at the discretion of our board of directors, ~~and~~subject ~~will~~to ~~depend~~applicable onlaws, ~~then-existing~~and ~~conditions,~~would ~~including~~depend on our financial condition, ~~operating~~ results, ~~contractual~~of ~~restrictions~~operations, capital requirements, general business ~~prospects~~conditions and other factors that our board of directors ~~may~~considers ~~deem~~ relevant. ~~In addition, we are currently prohibited from paying dividends on our common stock without the prior written consent of Innovatus Life Sciences Lending Fund I, LP, our senior lender.~~

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DILUTION

If you invest in our securities, your ownership interest will be diluted to the extent of the difference between the public offering price per share of our common stock and the as adjusted net tangible book value per share of our common stock immediately after the closing of this offering.

Our historical net tangible book value as of December 31, 2019 was $3.6 million, or $0.11 per share of common stock. Our historical net tangible book value is the amount of our total tangible assets less our liabilities. Historical net tangible book value per common share is our historical net tangible book value divided by the number of shares of common stock outstanding as of December 31, 2019.

After giving effect to the sale of shares of common stock and accompanying common warrants in this offering at an assumed public offering price of $0.85 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 9, 2020, and after deducting estimated underwriting discounts and commissions and estimated offering expenses payable by us, and excluding the proceeds, if any, from the exercise of the common warrants issued in this offering, our as adjusted net tangible book value as of December 31, 2019 would be $17.2 million, or $0.33 per share of common stock. This amount represents an immediate increase in as adjusted net tangible book value of $0.22 per share to our existing stockholders and an immediate dilution of $0.52 per share to investors participating in this offering. We determine dilution per share to investors participating in this offering by subtracting as adjusted net tangible book value per share after this offering from the assumed public offering price per share paid by investors participating in this offering.

The following table illustrates this dilution on a per share basis to new investors:

Assumed public offering price per share and accompanying common warrant			$	0.85
Historical net tangible book value per share as of December 31, 2019	$	0.11
Increase in as adjusted net tangible book value per share attributable to this offering		0.22
As adjusted net tangible book value per share after giving effect to this offering				0.33
Dilution per share to new investors in this offering			$	0.52

The as-adjusted dilution information discussed above is illustrative only and will change based on the actual public offering price. Each $0.25 increase (decrease) in the assumed public offering price of $0.85 per share and accompanying common warrant, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 9, 2020, would increase (decrease) the as-adjusted net tangible book value per share by $0.08 per share and the dilution per share to investors participating in this offering by $0.69 per share, assuming that the number of shares and accompanying common warrants offered by us, as set forth on the cover page of this prospectus, remains the same and after deducting estimated underwriting discounts and commissions and estimated offering expenses payable by us, and excluding the proceeds, if any, from the exercise of the common warrants issued in this offering.

We may also increase or decrease the number of shares we are offering. A 1.0 million share increase in the number of shares and accompanying common warrants offered by us, as set forth on the cover page of this prospectus, would increase the as adjusted net tangible book value per share by $0.01 and decrease the dilution per share to new investors participating in this offering by $0.01, assuming the assumed public offering price of $0.85 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 9, 2020, remains the same and after deducting estimated underwriting discounts and commissions and estimated offering expenses payable by us, and excluding the proceeds, if any, from the exercise of the common warrants issued in this offering. A 1.0 million share decrease in the number of shares and accompanying common warrants offered by us, as set forth on the cover page of this prospectus, would decrease the as adjusted net tangible book value per share after this offering by $0.01 and increase the dilution per share to new investors participating in this offering by $0.01, assuming the assumed public offering price of $0.85 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on March 9, 2020, remains the same and after deducting estimated underwriting discounts and commissions and estimated offering expenses payable by us, and excluding the proceeds, if any, from the exercise of the common warrants issued in this offering. The information discussed above is illustrative only and will adjust based on the actual public offering price, the actual number of shares and common warrants that we offer in this offering, and other terms of this offering determined at pricing. The discussion and table above assume (i) no sale of pre-funded warrants, which, if sold, would reduce the number of shares of common stock that we are offering on a one-for-one basis and (ii) no exercise of common warrants accompanying the shares of common stock sold in this offering.

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SELECTED FINANCIAL DATA

The selected statements of operations data for the years ended December 31, 2018 and 2019 and the balance sheet data as of December 31, 2018 and 2019 are derived from our audited financial statements appearing in our Annual Report on Form 10-K for the year ended December 31, 2019, which is incorporated by reference herein. Our historical results are not necessarily indicative of our results in any future period and results from our interim period may not necessarily be indicative of the results of the entire year.

You should read the following selected financial data together with “Management’s Discussion and Analysis of Financial Condition and Results of Operations” section and our financial statements and the related notes in our Annual Report on Form 10-K for the year ended December 31, 2019, which is incorporated by reference herein. The selected financial data in this section are not intended to replace our financial statements and the related notes and are qualified in their entirety by the financial statements and related notes included elsewhere in this prospectus.

	Year EndedDecember 31,
	2018			2019
Total revenue	$	12,000,735		$	10,129,508
Operating expenses:
Cost of revenue		8,711,326			6,768,147
Research and development		9,484,163			9,080,891
Selling, general and administrative		14,220,331			20,155,376
Total cost of revenue and operating expenses		32,415,820			36,004,414
Interest expense		(1,381,024	)		(2,286,196	)
Other income (expense)		3,315,228			(1,632,920	)
Provision for income taxes		(15,511	)		(21,048	)
Net loss	$	(18,496,392	)	$	(29,815,070	)
Net loss per share:
Basic and diluted	$	(2.61	)	$	(1.99	)

	As of December 31
	2018			2019
Balance Sheet Data:
Cash and cash equivalents	$	16,522,729		$	17,311,373
Working capital		18,502,256			1,891,220
Total assets		24,802,421			30,207,866
Long-term debt		9,029,374			—
Total liabilities		14,665,070			26,594,148
Accumulated deficit		(72,762,428	)		(102,577,498	)
Total stockholders' (deficit) equity		10,137,351			3,613,718

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PRINCIPAL STOCKHOLDERS

The following table sets forth information regarding beneficial ownership of our capital stock as of December 31, 2019 by:

• each person, or group of affiliated persons, known by us to beneficially own more than 5% of our common stock;

• each of our directors;

• each of our named executive officers; and

• all of our current executive officers and directors as a group.

The percentage ownership information shown in the column titled “Before Offering” in the table is based on 34,274,469 shares of common stock outstanding as of December 31, 2019. The percentage ownership information shown in the column titled “After Offering” in the table is based upon shares, assuming the sale of shares of our common stock and accompanying common warrants by us in this offering.

We have determined beneficial ownership in accordance with the rules of the SEC. These rules generally attribute beneficial ownership of securities to persons who possess sole or shared voting power or investment power with respect to those securities. In addition, the rules include shares of common stock issuable pursuant to the exercise of stock options or warrants that are exercisable as of February 29, 2020, which is 60 days after December 31, 2019. These shares are deemed to be outstanding and beneficially owned by the person holding those options or warrants for the purpose of computing the percentage ownership of that person, but they are not treated as outstanding for the purpose of computing the percentage ownership of any other person.

The following table is based upon information supplied by officers, directors and principal stockholders and Schedules 13D and 13G, if any, filed with the SEC. Unless otherwise indicated in the footnotes to this table and subject to community property laws where applicable, we believe that each of the stockholders named in this table has sole voting and investment power with respect to the shares indicated as beneficially owned.

Unless otherwise indicated, the address for each beneficial owner listed in the table below is c/o Bionano Genomics, Inc., 9540 Towne Centre Drive, Suite 100, San Diego, California 92121.

			Percentage of SharesBeneficially Owned
Name of Beneficial Owner	Number of SharesBeneficially Owned		BeforeOffering			AfterOffering
Greater than 5% Stockholders
LC Fund VI, L.P. and Related Entities(1)		2,906,915		8.5	%		%
Hudson Bay Capital Management LP(2)		2,020,000		5.6	%		%
Wealth Strategy Holding Limited(3)		1,950,000		5.5	%		%
Entities affiliated with Innovatus Life Sciences GP, LP(4)		1,891,408		5.4	%		%
Directors and Named Executive Officers							%
David L. Barker, Ph.D.(5)		40,454			*		*
R. Erik Holmlin, Ph.D.(6)		34,167			*		*
Albert Luderer, Ph.D.(7)		28,461			*		*
Mark Oldakowski(8)		88,907			*		*
Warren Robinson(9)		85,642			*		*
Christopher Twomey(10)		58,280			*		*
Junfeng Wang(1)		2,926,195		8.5	%		%
Mike Ward(11)		66,416			*		*
Kristiina Vuori, M.D., Ph.D.(12)		6,727			*		*
All directors and executive officers as a group (9 persons)(13)				9.6	%		%

* Represents beneficial ownership of less than 1%.

(1) Based solely on a Schedule 13G filed with the SEC by the reporting persons on June 7, 2019, the indicated ownership consists of (i) 426,900 shares of common stock held by LC Fund VI, L.P., (ii) 20,656 shares of common stock held by LC Parallel Fund VI, L.P., (iii) 1,325,359 shares of common stock held by LC Healthcare Fund I, L.P., and (iv) 1,134,000 shares of common stock held by Rosy Shine Limited and (v) 19,280 shares of common stock subject to options exercisable as of February 29, 2020 held by Junfeng Wang. Each of LC Fund VI, L.P., LC Parallel Fund VI, L.P., and LC Healthcare Fund I, L.P., collectively referred to as the LC Funds, are ultimately controlled and managed by Legend Capital, a limited liability Chinese company. Legend Capital is ultimately controlled by a management team consisting of three key individuals, Linan Zhu, Hao Chen, and Nengguang Wang. In addition, Junfeng Wang and Quan Zhou are Managing

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Directors of Legend Capital. Each of these individual managers of Legend Capital shares voting and investment power over the shares held by the LC Funds. Rosy Shine Limited is ultimately controlled and managed by Legend Holdings, a limited liability Chinese joint stock company listed on a Stock Exchange of Hong Kong (3396). The board of directors of Legend Holdings has sole voting and investment power over the shares held by Rosy Shine Limited. None of the members of the board of directors has individual voting or investment power with respect to such shares and each disclaims beneficial ownership of such shares. The address of the principal place of business for each of the above entities except Legend Holdings is Legend Capital, 16/F, Tower B, Raycom Infotech Park, No.2 Kexueyuan South Road, Zhongguancun, Haidian District, Beijing 100190, People’s Republic of China. The Schedule 13G filed by the reporting persons provides information as of April 2, 2019 and, consequently, the beneficial ownership of the reporting persons may have changed between April 2, 2019 and December 31, 2019. The address of the principal place of business for Legend Holdings is Room 1701, 17/F, Block 1, Court No. 2, Ke Xue Yuan Nanlu, Haidian District, Beijing, People’s Republic of China.

(2) Based solely on a Schedule 13G filed with the SEC by the reporting person January 31, 2020, the indicated ownership consists of 2,020,000 shares of common stock issuable upon the exercise of warrants held by Hudson Bay Master Fund Ltd. According to the Schedule 13G, Hudson Bay Capital Management LP acts as investment manager to Hudson Bay Master Fund Ltd., and Mr. Sander Gerber, a United States citizen, serves as managing member of Hudson Bay Capital GP LLC, which is a general partner of Hudson Bay Capital Management LP. Hudson Bay Capital Management LP and Mr. Sander Gerber may be deemed to have shared voting and dispositive power with respect to the shares held by Hudson Bay Master Fund Ltd. The address for Hudson Bay Capital Management LP and Mr. Sander Gerber listed in the Schedule 13G is 777 Third Avenue, 30th Floor, New York, NY 10017.

(3) Based solely on a Schedule 13G filed with the SEC by the reporting person on December 14, 2018, the indicated ownership consists of 975,000 shares of common stock and 975,000 shares of common stock issuable upon the exercise of warrants held by Wealth Strategy Holding Limited. According to the Schedule 13G, Mr. Kung Hung Ka may be deemed to have sole voting and dispositive power with respect to the shares held by Wealth Strategy Holding Limited. The Schedule 13G/A filed by the reporting person provides information as of August 21, 2018 and, consequently, the beneficial ownership of the reporting person may have changed between August 21, 2018 and December 31, 2019. The address for Wealth Strategy Holding Limited listed in the Schedule 13G is Level 12, International Commerce Centre, 1 Austin Road West, Kowloon, Hong Kong.

(4) The indicated ownership consists of (i) 839,781 shares of common stock and 332,948 shares of common stock issuable upon the exercise of warrants held by Innovatus Life Sciences Lending Fund I, LP, or Innovatus, and (ii) 514,640 shares of common stock and 204,039 shares of common stock issuable upon the exercise of warrants held by Innovatus Life Sciences Offshore Fund I-A, LP., or Innovatus Offshore. Innovatus Life Sciences GP, LP, or Innovatus GP, is the general partner of Innovatus Life Sciences Lending Fund I, LP, or Innovatus. Innovatus Capital Partners LLC, or Innovatus Manager, serves as investment manager to each of Innovatus and Innovatus Life Sciences Offshore Fund I-A, LP, or Innovatus Offshore. Innovatus Life Sciences Offshore GP, LP, or Innovatus Offshore GP, is the general partner of Innovatus Offshore. Each of Innovatus GP, Innovatus, Innovatus Manager, Innovatus Offshore GP and Innovatus Offshore are collectively referred to as the Innovatus Entities. Innovatus Flagship Parent GP, LLC, or Innovatus Holdings, is the parent company of Innovatus GP and Innovatus Offshore Parent GP, LLC, or Innovatus Offshore Holdings. David Schiff, a citizen of the United States, is the principal shareholder of each of Innovatus Holdings and Innovatus Offshore Holdings, collectively referred to as the Parent Entities, and could be deemed to exercise voting and investment power over the Parent Entities and the Innovatus Entities. The address of the principal place of business for each of the Parent Entities and David Schiff is 777 Third Avenue, 25th Floor New York, NY 10017.

(5) Consists of (i) 3,894 shares of common stock, (ii) 32,666 shares of common stock subject to options exercisable as of February 29, 2020 and (iii) 3.894 shares of common stock issuable upon the exercise of warrants.

(6) Consists of (i) 3,026 shares of common stock, (ii) 29,511 shares of common stock subject to options exercisable as of February 29, 2020 and (iii) 1,630 shares of common stock issuable upon the exercise of warrants.

(7) Consists of (i) 28,461 shares of common stock subject to options exercisable as of February 29, 2020.

(8) Consists of (i) 9,736 shares of common stock, (ii) 78,356 shares of common stock subject to options exercisable as of February 29, 2020 and (iii) 815 shares of common stock issuable upon the exercise of warrants.

(9) Consists of (i) 3,932 shares of common stock and (ii) 81,710 shares of common stock subject to options exercisable as of February 29, 2020.

(10) Consists of (i) 19,500 shares of common stock, (ii) 19,280 shares of common stock subject to options exercisable as of February 29, 2020 and (iii) 19,500 shares of common stock issuable upon the exercise of warrants.

(11) Consists of 66,416 shares of common stock subject to options exercisable as of February 29, 2020. Mr. Ward terminated service with us effective December 6, 2019.

(12) Consists of 6,727 shares of common stock subject to options exercisable as of February 29, 2020.

(13) Consists of (i) 2,937,503 shares of common stock, (ii) 362,407 shares of common stock subject to options exercisable as of February 29, 2020 and (iii) 16,339 shares of common stock issuable upon the exercise of warrants.

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DESCRIPTION OF CAPITAL STOCK

The following ~~description~~summary ofdescribes our ~~capital~~securities ~~stock~~registered under Section 12 of the Exchange Act, certain provisions of our amended and restated certificate of incorporation, as amended (“Restated Certificate”), our amended and restated and bylaws, as amended (“Bylaws”), and certain provisions of ~~Delaware~~the ~~law~~General ~~are~~Corporation ~~summaries~~Law of the State of Delaware (“DGCL”). ~~The~~Because it is only a summary, the following description of our capital stock is not complete and does not contain all of the information that may be important to you. The following summary is subject to and qualified in its entirety by reference to our ~~certificate~~Restated Certificate and Bylaws, copies of ~~incorporation~~which are filed as exhibits to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2025, filed with the SEC on August 14, 2025, and ~~bylaws~~the forms of securities, copies of which are filed as exhibits to the registration statement of which this prospectus isforms a part, aswhich ~~well~~are asincorporated ~~the~~by ~~relevant~~reference ~~provisions of the Delaware General Corporation Law~~herein.

AsGeneral of the date of this prospectus, our certificate of incorporation authorized us to issue 200,000,000 shares of common stock, par value $0.0001 per share, and 10,000,000 shares of preferred stock, par value $0.0001 per share.

The Restated Certificate authorizes us to issue 400,000,000 shares of common stock, par value $0.0001 per share, and 10,000,000 shares of preferred stock, par value $0.0001 per share. Our board of directors has the authority, without stockholder approval, except as required by the listing standards of The Nasdaq Stock Market LLC, to issue additional shares of our capital stock. In addition, our board of directors has the authority, without further action by our stockholders, to designate the rights, preferences, privileges, qualifications and restrictions of our preferred stock in one or more series.

As of September 9, 2025, there were 4,755,265 shares of common stock outstanding. Our authorized but unissued shares of common stock and preferred stock are available for issuance without further action by our stockholders, unless such action is required by applicable law or the rules of any stock exchange or automated quotation system on which our securities may be listed or traded in the future.

Common Stock

Voting Rights

Our common stock is entitled to one vote for each share held of record on all matters submitted to a vote of the stockholders, including the election of directors, and does not have cumulative voting rights. ~~Our~~The ~~amended~~Restated ~~and~~Certificate ~~restated certificate of incorporation~~ establishes a classified board of directors that is divided into three classes with staggered three-year terms. Only the directors in one class will be subject to election by a plurality of the votes cast at each annual meeting of our stockholders, with the directors in the other classes continuing for the remainder of their respective three-year terms.

Economic Rights

Except as otherwise expressly provided in ~~our~~the ~~certificate~~Restated ofCertificate ~~incorporation~~ or required by applicable law, all shares of common stock have the same rights and privileges and rank equally, share ratably, and are identical in all respects for all matters, including those described below.

Dividends. Subject to preferences that may be applicable to any then-outstanding preferred stock, the holders of common stock are entitled to receive dividends, if any, as may be declared from time to time by our board of directors out of legally available funds.

Liquidation Rights. In the event of our liquidation, dissolution or winding-up, holders of our common stock are entitled to share ratably in the net assets legally available for distribution to stockholders after the payment of all of our debts and other liabilities, subject to the satisfaction of any liquidation preference granted to the holders of any outstanding shares of preferred stock.

No Preemptive or Similar Rights

The holders of our shares of common stock are not entitled to preemptive rights, and are not subject to conversion, redemption or sinking fund provisions. The rights, preferences and privileges of the holders of our common stock are subject to, and may be adversely affected by, the rights of the holders of shares of any series of our preferred stock that we may designate and issue in the future.

~~Fully~~Preferred ~~Paid~~Stock ~~and Non-Assessable~~

~~All~~Our board of ~~our~~directors ~~outstanding~~may ~~shares~~authorize the issuance of ~~common~~preferred stock ~~are,~~with ~~and~~voting ~~the~~or ~~shares~~conversion ofrights ~~common~~that ~~stock~~could toadversely beaffect ~~issued~~the invoting ~~this~~power ~~offering~~or ~~will~~other ~~be,~~rights ~~fully~~of ~~paid~~the ~~and~~holders ~~nonassessable~~of the common stock. The issuance of preferred stock,

~~Convertible Preferred Stock~~11

~~Our~~TABLE ~~board~~OF of directors may authorize the issuance of preferred stock with voting or conversion rights that could adversely affect the voting power or other rights of the holders of the common stock. The issuance of preferred stock, while providing flexibility in connection with possible acquisitions and other corporate purposes, could, among other things, have the effect of delaying, deferring or preventing a change in our control that may otherwise benefit holders of our common stock and may adversely affect the market price of the common stock and the voting and other rights of the holders of common stock. We have no current plans to issue any shares of preferred stock.CONTENTS

while providing flexibility in connection with possible acquisitions and other corporate purposes, could, among other things, have the effect of delaying, deferring or preventing a change in our control that may otherwise benefit holders of our common stock and may adversely affect the market price of the common stock and the voting and other rights of the holders of common stock.

Anti-Takeover Provisions

The provisions of ~~Delaware~~the ~~law~~DGCL, ~~our~~the ~~eighth~~Restated ~~amended~~Certificate and ~~restated~~the ~~certificate of incorporation and our amended and restated bylaws~~Bylaws, certain provisions of which are summarized below, may have the effect of delaying, deferring or discouraging another person from acquiring control of our company. They are also designed, in part, to encourage persons seeking to acquire control of us to negotiate first with our board of directors. We believe that the benefits of increased protection of our potential ability to negotiate with an unfriendly or unsolicited acquirer outweigh the disadvantages of discouraging a proposal to acquire us because negotiation of these proposals could result in an improvement of their terms.

15Section 203 of the Delaware General Corporation Law

We are subject to Section 203 of the DGCL, which prohibits a Delaware corporation from engaging in any business combination with any interested stockholder for a period of three years after the date that such stockholder became an interested stockholder, with the following exceptions:

•	before such date, the board of directors of the corporation approved either the business combination or the transaction that resulted in the stockholder becoming an interested stockholder;

•

upon completion of the transaction that resulted in the stockholder becoming an interested stockholder, the interested stockholder owned at least 85% of the voting stock of the corporation outstanding at the time the transaction began, excluding for purposes of determining the voting stock outstanding (but not the outstanding voting stock owned by the interested stockholder) those shares owned (i) by persons who are directors and also officers and (ii) employee stock plans in which employee participants do not have the right to determine confidentially whether shares held subject to the plan will be tendered in a tender or exchange offer; or

•

on or after such date, the business combination is approved by the board of directors and authorized at an annual or special meeting of the stockholder, and not by written consent, by the affirmative vote of at least 66 2/3% of the outstanding voting stock that is not owned by the interested stockholder.

In general, Section 203 defines a “business combination” to include the following:

•	any merger or consolidation involving the corporation and the interested stockholder;

•	any sale, transfer, pledge or other disposition of 10% or more of the assets of the corporation involving the interested stockholder;

•	subject to certain exceptions, any transaction that results in the issuance or transfer by the corporation of any stock of the corporation to the interested stockholder;

•	any transaction involving the corporation that has the effect of increasing the proportionate share of the stock or any class or series of the corporation beneficially owned by the interested stockholder; or

•	the receipt by the interested stockholder of the benefit of any loss, advances, guarantees, pledges or other financial benefits by or through the corporation.

In general, Section 203 defines an “interested stockholder” as an entity or person who, together with the person’s affiliates and associates, beneficially owns, or is an affiliate or associate of the corporation and within three years prior to the time of determination of interested stockholder status did own, 15% or more of the outstanding voting stock of the corporation.

A Delaware corporation may “opt out” of these provisions with an express provision in its certificate of incorporation. We have not opted out of these provisions, which may as a result, discourage or prevent mergers or other takeover or change of control attempts of us.

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~~persons~~Certificate ~~seeking to acquire control~~ of usIncorporation toand ~~negotiate~~Bylaws first with our board of directors. We believe that the benefits of increased protection of our potential ability to negotiate with an unfriendly or unsolicited acquirer outweigh the disadvantages of discouraging a proposal to acquire us because negotiation of these proposals could result in an improvement of their terms.

~~Certificate~~Among ofother ~~Incorporation~~things, ~~and~~the ~~Bylaws~~Restated toCertificate beand ~~in Effect upon~~ the ~~Closing~~Bylaws: ~~of this Offering~~

~~Because~~• ~~our stockholders~~ do not ~~have~~provide stockholders with cumulative voting rights, such that stockholders holding a ~~majority~~plurality of the voting power of our shares of common stock ~~may~~would be able to elect all of our directors. Our amended and restated certificate of incorporation and amended and restated bylaws provide for stockholder actions at a duly called meeting of stockholders or, before the date on which all shares of common stock convert into a single class, by written consent. A special meeting of stockholders may be called by a majority of our board of directors, the chair of our board of directors, or our chief executive officer. Our amended and restated bylaws establish an advance notice procedure for stockholder proposals to be brought before an annual meeting of our stockholders, including proposed nominations of persons for election to our board of directors. Our board of directors is divided into three classes with staggered three-year terms.;

~~The~~• ~~foregoing~~provide ~~provisions make it difficult~~ for ~~another~~stockholder ~~party~~actions to ~~obtain~~be ~~control~~taken ofat usa byduly ~~replacing~~called ~~our~~meeting ~~board~~ of ~~directors.~~stockholders ~~Since our board of directors has the power to retain~~ and ~~discharge~~not ~~our~~by ~~officers,~~written these provisions could also make it more difficult for existing stockholders or another party to effect a change in management. In addition, the authorization of undesignated preferred stock makes it possible for our board of directors to issue preferred stock with voting or other rights or preferences that could impede the success of any attempt to change our control.consent;

•	provide that a special meeting of stockholders may only be called by a majority of our board of directors, the chair of our board of directors or our chief executive officer;

•	establish an advance notice procedure for stockholder proposals to be brought before an annual meeting of our stockholders, including proposed nominations of persons for election to our board of directors;

•	divide our board of directors into three classes with staggered three-year terms;

•	provide that the authorized number of directors may be changed only by resolution adopted by a majority of the authorized number of directors constituting the board of directors;

•	provide that the board of directors or any individual director may only be removed with cause and the affirmative vote of the holders of at least 66 2/3% of the voting power of all of our then outstanding shares of common stock; and

•

provide that all vacancies, including newly created directorships, may, except as otherwise required by law or subject to the rights of holders of preferred stock as designated from time to time, be filled by the affirmative vote of a majority of directors then in office, even if less than a quorum.

The foregoing provisions make it difficult for another party to obtain control of us by replacing our board of directors. Since our board of directors has the power to retain and discharge our officers, these provisions could also make it more difficult for existing stockholders or another party to effect a change in management. In addition, the authorization of undesignated preferred stock makes it possible for our board of directors to issue preferred stock with voting or other rights or preferences that could impede or discourage an attempt to obtain control of us by means of a merger, tender offer, proxy contest or otherwise.

These provisions are designed to reduce our vulnerability to an unsolicited acquisition proposal and to discourage certain tactics that may be used in proxy fights. However, such provisions could have the effect of discouraging others from making tender offers for our shares and may have the effect of deterring hostile takeovers or delaying changes in our control or management. As a consequence, these provisions may also inhibit fluctuations in the market price of our stock that could result from actual or rumored takeover attempts.

Section 203 of the Delaware General Corporation Law

We are subject to Section 203 of the Delaware General Corporation Law, which prohibits a Delaware corporation from engaging in any business combination with any interested stockholder for a period of three years after the date that such stockholder became an interested stockholder, subject to certain exceptions.

Choice of Forum

~~Our~~The ~~amended~~Restated ~~and~~Certificate ~~restated certificate of incorporation~~ provides that the Court of Chancery of the State of Delaware is the exclusive forum for: (i) any derivative action or proceeding brought on our behalf; (ii) any action asserting a claim of breach of fiduciary duty owed by any of our directors, officers or other employees to us or our stockholders; (iii) any action asserting a claim against us or any of our directors or officers or other employees arising under the Delaware General Corporation Law, ~~our~~the ~~amended~~Restated ~~and~~Certificate ~~restated certificate of incorporation~~ or ~~our~~the ~~amended and restated bylaws~~Bylaws; or (iv) any action asserting a claim against us or any of our directors or officers or other employees that is governed by the internal affairs doctrine. ~~Our~~The ~~amended~~Restated ~~and~~Certificate ~~restated certificate of incorporation~~ further provides that U.S. federal district courts iswill be the exclusive forum for resolving any complaint asserting a cause of action arising under the Securities Act. ~~However,~~of ~~a Delaware court recently held that such an exclusive forum provision relating to federal courts was unenforceable under Delaware law~~1933, ~~and~~as unless and until the Delaware court decision is reversed on appeal or otherwise abrogated, we do not intend to enforce such a provision in the event of a complaint asserting a cause of action arising under the Securities Actamended. These choice of forum provisions of ~~our~~the ~~amended~~Restated ~~and~~Certificate ~~restated certificate of incorporation~~ will not apply to suits brought to enforce a duty or liability created by the ~~Securities~~ Exchange Act ~~of 1934, as amended~~.

16Transfer Agent and Registrar

The transfer agent and registrar for our common stock is Equiniti Trust Company, LLC.

Listing on the Nasdaq Capital Market

Our common stock is currently listed on the Nasdaq Capital Market under the symbol “BNGO.”

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DESCRIPTION OF SECURITIES WE ARE OFFERING

We are offering ~~(i)~~up 17to 2,~~648~~032,~~000~~520 shares of our common stock, orSeries E ~~pre-funded~~Warrants ~~warrants~~ to purchase up to 2,032,520 shares of ~~our~~ common stock and ~~(ii)~~Series F ~~common~~Warrants ~~warrants~~ to purchase up to an2,032,520 ~~aggregate~~shares of 17common stock. We are also offering Pre-Funded Warrants to those purchasers whose purchase of shares of common stock in this offering would result in the purchaser,~~648~~ together with its affiliates and certain related parties,~~000~~ ~~shares~~beneficially owning more than 4.99% (or, at the election of the purchaser, 9.99%) of our outstanding shares of common stock following the consummation of this offering in lieu of the shares of common stock that would result in such excess ownership. Each Pre-Funded Warrant will be exercisable for one share of common stock. orEach ~~pre~~Pre-~~funded~~Funded ~~warrant~~Warrant is being ~~sold~~issued together with athe ~~common~~same ~~warrant~~Warrants todescribed ~~purchase~~above ~~one~~being issued with each share of common stock. For each Pre-Funded Warrant we sell, the number of shares of common stock we are offering will be decreased on a one-for-one basis. The shares of common stock or ~~pre~~Pre-~~funded~~Funded ~~warrants~~Warrants, as the case may be, and the accompanying Warrants, can only be purchased together in this offering, but the shares of common ~~warrants~~stock and Pre-Funded Warrants and accompanying Warrants are immediately separable and will be issued separately in this offering. We are also registering the shares of common stock issuable from time to time upon exercise of the ~~pre~~Pre-~~funded~~Funded ~~warrants~~Warrants and ~~common~~Warrants ~~warrants~~ offered hereby.

Common Stock

The material terms and provisions of our common stock ~~and each other class of our securities which qualifies or limits our common stock~~ are described under the ~~caption~~section “Description of Capital Stock” in this prospectus.

Warrants

The following is a summary of certain terms and provisions of the Series E Warrants and Series F Warrants that are being offered hereby is not complete and is subject to, and qualified in its entirety by, the provisions of the Warrants, the forms of which will be filed as exhibits to the registration statement of which this prospectus forms a part. Prospective investors should carefully review the terms and provisions of the form of Series E Warrant and form of Series F Warrant for a complete description of the terms and conditions of the applicable Warrants. The Series E Warrants and Series F Warrants are identical except with regard to their duration, as described below.

Duration and Exercise Price

Each Warrant offered hereby will have an assumed exercise price equal to $4.92 (representing 100% of the assumed combined price at which a share of common stock and accompanying Warrants are sold to the public in this offering). The Warrants will be exercisable beginning on the effective date of Warrant Stockholder Approval; provided, however, that if the Pricing Conditions are met, the Warrants will be exercisable upon issuance (the “Initial Exercise Date”). The Series E Warrants will expire on the five-year anniversary of the Initial Exercise Date. The Series F Warrants will expire on the 18-month anniversary of the Initial Exercise Date. The exercise price and number of shares of common stock issuable upon exercise of the Warrants is subject to appropriate adjustment in the event of stock dividends, stock splits, reorganizations or similar events affecting our common stock and the exercise price. The Warrants will be issued separately from the common stock or Pre-Funded Warrants, respectively, and may be transferred separately immediately thereafter. The Warrants will be issued in certificated form only.

We intend to promptly, and in no event later than 90 days after the consummation of this offering, seek Warrant Stockholder Approval for the issuance of shares of common stock issuable upon exercise of the Warrants but we cannot assure you that such stockholder approval will be obtained; provided, however, that, if and only if the Pricing Conditions are satisfied, then we will not seek Warrant Stockholder Approval. We have agreed with the investors in this offering that, if we do not obtain Warrant Stockholder Approval for the issuance of the shares of common stock upon exercise of the Warrants at the first stockholder meeting for such purpose after this offering, we will call a stockholder meeting every 90 days thereafter until the earlier of the date we obtain such approval or the Warrants are no longer outstanding, provided, however, that, if and only if the Pricing Conditions are satisfied, then we will not seek Warrant Stockholder Approval.

Exercisability

The Warrants will be exercisable, at the option of each holder, in whole or in part, by delivering to us a duly executed exercise notice accompanied by payment in full for the number of shares of our common stock purchased upon such exercise (except in the case of a cashless exercise as discussed below). A holder (together with its affiliates) may not exercise any portion of such holder’s Warrants to the extent that the holder would own more than 4.99% of the

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outstanding common stock immediately after exercise, except that upon at least 61 days’ prior notice from the holder to us, the holder may increase the amount of ownership of outstanding stock after exercising the holder’s Warrants up to 9.99% of the number of shares of our common stock outstanding immediately after giving effect to the exercise, as such percentage ownership is determined in accordance with the terms of the Warrants.

Cashless Exercise

If, at the time a holder exercises its Warrants, a registration statement registering the issuance or resale of the shares of common stock underlying the Warrants under the Securities Act is not then effective or available for the issuance of such shares, then in lieu of making the cash payment otherwise contemplated to be made to us upon such exercise in payment of the aggregate exercise price, the holder may elect instead to receive upon such exercise (either in whole or in part) the net number of shares of common stock determined according to a formula set forth in the Warrant.

Fundamental Transactions

In the event of any fundamental transaction, as described in the Warrants and generally including any merger or consolidation with or into another entity, sale of all or substantially all of our assets, tender offer or exchange offer, or reclassification of our common stock, then upon any subsequent exercise of a Warrant, the holder will have the right to receive as alternative consideration, for each share of our common stock that would have been issuable upon such exercise immediately prior to the occurrence of such fundamental transaction, the number of shares of common stock of the successor or acquiring corporation or of our Company, if it is the surviving corporation, and any additional consideration receivable upon or as a result of such transaction by a holder of the number of shares of our common stock for which the Warrant is exercisable immediately prior to such event. Notwithstanding the foregoing, in the event of a fundamental transaction, the holders of the Warrants have the right to require us or a successor entity to redeem the Warrants for cash in the amount of the Black-Scholes Value (as defined in each Warrant) of the remaining unexercised portion of the Warrants on the date of the consummation of such fundamental transaction, concurrently with or within 30 days following the consummation of a fundamental transaction.

However, in the event of a fundamental transaction which is not in our control, including a fundamental transaction not approved by our board of directors, the holders of the Warrants will only be entitled to receive from us or our successor entity, as of the date of consummation of such fundamental transaction the same type or form of consideration (and in the same proportion), at the Black Scholes Value of the unexercised portion of the Warrant that is being offered and paid to the holders of our common stock in connection with the fundamental transaction, whether that consideration is in the form of cash, stock or any combination of cash and stock, or whether the holders of our common stock are given the choice to receive alternative forms of consideration in connection with the fundamental transaction.

Transferability

Subject to applicable laws, a Warrant may be transferred at the option of the holder upon surrender of the Warrant to us together with the appropriate instruments of transfer.

Fractional Shares

No fractional shares of common stock will be issued upon the exercise of the Warrants. Rather, the number of shares of common stock to be issued will, at our election, either be rounded up to the nearest whole number or we will pay a cash adjustment in respect of such final fraction in an amount equal to such fraction multiplied by the exercise price.

Trading Market

There is no established trading market for the Warrants, and we do not expect an active trading market to develop. We do not intend to apply to list the Warrants on the Nasdaq Capital market or any other securities exchange or other trading market. Without a trading market, the liquidity of the Warrants will be extremely limited. The shares of common stock issuable upon exercise of the Warrants are currently traded on the Nasdaq Capital Market.

Right as a Stockholder

Except as otherwise provided in the Warrants or by virtue of the holder’s ownership of shares of our common stock, such holder of Warrants does not have the rights or privileges of a holder of our common stock, including any voting rights, until such holder exercises such holder’s Warrants.

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Waivers and Amendments.

No term of the Warrants may be amended or waived without the written consent of the majority of the holders of the Warrants purchased in this offering.

Pre-Funded Warrants

The following summary of certain terms and provisions of ~~pre~~the Pre-~~funded~~Funded ~~warrants~~Warrants that are being offered hereby is not complete and is subject to, and qualified in its entirety by, the provisions of the ~~pre~~Pre-~~funded~~Funded ~~warrant~~Warrant, the form of which iswill be filed as an exhibit to the registration statement of which this prospectus forms a part. Prospective investors should carefully review the terms and provisions of the form of ~~pre~~Pre-~~funded~~Funded ~~warrant~~Warrant for a complete description of the terms and conditions of the ~~pre~~Pre-~~funded~~Funded ~~warrants~~Warrants.

Duration and Exercise Price. Each pre-funded warrant offered hereby will have an initial exercise price per share equal to $0.001. The pre-funded warrants will be immediately exercisable and may be exercised at any time until the pre-funded warrants are exercised in full. The exercise price and number of shares of common stock issuable upon exercise is subject to appropriate adjustment in the event of stock dividends, stock splits, reorganizations or similar events affecting our common stock and the exercise price. The pre-funded warrants will be issued separately from the accompanying common warrants, and may be transferred separately immediately thereafter.

~~Exercisability.~~Each ~~The pre~~Pre-~~funded~~Funded ~~warrants~~Warrant ~~will~~offered behereby ~~exercisable,~~will athave ~~the~~an ~~option~~initial ~~of each holder, in whole or in part, by delivering to us a duly executed~~ exercise ~~notice~~price ~~accompanied~~per byshare ~~payment in full for the number~~ of ~~shares of our~~ common stock ~~purchased~~equal ~~upon~~to ~~such exercise (except in the case of a cashless exercise as discussed below)~~$0.0001. ~~Purchasers~~The ~~of the pre~~Pre-~~funded~~Funded ~~warrants~~Warrants inwill ~~this~~be ~~offering~~immediately ~~may~~exercisable ~~elect to deliver their exercise notice following the pricing of the offering~~ and ~~prior~~will toexpire ~~the~~when ~~issuance of the pre-funded warrants at closing to have their pre-funded warrants~~ exercised ~~immediately~~in ~~upon issuance and receive shares of common stock underlying the pre-funded warrants upon closing of this offering~~full. AThe ~~holder (together with its affiliates) may not~~ exercise ~~any~~price ~~portion~~and of the pre-funded warrant to the extent that the holder would own more than 4.99% of the outstanding common stock immediately after exercise, except that upon at least 61 days’ prior notice from the holder to us, the holder may increase the amount of ownership of outstanding stock after exercising the holder’s pre-funded warrants up to 9.99% of the number of shares of ~~our~~ common stock ~~outstanding~~issuable ~~immediately~~upon ~~after giving effect to the~~ exercise, ~~as such percentage ownership~~ is ~~determined~~subject into ~~accordance~~appropriate ~~with~~adjustment ~~the terms of the pre-funded warrants. Purchasers of pre-funded warrants~~ in ~~this offering may also elect prior to~~ the ~~issuance~~event of ~~the~~share ~~pre-funded~~dividends, ~~warrants~~share tosplits, ~~have~~reorganizations ~~the~~or ~~initial~~similar ~~exercise~~events ~~limitation~~affecting ~~set at 9.99% of~~ our ~~outstanding common stock. No fractional~~ shares of common stock ~~will~~and ~~be issued in connection with~~ the exercise ~~of a pre-funded warrant~~price. ~~In lieu of fractional shares, we will round down to the next whole share.~~

~~Cashless~~Exercisability Exercise. If, at the time a holder exercises its pre-funded warrants, a registration statement registering the issuance of the shares of common stock underlying the pre-funded warrants under the Securities Act is not then effective or available, then in lieu of making the cash payment otherwise contemplated to be made to us upon such exercise in payment of the aggregate exercise price, the holder may elect instead to receive upon such exercise (either in whole or in part) the net number of shares of common stock determined according to a formula set forth in the pre-funded warrants.

~~Transferability.~~The ~~Subject~~Pre-Funded toWarrants ~~applicable~~will ~~laws~~be exercisable, at the option of each holder, in whole or in part, by delivering to us a ~~pre-funded~~duly ~~warrant~~executed ~~may~~exercise benotice ~~transferred~~accompanied atby payment in full for the ~~option~~number of shares of common stock purchased upon such exercise (except in the case of a cashless exercise as discussed below). A holder ~~upon~~(together ~~surrender~~with its affiliates) may not exercise any portion of the ~~pre~~Pre-~~funded~~Funded ~~warrant~~Warrant to the extent that the holder would own more than 4.99% of the outstanding shares of common stock immediately after exercise, except that upon at least 61 days’ prior notice from the holder to us, ~~together~~the holder may increase the amount of beneficial ownership of outstanding shares after exercising the holder’s Pre-Funded Warrants up to 9.99% of the number of our shares of common stock outstanding immediately after giving effect to the exercise, as such percentage ownership is determined in accordance with the ~~appropriate~~terms ~~instruments~~of the Pre-Funded Warrants. Purchasers of ~~transfer~~Pre-Funded Warrants in this offering may also elect prior to the issuance of the Pre-Funded Warrants to have the initial exercise limitation set at 9.99% of our outstanding shares of common stock.

~~Exchange~~Cashless ~~Listing.~~Exercise There is no trading market available for the pre-funded warrants on any securities exchange or nationally recognized trading system. We do not intend to list the pre-funded warrants on any securities exchange or nationally recognized trading system.

In lieu of making the cash payment otherwise contemplated to be made to us upon such exercise in payment of the aggregate exercise price, the holder may elect instead to receive upon such exercise (either in whole or in part) the number of shares of common stock determined according to a formula set forth in the Pre-Funded Warrants.

Fractional Shares

No fractional shares of common stock will be issued upon the exercise of the Pre-Funded Warrants. Rather, at our election, the number of shares of common stock to be issued will be rounded up to the nearest whole number or we will pay a cash adjustment in an amount equal to such fraction multiplied by the exercise price.

Transferability

Subject to applicable laws, a Pre-Funded Warrant may be transferred at the option of the holder upon surrender of the Pre-Funded Warrants to us together with the appropriate instruments of transfer.

Trading Market

There is no trading market available for the Pre-Funded Warrants on any securities exchange or nationally recognized trading system, and we do not expect a trading market to develop. We do not intend to list the Pre-Funded Warrants on the Nasdaq Capital Market or any other securities exchange or nationally recognized trading market. Without a trading market, the liquidity of the Pre-Funded Warrants will be extremely limited. The shares of common stock issuable upon exercise of the Pre-Funded Warrants are currently traded on the Nasdaq Capital Market.

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Right as a Shareholder

Except as otherwise provided in the Pre-Funded Warrants or by virtue of such holder’s ownership of shares of common stock, the holders of the Pre-Funded Warrants do not have the rights or privileges of holders of our shares of common stock, including any voting rights, until they exercise their Pre-Funded Warrants. The Pre-Funded Warrants will provide that holders have the right to participate in distributions or dividends paid on our shares of common stock.

Fundamental Transaction

In the event of a fundamental transaction, as described in the Pre-Funded Warrants and generally including any reorganization, recapitalization or reclassification of our shares of common stock, the sale, transfer or other disposition of all or substantially all of our properties or assets, our consolidation or merger with or into another person, the acquisition of 50% or more of our outstanding securities, or any person or group becoming the beneficial owner of 50% or more of the voting power represented by our outstanding shares of securities, the holders of the Pre-Funded Warrants will be entitled to receive upon exercise of the Pre-Funded Warrants the kind and amount of securities, cash or other property that the holders would have received had they exercised the Pre-Funded Warrants immediately prior to such fundamental transaction.

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~~Right~~PLAN asOF aDISTRIBUTION Stockholder. Except as otherwise provided in the pre-funded warrants or by virtue of such holder’s ownership of shares of our common stock, the holders of the pre-funded warrants do not have the rights or privileges of holders of our common stock, including any voting rights, until they exercise their pre-funded warrants.

~~Fundamental~~Pursuant ~~Transaction.~~to Inan ~~the~~engagement ~~event~~agreement, ofdated aJuly ~~fundamental transaction~~9, as2025 ~~described in~~ (the ~~pre-funded~~“Engagement ~~warrants~~Agreement”), ~~and~~we ~~generally~~have ~~including~~engaged ~~any~~H.C. Wainwright ~~reorganization~~& Co., ~~recapitalization~~LLC orto ~~reclassification~~act ofas our ~~common~~exclusive ~~stock,~~placement ~~the~~agent ~~sale,~~to ~~transfer~~solicit oroffers ~~other~~to ~~disposition~~purchase ofthe ~~all~~securities oroffered ~~substantially~~by ~~all~~this ofprospectus ~~our~~on ~~properties~~a orreasonable ~~assets,~~best ~~our~~efforts ~~consolidation~~basis. orThe ~~merger~~Engagement ~~with~~Agreement ordoes ~~into~~not ~~another~~give ~~person,~~rise to any commitment by the ~~acquisition~~placement ofagent ~~more~~to ~~than~~purchase ~~50%~~any of our ~~outstanding~~securities, ~~common~~and ~~stock,~~the orplacement ~~any~~agent ~~person~~will orhave ~~group~~no ~~becoming~~authority ~~the~~to ~~beneficial~~bind ~~owner~~us ofby ~~50%~~virtue of the ~~voting~~Engagement ~~power~~Agreement. ~~represented~~The byplacement ~~our~~agent ~~outstanding~~is ~~common~~not ~~stock,~~purchasing ~~the~~or ~~holders~~selling ofany ~~the~~securities, ~~pre-funded~~nor ~~warrants~~is ~~will~~it berequired ~~entitled~~ to ~~receive~~arrange ~~upon~~for ~~exercise~~the ofpurchase ~~the~~and ~~pre-funded~~sale ~~warrants~~of ~~the~~any ~~kind~~specific ~~and~~number or dollar amount of securities, ~~cash~~other orthan ~~other~~to ~~property~~use ~~that~~its ~~the~~“reasonable ~~holders~~best ~~would~~efforts” ~~have~~to ~~received~~arrange ~~had~~for ~~they~~the ~~exercised~~sale of the ~~pre-funded~~securities ~~warrants~~by ~~immediately~~us. ~~prior~~Therefore, towe ~~such~~may ~~fundamental~~not ~~transaction~~sell the entire amount of securities being offered.

~~Common~~The ~~Warrants~~terms of this offering are subject to market conditions and negotiations between us, the placement agent and prospective investors. The placement agent will have no authority to bind us by virtue of the engagement letter. This is a best efforts offering and there is no minimum amount of proceeds that is a condition to closing of this offering. Investors purchasing securities offered hereby will have the option to execute a securities purchase agreement with us. In addition to rights and remedies available to all purchasers in this offering under federal securities and state law, the purchasers which enter into a securities purchase agreement will also be able to bring claims of breach of contract against us. The placement agent may engage one or more sub-agents or selected dealers in connection with the offering. The ability to pursue a claim for breach of contract is material to larger purchasers in this offering as a means to enforce the following covenants uniquely available to them under the securities purchase agreement: (i) a covenant to not enter into variable rate financings for a period of one year following the closing of the offering, subject to certain exceptions; and (ii) a covenant to not enter into any equity financings for 30 days from closing of the offering, subject to certain exceptions.

The ~~following~~nature ~~summary~~ of ~~certain terms and provisions of Common Warrants that are being offered hereby is not complete and is subject to, and qualified in its entirety by,~~ the ~~provisions of the Common Warrants~~representations, ~~the~~warranties ~~form of which is filed as an exhibit to the registration statement of which this prospectus forms a part. Prospective investors should carefully review the terms~~ and ~~provisions~~covenants ofin the ~~form~~securities ofpurchase ~~Common~~agreements ~~Warrants~~will ~~for~~include: ~~a complete description of the terms and conditions of the common warrants.~~

~~Duration~~• standard and ~~Exercise~~customary ~~Price.~~issuer ~~Each~~representations ~~common~~and ~~warrant~~warranties ~~offered~~on ~~hereby~~matters ~~will~~such ~~have~~as andue ~~initial~~organization, ~~exercise~~qualification, ~~price~~authorization, ~~per~~no ~~share~~conflict, ~~equal~~no togovernmental ~~$ .~~filings ~~The~~required, ~~common~~currentness ~~warrants will be immediately exercisable~~ and ~~will~~accuracy ~~expire on the fifth anniversary~~ of ~~the~~SEC ~~original~~filings, ~~issuance~~absence ~~date. The exercise price and number~~ of ~~shares~~litigation, oflabor ~~common~~or ~~stock~~other ~~issuable~~compliance ~~upon exercise is subject to appropriate adjustment in the event of stock dividends~~issues, ~~stock splits~~environmental, ~~reorganizations~~intellectual orproperty ~~similar~~and ~~events~~title ~~affecting~~matters ~~our common stock~~ and ~~the~~compliance ~~exercise~~with ~~price.~~various ~~The~~laws ~~common~~such ~~warrants~~as ~~will be issued separately from~~ the ~~common~~Foreign ~~stock,~~Corrupt ~~and~~Practices ~~may~~Act; ~~be transferred separately immediately thereafter. A common warrant to purchase one share of our common stock will be issued for every one share of common stock purchased in this offering.~~and

~~Exercisability.~~• ~~The~~covenants ~~common~~regarding ~~warrants~~matters ~~will~~such beas ~~exercisable,~~registration atof the ~~option~~offering of ~~each holder, in whole or in part, by delivering to us a duly executed exercise notice accompanied by payment in full for~~ the ~~number~~warrant of shares, ~~of our common stock purchased upon such exercise (except in~~ the ~~case~~filing of a ~~cashless~~Current ~~exercise~~Report ason ~~discussed~~Form ~~below).~~8-K ~~A holder (together with its affiliates) may not exercise any portion of the common warrant~~ to ~~the~~disclose ~~extent~~entering ~~that~~into ~~the~~these ~~holder~~securities ~~would~~purchase ~~own more than 4.99% of the outstanding common stock immediately after exercise~~agreements, ~~except that upon at least 61 days’ prior notice from~~ the ~~holder~~providing ~~to us, the holder may increase the amount~~ of ~~ownership~~material ofnonpublic ~~outstanding~~information, ~~stock~~use ~~after exercising the holder’s common warrants up to 9.99%~~ of ~~the~~proceeds, ~~number~~indemnification of ~~shares of our common stock outstanding immediately after giving effect to the exercise~~purchasers, asreservation ~~such~~and ~~percentage~~listing ~~ownership is determined in accordance with the terms~~ of ~~the~~ common ~~warrants. No fractional shares of common~~ stock ~~will be issued in connection with the exercise of a common warrant. In lieu of fractional shares~~, weand ~~will~~prohibitions ~~round~~on ~~down~~subsequent toequity ~~the~~sales ~~next~~for ~~whole~~30 ~~share~~days.

~~Cashless~~Delivery ~~Exercise. If, at the time a holder exercises its common warrants, a registration statement registering the issuance~~ of the ~~shares~~securities ofoffered ~~common~~hereby ~~stock underlying the common warrants under the Securities Act~~ is ~~not~~expected ~~then~~to ~~effective~~occur on or ~~available and an exemption from registration under the Securities Act is not available for the issuance of such shares~~about , ~~then in lieu of making the cash payment otherwise contemplated to be made to us upon such exercise in payment of the aggregate exercise price~~2025, ~~the~~subject ~~holder may elect instead~~ to ~~receive~~satisfaction ~~upon such exercise (either in whole or in part) the net number~~ of ~~shares~~certain ofcustomary ~~common~~closing ~~stock determined according to a formula set forth in the common warrants~~conditions.

~~Transferability.~~Fees ~~Subject to applicable laws, a common warrant in book entry form may be transferred at the option of the holder through the facilities of the Depository Trust Company~~ and ~~common~~Expenses ~~warrants in physical form may be transferred upon surrender of the common warrant to the warrant agent together with the appropriate instruments of transfer.~~

~~Exchange~~The ~~Listing.~~following ~~There~~table isshows nothe ~~established~~per ~~public~~share ~~trading~~and ~~market~~accompanying ~~for the common warrants~~Warrants, and weper doPre-Funded ~~not~~Warrant ~~expect~~and aaccompanying ~~market to develop. In addition~~Warrants, weand dototal ~~not~~placement ~~intend~~agent tofees ~~list~~we ~~the~~will ~~common~~pay ~~warrants~~in onconnection ~~any~~with ~~securities exchange or nationally recognized trading system. Without an active trading market,~~ the ~~liquidity~~sale of the ~~common~~securities ~~warrants~~in ~~will~~this ~~be limited~~offering.

~~Right~~Per asShare aand ~~Stockholder.~~Accompanying ~~Except~~Warrants asPer ~~otherwise~~Pre-Funded ~~provided~~Warrant inand ~~the~~Accompanying ~~common~~Warrants ~~warrants~~Total orCombined bypublic ~~virtue~~offering ofprice ~~such~~$ ~~holder’s~~$ ~~ownership~~$ ofPlacement ~~shares~~agent offees ~~our~~$ ~~common~~$ ~~stock,~~$ ~~the~~Proceeds ~~holders~~to ~~of the common warrants do not have the rights or privileges of holders of our common stock~~us, ~~including~~before ~~any~~expenses ~~voting~~$ ~~rights,~~$ ~~until they exercise their common warrants.~~$

We have agreed to pay the placement agent a total cash fee equal to 6.0% of the aggregate gross proceeds raised in the offering and a management fee equal to 0.5% of the gross proceeds raised in this offering. We will reimburse the placement agent a nonaccountable expense allowance of $50,000, its legal fees and expenses and other out-of-pocket expenses in an amount up to $100,000, road show expenses in an amount up to $5,000, and its clearing expense in an amount up to $15,950 in connection with this offering. We estimate the total offering expenses of this offering that will be payable by us, excluding the placement agent fees and expenses, will be approximately $160,093. After deducting the placement agent fees and our estimated offering expenses, we expect the net proceeds from this offering to be approximately $9.0 million.

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~~Fundamental~~Right ~~Transaction. In the event~~ of aFirst ~~fundamental~~Refusal transaction, as described in the form of common warrant, and generally including any reorganization, recapitalization or reclassification of our common stock, the sale, transfer or other disposition of all or substantially all of our properties or assets, our consolidation or merger with or into another person, the acquisition of more than 50% of our outstanding common stock, or any person or group becoming the beneficial owner of 50% of the voting power represented by our outstanding common stock, the holders of the common warrants will be entitled to receive upon exercise of the common warrants the kind and amount of securities, cash or other property that the holders would have received had they exercised the common warrants immediately prior to such fundamental transaction.

Subject to consummation of the offering, we have granted a right of first refusal to the placement agent pursuant to which it has the right to act as the exclusive book-running manager, underwriter or placement agent, as applicable, if we decide to raise capital through a public offering (including an at-the-market facility) or private placement or any other capital-raising financing of equity, equity-linked or debt securities (other than a traditional debt facility or venture debt facility or an equity line of credit) at any time prior to the nine months following the consummation of this offering.

Tail

In the event that any investors that were contacted by the placement agent or were introduced to us by the placement agent during the term of our engagement agreement with the placement agent provide any capital to us in a public or private offering or other financing or capital-raising transaction of any kind (each, a “Tail Financing”) within nine months following the termination or expiration of our engagement agreement with the placement agent, we shall pay the placement agent the cash and warrant compensation provided above on the gross proceeds raised in such Tail Financing from such investors.

Determination of Offering Price

The combined public offering price per share and accompanying Warrants and the combined public offering price per Pre-Funded Warrant and accompanying Warrants we are offering and the exercise prices and other terms of the Pre-Funded Warrants and Warrants were negotiated between us and the investors, in consultation with the placement agent based on the trading of our common stock prior to this offering, among other things. Other factors considered in determining the public offering prices of the securities we are offering and the exercise prices and other terms of the Pre-Funded Warrants and Warrants include the history and prospects of our Company, the stage of development of our business, our business plans for the future and the extent to which they have been implemented, an assessment of our management, general conditions of the securities markets at the time of the offering and such other factors as were deemed relevant.

Lock-up Agreements

Each of our officers and directors have agreed with the placement agent to be subject to a lock-up period of 60 days following the date of this prospectus. This means that, during the applicable lock-up period, we may not offer for sale, contract to sell, or sell any shares of our common stock or any securities convertible into, or exercisable or exchangeable for, shares of our common stock subject to certain customary exception such as issuing stock options to directors, officers, employees and consultants under our existing plans. The placement agent may, in its sole discretion and without notice, waive the terms of any of these lock-up agreements. In addition, we have agreed to not issue any shares of common stock or securities exercisable or convertible into shares of common stock for a period of 30 days following the closing date of this offering, subject to certain exceptions, and to not issue any securities that are subject to a price reset based on trading prices of our common stock or upon a specified or contingent event in the future, or enter into an agreement to issue securities at a future determined price, until the date that is one year following the closing date of the offering.

Transfer Agent and Registrar

The transfer agent for our common stock is Equiniti Trust Company, LLC.

Listing on the Nasdaq Capital Market

Our common stock is currently listed on the Nasdaq Capital Market under the symbol “BNGO.” On September 10, 2025, the closing price per share of our common stock was $4.92.

Indemnification

We have agreed to indemnify the placement agent against certain liabilities, including certain liabilities arising under the Securities Act and liabilities arising from breaches of representations and warranties contained in our engagement letter with the placement agent. We have also agreed to contribute to payments that the placement agent may be required to make for these liabilities.

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~~UNDERWRITING~~In addition, we will indemnify the purchasers of securities in this offering who enter into a securities purchase agreement with us against liabilities arising out of or relating to (i) any breach of any of the representations, warranties, covenants or agreements made by us in the securities purchase agreement or related documents or (ii) any action instituted against a purchaser by a third party (other than a third party who is affiliated with such purchaser) with respect to the securities purchase agreement or related documents and the transactions contemplated thereby, subject to certain exceptions.

WeRegulation ~~entered~~M into an underwriting agreement with the underwriters named below on , 2020. Oppenheimer & Co. Inc. is acting as the sole book-running manager and representative of the underwriters. The underwriting agreement provides for the purchase of a specific number of shares of common stock and/or pre-funded warrants and accompanying common warrants to purchase shares of common stock by each of the underwriters. The underwriters' obligations are several, which means that each underwriter is required to purchase a specified number of shares of common stock and/or pre-funded warrants and accompanying common warrants, but is not responsible for the commitment of any other underwriter to purchase shares of common stock and/or pre-funded warrants and accompanying common warrants. Subject to the terms and conditions of the underwriting agreement, each underwriter has severally agreed to purchase the number of shares set forth opposite its name below:

~~Underwriter~~The ~~Number~~placement ~~ofShares~~agent may be deemed to be an underwriter within the meaning of ~~Common~~Section 2(a)(11) ~~Stock~~of ~~Number~~the ~~ofPre~~Securities Act and any fees received by it and any profit realized on the sale of the securities by it while acting as principal might be deemed to be underwriting discounts or commissions under the Securities Act. The placement agent will be required to comply with the requirements of the Securities Act and the Exchange Act, including, without limitation, Rule 10b-~~Funded~~5 ~~Warrants~~and ~~Number~~Regulation ~~ofCommon~~M ~~Warrants~~under ~~Oppenheimer~~the &Exchange CoAct. ~~Inc~~These rules and regulations may limit the timing of purchases and sales of our securities by the placement agent. ~~Roth~~Under ~~Capital~~these ~~Partners~~rules and regulations, ~~LLC~~the ~~Maxim~~placement ~~Group~~agent ~~LLC~~may ~~Total~~not (i) engage in any stabilization activity in connection with our securities; and (ii) bid for or purchase any of our securities or attempt to induce any person to purchase any of our securities, other than as permitted under the Exchange Act, until it has completed its participation in the distribution.

~~The~~Other ~~underwriters~~Relationships ~~have agreed to purchase all of the shares of common stock and/or pre-funded warrants and accompanying common warrants offered by this prospectus, if any are purchased.~~

The ~~shares~~placement ofagent ~~common~~and ~~stock~~its ~~and/or~~affiliates ~~pre-funded~~have ~~warrants~~in the past and ~~accompanying~~may ~~common~~in ~~warrants~~the ~~offered~~future ~~hereby~~engage ~~are~~in ~~expected~~investment tobanking betransactions ~~ready~~and ~~for~~other ~~delivery~~commercial ondealings in the ordinary course of business with us or ~~about ,~~our ~~2020~~affiliates. ~~against~~The ~~payment~~placement agent may in ~~immediately~~the ~~available~~future ~~funds~~receive customary fees and commissions for these transactions.

~~The~~In ~~underwriters~~addition, ~~are~~in ~~offering~~ the ~~shares~~ordinary course of ~~common~~their ~~stock~~business ~~and/or~~activities, ~~pre-funded~~the ~~warrants~~placement agent and ~~accompanying~~its ~~common~~affiliates ~~warrants subject to various conditions and~~ may ~~reject~~make ~~all~~ or ~~part~~hold ofa ~~any~~broad ~~order.~~array ~~The representative~~ of ~~the~~investments ~~underwriters~~and ~~has~~actively ~~advised~~trade usdebt ~~that~~and ~~the~~equity ~~underwriters~~securities ~~propose~~(or ~~initially~~related toderivative ~~offer~~securities) ~~the~~for ~~shares~~their ofown ~~common~~account ~~stock~~ and~~/or~~ ~~pre-funded~~for ~~warrants~~the ~~and~~accounts ~~accompanying common warrants to purchase shares~~ of ~~common~~their ~~stock~~customers. toSuch ~~the~~investments ~~public~~and atsecurities ~~the~~activities ~~public~~may ~~offering~~involve ~~price~~securities ~~set forth on the cover page of this prospectus~~ and/or toinstruments ~~dealers at a price less a concession not in excess~~ of ~~$ per~~ours ~~share~~or ~~and~~our ~~accompanying~~affiliates. ~~common~~The ~~warrant~~placement oragent ~~$ per pre-funded warrant~~ and ~~accompanying~~its ~~common~~affiliates ~~warrant,~~may ~~based~~also onmake ~~the~~investment ~~combined~~recommendations ~~public offering price per share~~ and/or ~~accompanying~~publish ~~common warrant~~ or ~~pre-funded~~express ~~warrant~~independent ~~and~~research ~~accompanying~~views ~~common~~in ~~warrant,~~respect ~~to brokers and dealers. After the shares~~ of ~~common~~such ~~stock~~securities ~~and/~~or ~~pre-funded~~financial ~~warrants~~instruments and ~~accompanying~~may ~~common~~hold, ~~warrants~~or ~~are~~recommend ~~released for sale~~ to ~~the~~clients ~~public,~~that ~~the~~they ~~representative may change the offering price~~acquire, ~~the~~long ~~concession,~~ and/or ~~other~~short ~~selling~~positions ~~terms~~in atsuch ~~various~~securities ~~times~~and instruments.

~~The~~Except ~~following~~as ~~table~~disclosed ~~provides~~in ~~information~~this ~~regarding~~prospectus, ~~the~~we ~~amount~~have ofno present arrangements with the ~~discounts~~placement ~~and~~agent ~~commissions~~for toany befurther ~~paid~~services. toThe ~~the~~placement ~~underwriters~~agent byacted usas our exclusive placement agent for registered direct offerings in January 2025, ~~before~~October ~~expenses:~~2024, July 2024 and April 2024, and currently acts as our exclusive sales agent under our at-the-market offering program.

Per Share

PerPre-FundedWarrant

PerCommonWarrant

Total PerShare andAccompanyingCommon Warrant

Total PerPre-Funded Warrantand Accompanying Common Warrant

Public offering price

Underwriting discounts and commissions(1)

Proceeds, before expenses, to us

Electronic Distribution

~~(1)~~A Weprospectus ~~have~~in ~~agreed~~electronic toformat ~~pay~~may ~~the~~be ~~underwriters~~made available on a ~~commission~~website ofmaintained 7%by the placement agent and the placement agent may distribute prospectuses electronically. Other than the prospectus in electronic format, the information on these websites is not part of this prospectus or the ~~gross~~registration ~~proceeds~~statement of which this ~~offering~~prospectus forms a part, has not been approved and/or endorsed by us or the placement agent and should not be relied upon by investors.

We estimate that our total expenses of the offering, excluding the estimated underwriting discounts and commissions, will be approximately $ , which includes the fees and expenses for which we have agreed to reimburse the underwriters, provided that any such fees and expenses in excess of an aggregate of $ will be subject to our prior written approval.

We have agreed to indemnify the underwriters against certain liabilities, including liabilities under the Securities Act of 1933.

We, our officers and directors have agreed to a 90-day “lock-up” with respect to shares of our common stock and other of our securities that they beneficially own, including securities that are convertible into shares of common

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~~stock~~INFORMATION ~~and~~INCORPORATED ~~securities~~BY ~~that~~REFERENCE are exchangeable or exercisable for shares of common stock. This means that, subject to certain exceptions, for a period of 90 days following the date of this prospectus, we and such persons may not offer, sell, pledge or otherwise dispose of these securities without the prior written consent of Oppenheimer & Co. Inc.

~~Rules~~The ofSEC ~~the~~allows ~~Securities~~us ~~and~~to ~~Exchange~~“incorporate ~~Commission~~by ~~may~~reference” ~~limit~~information ~~the~~that ~~ability~~we offile ~~the~~with ~~underwriters~~it into this prospectus, which means that we can disclose important information to ~~bid~~you ~~for~~by orreferring ~~purchase~~you ~~shares~~to ~~before~~those ~~the~~documents ~~distribution~~filed ofseparately with the ~~shares~~SEC. The information incorporated by reference is ~~completed~~an important part of this prospectus. ~~However,~~The ~~the~~information ~~underwriters~~incorporated ~~may~~by ~~engage~~reference inis ~~the~~considered ~~following~~to ~~activities~~be ina ~~accordance~~part of this prospectus, and information that we file later with the ~~rules:~~SEC will automatically update and supersede information contained in this prospectus.

•This ~~Stabilizing~~prospectus ~~transactions~~incorporates -by ~~the~~reference ~~representative may make bids or purchases for~~ the ~~purpose~~documents ofand ~~pegging,~~reports ~~fixing~~listed orbelow: ~~maintaining the price of the shares, so long as stabilizing bids do not exceed a specified maximum.~~

• ~~Penalty~~our ~~bids~~Annual -Report ifon ~~the~~Form ~~representative~~10-K ~~purchases~~for ~~shares in~~ the ~~open~~year ~~market~~ended inDecember a31, ~~stabilizing transaction or syndicate covering transaction~~2024, itfiled ~~may~~with ~~reclaim a selling concession from~~ the ~~underwriters~~SEC ~~and~~on ~~selling~~March ~~group~~31, ~~members who sold those shares as part of this offering.~~2025;

• ~~Passive~~our ~~market~~Quarterly ~~making~~Reports -on ~~market~~Form ~~makers~~10-Q infor the ~~shares~~quarters ~~who~~ended ~~are~~March ~~underwriters~~31, or2025 ~~prospective~~and ~~underwriters~~June ~~may~~30, ~~make~~2025, ~~bids~~filed ~~for~~with orthe ~~purchases~~SEC ofon ~~shares,~~May ~~subject to limitations~~14, ~~until~~2025 ~~the~~and ~~time~~August 14, ~~if ever~~2025, ~~at which a stabilizing bid is made.~~respectively;

~~Similar~~• toour ~~other~~Current ~~purchase~~Reports ~~transactions,~~on ~~the~~Form ~~underwriters'~~8-K ~~purchases~~(other tothan ~~cover~~information ~~the~~furnished ~~syndicate~~rather ~~short~~than ~~sales~~filed) orfiled towith ~~stabilize~~ the ~~market~~SEC ~~price~~on ofJanuary ~~our~~3, ~~common~~2025 ~~stock~~(with ~~may~~respect ~~have~~to ~~the~~Items ~~effect~~1.01, of3.02 ~~raising~~and or9.01 ~~maintaining~~only), ~~the~~January ~~market~~6, ~~price~~2025 of(with ~~our~~respect ~~common~~to ~~stock~~Items or1.01, ~~preventing~~8.01 orand ~~mitigating a decline in the market price of our common stock~~9.01 Asonly), aJanuary ~~result~~13, ~~the~~2025, ~~price~~January of16, ~~the~~2025, ~~shares~~January of27, ~~our~~2025 ~~common~~(with ~~stock~~respect ~~may~~to beItems ~~higher~~3.03, ~~than~~5.03 ~~the~~and ~~price~~9.01 ~~that~~only), ~~might~~February ~~otherwise~~10, ~~exist~~2025, inFebruary ~~the~~21, ~~open~~2025 ~~market.~~and ~~The~~June ~~imposition~~13, of2025, aand ~~penalty~~on ~~bid~~Form ~~might~~8-K/A, ~~also~~filed ~~have~~with anthe ~~effect~~SEC on ~~the~~June ~~price~~18, ~~of the shares if it discourages resales of the shares.~~2025;

~~Neither~~• weour ~~nor~~Definitive ~~the~~Proxy ~~underwriters~~Statement ~~make~~on ~~any~~Schedule ~~representation~~14A, orfiled ~~prediction~~with asthe toSEC ~~the~~on ~~effect~~April ~~that~~28, ~~the~~2025 ~~transactions~~(solely ~~described~~those ~~above~~portions ~~may~~that ~~have~~were onincorporated ~~the~~by ~~price~~reference ofinto ~~the~~Part ~~shares.~~III ~~These~~of ~~transactions~~our ~~may~~Annual ~~occur~~Report on ~~The~~Form ~~Nasdaq~~10-K ~~Capital~~for ~~Market~~the orfiscal ~~otherwise.~~year Ifended ~~such~~December ~~transactions are commenced~~31, ~~they~~2024); ~~may be discontinued without notice at any time.~~and

~~Electronic~~• ~~Delivery~~the description of ~~Prospectus:~~the ACompany’s ~~prospectus~~Common Stock contained in ~~electronic~~the ~~format~~Company’s ~~may~~Registration beStatement ~~delivered~~on toForm ~~potential~~8-A/A, ~~investors~~filed bywith ~~one~~the orSEC ~~more~~on ofAugust ~~the~~17, ~~underwriters~~2018, ~~participating~~as inupdated ~~this~~by ~~offering.~~the ~~The~~description ~~prospectus~~of incapital ~~electronic~~stock ~~format~~contained ~~will~~in beExhibit ~~identical~~4.5 to the ~~paper~~Annual ~~version~~Report ofon ~~such~~Form ~~prospectus.~~10-K ~~Other~~for ~~than~~ the ~~prospectus~~year inended ~~electronic~~December ~~format~~31, 2023, filed with the ~~information~~SEC on ~~any~~March ~~underwriter's~~5, ~~website~~2024, and ~~any~~including ~~information contained in~~ any ~~other~~amendments ~~website~~or ~~maintained~~reports byfiled anfor ~~underwriter is not part of this prospectus or~~ the ~~registration~~purposes ~~statement~~ of ~~which~~updating this ~~prospectus forms a part~~description.

~~Notice~~All other reports and documents filed by us pursuant to ~~Non-U~~Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act after the date that this registration statement becomes effective and after the date of this prospectus but before the termination of the offering of the securities described in this prospectus (excluding information furnished pursuant to Items 2.S02 and 7.01 ~~Investors~~of Form 8-K) shall be deemed to be incorporated by reference into this prospectus.

~~Belgium~~Notwithstanding the statements in the preceding paragraphs, no document, report or exhibit (or portion of any of the foregoing) or any other information that we have “furnished” to the SEC pursuant to the Exchange Act shall be incorporated by reference into this prospectus.

~~The~~Any ~~offering~~statement iscontained ~~exclusively~~in ~~conducted~~this ~~under~~prospectus ~~applicable~~or ~~private~~contained ~~placement~~in ~~exemptions~~a ~~and~~document ~~therefore~~incorporated itor ~~has~~deemed ~~not~~to ~~been~~be ~~and~~incorporated by reference into this prospectus will ~~not~~be deemed to be ~~notified~~modified or superseded to, ~~and~~the extent that a statement contained in this ~~document~~prospectus or any ~~other~~subsequently ~~offering~~filed ~~material~~supplement ~~relating~~ to ~~the~~this ~~shares~~prospectus, ~~has~~or ~~not~~document ~~been~~deemed ~~and~~to ~~will not~~ be ~~approved~~incorporated by, ~~the~~reference ~~Belgian~~into ~~Banking~~this prospectus, ~~Finance~~modifies ~~and~~or ~~Insurance~~supersedes ~~Commission~~such ~~(“Commission~~statement. ~~bancaire,~~Any ~~financière~~statements etso ~~des~~modified ~~assurances/Commissie~~or ~~voor~~superseded ~~het~~shall ~~Bank~~not be deemed, ~~Financie~~except enas ~~Assurantiewezen”).~~so ~~Any~~modified ~~representation~~or superseded, to ~~the~~constitute ~~contrary~~a ispart ~~unlawful~~of this prospectus.

~~Each~~You ~~underwriter~~can ~~has~~obtain ~~undertaken not to offer sell, resell, transfer or deliver directly or indirectly,~~ any ~~shares,~~of orthe tofilings ~~take~~incorporated ~~any~~by ~~steps~~reference ~~relating/ancillary~~into ~~thereto,~~this ~~and~~prospectus ~~not~~through tous ~~distribute~~ or ~~publish~~from ~~this document or any other material relating to~~ the ~~shares~~SEC orthrough to the ~~offering~~SEC’s inwebsite aat ~~manner~~www.sec.gov. ~~which~~We ~~would~~will befurnish ~~construed~~without ~~as:~~charge ~~(a)~~to ayou, ~~public~~upon ~~offering~~written ~~under~~or ~~the~~oral ~~Belgian~~request, ~~Royal~~a ~~Decree~~copy of 7any ~~July 1999 on the public character of financial transactions;~~ or ~~(b)~~all ~~an offering~~ of ~~securities to~~ the ~~public~~documents ~~under~~incorporated ~~Directive~~by ~~2003/71/EC~~reference, ~~which~~including ~~triggers~~exhibits ~~an obligation~~ to ~~publish a prospectus in Belgium. Any action contrary to~~ these ~~restrictions~~documents ~~will~~by ~~cause~~writing ~~the~~or ~~recipient~~telephoning ~~and~~us ~~the~~at ~~company to be in violation of~~ the ~~Belgian~~following ~~securities~~address: ~~laws.~~

~~Canada~~Bionano Genomics, Inc.

~~This~~9540 ~~document~~Towne ~~constitutes~~Centre anDrive, ~~“exempt~~Suite ~~offering~~100 document” as defined in and for the purposes of applicable Canadian securities laws. No prospectus has been filed with any securities commission or similar regulatory authority in Canada in connection with the offer and sale of the securities described herein (the “Securities”). No securities commission or similar regulatory authority in Canada has reviewed or in any way passed upon this document or on the merits of the Securities and any representation to the contrary is an offence.

~~Canadian~~San ~~investors are advised that this document has been prepared in reliance on section 3A.3 of National Instrument 33-105 Underwriting Conflicts (“NI 33-105”). Pursuant to section 3A.3 of NI 33-105~~Diego, ~~this~~California ~~document~~92121

Telephone: (858) 888-7600

You should rely only on the information incorporated by reference or provided in this prospectus. We have not authorized anyone else to provide different or additional information on our behalf. An offer of these securities is not being made in any jurisdiction where the offer or sale is not permitted. You should not assume that the information in this prospectus is accurate as of any date other than the date of those respective documents.

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isWHERE ~~exempt~~YOU ~~from~~CAN ~~the~~FIND ~~requirement~~MORE toINFORMATION provide investors with certain conflicts of interest disclosure pertaining to “connected issuer” and/or “related issuer” relationships as would otherwise be required pursuant to subsection 2.1(1) of NI 33-105.

~~Resale~~This ~~Restrictions~~prospectus is part of a registration statement we filed with the SEC. This prospectus does not contain all of the information set forth in the registration statement and the exhibits to the registration statement.

~~The~~For ~~offer~~further ~~and~~information ~~sale~~with ofrespect to us and the securities inwe ~~Canada~~are isoffering ~~being~~under ~~made~~this onprospectus, awe ~~private~~refer ~~placement~~you ~~basis~~to ~~only~~the ~~and~~registration isstatement ~~exempt~~and ~~from~~ the ~~requirement~~exhibits toand ~~prepare~~schedules ~~and~~filed ~~file~~as a ~~prospectus~~part ~~under~~of ~~applicable~~the ~~Canadian~~registration ~~securities laws~~statement. ~~Any~~You ~~resale~~should ofrely ~~Securities~~only ~~acquired~~on bythe ainformation ~~Canadian~~contained ~~investor~~ in this ~~offering~~prospectus ~~must~~or beincorporated ~~made~~by inreference ~~accordance~~into ~~with~~this ~~applicable~~prospectus. ~~Canadian~~We ~~securities~~have ~~laws,~~not ~~which~~authorized ~~may~~anyone ~~vary~~else ~~depending~~to onprovide ~~the~~you ~~relevant~~with ~~jurisdiction,~~different ~~and~~information. ~~which~~We ~~may~~are ~~require~~not ~~resales~~making toan beoffer ~~made~~of inthese ~~accordance~~securities ~~with~~in ~~Canadian~~any ~~prospectus~~jurisdiction ~~requirements,~~where athe ~~statutory~~offer ~~exemption~~is ~~from~~not ~~the~~permitted. ~~prospectus~~You ~~requirements,~~should inassume athat ~~transaction~~the ~~exempt~~information ~~from~~contained ~~the~~in this prospectus, ~~requirements~~ or ~~otherwise~~any ~~under~~document aincorporated ~~discretionary~~by ~~exemption~~reference ~~from~~in ~~the~~this prospectus, ~~requirements~~is ~~granted~~accurate byonly ~~the~~as ~~applicable~~of ~~local~~the ~~Canadian~~date ~~securities~~of ~~regulatory~~those ~~authority.~~respective ~~These~~documents, ~~resale~~regardless ~~restrictions~~of ~~may~~the ~~under~~time ~~certain~~of ~~circumstances~~delivery ~~apply~~of tothis ~~resales~~prospectus ofor ~~the~~any ~~Securities~~sale ~~outside~~ of ~~Canada~~our securities.

~~Representations~~We offile ~~Purchasers~~annual, quarterly and current reports, proxy statements and other information with the SEC. Our SEC filings are available to the public from commercial document retrieval services and over the Internet at the SEC’s website at http://www.sec.gov.

~~Each~~We ~~Canadian~~maintain ~~investor~~a ~~who~~website ~~purchases~~at ~~the~~www.bionanogenomics.com. ~~securities~~You ~~will~~may beaccess ~~deemed~~our toannual ~~have~~reports ~~represented~~on toForm 10-K, ~~the~~quarterly ~~issuer~~reports ~~and~~on toForm 10-Q, ~~each~~current ~~dealer~~reports ~~from~~on ~~whom~~Form 8-K aand ~~purchase~~amendments ~~confirmation~~to isthose ~~received,~~reports asfiled ~~applicable,~~or ~~that~~furnished ~~the~~pursuant ~~investor~~to Section 13(ia) ~~is purchasing as principal,~~ or is15(d) ~~deemed~~of tothe beExchange ~~purchasing~~Act ~~as principal in accordance~~ with ~~applicable~~the ~~Canadian~~SEC ~~securities~~free ~~laws,~~of ~~for~~charge ~~investment~~at ~~only~~our ~~and~~website ~~not~~as ~~with~~soon aas ~~view~~reasonably topracticable ~~resale~~after ~~or redistribution; (ii) is an “accredited investor” as~~ such ~~term~~material is ~~defined~~electronically infiled ~~section~~with, ~~1.1 of National Instrument 45-106 Prospectus Exemptions (“NI 45-106”)~~ or, infurnished ~~Ontario~~to, asthe ~~such~~SEC. ~~term~~The isinformation ~~defined~~contained in, ~~section~~or ~~73.3(1)~~that ofcan ~~the~~be ~~Securities~~accessed ~~Act~~through, ~~(Ontario);~~our ~~and~~website ~~(iii)~~ is anot ~~“permitted~~incorporated ~~client”~~by asreference ~~such~~into, ~~term~~and is ~~defined~~not inpart ~~section 1.1~~ of ~~National Instrument 31-103 Registration Requirements~~, ~~Exemptions~~this ~~and Ongoing Registrant Obligations~~prospectus.

Taxation and Eligibility for Investment

Any discussion of taxation and related matters contained in this document does not purport to be a comprehensive description of all of the tax considerations that may be relevant to a Canadian investor when deciding to purchase the securities and, in particular, does not address any Canadian tax considerations. No representation or warranty is hereby made as to the tax consequences to a resident, or deemed resident, of Canada of an investment in the securities or with respect to the eligibility of the securities for investment by such investor under relevant Canadian federal and provincial legislation and regulations.

Rights of Action for Damages or Rescission

Securities legislation in certain of the Canadian jurisdictions provides certain purchasers of securities pursuant to an offering memorandum, including where the distribution involves an “eligible foreign security” as such term is defined in Ontario Securities Commission Rule 45-501 Ontario Prospectus and Registration Exemptions and in Multilateral Instrument 45-107 Listing Representation and Statutory Rights of Action Disclosure Exemptions, as applicable, with a remedy for damages or rescission, or both, in addition to any other rights they may have at law, where the offering memorandum, or other offering document that constitutes an offering memorandum, and any amendment thereto, contains a “misrepresentation” as defined under applicable Canadian securities laws. These remedies, or notice with respect to these remedies, must be exercised or delivered, as the case may be, by the purchaser within the time limits prescribed under, and are subject to limitations and defences under, applicable Canadian securities legislation. In addition, these remedies are in addition to and without derogation from any other right or remedy available at law to the investor.

Language of Documents

Upon receipt of this document, each Canadian investor hereby confirms that it has expressly requested that all documents evidencing or relating in any way to the sale of the securities described herein (including for greater certainty any purchase confirmation or any notice) be drawn up in the English language only. Par la réception de ce document, chaque investisseur canadien confirme par les présentes qu'il a expressément exigé que tous les documents faisant foi ou se rapportant de quelque manière que ce soit à la vente des valeurs mobilières décrites aux présentes (incluant, pour plus de certitude, toute confirmation d'achat ou tout avis) soient rédigés en anglais seulement.

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France

Neither this prospectus nor any other offering material relating to the shares has been submitted to the clearance procedures of the Autorité des marchés financiers in France. The shares have not been offered or sold and will not be offered or sold, directly or indirectly, to the public in France. Neither this prospectus nor any other offering material relating to the shares has been or will be: (a) released, issued, distributed or caused to be released, issued or distributed to the public in France; or (b) used in connection with any offer for subscription or sale of the shares to the public in France. Such offers, sales and distributions will be made in France only: (i) to qualified investors (investisseurs qualifiés) and/or to a restricted circle of investors (cercle restreint d'investisseurs), in each case investing for their own account, all as defined in and in accordance with Articles L.411-2, D.411-1, D.411-2, D.734-1, D.744-1, D.754-1 and D.764-1 of the French Code monétaire et financier; (ii) to investment services providers authorised to engage in portfolio management on behalf of third parties; or (iii) in a transaction that, in accordance with article L.411-2-II-1°-or-2°-or 3° of the French Code monétaire et financier and article 211-2 of the General Regulations (Règlement Général) of the Autorité des marchés financiers, does not constitute a public offer (appel public à l'épargne). Such shares may be resold only in compliance with Articles L.411-1, L.411-2, L.412-1 and L.621-8 through L.621-8-3 of the French Code monétaire et financier.

United Kingdom/Germany/Norway/The Netherlands

In relation to each Member State of the European Economic Area which has implemented the Prospectus Directive (each, a “Relevant Member State”) an offer to the public of any shares which are the subject of the offering contemplated by this prospectus may not be made in that Relevant Member State other than the offers contemplated in this prospectus in name(s) of Member State(s) where prospectus will be approved or passported for the purposes of a non-exempt offer once this prospectus has been approved by the competent authority in such Member State and published and passported in accordance with the Prospectus Directive as implemented in name(s) of relevant Member State(s) except that an offer to the public in that Relevant Member State of any shares may be made at any time under the following exemptions under the Prospectus Directive, if they have been implemented in that Relevant Member State:

(a) to legal entities which are authorised or regulated to operate in the financial markets or, if not so authorised or regulated, whose corporate purpose is solely to invest in securities;

(b) to any legal entity which has two or more of (1) an average of at least 250 employees during the last financial year; (2) a total balance sheet of more than €43,000,000 and (3) an annual net turnover of more than €50,000,000, as shown in its last annual or consolidated accounts;

(c) by the representative to fewer than 100 natural or legal persons (other than qualified investors as defined in the Prospectus Directive); or

(d) in any other circumstances falling within Article 3(2) of the Prospectus Directive, provided that no such offer of shares shall result in a requirement for the publication by the company or any underwriter of a prospectus pursuant to Article 3 of the Prospectus Directive.

For the purposes of this provision, the expression an “offer to the public” in relation to any shares in any Relevant Member State means the communication in any form and by any means of sufficient information on the terms of the offer and any shares to be offered so as to enable an investor to decide to purchase any shares, as the same may be varied in that Member State by any measure implementing the Prospectus Directive in that Member State and the expression “Prospectus Directive” means Directive 2003/71/EC and includes any relevant implementing measure in each Relevant Member State.

Each underwriter has represented, warranted and agreed that:

(a) it has only communicated or caused to be communicated and will only communicate or cause to be communicated any invitation or inducement to engage in investment activity (within the meaning of section 21 of the Financial Services and Markets Act 2000 (the FSMA)) received by it in connection with the issue or sale of any shares in circumstances in which section 21(1) of the FSMA does not apply to the company; and

(b) it has complied with and will comply with all applicable provisions of the FSMA with respect to anything done by it in relation to the shares in, from or otherwise involving the United Kingdom.

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Israel

In the State of Israel, the shares offered hereby may not be offered to any person or entity other than the following:

(a) a fund for joint investments in trust (i.e., mutual fund), as such term is defined in the Law for Joint Investments in Trust, 5754-1994, or a management company of such a fund;

(b) a provident fund as defined in Section 47(a)(2) of the Income Tax Ordinance of the State of Israel, or a management company of such a fund;

(c) an insurer, as defined in the Law for Oversight of Insurance Transactions, 5741-1981, (d) a banking entity or satellite entity, as such terms are defined in the Banking Law (Licensing), 5741-1981, other than a joint services company, acting for their own account or for the account of investors of the type listed in Section 15A(b) of the Securities Law 1968;

(d) a company that is licensed as a portfolio manager, as such term is defined in Section 8(b) of the Law for the Regulation of Investment Advisors and Portfolio Managers, 5755-1995, acting on its own account or for the account of investors of the type listed in Section 15A(b) of the Securities Law 1968;

(e) a company that is licensed as an investment advisor, as such term is defined in Section 7(c) of the Law for the Regulation of Investment Advisors and Portfolio Managers, 5755-1995, acting on its own account;

(f) a company that is a member of the Tel Aviv Stock Exchange, acting on its own account or for the account of investors of the type listed in Section 15A(b) of the Securities Law 1968;

(g) an underwriter fulfilling the conditions of Section 56(c) of the Securities Law, 5728-1968;

(h) a venture capital fund (defined as an entity primarily involved in investments in companies which, at the time of investment, (i) are primarily engaged in research and development or manufacture of new technological products or processes and (ii) involve above-average risk);

(i) an entity primarily engaged in capital markets activities in which all of the equity owners meet one or more of the above criteria; and

(j) an entity, other than an entity formed for the purpose of purchasing shares in this offering, in which the shareholders equity (including pursuant to foreign accounting rules, international accounting regulations and U.S. generally accepted accounting rules, as defined in the Securities Law Regulations (Preparation of Annual Financial Statements), 1993) is in excess of NIS 50 million.

Any offeree of the shares offered hereby in the State of Israel shall be required to submit written confirmation that it falls within the scope of one of the above criteria. This prospectus will not be distributed or directed to investors in the State of Israel who do not fall within one of the above criteria.

Italy

The offering of the shares offered hereby in Italy has not been registered with the Commissione Nazionale per la Società e la Borsa (“CONSOB”) pursuant to Italian securities legislation and, accordingly, the shares offered hereby cannot be offered, sold or delivered in the Republic of Italy (“Italy”) nor may any copy of this prospectus or any other document relating to the shares offered hereby be distributed in Italy other than to professional investors (operatori qualificati) as defined in Article 31, second paragraph, of CONSOB Regulation No. 11522 of 1 July, 1998 as subsequently amended. Any offer, sale or delivery of the shares offered hereby or distribution of copies of this prospectus or any other document relating to the shares offered hereby in Italy must be made:

(a) by an investment firm, bank or intermediary permitted to conduct such activities in Italy in accordance with Legislative Decree No. 58 of 24 February 1998 and Legislative Decree No. 385 of 1 September 1993 (the “Banking Act”);

(b) in compliance with Article 129 of the Banking Act and the implementing guidelines of the Bank of Italy; and

(c) in compliance with any other applicable laws and regulations and other possible requirements or limitations which may be imposed by Italian authorities.

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Sweden

This prospectus has not been nor will it be registered with or approved by Finansinspektionen (the Swedish Financial Supervisory Authority). Accordingly, this prospectus may not be made available, nor may the shares offered hereunder be marketed and offered for sale in Sweden, other than under circumstances which are deemed not to require a prospectus under the Financial Instruments Trading Act (1991: 980).

Switzerland

The shares offered pursuant to this prospectus will not be offered, directly or indirectly, to the public in Switzerland and this prospectus does not constitute a public offering prospectus as that term is understood pursuant to art. 652a or art. 1156 of the Swiss Federal Code of Obligations. The company has not applied for a listing of the shares being offered pursuant to this prospectus on the SWX Swiss Exchange or on any other regulated securities market, and consequently, the information presented in this prospectus does not necessarily comply with the information standards set out in the relevant listing rules. The shares being offered pursuant to this prospectus have not been registered with the Swiss Federal Banking Commission as foreign investment funds, and the investor protection afforded to acquirers of investment fund certificates does not extend to acquirers of shares.

Investors are advised to contact their legal, financial or tax advisers to obtain an independent assessment of the financial and tax consequences of an investment in shares.

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LEGAL MATTERS

~~Cooley~~The ~~LLP,~~validity ~~San~~of ~~Diego,~~the ~~California,~~securities ~~which~~being ~~has~~offered ~~acted~~hereby asand ~~our~~certain ~~counsel~~other inlegal ~~connection~~matters ~~with~~will ~~this~~be ~~offering,~~passed ~~will~~upon ~~pass~~for onus ~~certain~~by ~~legal~~Troutman ~~matters~~Pepper ~~with~~Locke ~~respect~~LLP, toCharlotte, UNorth Carolina.S. ~~federal~~Certain ~~law~~legal inmatters ~~connection~~will ~~with~~be ~~this~~passed ~~offering.~~upon ~~Mintz,~~for ~~Levin,~~the ~~Cohn,~~placement ~~Ferris,~~agent ~~Glovsky~~by Haynes and ~~Popeo~~Boone, ~~P.C.~~LLP, New York, New York ~~has acted as counsel to the underwriters in connection with this offering~~.

EXPERTS

The consolidated financial statements ~~incorporated~~of inBionano ~~this~~Genomics, ~~Prospectus~~Inc. by(the ~~reference~~Company) ~~from~~as ~~the~~of ~~Company’s~~December ~~Annual~~31, ~~Report~~2024 onand ~~Form~~2023 ~~10-K~~and for each of the ~~year~~years then ended ~~December~~incorporated ~~31,~~by ~~2019~~reference in this prospectus and in the registration statement have been ~~audited~~so byincorporated ~~Deloitte~~in &reliance ~~Touche~~on ~~LLP~~the report of BDO USA, P.C., an independent registered public accounting firm, asgiven ~~stated~~on inthe ~~their~~authority ~~report,~~of ~~which~~said isfirm ~~incorporated~~as ~~herein~~experts byin ~~reference~~auditing ~~(which~~and ~~report~~accounting. ~~expresses~~The anreport ~~unqualified opinion~~ on the consolidated financial statements ~~and~~contains ~~includes~~ an explanatory paragraph ~~referring~~regarding to the Company’s ability to continue as a going concern). ~~Such financial statements have been so incorporated in reliance upon the report of such firm given upon their authority as experts in accounting and auditing.~~

~~WHERE YOU CAN FIND MORE INFORMATION~~23

We have filed with the SEC a registration statement on Form S-1 under the Securities Act, with respect to the securities being offered by this prospectus. This prospectus does not contain all of the information in the registration statement and its exhibits. For further information with respect to us and the securities offered by this prospectus, we refer you to the registration statement and its exhibits. Statements contained in this prospectus as to the contents of any contract or any other document referred to are not necessarily complete, and in each instance, we refer you to the copy of the contract or other document filed as an exhibit to the registration statement. Each of these statements is qualified in all respects by this reference.

We are subject to the information and periodic reporting requirements of the Exchange Act, and we file periodic reports, proxy statements and other information with the SEC. You can read our SEC filings, including the registration statement, over the Internet at the SEC’s website at www.sec.gov. You may also request a copy of these filings, at no cost, by writing us at 9540 Towne Centre Drive, Suite 100, San Diego, California 92121 or telephoning us at (858) 888-7600. We also maintain a website at www.bionanogenomics.com, at which you may access these materials free of charge after they are electronically filed with, or furnished to, the SEC. The information contained in, or that can be accessed through, our website is not incorporated by reference in, and is not part of, this prospectus.

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~~INCORPORATION~~Up OFto ~~CERTAIN~~2,032,520 ~~INFORMATION~~Shares BYof ~~REFERENCE~~Common Stock

~~The~~Up ~~SEC allows us~~ to ~~“incorporate by reference” information from other documents that we file with it~~2,032,520 ~~which~~Pre-Funded ~~means~~Warrants ~~that we can disclose important information~~ to ~~you~~Purchase byup ~~referring you~~ to ~~those~~2,032,520 ~~documents.~~Shares ~~The information incorporated by reference is considered to be part~~ of ~~this~~Common ~~prospectus.~~Stock

WeUp ~~incorporate~~to ~~by reference into this prospectus and the registration statement of which this prospectus form a part the information or documents listed below that we have filed with the SEC~~2, ~~and any future filings we will make with the SEC under Sections 13(a)~~032,520 ~~13(c),~~Series E ~~14,~~Warrants orto ~~15(d)~~Purchase ofup ~~the Exchange Act after the date of the initial filing of the registration statement of which this prospectus is a part and prior~~ to ~~effectiveness of such registration statement~~2,032,520 ~~and~~Shares ~~until the termination~~ of ~~the~~Common ~~offering of the shares covered by this prospectus (other than information furnished under Item 2.02 or Item 7.01 of Form 8-K):~~Stock

•Up ~~our~~to ~~Annual~~2,032,520 ~~Report~~Series F onWarrants ~~Form~~to ~~10-K~~Purchase ~~for~~up ~~the~~to ~~year ended December 31~~2,032,520 ~~2019~~Shares ~~filed~~of ~~with~~Common ~~the~~Stock ~~SEC on March 10, 2020;~~

•Up ~~our~~to ~~Current~~6,097,560 ~~Reports~~Shares onof ~~Form~~Common ~~8-K~~Stock ~~(other~~Issuable ~~than~~Upon ~~information~~Exercise ~~furnished~~of ~~rather than filed) filed with~~ the ~~SEC on January 30, 2020 and March 2, 2020; and~~

~~• the description of our common stock which is registered under Section 12 of the Exchange Act, in our registration statement on Form 8~~Pre-A,Funded ~~filed on August 17~~Warrants, ~~2018,~~Series E ~~including~~Warrants ~~any~~and ~~amendment~~Series F orWarrants ~~reports filed for the purposes of updating this description.~~

~~Any~~PRELIMINARY ~~statement~~PROSPECTUS contained in this prospectus or in a document incorporated or deemed to be incorporated by reference into this prospectus will be deemed to be modified or superseded for purposes of this prospectus to the extent that a statement contained in this prospectus or any other subsequently filed document that is deemed to be incorporated by reference into this prospectus modifies or supersedes the statement. Any statements so modified or superseded shall not be deemed, except as so modified or superseded, to constitute a part of this prospectus.

~~We will furnish without charge to you, on written or oral request, a copy of any or all of the documents incorporated by reference in this prospectus, including exhibits to these documents~~H. ~~You should direct any requests for documents to Bionano Genomics, Inc~~C. ~~9540~~Wainwright ~~Towne~~& ~~Centre Drive, Suite 100, San Diego, California 92121; telephone: (858) 888-7600~~Co.

~~You~~The ~~also~~date ~~may~~of ~~access these filings on our website at www.bionanogenomics.com. We do not incorporate the information on our website into~~ this prospectus ~~or any supplement to this prospectus and you should not consider any information on~~is , or that can be accessed through, our website as part of this prospectus or any supplement to this prospectus (other than those filings with the SEC that we specifically incorporate by reference into this prospectus)2025.

DISCLOSURE OF COMMISSION POSITION ON INDEMNIFICATION FOR SECURITIES ACT LIABILITY

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to our directors, officers, and controlling persons, we have been advised that in the opinion of the SEC this indemnification is against public policy as expressed in the Securities Act and is therefore, unenforceable.

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17,648,000 Shares of Common StockPre-Funded Warrants to Purchase Shares of Common StockWarrants to Purchase up to 17,648,000 Shares of Common Stock

PROSPECTUS

Sole Book-Running Manager

Oppenheimer & Co.

Lead Manager Co-Lead Manager Roth Capital Partners Maxim Group LLC

You should rely only on the information contained in this prospectus. No dealer, salesperson or other person is authorized to give information that is not contained in this prospectus. This prospectus is not an offer to sell nor is it seeking an offer to buy these securities in any jurisdiction where the offer or sale is not permitted. The information contained in this prospectus is correct only as of the date of this prospectus, regardless of the time of the delivery of this prospectus or any sale of these securities.

The date of this prospectus is , 2020

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PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

Item 13. Other Expenses of Issuance and Distribution.

The following table sets forth the ~~expenses~~costs toand beexpenses, ~~incurred~~other inthan ~~connection~~placement ~~with~~agent ~~the~~fees ~~offering~~and ~~described~~commissions, inpayable ~~this~~by ~~registration~~us ~~statement,~~in ~~all~~connection ofwith ~~which~~the ~~will~~sale beand ~~paid~~distribution byof the ~~registrant~~securities being registered. All of the amounts shown are estimates, except for the SEC registration fee. and the FINRA filing fee:

	Amount
			Amount to be paid
SEC registration fee	$	~~3,895~~	$4,593
FINRA filing fee	$	~~5,000~~	5,000
Printing and engraving expenses	$	20,000
Legal fees and expenses			100,000
Legal fees and expenses	$	250,000
Accounting fees and expenses			45,000
Accounting fees and expenses	$	30,000
Miscellaneous			5,500
Transfer agent and registrar fees	$	5,000
Total expenses			$160,093
Miscellaneous fees and expenses	$	21,105
Total	$	335,000

Item 14. Indemnification of Directors and Officers.

We are incorporated under the laws of the State of Delaware. Section 145 of the ~~Delaware~~ General Corporation Law of the State of Delaware provides that a Delaware corporation may indemnify any persons who were, are, or are threatened to be made, parties to any threatened, pending or completed action, suit or proceeding, whether civil, criminal, administrative or investigative (other than an action by or in the right of such corporation), by reason of the fact that such person is or was an officer, director, employee or agent of such corporation, or is or was serving at the request of such corporation as an officer, director, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys’ fees), judgments, fines and amounts paid in settlement actually and reasonably incurred by such person in connection with such action, suit or proceeding, provided that such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation’s best interests and, with respect to any criminal action or proceeding, had no reasonable cause to believe that his or her conduct was illegal. A Delaware corporation may indemnify any persons who were, are, or are threatened to be made, a party to any threatened, pending or completed action or suit by or in the right of the corporation by reason of the fact that such person is or was a director, officer, employee or agent of such corporation, or is or was serving at the request of such corporation as a director, officer, employee or agent of another corporation or enterprise. The indemnity may include expenses (including attorneys’ fees) actually and reasonably incurred by such person in connection with the defense or settlement of such action or suit provided such person acted in good faith and in a manner he or she reasonably believed to be in or not opposed to the corporation’s best interests except that no indemnification is permitted without judicial approval if the officer or director is adjudged to be liable to the corporation. Where an officer or director is successful on the merits or otherwise in the defense of any action referred to above, the corporation must indemnify him or her against the expenses (including attorneys’ fees) actually and reasonably incurred.

Our amended and restated certificate of incorporation, as amended, and our amended and restated bylaws provide for the indemnification of our directors and officers to the fullest extent permitted under the General Corporation Law of the State of Delaware. Section 102(b)(7) of the General Corporation Law. of the State of Delaware permits a corporation to provide in its certificate of incorporation that a director or officer of the corporation shall not be personally liable to the corporation or its stockholders for monetary damages for breach of fiduciary duties as a director or officer, except for liability for any:

~~Section~~• ~~102(b)(7)~~transaction offrom which the ~~Delaware General Corporation Law permits a corporation to provide in its certificate of incorporation that a~~ director ~~of the corporation shall not be personally liable to the corporation~~ or ~~its~~officer ~~stockholders~~derives ~~for~~an ~~monetary~~improper ~~damages~~personal ~~for breach of fiduciary duties as a director, except for liability for any:~~benefit;

• transaction from which the director derives an improper personal benefit;

•	act or omission not in good faith or that involves intentional misconduct or a knowing violation of law;

• in the case of a director, unlawful payment of dividends or redemption of shares; or

• breach of a director’s duty of loyalty to the corporation or its stockholders.; or

•	in the case of an officer, action by or in the right of the corporation.

Our amended and restated certificate of incorporation, as amended, includes such a provision with respect to our directors. Expenses incurred by any officer or director in defending any such action, suit or proceeding in advance

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~~Our amended and restated certificate~~ of ~~incorporation includes such a provision. Expenses incurred by any officer or director in defending any such action, suit or proceeding in advance of~~ its final disposition will be paid by us upon delivery to us of an undertaking, by or on behalf of such director or officer, to repay all amounts so advanced if it shall ultimately be determined that such director or officer is not entitled to be indemnified by us.

Section 174 of the ~~Delaware~~ General Corporation Law of the State of Delaware provides, among other things, that a director who willfully or negligently approves of an unlawful payment of dividends or an unlawful stock purchase or redemption, may be held liable for such actions. A director who was either absent when the unlawful actions were approved or dissented at the time may avoid liability by causing his or her dissent to such actions to be entered in the books containing minutes of the meetings of the board of directors at the time such action occurred or immediately after such absent director receives notice of the unlawful acts.

As permitted by the ~~Delaware~~ General Corporation Law of the State of Delaware, we have entered ~~into~~, and continue to enter, into separate indemnity agreements with each of our directors and executive officers that require us to indemnify such persons against any and all costs and expenses (including attorneys’, witness or other professional fees) actually and reasonably incurred by such persons in connection with any action, suit or proceeding (including derivative actions), whether actual or threatened, to which any such person may be made a party by reason of the fact that such person is or was a director or officer or is or was acting or serving as an officer, director, employee or agent of ours or any of our affiliated enterprises. Under these agreements, we are not required to provide indemnification for certain matters, including:

• indemnification beyond that permitted by the ~~Delaware~~ General Corporation Law of the State of Delaware;

•	indemnification for any proceeding with respect to the unlawful payment of remuneration to the director or officer;

•	indemnification for certain proceedings involving a final judgment that the director or officer is required to disgorge profits from the purchase or sale of our stock;

•	indemnification for proceedings involving a final judgment that the director’s or officer’s conduct was in bad faith, knowingly fraudulent or deliberately dishonest or constituted willful misconduct or a breach of his or her duty of loyalty, but only to the extent of such specific determination;

• indemnification for proceedings or claims brought by an officer or director against us or any of our directors, officers, employees or agents, except for (1) claims to establish a right of indemnification or proceedings, (2) claims approved by our board of directors, (3) claims required by law, (4) when there has been a change of control as defined in the indemnification agreement with each director or officer, or (5) by us in our sole discretion pursuant to the powers vested to us under the ~~Delaware~~ General ~~Corporate~~Corporation Law of the State of Delaware;

•	indemnification for settlements the director or officer enters into without our consent; or

• indemnification in violation of any undertaking required by the Securities Act ~~of 1933, as amended,~~ or ~~the Securities Act, or~~ in any registration statement we file.

The indemnification agreements also set forth certain procedures that will apply in the event of a claim for indemnification thereunder.

There is at present no pending litigation or proceeding involving any of our directors or executive officers as to which indemnification is required or permitted, and we are not currently aware of any threatened litigation or proceeding that may result in a claim for indemnification.

We have an insurance policy in place that covers our officers and directors with respect to certain liabilities, including liabilities arising under the Securities Act or otherwise.

~~Any~~Pursuant ~~underwriting~~to ~~agreement~~certain ~~that~~underwriting agreements we may enter, ~~into may provide that~~ the underwriters are obligated, under some circumstances, to indemnify our directors, officers and controlling persons against specified liabilities, including liabilities under the Securities Act.

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Item 15. Recent Sales of Unregistered Securities.

~~Set~~The ~~forth~~following ~~below~~list issets forth information ~~regarding~~as ~~shares~~to ofall ~~common~~unregistered ~~stock~~securities ~~and~~we ~~preferred~~have ~~stock~~sold ~~issued, and options granted, by us~~ since January 1, ~~2017~~2022 ~~that~~through ~~were not registered under~~ the ~~Securities~~date ~~Act~~ of ~~1933, as amended (~~the ~~Securities~~prospectus ~~Act).~~that ~~Also included~~ is ~~the~~a ~~consideration,~~part ~~if any, received by us for such shares and options and information relating to the section~~ of ~~the~~this ~~Securities Act, or rule of the Securities and Exchange Commission, under which exemption from~~ registration ~~was~~statement: ~~claimed.~~

~~(a)~~April 2023 ~~Issuances~~Private ofPlacement ~~Securities~~

On ~~March 2~~April 13, ~~2020~~2023, we entered into a ~~Warrants~~Purchase ~~Amendment and~~ Agreement, or (the ~~Warrant~~“April 2023 ~~Inducement~~Purchase Agreement,”) with ~~certain~~David ~~holders~~Barker ~~of the common warrants issued in our October 23, 2019 underwritten public offering, whereby we agreed~~ (i)“April 2023 ~~to amend such warrants~~Purchaser”), or the ~~Amended~~Chair ~~Warrants,~~of ~~held by~~ the ~~holders~~Company’s ~~and~~board ~~exercisable for up to an aggregate~~ of 3directors,~~200,000~~ ~~shares~~pursuant ~~of common stock~~ to ~~reduce~~which ~~the~~we ~~exercise~~agreed ~~price~~to ofissue ~~the~~and ~~Amended~~sell ~~Warrants~~one inshare ~~the event~~ of athe ~~cash~~Company’s ~~exercise~~Series A ~~(and~~Preferred ~~not~~Stock, apar ~~cashless~~value ~~exercise) to~~ $0.750001 per share ~~until 9:15 a.m. Eastern Time on March 3~~, ~~2020~~to ~~and~~the ~~(ii)~~April 2023 ~~that~~Purchaser ~~if and only if such holders exercised~~ for ~~cash all of the Amended Warrants no later than 9:15~~ a~~.m.~~ ~~Eastern Time on March 3, 2020, to issue to such holders new warrants, or the Inducement Warrants, to~~ purchase ~~shares of our common stock, initially exercisable for the same number of shares of common stock issued to such holders pursuant to the exercise of the Amended Warrants, at an exercise~~ price of $1100.~~06 per share~~00. The ~~holders~~closing ~~timely~~of ~~exercised for cash all~~ the ~~Amended~~sale ~~Warrants~~and onpurchase ~~March 3, 2020, resulting in gross proceeds to us~~ of ~~$2.4 million. In accordance with~~ the ~~Warrant~~share ~~Inducement~~of ~~Agreement,~~Series A wePreferred ~~issued~~was ~~these~~completed ~~holders the Inducement Warrants~~ on ~~March 3~~April 13, ~~2020, which will be exercisable commencing on the six-month anniversary of the issuance date for a period of five years thereafter~~2023. The ~~issuance~~April 2023 ofPurchaser ~~the~~is ~~Inducement~~an ~~Warrants~~“accredited investor” and the ~~shares~~offer ofand ~~our~~sale ~~common stock issuable upon exercise~~ of the ~~Inducement~~share ~~Warrants~~of isSeries A Preferred was exempt from registration under ~~the Securities Act, pursuant to the exemption for transactions by an issuer not involving any public offering under~~ Section 4(a)(2) of the Securities Act. ~~The foregoing description is subject to, and qualified in its entirety by, the Form of Warrant Inducement Agreement filed as an exhibit hereto and incorporated herein by reference.~~

OnOctober 2023 ~~March~~Private ~~14,~~Placement 2019, we entered into a Loan and Security Agreement, or the Innovatus Loan Agreement, with Innovatus Life Sciences Lending Fund I, LP, or Innovatus, a Delaware limited partnership, as collateral agent and the Lenders listed on Schedule 1.1 thereto, including East West Bank, pursuant to which Innovatus agreed, among other things, to make a first term loan of $17.5 million to us, or the Term A-1 Loan, a second term loan of $2.5 million to us, or the Term A-2 Loan, and a third term loan of $5.0 million to us, each upon satisfaction of certain funding conditions as set forth in the Innovatus Loan Agreement. In connection with the funding of any of the term loans, we agreed to issue warrants to Innovatus to purchase shares of our common stock. The warrants will be issued on the funding date of each tranche and will expire ten (10) years from such issue date.

On ~~March 22~~October 11, ~~2019~~2023, inwe ~~connection~~entered ~~with~~into a securities purchase agreement (the ~~receipt~~“October 2023 ofPurchase ~~funding~~Agreement”) with ~~respect~~High toTrail ~~the~~Special ~~Term~~Situations ~~A-1~~LLC ~~Loan~~(the ~~and~~“October 2023 ~~Term~~Purchaser”) ~~A-2~~pursuant ~~Loan,~~to which we issued to ~~Innovatus~~the October 2023 Purchaser: (i) in a ~~warrant~~registered offering (the “October 2023 Registered Offering”) (a) $45.0 million aggregate principal amount of senior secured convertible notes due 2025 (the “Registered Notes”) initially convertible into 261,894 shares of our common stock (as adjusted for the reverse stock split) and (b) warrants to purchase up to ~~161~~361,~~987~~011 shares of our common stock at(as anadjusted ~~exercise~~for the reverse stock split) (the “Registered Warrants”); and (ii) in a concurrent private placement (the “October 2023 Private Placement”), $35.0 million aggregate principal amount of senior secured convertible notes due 2025 initially convertible at a price of $4171.6360 (as ~~per~~adjusted ~~share.~~for ~~The~~the ~~foregoing~~reverse ~~description~~stock issplit) ~~subject~~into to203,696 ~~and~~shares ~~qualified~~of inour ~~its~~common ~~entirety~~stock ~~by,~~(as adjusted for the ~~Loan~~reverse ~~and~~stock ~~Security~~split) ~~Agreement~~(the “Private Placement Notes” and together with the ~~form~~Registered ofNotes, ~~Warrant~~the to“Notes”). ~~Purchase~~The ~~Common~~October 2023 ~~Stock~~Registered ~~filed~~Offering asand ~~exhibits~~the ~~hereto~~October 2023 ~~and~~Private ~~incorporated~~Placement ~~herein~~closed byon ~~reference~~October 13, 2023.

InPursuant ~~connection~~to ~~with~~ the ~~Innovatus~~October 2023 ~~Loan~~Purchase Agreement, ~~on March 14, 2019,~~ we ~~entered~~also ~~into~~granted ~~a Common Stock Purchase Agreement, or~~ the ~~Innovatus~~October 2023 ~~Purchase~~Purchaser ~~Agreement,~~an ~~with~~option ~~certain~~to ~~entities~~purchase ~~affiliated~~up ~~with~~to ~~Innovatus,~~an oradditional ~~the~~$25.0 million ~~Innovatus~~aggregate ~~Investors,~~principal ~~pursuant~~amount toof ~~which~~Private wePlacement ~~agreed~~Notes toinitially ~~issue~~convertible ~~and~~into ~~sell 406~~145,~~504~~497 shares of our common stock at(as ~~$3.69~~adjusted ~~per share~~ for ~~proceeds~~the ofreverse ~~$1.5~~stock ~~million,~~split) or (the ~~Innovatus~~“Subsequently ~~Shares.~~Purchased ~~The~~Notes”) ~~foregoing~~and ~~description~~warrants is(the ~~subject~~“Private ~~to,~~Placement Warrants” and ~~qualified~~together inwith ~~its~~the ~~entirety~~Registered byWarrants, the ~~Innovatus~~“October 2023 ~~Purchase~~Warrants”) ~~Agreement~~to ~~filed~~purchase asup anto ~~exhibit~~112,816 ~~hereto~~shares ~~and~~of ~~incorporated~~our ~~herein~~common bystock ~~reference.~~(as Onadjusted ~~November~~for 8,the ~~2019,~~reverse westock ~~entered~~split) ~~into~~in a ~~Common~~subsequent ~~Stock~~private ~~Issuance~~placement ~~Agreement~~on ~~with~~the ~~Innovatus,~~same ~~pursuant~~terms toas ~~which~~the weOctober 2023 ~~issued~~Notes toand ~~Innovatus~~the ~~572,917~~Registered ~~shares~~Warrants of(any ~~our~~such ~~common~~subsequent ~~stock.~~private placement, a “Subsequent Private Placement”).

OnCowen ~~March~~and 14Company, ~~2019,~~LLC weand ~~entered~~Stifel, ~~into~~Nicolaus ~~the~~& ~~Common~~Company, ~~Stock~~Incorporated ~~Purchase~~acted ~~Agreement,~~as orco-lead ~~the~~placement ~~Aspire~~agents ~~Agreement~~and BTIG, ~~with~~LLC ~~Aspire~~as ~~Capital~~placement ~~Fund,~~agent ~~LLC~~(together, orthe ~~Aspire~~“Placement ~~Capital.~~Agents”) ~~Pursuant~~for to the ~~terms~~sale of the ~~Aspire~~October 2023 ~~Agreement,~~Notes ~~Aspire~~and ~~Capital~~the ~~purchased~~October 2023 ~~272~~Warrants,~~479~~ ~~shares~~pursuant ofto ~~our~~a ~~common~~placement ~~stock~~agent atagreement, ~~$3.67~~by ~~per~~and ~~share~~between us and wethe ~~issued~~Placement 69Agents dated October 11,~~444~~ ~~shares~~2023. ofWe ~~our~~paid ~~common~~the ~~stock~~Placement Agents a cash fee equal to ~~Aspire~~$2.7 ~~Capital~~million inand ~~consideration~~agreed ~~for~~to ~~entering~~pay ~~into~~a cash fee equal to 6.0% of the ~~Aspire~~gross ~~Agreement~~proceeds from the sale of any Subsequent Private Placement.

OnThe ~~November~~Private ~~19,~~Placement ~~2018,~~Notes weand ~~entered~~the ~~into~~shares anof ~~Amendment~~common ~~Agreement,~~stock orunderlying the ~~Amendment~~Private ~~Agreement,~~Placement ~~with~~Notes ~~Western~~were ~~Alliance~~issued ~~Bank,~~in anreliance ~~Arizona~~upon ~~corporation~~Rule 506 (of Regulation D promulgated under the ~~“Holder”)~~Securities Act, inas ~~order~~a totransaction ~~amend~~not ~~(i)~~requiring ~~that~~registration ~~certain~~under ~~Warrant~~the toSecurities ~~Purchase~~Act ~~Stock,~~and ~~dated~~was ~~March~~made 8,without ~~2016,~~general ~~(ii)~~solicitation ~~that~~or ~~certain~~advertising. ~~Warrant~~Pursuant to the October 2023 Purchase ~~Stock~~Agreement, ~~dated~~the ~~December~~October 2023 9,Purchaser ~~2016,~~represented ~~or,~~that ~~(i)~~it is an accredited investor and ~~(ii)~~that ~~collectively,~~it is acquiring the ~~Bank~~securities ~~Warrants,~~for investment purposes only and ~~(iii)~~not ~~that~~with ~~certain~~a ~~Loan~~view ~~and~~to ~~Security~~any ~~Agreement~~resale, ~~dated~~distribution asor other disposition of ~~March~~such 8,securities ~~2016,~~in asviolation ~~amended,~~of orthe Securities Act.

May 2024 Private Placement

On May 24, 2024, we entered into a securities purchase agreement (the “May 2024 Purchase Agreement”) with certain accredited investors (the “May 2024 Investors”) and JGB Collateral LLC, as collateral agent, pursuant to which we issued to the May 2024 Investors in a private placement (the “May 2024 Private Placement”): (i) 37,500 shares of our common stock (as adjusted for the reverse stock split) (the “May 2024 Shares”), and (ii) Senior Secured Convertible Debentures in the aggregate principal amount of $20,000,000 (the “May 2024 Debentures”), for an aggregate purchase price of $18,000,000.

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Canaccord Genuity LLC (“Canaccord”) acted as the ~~Loan~~exclusive placement agent for the May 2024 Private Placement, which was conducted on a “reasonable best efforts” basis, pursuant to a placement agent agreement (the “Placement Agent Agreement”), dated May 24, 2024, by and between us and Canaccord. Pursuant to the ~~Amendment~~Placement Agent Agreement, we paid Canaccord a cash fee equal to 6.0% of the ~~exercise~~of ~~price~~the aggregate face value of the ~~Bank~~May 2024 ~~Warrants~~Debentures ~~was~~issued ~~decreased~~in ~~from~~the ~~$20~~May 2024 Private Placement.56 ~~per~~In ~~share~~addition, we agreed to ~~$6.99~~reimburse ~~per~~Canaccord ~~share.~~for ~~The~~any ~~foregoing~~out-of-pocket ~~description~~expenses isincurred ~~subject~~by Canaccord in connection with the May 2024 Private Placement not to exceed $75,000. ~~and~~The ~~qualified~~May in2024 ~~its~~Private ~~entirety~~Placement byclosed on May 24, 2024, and the ~~Amendment~~Company ~~Agreement~~received ~~filed~~net asproceeds anof ~~exhibit~~approximately ~~hereto~~$16.6 million ~~and~~after ~~incorporated~~payment ~~herein~~of byplacement ~~reference~~agent fees, and other offering expenses.

OnThe ~~November~~May ~~19,~~2024 ~~2018,~~Shares ~~we issued (i) to LifeSci Capital, LLC, a warrant to purchase 44,183 shares of our common stock,~~ and ~~(ii)~~the toMay 2024 ~~Russell~~Debentures ~~Creative~~were ~~Group,~~issued ain ~~warrant~~reliance toupon ~~purchase~~Rule 506 ~~3,311 shares~~ of ~~our~~Regulation D promulgated ~~common~~under ~~stock, or, together,~~ the ~~Service~~Securities ~~Provider Warrants~~Act, ~~each~~as ~~having~~a antransaction ~~exercise~~not ~~price~~requiring ofregistration ~~$8.25~~under ~~per~~the ~~share~~Securities ofAct ~~our~~and ~~common~~was ~~stock~~made ~~and~~without ageneral ~~term~~solicitation ofor ~~five years~~advertising. ~~The~~Pursuant ~~Service Provider Warrants were issued in full satisfaction of our obligations~~ to ~~pay~~the ~~(i)~~May 2024 toPurchase ~~LifeSci Capital~~Agreement, ~~LLC~~the anMay 2024 ~~aggregate~~Investors ofeach ~~$150,000~~represented ~~for~~that ~~capital~~it ~~advisory~~is ~~and~~an accredited investor ~~relations services~~ and ~~(ii)~~that toit ~~Russell~~is ~~Creative~~acquiring ~~Group~~the ansecurities ~~aggregate~~for ofinvestment ~~$15,000~~purposes ~~for~~only ~~branding~~ and ~~marketing~~not ~~services.~~with ~~LifeSci~~a ~~Capital,~~view ~~LLC~~to ~~and~~any ~~Russell~~resale, ~~Creative~~distribution ~~Group~~or ~~are~~other ~~accredited~~disposition ~~investors and the issuance~~ of ~~the~~such ~~Service~~securities ~~Provider Warrants was exempt from registration under the Securities Act~~ in ~~reliance~~violation ~~on an exemption provided by Section 4(a)(2)~~ of the Securities Act. ~~The description of the Service Provider Warrants is qualified in its entirety by the form of Warrant to Purchase Common Stock filed as an exhibit hereto and incorporated herein by reference.~~

OnDecember 2024 ~~August~~Settlement ~~23,~~Agreement 2018, in connection with the underwriting agreement related to our IPO, we issued (i) to Roth Capital Partners, a warrant to purchase 68,040 shares of our common stock, (ii) to Maxim Partners LLC, a warrant to purchase 22,680 shares of our common stock and ~~(ii)~~Amendment to ~~LifeSci~~Securities Capital LLC, a warrant to purchase 10,080 shares of our common stock, or, together, the Underwriter Warrants, each having an exercise price of $9.1875 per share of our common stock and a term of five years. On August 30, 2018, pursuant to the exercise of the underwriters’ over-allotment option, we issued (i) to Roth Capital Partners, a warrant to purchase 10,206 shares of our common stock, (ii) to Maxim Partners LLC, a warrant to purchase 3,402 shares of our common stock and (ii) to LifeSci Capital LLC, a warrant to purchase 1,512 shares of our common stock, or, together, the Over-Allotment Warrants, each having an exercise price of $9.1875 per share of our common stock and a term of five years. The description of the Underwriter Warrants and the Over-Allotment Warrants is qualified in its entirety by the form of Warrant to Purchase ~~Common~~Agreement ~~Stock issued to the underwriters, filed as an exhibit hereto and incorporated herein by reference.~~

~~The~~On ~~offers~~December 31, ~~sales~~2024, ~~and~~we ~~issuances~~entered ofinto ~~the~~a ~~securities~~settlement ~~described~~agreement inand ~~this~~amendment ~~section~~ (athe “Amendment”) ofrelating ~~Item~~to 15our ~~were~~outstanding ~~deemed~~May 2024 toDebentures. bePursuant ~~exempt~~to ~~from~~the ~~registration~~Amendment, ~~under~~ the ~~Securities~~conversion ~~Act~~price into ~~reliance~~convert onoutstanding ~~Section~~principal ~~4(a)(2)~~amounts of the ~~Securities~~May 2024 ~~Act~~Debentures ~~and~~to ~~Rule~~shares ~~506~~of ~~promulgated~~our ~~under~~common ~~Regulation~~stock Dwas ~~promulgated~~adjusted. ~~thereunder~~As asa ~~transactions~~result byof anthis ~~issuer~~conversion ~~not~~price ~~involving~~adjustment, athe ~~public~~$15,000,000 ~~offering.~~outstanding ~~The~~aggregate ~~recipients~~principal amount of ~~securities~~the inMay 2024 ~~each~~Debentures ofwould ~~these~~be ~~transactions~~convertible ~~acquired~~into ~~the~~925,925 ~~securities~~shares ~~for~~of ~~investment~~common ~~only~~stock ~~and~~(as ~~not~~adjusted ~~with~~for athe ~~view~~reverse tostock orsplit), ~~for~~of ~~sale~~which in759,259 ~~connection~~shares ~~with~~(as ~~any~~adjusted ~~distribution~~for ~~thereof~~the ~~and~~reverse ~~appropriate~~stock ~~legends~~split) were ~~affixed~~not topreviously registered under the ~~securities~~Securities ~~issued~~Act in(the ~~these~~“Unregistered ~~transactions~~Conversion Shares”). ~~Each~~As ofconsideration for the ~~recipients~~Amendment, ofwe ~~securities~~issued inthe ~~these~~May 2024 ~~transactions~~Investors ~~was~~83,333 anshares ~~accredited~~of ~~investor~~our ~~within~~common ~~the~~stock ~~meaning~~(as ofadjusted ~~Rule~~for ~~501~~the ofreverse ~~Regulation~~stock Dsplit) ~~under~~ (the ~~Securities~~“New ~~Act~~Shares” and, ~~had~~together ~~adequate~~with ~~access,~~the ~~through~~Unregistered ~~employment~~Conversion Shares, ~~business~~the or“Shares”) ~~other~~and ~~relationships,~~ to ~~information~~forbear ~~about~~from issuing a redemption notice under the ~~Company.~~May 2024 NoDebentures ~~underwriters~~to ~~were~~the ~~involved~~May 2024 inInvestors ~~these~~prior ~~transactions~~to July 31, 2025.

The Shares were issued in a transaction not involving public offering under Section 4(ba)(2) ~~Stock~~of ~~Option~~the Securities Act as a transaction not requiring registration under the Securities Act and ~~Restricted~~was ~~Stock~~made ~~Grants~~without general solicitation or advertising. Pursuant to the Amendment, the May 2024 Investors each represented that it is an accredited investor and that it is acquiring the Shares for investment purposes only and not with a view to any resale, distribution or other disposition of such Shares in violation of the Securities Act.

~~From~~July 2024 ~~January~~Private 1,Placement 2017 to August 21, 2018, we granted stock options under our Amended and Restated 2006 Equity Compensation Plan to purchase an aggregate of 462,363 shares of our common stock, with exercise prices ranging from $1.30 to $6.00 per share to certain directors, officers, employees and consultants.

~~The~~On July 4, 2024, we entered into a securities ~~described~~purchase agreement (the “July 2024 Purchase Agreement”) with certain institutional investors (the “Purchasers”), pursuant to which we issued to the Purchasers: (i) in ~~this~~a ~~section~~registered direct offering priced at-the-market consistent with the rules of the Nasdaq Stock Market, (ba) an aggregate of ~~Item~~195,000 15shares ~~were~~of ~~deemed~~our common stock (as adjusted for the reverse stock split) and (b) pre-funded warrants to bepurchase ~~exempt~~up ~~from~~to ~~registration~~an ~~under~~aggregate of 96,885 shares of our common stock (as adjusted for the ~~Securities~~reverse ~~Act~~stock split); and (ii) in ~~reliance~~a onconcurrent ~~Rule~~private ~~701~~placement, inSeries A ~~that~~warrants to purchase up to an aggregate of 291,885 shares of our common stock (as adjusted for the ~~transactions~~reverse ~~were~~stock ~~under~~split) ~~compensatory~~(the ~~benefit~~“Series A ~~plans~~Warrants”) and ~~contracts~~Series B ~~relating~~warrants to ~~compensation~~purchase asup ~~provided~~to ~~under~~an ~~Rule~~aggregate ~~701.~~of ~~The~~291,885 ~~recipients~~shares of ~~such~~our ~~securities~~common ~~were~~stock ~~the~~(as ~~Registrant’s~~adjusted ~~employees,~~for ~~directors~~the orreverse ~~bona~~stock ~~fide~~split) ~~consultants~~(the “Series B Warrants”, and ~~received~~together with the ~~securities~~Series A ~~under~~Warrants, the ~~Company’s~~“July 2024 ~~2006~~Purchase ~~Equity~~Warrants”). ~~Incentive~~Each ~~Plan~~share ~~and~~of ~~2018~~common ~~Equity~~stock ~~Incentive~~and ~~Plan.~~each ~~Appropriate~~pre-funded ~~legends~~warrant ~~were~~sold ~~affixed~~pursuant to the ~~securities~~July 2024 ~~issued~~Purchase inAgreement ~~these~~was ~~transactions~~accompanied by one Series A Warrant and one Series B Warrant. ~~Each~~The combined purchase price of ~~the~~each ~~recipients~~share of ~~securities~~common instock ~~these~~and ~~transactions~~accompanying ~~had~~July 2024 ~~adequate~~Purchase ~~access,~~Warrants ~~through~~was ~~employment,~~$34.260 ~~business~~per orshare ~~other~~(as ~~relationships,~~adjusted tofor ~~information~~the ~~about~~reverse stock split). The combined purchase price of each pre-funded warrant and accompanying July 2024 Purchase Warrants was $34.259 (as adjusted for the ~~Company~~reverse stock split).

H.C. Wainwright & Co., LLC (“Wainwright”) acted as the exclusive placement agent for the Company on a “reasonable best efforts” basis in connection with the transactions pursuant to an engagement letter (the “Engagement Letter”), by and between us and Wainwright. Pursuant to the Engagement Letter, the Company paid Wainwright an aggregate cash fee equal to 6.0% of the gross proceeds received in the Offering and for certain expenses incurred by Wainwright in connection with the offering.

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~~Item~~We 16received gross proceeds of approximately $10.0 million ~~Exhibits~~(excluding up to $20.0 million of aggregate gross proceeds that may be received in the future upon the cash exercise of the July 2024 Purchase Warrants), before deducting placement agent fees and ~~Financial~~other ~~Statement~~offering ~~Schedules~~expenses payable by the Company. We received net proceeds of $9.3 million after deducting placement agent fees and other offering expenses of $0.7 million payable by us.

The July 2024 Purchase Warrants were issued in reliance upon an exemption from the registration requirements under the Securities Act afforded by Section 4(a)(2) ~~Exhibits~~thereof and/or Rule 506(b) of Regulation D promulgated thereunder.

Exhibit Number	Description
1.1†	Form of Underwriting Agreement.
3.1(1)	Amended and Restated Certificate of Incorporation.
3.2(1)	Amended and Restated Bylaws.
4.1(2)	Form of Common Stock Certificate.
4.2(2)	Form of Warrant to Purchase Series B-1 Preferred Stock issued to Square 1 Bank.
4.3(2)	Form of Warrant to Purchase Series D Preferred Stock issued to Western Alliance Bank.
4.4(2)	Warrant to Purchase Series D-1 Preferred Stock issued to Western Alliance Bank.
4.5(2)	Form of Warrant to Purchase Series D-1 Preferred Stock issued to Midcap Financial Trust.
4.6(2)	Form of Warrant to Purchase Common Stock Issued to Underwriters in Initial Public Offering.
4.7(2)	Form of Warrant Certificate (included in Exhibit 4.8).
4.8(2)	Form of Warrant Agent Agreement by and between the Registrant and American Stock Transfer & Trust Company LLC, as warrant agent.
4.9(3)	Form of Warrant to Purchase Common Stock for Service Providers.
4.10(4)	Form of Warrant to Purchase Common Stock for Innovatus.
4.11(4)	Registration Rights Agreement, dated March 14, 2019, between the Company and Aspire Capital Fund, LLC.
4.12(4)	Registration Rights Agreement, as amended, dated March 14, 2019, by and among the Company and the Innovatus Investors.
4.13(5)	Form of Warrant to Purchase Common Stock issued to Investors in October 2019 Public Offering.
4.14(5)	Form of Pre-Funded Warrant issued to Investors in October 2019 Public Offering.
4.15(6)	Form of Inducement Warrant.
4.16†	Form of Warrant to Purchase Common Stock.
4.17†	Form of Pre-Funded Warrant.
5.1†	Opinion of Cooley LLP.
10.1(2)	Fifth Amended and Restated Investors’ Rights Agreement, dated August 5, 2016 as amended.
10.2+(2)	Bionano Genomics, Inc. Amended and Restated 2006 Equity Compensation Plan (the “2006 Plan”).
10.3+(2)	Forms of grant notice, stock option agreement and notice of exercise under the 2006 Plan.
10.4+(7)	Bionano Genomics, Inc. 2018 Equity Incentive Plan (the “2018 Plan”).
10.5+(2)	Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan.
10.6+(7)	Bionano Genomics, Inc. 2018 Employee Stock Purchase Plan.
10.7+(2)	Form of Indemnification Agreement by and between the Registrant and each director and executive officer.
10.8+(2)	Bionano Genomics, Inc. Non-Employee Director Compensation Policy.
10.9(2)	Credit and Security Agreement by and between the Registrant, Midcap Financial Trust and the Lenders listed on the Schedule of Lenders attached thereto, dated June 29, 2018.
10.10+(2)	Employment Agreement by and between the Registrant and R. Erik Holmlin, Ph.D., dated November 7, 2017, as amended.
10.11+(2)	Employment Agreement by and between the Registrant and Han Cao, Ph.D., dated November 7, 2017, as amended.
10.12+(2)	Employment Agreement by and between the Registrant and Mike Ward, dated July 1, 2016.
10.13+(2)	Employment Agreement by and between the Registrant and Warren Robinson, dated November 7, 2017.
10.14+(2)	Employment Agreement by and between the Registrant and Mark Borodkin, dated November 7, 2017.
10.15(2)	Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated March 8, 2016.
10.16(2)	First Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated December 9, 2016.
10.17(2)	Second Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated May 2, 2017.

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Exhibit Number	Description
10.18(2)	Third Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated November 20, 2017.
10.19(2)	Forbearance and Fourth Amendment to the Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated February 9, 2018.
10.20(2)	Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012.
10.21(2)	First Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated September 10, 2013.
10.22(2)	Second Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated July 1, 2015.
10.23#(2)	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.
10.24#(2)	Manufacturing Services Agreement by and between the Registrant and Paramit Corporation, dated February 18, 2015.
10.25#(2)	License Agreement by and between Princeton University and the Registrant, dated January 7, 2004.
10.26#(2)	First Amendment to the License Agreement by and between Princeton University and the Registrant, dated December 17, 2004.
10.27#(2)	Second Amendment to the License Agreement by and between Princeton University and the Registrant, dated February 25, 2010.
10.28#(2)	Third Amendment to the License Agreement by and between Princeton University and the Registrant, dated October 17, 2011.
10.29#(2)	Fourth Amendment License Agreement by and between Princeton University and the Registrant, dated February 9, 2012.
10.30#(2)	Sublicense Agreement by and between the Registrant and Industry 3200 dated December 27, 2013.
10.31#(2)	License Agreement by and between the Registrant and Q Biotechnology CV dated May 1, 2014.
10.32#(2)	Amendment to Non-Exclusive Patent License Agreement by and between the Registrant and QBiotechnology CV dated May 1, 2014.
10.33#(2)	License Agreement by and between the Registrant and New York University dated November 4, 2013.
10.34#(2)	Option and Sublicense Agreement by and between the Registrant and Pacific Biosciences of California, Inc. dated February 2, 2016.
10.35(2)	Note Purchase Agreement by and among the Registrant and the Investors listed on Exhibit A thereto, dated February 9, 2018.
10.36(2)	First Amendment to Note Purchase Agreement by and among the Registrant and the Investors listed on the Schedule of Investors attached thereto, dated April 2, 2018.
10.37(2)	Fifth Amendment to Loan and Security Agreement by and between the Registrant and Western Alliance Bank, dated June 13, 2018.
10.38#(2)	Amendment to Patent Sublicense Agreement by and between the Registrant and Industry 3200, dated June 28, 2018.
10.39(2)	Second Amendment to Note Purchase Agreement by and between the Registrant and the Investors listed on the Schedule of Investors attached thereto, dated June 29, 2018.
10.40(2)	Omnibus Amendment to Convertible Promissory Notes by and among the Registrant and the Holders identified in the signature pages thereto, dated June 29, 2018.
10.41(2)	Omnibus Amendment to Convertible Promissory Notes by and among the Registrant and the Holders identified in the signature pages thereto, dated August 14, 2018.
10.42(2)	Omnibus Amendment to Warrants to Purchase Series B-1 Preferred Stock by and among the Registrant and the Holders identified in the signature pages thereto, dated August 14, 2018.
10.43(2)	Omnibus Amendment to Warrants to Purchase Series D Preferred Stock by and among the Registrant and the Holders identified in the signature pages thereto, dated August 14, 2018.
10.44(3)	Amendment Agreement, by and between the Registrant and Western Alliance Bank, dated November 19, 2018.
10.45(4)	Common Stock Purchase Agreement, dated March 14, 2019, between the Registrant and Aspire Capital Fund, LLC.

Item 16.

Exhibits.


Exhibit No.			Description
3.1			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).
3.2			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).
3.3			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).
3.4			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).
4.1			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).
4.2			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).
4.3			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).
4.4			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).
4.5			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).
4.6			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).
4.7			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).
4.8			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).
4.9^€			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).
4.10			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).
4.11			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).
4.12			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).
4.13			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).

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Exhibit Number	Description
Exhibit No.		Description
10.46(4)	Loan and Security Agreement, dated March 14, 2019, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and the Lenders listed on Schedule 1.1 thereto.
4.14		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).
10.47(8)	Waiver and First Amendment to Loan and Security Agreement, dated June 25, 2019, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and East West Bank.
4.15		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).
10.48(4)	Common Stock Purchase Agreement, dated March 14, 2019, by and among the Company and the Innovatus Investors.
4.16		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).
10.49(9)	Second Amendment to Loan and Security Agreement, dated March 6, 2020, by and among the Company, Innovatus Life Sciences Lending Fund I, LP and East West Bank.
4.17		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).
21.1(2)	Subsidiaries of the Registrant.
4.18		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).
23.1	Consent of Deloitte & Touche LLP, independent registered public accounting firm.
4.19*		Form of Pre-Funded Warrant issued in this Offering.
23.2†	Consent of Cooley LLP (included in Exhibit 5.1).
4.20*		Form of Series E/F Warrant issued in this Offering.
24.1	Power of Attorney (included on signature page).
5.1*		Opinion of Troutman Pepper Locke LLP.
10.1^€		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).
10.2^€		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).
10.3^€		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).
10.4^€		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).
10.5+		Bionano Genomics, Inc. 2018 Equity Incentive Plan, as amended (the “2018 Plan”) (incorporated by reference to Exhibit 99.1 of the Registrant’s Registration Statement on Form S-8 (File No. 333-245764), filed with the SEC on August 13, 2020).
10.5A+		Forms of grant notice, stock option agreement and notice of exercise under the 2018 Plan (incorporated by reference to Exhibit 10.2A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023).
10.5B+		Forms of director grant notice, stock option agreement and notice of exercise under the 2018 Plan (incorporated by reference to Exhibit 10.2B of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023).
10.5C+		Forms of double-trigger grant notice, stock option agreement and notice of exercise under the 2018 Plan (incorporated by reference to Exhibit 10.2C of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023).
10.5D+		Forms of international grant notice, stock option agreement and notice of exercise under the 2018 Plan (incorporated by reference to Exhibit 10.5 of the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended, filed with the SEC on August 17, 2018).
10.5E+		Forms of restricted stock unit grant notice and restricted stock unit award agreement under the Bionano Genomics, Inc. 2018 Equity Incentive Plan (incorporated by reference to Exhibit 10.1 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on August 4, 2021).
10.5F+		Bionano Genomics, Inc. 2018 Employee Stock Purchase Plan (incorporated by reference to Exhibit 99.5 of the Registrant’s Registration Statement on Form S-8 (File No. 333-227073), filed with the SEC on August 28, 2018).

+ Indicates management contract or compensatory plan.

# Confidential treatment has been requested with respect to certain portions of this exhibit. Omitted portions have been filed separately with the SEC.

† To be filed by amendment.

(1) Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2018.

(2) Incorporated by reference to the Registrant’s Registration Statement on Form S-1 (File No. 333-225970), as amended.

(3) Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on November 21, 2018.

(4) Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on March 14, 2019.

(5) Incorporated by reference to the Registrant’s Registration Statement on Form S-1 (File No. 333-233828), as amended.

(6) Incorporated by reference to the Registrant’s Current Report on Form 8-K, filed with the SEC on March 2, 2020.

(7) Incorporated by reference to the Registrant’s Registration Statement on Form S-8 (File No. 333-227073).

(8) Incorporated by reference to the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on August 8, 2019.

(9) Incorporated by reference to the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 10, 2020.

(b) Financial Statement Schedules

No financial statement schedules are provided because the information called for is not required or is shown either in the financial statements or related notes, which are incorporated herein by reference.

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Item 17. Undertakings


Exhibit No.			Description
10.5G+			Bionano Genomics, Inc. 2020 Inducement Plan, as amended (incorporated by reference to Exhibit 99.3 of the Registrant’s Registration Statement on Form S-8 (File No. 333-286325), filed with the SEC on March 31, 2025).
10.5H+			Form of Stock Option Grant Notice and Stock Option Agreement under the Bionano Genomics, Inc. 2020 Inducement Plan (incorporated by reference to Exhibit 10.2 of the Registrant’s Current Report on Form 8-K, filed with the SEC on August 24, 2020).
10.5I+			Bionano Genomics, Inc. Non-Employee Director Compensation Policy, as amended (incorporated by reference to Exhibit 10.7 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022).
10.6+			Form of Indemnification Agreement by and between the Registrant and each director and executive officer (incorporated by reference to Exhibit 10.7 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 10, 2020).
10.7+			Employment Agreement by and between the Registrant and R. Erik Holmlin, Ph.D., dated November 7, 2017, as amended (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.8+			Employment Agreement, effective as of August 31, 2020, by and between Alka Chaubey and the Company (incorporated by reference to Exhibit 10.7 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on November 13, 2020).
10.9+			Employment Agreement by and between the Registrant and Mark Oldakowski, dated November 7, 2017 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.10			Lease by and between the Registrant and The Irvine Company LLC, dated January 16, 2012 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.10A			First Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated September 10, 2013 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.10B			Second Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated July 1, 2015 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.10C			Third Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated December 19, 2019 (incorporated by reference to Exhibit 10.22 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021).
10.10D			Fourth Amendment to the Lease by and between the Registrant and The Irvine Company LLC, dated February 15, 2021 (incorporated by reference to Exhibit 10.23 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 23, 2021).
10.10E			Fifth Amendment to the Lease by and between the Registrant and The Irvine Company, LLC, dated January 12, 2022. (incorporated by reference to Exhibit 10.39 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022).
10.10F			Sixth Amendment to the Lease by and between the Registrant and Irvine Eastgate Office I LLC, dated June 27, 2025 (incorporated by reference to Exhibit 10.1 of the Registrant’s Quarterly Report on Form 10-Q, filed with the SEC on August 14, 2025).
10.11			Standard Industrial/Commercial Single-Tenant Lease, made effective as of November 23, 2021, by and between the Company and 6777 Nancy Ridge LLC (incorporated by reference to Exhibit 10.33 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022).
10.12			Commercial Single-Tenant Lease - Net, dated February 28, 2016, by and between Tesa Beach LLC and BioDiscovery, Inc. (incorporated by reference to Exhibit 10.38 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 1, 2022).
10.13			Lease, dated August 22, 2016, by and between SFF BBC, LLC and Purigen Biosystems, Inc. (incorporated by reference to Exhibit 10.14 of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023).

The undersigned registrant hereby undertakes to provide to the underwriters at the closing specified in the underwriting agreement certificates in such denominations and registered in such names as required by the underwriters to permit prompt delivery to each purchaser.II-8

~~Insofar~~TABLE asOF indemnification for liabilities arising under the Securities Act may be permitted to directors, officers and controlling persons of the registrant pursuant to the foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the Securities Act, and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question of whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.CONTENTS

The undersigned registrant hereby undertakes:


Exhibit No.			Description
10.13A			First Amendment to the Lease by and between Purigen Biosystems Inc, and SFF BBC, LLC, dated August 22, 2016 (incorporated by reference to Exhibit 10.14A of the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 9, 2023).
10.14			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).
10.15#			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 (incorporated by reference to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.16#			Manufacturing Services Agreement by and between the Registrant and Paramit Corporation, dated February 18, 2015 (incorporated by reference to Exhibit 10.24 to the Company’s Registration Statement on Form S-1 (File No. 333-225970), as amended).
10.17^			Securities Purchase Agreement, dated October 11, 2023, by and among the Company and the Purchaser named therein (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K, filed with the SEC on October 11, 2023).
10.18^			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).
10.19			Separation Agreement, effective as of February 20, 2025, by and between Gülsen Kama and the Company (incorporated by reference to Exhibit 10.19 to the Registrant’s Annual Report on Form 10-K, filed with the SEC on March 31, 2025).
10.20^#			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).
10.21^#			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).
10.22			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).
10.23			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).
10.24*			Form of Securities Purchase Agreement to be entered into in this Offering.
21.1			Subsidiaries of the Registrant (incorporated by reference to Exhibit 21.1 of the Company’s Annual Report on Form 10-K filed with the Commission on March 31, 2025).
23.1*			Consent of BDO USA, P.C., independent registered public accounting firm.
23.2*			Consent of Troutman Pepper Locke LLP (included as part of Exhibit 5.1).
24.1*			Power of Attorney (included in the signature page to this registration statement).
107*			Filing Fee Table.

*	Filed herewith.

^	Certain exhibits and schedules have been omitted pursuant to Item 601(a)(5) of Regulation S-K. The Registrant hereby undertakes to furnish supplementally a copy of any omitted exhibit or schedule upon request by the SEC.

+	Indicates a management contract or compensatory plan, contract or arrangement.

#	Portions of this exhibit have been omitted pursuant to Item 601(b)(2)(ii) of Regulation S-K. The Company agrees to furnish supplementally an unredacted copy of the Exhibits to the SEC upon its request.

€

Pursuant to Item 601(b)(10) of Regulation S-K, certain portions of this exhibit have been omitted (indicated by “[***]”) because the Company has determined that the information is not material and is the type that the Company treats as private or confidential. The Registrant hereby agrees to furnish supplementally to the SEC, upon its request, an unredacted copy of this exhibit.

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Item 17.

Undertakings.

(a)	The undersigned registrant hereby undertakes:

(1)	To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i) toTo include any prospectus required by Section 10(a)(3) of the Securities Act ~~of 1933~~;

(ii) toTo reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of prospectus filed with the ~~Commission~~SEC pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20% percent change in the maximum aggregate offering price set forth in the “Calculation of Filing Fee Tables” or “Calculation of Registration Fee” table, as applicable, in the effective registration statement; and

(iii) toTo include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement.;

~~(2)~~provided, ~~That~~however, ~~for~~that the ~~purpose~~undertakings ofset ~~determining~~forth ~~any~~in ~~liability~~paragraphs ~~under~~(a)(1)(i), (a)(1)(ii) and (a)(1)(iii) above do not apply if the ~~Securities~~information ~~Act~~required ofto ~~1933,~~be ~~each~~included ~~such~~in a post-effective amendment ~~shall~~by bethose ~~deemed~~paragraphs tois becontained ain ~~new~~reports ~~registration~~filed ~~statement~~with ~~relating~~or furnished to the ~~securities~~SEC ~~offered~~by ~~therein,~~the ~~and~~registrant ~~the~~pursuant ~~offering~~to section 13 or section 15(d) of ~~such~~the ~~securities~~Securities atExchange Act of 1934 that ~~time~~are ~~shall~~incorporated beby ~~deemed~~reference in this registration statement or are contained in a form of prospectus filed pursuant to beRule 424(b) ~~the~~that ~~initial~~is ~~bona~~part ~~fide~~of ~~offering~~this ~~thereof~~registration statement.

(2)

That, for the purpose of determining any liability under the Securities Act, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(3)	To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(4) That, for the purpose of determining liability under the Securities Act of 1933 to any purchaser, ineach ~~the~~prospectus ~~initial~~filed ~~distribution~~pursuant to Rule 424(b) as part of ~~the~~a ~~securities~~registration statement relating to an offering, ~~the~~other ~~undersigned~~than ~~registrant~~registration ~~undertakes~~statements ~~that~~relying on Rule 430B or other than prospectuses filed in areliance ~~primary~~on ~~offering~~Rule 430A, shall be deemed to be part of ~~securities~~and included in the registration statement as of the ~~undersigned~~date ~~registrant~~it ~~pursuant~~is tofirst ~~this~~used after effectiveness. Provided, however, that no statement made in a registration statement, ~~regardless~~or prospectus that is part of the ~~underwriting~~registration ~~method~~statement ~~used~~or tomade ~~sell~~in ~~the~~a ~~securities~~document toincorporated ~~the~~or ~~purchaser,~~deemed ifincorporated ~~the~~by ~~securities~~reference ~~are~~into ~~offered~~the registration statement or ~~sold~~prospectus that is part of the registration statement will, as to ~~such~~a purchaser bywith ~~means~~a time of ~~any~~contract of ~~the~~sale ~~following~~prior ~~communications~~to such first use, ~~the~~supersede ~~undersigned~~or ~~registrant~~modify ~~will~~any bestatement athat ~~seller~~was tomade in the ~~purchaser~~registration ~~and~~statement ~~will~~or beprospectus ~~considered~~that towas ~~offer~~part of the registration statement or ~~sell~~made in any such ~~securities~~document immediately prior to such ~~purchaser:~~date of first use.

(i5) ~~Any~~That, ~~preliminary~~for ~~prospectus~~the orpurpose ~~prospectus~~of determining liability of the registrant under the Securities Act to any purchaser in the initial distribution of the securities, the undersigned registrant ~~relating~~undertakes that in a primary offering of securities of the undersigned registrant pursuant to this registration statement, regardless of the ~~offering~~underwriting ~~required~~method used to besell ~~filed~~the ~~pursuant~~securities to ~~Rule~~the ~~424~~purchaser, ~~(§230.424~~if the securities are offered or sold to such purchaser by means of ~~this~~any ~~chapter);~~of the following communications, the undersigned registrant will be a seller to the purchaser and will be considered to offer or sell such securities to such purchaser:

(i)	Any preliminary prospectus or prospectus of the undersigned registrant relating to the offering required to be filed pursuant to Rule 424;

(ii)	Any free writing prospectus relating to the offering prepared by or on behalf of the undersigned registrant or used or referred to by the undersigned registrant;

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(iii)

The portion of any other free writing prospectus relating to the offering containing material information about the undersigned registrant or its securities provided by or on behalf of the undersigned registrant; and

(iv)	Any other communication that is an offer in the offering made by the undersigned registrant to the purchaser.

~~II-8~~(b) The undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act, each filing of the registrant's annual report pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan's annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(c)

Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the registrant pursuant to the foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the registrant of expenses incurred or paid by a director, officer or controlling person of the registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.

(d)	The undersigned registrant hereby undertakes hat:

(1)

For purposes of determining any liability under the Securities Act of 1933, the information omitted from the form of prospectus filed as part of this registration statement in reliance upon Rule 430A and contained in a form of prospectus filed by the registrant pursuant to Rule 424(b)(1) or (4) or 497(h) under the Securities Act shall be deemed to be part of this registration statement as of the time it was declared effective.

(2)

For the purpose of determining any liability under the Securities Act of 1933, each post-effective amendment that contains a form of prospectus shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

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(5) The undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act, each filing of the registrant’s annual report pursuant to section 13(a) or section 15(d) of the Securities Exchange Act of 1934, as amended, or the Exchange Act, (and, where applicable, each filing of an employee benefit plan’s annual report pursuant to section 15(d) of the Exchange Act) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(6) For purposes of determining any liability under the Securities Act, the information omitted from the form of prospectus filed as part of this Registration Statement in reliance upon Rule 430A and contained in a form of prospectus filed by the Registrant pursuant to Rule 424(b)(1) or (4) or 497(h) under the Securities Act shall be deemed to be part of this Registration Statement as of the time it was declared effective.

(7) For the purpose of determining any liability under the Securities Act, each post-effective amendment that contains a form of prospectus shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the ~~Registrant~~registrant has duly caused this ~~Registration~~registration ~~Statement~~statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of San Diego, State of California, on ~~March~~ September 11, ~~2020~~2025.

~~Bionano~~BIONANO ~~Genomics~~GENOMICS, ~~Inc~~INC. By: /s/ R. Erik Holmlin, Ph.D. R. Erik Holmlin, Ph.D. President and Chief Executive Officer (Principal Executive Officer and Principal Financial Officer)

POWER OF ATTORNEY

~~KNOW~~We, ~~ALL~~the ~~PERSONS~~undersigned BYofficers ~~THESE~~and ~~PRESENTS,~~directors ~~that~~of ~~each~~Bionano ~~person~~Genomics ~~whose~~Inc., ~~signature~~hereby ~~appears~~severally ~~below~~constitute ~~constitutes~~ and ~~appoints~~appoint R. Erik Holmlin, Ph.D. ~~his~~and orMark ~~her~~Adamchak, ~~true~~ and ~~lawful~~each ~~attorney-in-fact~~of ~~and~~them ~~agent,~~singly (with full power ofto ~~substitution~~each ~~and~~of ~~resubstitution,~~them ~~for him or her and in his or her name, place, and stead, in any and all capacities,~~ to ~~(i)~~ act onalone), to sign ~~and file with the Securities and Exchange Commission~~ any and all amendments (including post-effective amendments) to this registration statement ~~together~~(or ~~with~~any ~~all~~other ~~schedules~~registration ~~and~~statement ~~exhibits~~for ~~thereto~~the ~~and~~same ~~any~~offering ~~subsequent~~that ~~registration~~is ~~statement~~to ~~filed~~be effective upon filing pursuant to Rule 462(b) under the Securities Act of 1933), asand ~~amended,~~to ~~together~~file the same, with all ~~schedules and~~ exhibits thereto, ~~(ii) act on, sign~~ and ~~file such certificates, instruments, agreements and~~ other documents ~~as may be necessary or appropriate~~ in connection therewith, ~~(iii)~~with ~~act~~the onSecurities and ~~file~~Exchange ~~any~~Commission, ~~supplement~~granting tounto ~~any~~said ~~prospectus included~~ attorneys-in-fact ~~this~~and ~~registration~~agents, ~~statement~~and oreach ~~any~~of ~~such~~them, ~~amendment~~full orpower ~~any~~and ~~subsequent~~authority ~~registration statement filed pursuant~~ to ~~Rule~~do ~~462(b)~~and ~~under~~perform ~~the~~each ~~Securities Act of 1933, as amended,~~ and ~~(iv)~~every ~~take~~act ~~any~~ and ~~all~~thing ~~actions~~requisite ~~which~~or ~~may~~necessary to be ~~necessary~~done orin ~~appropriate~~and toabout bethe ~~done~~premises, as ~~fully~~full ~~for~~to all intents and purposes as he ~~or she~~ might or could do in person, hereby ratifying and confirming all that said ~~attorney~~attorneys-in-fact and ~~agent~~agents or any of them, or ~~his~~their or ~~her~~his substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this ~~Registration~~registration ~~Statement~~statement has been signed by the following persons inon ~~the~~September 11, ~~capacities~~2025 ~~indicated~~in on the ~~dates~~capacities indicated.

Signature	~~Title~~	~~Date~~	Title	Date
/s/ R. Erik Holmlin, Ph.D.	~~Chief Executive Officer and Director~~	~~March 11, 2020~~	President, Chief Executive Officer and Director(Principal Executive Officer andPrincipal Financial Officer)	September 11, 2025
R. Erik Holmlin, Ph.D.	~~(Principal Executive and Financial Officer)~~
/s/ Mark Adamchak	~~Controller~~	~~March 11, 2020~~	VP, Accounting(Principal Accounting Officer)	September 11, 2025
Mark Adamchak	~~(Principal Accounting Officer)~~
/s/ David L. Barker, Ph.D.	~~Director~~	~~March 11, 2020~~	Director	September 11, 2025
David L. Barker, Ph.D.
/s/ Albert A. Luderer, Ph.D.	Director	March 11, 2020
/s/ Yvonne Linney, Ph.D.			Director	September 11, 2025
Albert A. Luderer, Ph.D.
Yvonne Linney, Ph.D.
/s/ Junfeng Wang	Director	March 11, 2020
/s/ Albert A. Luderer, Ph.D.			Director	September 11, 2025
Junfeng Wang
Albert A. Luderer, Ph.D.
/s/ Christopher Twomey	Director	March 11, 2020
/s/ Hannah Mamuszka			Director	September 11, 2025
Christopher Twomey
Hannah Mamuszka
/s/ Kristiina Vuori, M.D., Ph.D.	Director	March 11, 2020
/s/ Aleksandar Rajkovic, M.D., Ph.D.			Director	September 11, 2025
Kristiina Vuori, M.D., Ph.D.
Aleksandar Rajkovic, M.D., Ph.D.
/s/ Christopher Twomey			Director	September 11, 2025
Christopher Twomey
/s/ Kristiina Vuori, M.D., Ph.D.			Director	September 11, 2025
Kristiina Vuori, M.D., Ph.D.

II-12

(State or other jurisdiction of incorporation or organization)

(Primary Standard Industrial Classification Code Number)

(I.R.S. Employer
Identification No.)

Filing Compare · Bionano Genomics, Inc.