SecProbe.io

CORRESP
 1
 filename1.htm

 September 11, 2025

 VIA EDGAR

 U.S. Securities and Exchange Commission
 Division of Corporation Finance
 Washington, DC 20549

 Re:

 Bionano Genomics, Inc.
 Registration Statement on Form S-1 (File No. 333-290187) – Concurrence in Acceleration Request

 Ladies and Gentlemen:

 H.C. Wainwright & Co., LLC (“ Wainwright ”),
 solely acting as placement agent on a best efforts basis in an offering pursuant to the registration statement on Form S-1 (File No. 333-290187) (the “ Registration
 Statement ”), hereby concurs in the request by Bionano Genomics, Inc. that the effective date of the above-referenced registration statement be accelerated to 9:00 A.M (Eastern Time), or as soon as practicable thereafter, on September
 15, 2025, pursuant to Rule 461 under the Securities Act of 1933, as amended (the “ Securities Act ”). Wainwright affirms that it is aware of its obligations
 under the Securities Act as they pertain to the best efforts offering pursuant to the Registration Statement.

 Very truly yours,

 H.C. WAINWRIGHT & CO., LLC

 By:

 /s/ Edward. D. Silvera

 Name: Edward D. Silvera

 Title: Chief Operating Officer

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

 VIA EDGAR

 September 11, 2025

 Securities and Exchange Commission
 Division of Corporation Finance
 Office of Life Sciences
 100 F Street, N.E.
 Washington, D.C. 20549
 Attn: Conlon Danberg

 Re:

 Bionano Genomics, Inc.

 Registration Statement on Form S-1 (File No. 333-290187)

 Request for Acceleration of Effective Date

 Ladies and Gentlemen:

 Pursuant to Rule 461 under the Securities Act of 1933, as amended, Bionano Genomics, Inc. (the “ Company ”) hereby requests that the Securities and Exchange Commission (the “ Commission ”)
 accelerate the effective date of the above-referenced Registration Statement on Form S-1 (the “ Registration Statement ”) so that the Registration
 Statement will be declared effective as of 9:00 a.m. Eastern time, on September 15, 2025, or as soon as practicable thereafter. The Company hereby authorizes David S. Wolpa or Rakesh Gopalan, both of whom are attorneys at the Company’s outside legal
 counsel, Troutman Pepper Locke LLP, to orally modify or withdraw this request for acceleration.

 Once the Registration Statement has been declared effective, please orally confirm that event with Mr. Wolpa at (704) 916-2375 or Mr.
 Gopalan at (704) 916-2374.

 Thank you for your assistance in this matter.

 Very truly yours,

 Bionano Genomics, Inc.

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

 Name:

 R. Erik Holmlin, Ph.D.

 Title:

 President and Chief Executive Officer

 cc (via email):

 Jonathan Dixon, Bionano Genomics, Inc.
 David S. Wolpa, Troutman Pepper Locke LLP
 Rakesh Gopalan, Troutman Pepper Locke LLP

<DOCUMENT>
<TYPE>TEXT-EXTRACT
<SEQUENCE>2
<FILENAME>filename2.txt
<TEXT>
 August 1, 2025

R. Erik Holmlin, Ph.D.
President, Chief Executive Officer and Director
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121

 Re: Bionano Genomics, Inc.
 Draft Registration Statement on Form S-1
 Submitted July 30, 2025
 CIK No. 0001411690
Dear R. Erik Holmlin, Ph.D.:

 This is to advise you that we do not intend to review your registration
statement.

 We request that you publicly file your registration statement at least
two business
days prior to the requested effective date and time. Please refer to Rules 460
and 461
regarding requests for acceleration. We remind you that the company and its
management are
responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review,
comments, action or absence of action by the staff.

 Please contact Conlon Danberg at 202-551-4466 with any questions.

 Sincerely,

 Division of
Corporation Finance
 Office of
Industrial Applications and
 Services
cc: David S. Wolpa, Esq.
</TEXT>
</DOCUMENT>

CORRESP
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    BIONANO GENOMICS, INC.

    9540 Towne Centre Drive, Suite 100

    San Diego, CA 92121

    VIA EDGAR

    January 8, 2025

    U.S. Securities and Exchange Commission

    Division of Corporation Finance

    Office of Industrial Applications and Services

    100 F Street, N.E.

    Washington, D.C. 20549

    Attn: Abby Adams

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-3

            File No. 333-284124

            Acceleration Request

            Requested Date:

            January 10, 2025

            Requested Time:

            4:30 p.m. Eastern Time

    Ladies and Gentlemen:

    In accordance with Rule 461 under the Securities Act of 1933, as amended, Bionano Genomics, Inc. hereby requests that the Securities and Exchange Commission take appropriate action to cause the above-referenced Registration Statement on Form S-3
      (File No. 333-284124) (the “Registration Statement”) to become effective on January 10, 2025, at 4:30 p.m. Eastern Time, or as soon thereafter as is practicable.

    Once the Registration Statement has been declared effective, please orally confirm that event with Thomas Coll or Alexander Gefter of Cooley LLP, our outside counsel, at (858) 550-6013 or (310) 883-6438. Thank you for your assistance with this
      matter.

            Sincerely,

            BIONANO GENOMICS, INC.

            By:

              /s/ Jonathan Dixon

            Jonathan Dixon

            General Counsel and Secretary

January 8, 2025
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed January 3, 2025
File No. 333-284124
Dear R. Erik Holmlin Ph.D.:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration. We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Margaret Sawicki at 202-551-7153 with any questions.
Sincerely,
Division of Corporation Finance
Office of Industrial Applications and
Services
cc:Tom Coll, Esq.

CORRESP
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    BIONANO GENOMICS, INC.

    9540 Towne Centre Drive, Suite 100

    San Diego, CA 92121

    VIA EDGAR

    August 8, 2024

    U.S. Securities and Exchange Commission

    Division of Corporation Finance

    Office of Industrial Applications and Services

    100 F Street, N.E.

    Washington, D.C. 20549

    Attn: Abby Adams

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-3

            File No. 333-281138

            Acceleration Request

            Requested Date:

            August 12, 2024

            Requested Time:

            4:30 p.m. Eastern Time

    Ladies and Gentlemen:

    In accordance with Rule 461 under the Securities Act of 1933, as amended, Bionano Genomics, Inc. hereby requests that the Securities and Exchange Commission
      take appropriate action to cause the above-referenced Registration Statement on Form S-3 (File No. 333-281138) (the “Registration
        Statement”) to become effective on August 12, 2024, at 4:30 p.m. Eastern Time, or as soon thereafter as is practicable.

    Once the Registration Statement has been declared effective, please orally confirm that event with Thomas Coll or Alexander Gefter of Cooley LLP, our outside
      counsel, at (858) 550-6013 or (310) 883-6438. Thank you for your assistance with this matter.

            Sincerely,

            BIONANO GENOMICS, INC.

            By:

              /s/Jonathan Dixon

            Jonathan Dixon

            General Counsel and Secretary

August 7, 2024
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed July 31, 2024
File No. 333-281138
Dear R. Erik Holmlin Ph.D.:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration. We remind you that
the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Abby Adams at 202-551-6902 with any questions.
Sincerely,
Division of Corporation Finance
Office of Industrial Applications and
Services

CORRESP
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  Bionano Genomics, Inc.

    9540 Towne Centre Drive, Suite 100

  San Diego, California 92121

  June 17, 2024

  VIA EDGAR

  United States Securities and Exchange Commission

  Division of Corporation Finance

  Office of Industrial Applications and Services

  100 F Street, NE

  Washington, DC 20549

  Attention: Jane Park

  Re:        Bionano Genomics, Inc.

  Registration Statement on Form S-3

  Filed June 10, 2024

  File No. 333-280098

  Ladies and Gentlemen:

  Pursuant to Rule 461 of the Securities Act of 1933, as amended, Bionano Genomics, Inc. (the “Company”), hereby respectfully requests
    that the effective date for the Registration Statement referred to above be accelerated so that it will be declared effective at 4:30 P.M. (Eastern Time) on June 19, 2024, or as soon thereafter as possible on such date.

          Very truly yours,

        Bionano Genomics, Inc.

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

        Name:
        R. Erik Holmlin, Ph.D.

        Title:
        President and Chief Executive Officer

United States securities and exchange commission logo
June 14, 2024
R. Erik Holmlin, Ph.D.
Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed June 10, 2024
File No. 333-280098
Dear R. Erik Holmlin:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration. We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Jane Park at 202-551-7439 with any questions.
Sincerely,
Division of Corporation Finance
Office of Industrial Applications and
Services
cc:       Marc Rivera, Esq.

CORRESP
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    Bionano Genomics, Inc.

    9540 Towne Centre Drive, Suite 100

    San Diego, California 92121

    (858) 888-7600

    November 2, 2023

    Via Edgar

    United States Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

              Attn:

              Jessica Ansart

              Re:

              Bionano Genomics, Inc.

                Registration Statement on Form S-3

                File No. 333-275181

    Ladies and Gentlemen:

    Pursuant to Rule 461 under the Securities Act of 1933, as amended, the undersigned registrant hereby requests that the Securities and Exchange Commission
      take appropriate action to cause the above-referenced Registration Statement on Form S-3 to become effective at 4:30 p.m. Eastern Time on November 6, 2023, or as soon thereafter as is practicable.

    Once the above-referenced Registration Statement has been declared effective, please orally confirm that event with Su Lian Lu of Cooley LLP, counsel to
      the Registrant, at (310) 883-6555.

    Bionano Genomics, Inc.

            By:

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

            R. Erik Holmlin, Ph.D.

              President and Chief Executive Officer

            cc:

            Su Lian Lu, Cooley LLP

United States securities and exchange commission logo
November 2, 2023
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed October 26, 2023
File No. 333-275181
Dear R. Erik Holmlin:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration. We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Jessica Ansart at 202-551-4511 with any questions.
Sincerely,
Division of Corporation Finance
Office of Industrial Applications and
Services
cc:       Su Lian Lu

CORRESP
1
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    Bionano Genomics, Inc.

    9540 Towne Centre Drive, Suite 100

    San Diego, California 92121

    (858) 888-7600

    May 8, 2023

    Via Edgar

    United States Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

          Attn:

            Jane Park

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-3

            File No. 333-270459

    Ladies and Gentlemen:

    Pursuant to Rule 461 under the Securities Act of 1933, as amended, the undersigned registrant hereby requests that the Securities and Exchange Commission take appropriate action to cause the above-referenced
      Registration Statement on Form S-3 to become effective at 5:30 p.m. Eastern Time on May 10, 2023, or as soon thereafter as is practicable.

    Once the above-referenced Registration Statement has been declared effective, please orally confirm that event with Phillip S. McGill of Cooley LLP, counsel to the Registrant, at (858) 550-6193.

            Bionano Genomics, Inc.

          By:

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

            R. Erik Holmlin, Ph.D.

            President and Chief Executive Officer

          cc:

            Phillip S. McGill, Cooley LLP

United States securities and exchange commission logo
March 17, 2023
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed March 10, 2023
File No. 333-270459
Dear R. Erik Holmlin:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Jane Park at 202-551-7439 with any questions.
Sincerely,
Division of Corporation Finance
Office of Industrial Applications and
Services
cc:       Phillip McGill, Esq.

United States securities and exchange commission logo
July 29, 2022
Christopher Stewart
Chief Financial Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive
Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc.
Form 10-K for the Fiscal Year Ended December 31, 2021
Filed March 1, 2022
File No. 001-38613
Dear Mr. Stewart:
            We have completed our review of your filings.  We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence of action by the staff.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

CORRESP
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        Confidential Treatment Requested

          By Bionano Genomics, Inc.

                CERTAIN PORTIONS OF THIS LETTER HAVE BEEN OMITTED FROM THE VERSION FILED VIA EDGAR. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT TO THE
                  OMITTED PORTIONS. INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS LETTER WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[***]”.

        July 18, 2022

        United States Securities and Exchange Commission

        Division of Corporation Finance

        Office of Life Sciences

        100 F Street, N.E.

        Washington, D.C. 20549

              Attn:

                Gary Newberry

        Tara Harkins

              Re:

                Bionano Genomics, Inc.

        Form 10-K for the Fiscal Year Ended December 31, 2021

        Form 8-K filed on October 19, 2021

        File No. 001-38613

        Ladies and Gentlemen:

        We are in receipt of the comment letter, dated June 23, 2022, from the staff (the “Staff”) of the Securities
          and Exchange Commission (the “SEC”) regarding the above captioned filings on Form 10-K for the fiscal year ended December 31, 2021 (the “Form 10-K”) and Form 8-K, filed on October 19, 2021 (the “Form 8-K”). Below is the response of Bionano Genomics, Inc. (the “Company,” “we,” “our” or similar terminology) to the Staff’s comments.

        For the Staff’s convenience, we have incorporated the Staff’s comments into this response letter in italics. The Company acknowledges that it is responsible for the
          adequacy and accuracy of the disclosure in the Form 10-K and the Form 8-K.

        Confidential Treatment Request

        Due to the commercially sensitive nature of information contained in this letter, the Company hereby requests, pursuant to 17 C.F.R. § 200.83, that certain portions of
          this letter be maintained in confidence, not be made part of any public record and not be disclosed to any person. The Company has filed a separate copy of this letter, marked to show the portions redacted from the version filed via EDGAR and for
          which the Company is requesting confidential treatment.

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

              Confidential Treatment Requested

                By Bionano Genomics, Inc.

        Form 10-K for the Fiscal Year Ended December 31, 2021

        Item 9A. Controls and Procedures

        Evaluation of Disclosure Controls and Procedures, page 106

              1.

                Consistent with Item 307 of Regulation S-K, please amend your filing to disclose the conclusions of your principal executive and principal financial officers regarding the effectiveness of your disclosure controls and procedures as of the end of the period covered by the report – i.e., December 31, 2021.

        Response:  The Company respectfully acknowledges the Staff’s comment and confirms that it inadvertently included a typographical
          error referencing effectiveness of its internal control over financial reporting (“ICFR”) rather than effectiveness of its disclosure controls and procedures in the second paragraph
          under the heading “Evaluation of Disclosure Controls and Procedures” in Item 9A of the Form 10‑K. The Company acknowledges that the disclosures regarding disclosure controls and procedures required by Item 307 of Regulation S-K are separate from
          the disclosures regarding ICFR required by Item 308(a) of Regulation S-K.

        The Company respectfully directs the Staff’s attention to the first paragraph under the heading “Evaluation of Disclosure Controls and Procedures” in Item 9A of the
          Form 10-K, in which the Company disclosed that its management, including its principal executive and principal financial officers, evaluated the effectiveness of the Company’s disclosure controls and procedures as of December 31, 2021, and
          provided a description of the meaning and purpose of “disclosure controls and procedures” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended. The Company advises the Staff that, following such
          evaluation, its management, with the participation of its principal executive and principal financial officers, concluded that such disclosure controls and procedures were effective as of December 31, 2021, and intended to include a statement to
          this effect in the Form 10-K, as it has in prior periodic reports, had the Company not inadvertently included the typographical error referencing ICFR.

        The Company also respectfully advises the Staff that the Company’s Quarterly Report on Form 10-Q for the period ended March 31, 2022, filed with the SEC on May 5, 2022,
          also contained separate statements regarding management’s evaluation of the Company’s disclosure controls and procedures as of March 31, 2022 pursuant to Item 307 of Regulation S-K, with a corresponding conclusion that the Company’s management,
          with the participation of its principal executive and principal financial officers, concluded that such disclosure controls and procedures were effective.

        On the basis of the foregoing, the Company respectfully requests that the Staff permit the Company to confirm hereby future compliance with Item 307 of Regulation S-K
          for future periodic filings with the SEC, in lieu of requiring the Company to amend the Form 10-K. Accordingly, should the Staff grant the Company’s request, the Company hereby confirms that it will include in its future filings with the SEC,
          where applicable, the disclosure required by Item 307 of Regulation S-K as to the conclusions of its principal executive and principal financial officers regarding the effectiveness of its disclosure controls and procedures as of the end of the
          period covered by the applicable filing.

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

              Confidential Treatment Requested

                By Bionano Genomics, Inc.

        Form 8-K Filed on October 19, 2021

        Exhibits

              2.

                We note from Item 9.01 that you acquired BioDiscovery, LLC for $75 million in October 2021. Please provide to us your significance calculations under Rule 3-05
                  of Regulation S-X for this acquisition. To the extent that separate financial statements are required to be included under Rule 3-05 of Regulation S-X, please revise to include these financial statements and the related pro forma
                  financial statements under Article 11 of Regulation S-X.

          Response: The Company respectfully advises the Staff that it considered the requirements of Rule 3-05 and
            Article 11 of Regulation S-X and determined that it was not required to include audited financial statements of, and pro forma financial information relating to the acquisition of, BioDiscovery, LLC (“BioDiscovery”). The acquisition of BioDiscovery constituted an acquisition of a “business” within the
            meaning of Rule 11-01(d) of the Securities Act. The Company compared (i) the amount of the Company’s investment in BioDiscovery, against the Company’s market capitalization (the “Investment
              Test”); (ii) the total assets of BioDiscovery as of December 31, 2020, against the Company’s total consolidated assets as of December 31, 2020 (the “Asset Test”); and (iii) the lower of (a) the revenue of BioDiscovery for the year ended December 31, 2020, against the Company’s consolidated revenue for the year ended December 31, 2020 (the “Revenue Component”) and (b) the absolute value of the pre-tax income or loss, as applicable, of BioDiscovery for the year ended December 31, 2020, against the absolute value of the
            Company’s pre-tax income or loss, as applicable, for the year ended December 31, 2020 (the “Income Component” and, together with the Revenue Component, the “Income Test”). The Company respectfully advises the Staff that its acquisition of BioDiscovery did not meet the threshold to be considered a
            significant acquisition pursuant to Rule 3-05 or Article 11 of Regulation S-X as none of the Asset Test, the Investment Test or the Income Test exceeded the 20% significance threshold as applied to the acquisition of a “business” (as defined in
            Rule 11-01(d) of Regulation S-X), as shown in the table below. Moreover, each of the Asset Test, Investment Test and Income Test were below 10% significance.

        The Company’s calculations of the significance tests for the BioDiscovery acquisition are as follows:

                Investment Test – 4.92%

                Asset Test – [***]%

                Income Test – [***]%

        The percentages were calculated as follows (the dollar amounts below are in U.S. dollars and based on U.S. GAAP audited financial statements of the Company and the most
          recent pre-acquisition annual financial statements of BioDiscovery):

                Investment Test:

                Total investment in BioDiscovery

                $

                74,756,000

                =

                4.92%

                Aggregate worldwide market value of the Company’s voting and non-voting common equity1

                $

                1,518,521,682

                Asset Test:

                Total assets of BioDiscovery as of December 31, 2020

                $

                [***]

                =

                [***]%

                Consolidated total assets of the Company as of December 31, 2020

                $

                60,449,526

                Income Test2 –

                Income Component:

                Pre-tax income (loss) of BioDiscovery for the year ended December 31, 2020

                $

                [***]

                =

                [***]%

                Pre-tax income (loss) of the Company for the year ended December 31, 2020

                $

                41,077,158

        * * * * *

        1 Calculated using the average of the daily closing price of the Company’s shares of common stock for the last five trading days of the Company’s
          most recently completed month ending prior to date of the definitive acquisition agreement.

        2 As discussed above, the Income Test is equal to the lower of the Income Component and the Revenue Component. The Revenue Component was determined as
          follows: a quotient obtained by dividing (i) the revenue of BioDiscovery for the year ended December 31, 2020, which was equal to $[***], by (ii) the consolidated revenue of the Company for the year ended December 31, 2020, which was equal to
          $8,502,984, resulting in the Revenue Component equaling [***]%. However, because the Income Component is [***]% and lower than the Revenue Component, the Income Test is determined by the Income Component and not significant.

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

              Confidential Treatment Requested

                By Bionano Genomics, Inc.

        Please advise us if we can provide any further information or assistance to facilitate your review. Please direct any questions or further comments
          regarding this response letter to the undersigned at (858) 888-7614. Thank you.

        Sincerely,

                /s/ Christopher Stewart

                Christopher Stewart

                Chief Financial Officer

                Bionano Genomics, Inc.

              cc:

                Erik Holmlin, Bionano Genomics, Inc.

        Thomas A. Coll, Cooley LLP

        Sarah K. Sellers, Cooley LLP

        Reid S. Hooper, Cooley LLP

        Phillip S. McGill, Cooley LLP

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

CORRESP
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      July 8, 2022

      United States Securities and Exchange Commission

      Division of Corporation Finance

      Office of Life Sciences

      100 F Street, N.E.

      Washington, D.C. 20549

              Attn:

                  Gary Newberry

                  Tara Harkins

              Re:

                  Bionano Genomics, Inc.

                  Form 10-K for the Fiscal Year Ended December 31, 2021

                  Form 8-K filed on October 19, 2021

                  File No. 001-38613

      Ladies and Gentlemen:

      We are in receipt of the comment letter, dated June 23, 2022, from the staff (the “Staff”) of the Securities and Exchange Commission regarding the above
        captioned filings on Form 10-K for the fiscal year ended December 31, 2021 and Form 8-K, filed on October 19, 2021.

      The comment letter requested that Bionano Genomics, Inc. (the “Company,” “we,” “our” or similar terminology) respond within ten business days or advise the Staff when the Company will respond. As we discussed with Mr. Newberry via phone call on July 7, 2022, we
            respectfully request an extension of ten business days to respond. The Company plans to provide a response to the Staff’s comment letter on or before Friday, July 22, 2022.

      * * * * *

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

      Thank you for your consideration of our request for an extension. If you have any questions, please do not hesitate to call the undersigned at (858) 888-7614.

      Sincerely,

      /s/ Christopher Stewart

      Christopher Stewart

      Chief Financial Officer

      Bionano Genomics, Inc.

                cc:

                  Erik Holmlin, Bionano Genomics, Inc.

                  Thomas A. Coll, Cooley LLP

                  Sarah K. Sellers, Cooley LLP

                  Phillip S. McGill, Cooley LLP

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

United States securities and exchange commission logo
June 23, 2022
Christopher Stewart
Chief Financial Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive
Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc.
Form 10-K for the Fiscal Year Ended December 31, 2021
Form 8-K filed on October 19, 2021
File No. 001-38613
Dear Mr. Stewart:
            We have limited our review of your filing to the financial statements and related
disclosures and have the following comments.  In some of our comments, we may ask you to
provide us with information so we may better understand your disclosure.
            Please respond to these comments within ten business days by providing the requested
information or advise us as soon as possible when you will respond.  If you do not believe our
comments apply to your facts and circumstances, please tell us why in your response.
            After reviewing your response to these comments, we may have additional comments.
Form 10-K for the Fiscal Year Ended December 31, 2021
Item 9A. Controls and Procedures
Evaluation of Disclosure Controls and Procedures, page 106
1.Consistent with Item 307 or Regulation S-K, please amend your filing to disclose the
conclusions of your principal executive and principal financial officers regarding the
effectiveness of your disclosure controls and procedures as of the end of the period
covered by the report - i.e., December 31, 2021.

 FirstName LastNameChristopher Stewart
 Comapany NameBionano Genomics, Inc.
 June 23, 2022 Page 2
 FirstName LastName
Christopher Stewart
Bionano Genomics, Inc.
June 23, 2022
Page 2
Form 8-K filed on October 19, 2021
Exhibits
2.We note from Item 9.01 that you acquired BioDiscovery, LLC for $75 million in October
2021.  Please provide to us your significance calculations under Rule 3-05 of Regulation
S-X for this acquisition.  To the extent that separate financial statements are required to be
included under Rule 3-05 of Regulation S-X, please revise to include these financial
statements and the related pro forma financial statements under Article 11 of Regulation
S-X.
            In closing, we remind you that the company and its management are responsible for the
accuracy and adequacy of their disclosures, notwithstanding any review, comments, action or
absence of action by the staff.
            You may contact Gary Newberry at (202) 551-3761 or Tara Harkins, Senior
Accountant, at (202) 551-3639 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

CORRESP
1
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      Bionano Genomics, Inc.

    9540 Towne Centre Drive, Suite 100

    San Diego, California 92121

    (858) 888-7600

    August 21, 2020

    Via Edgar

    United States Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

    Attn:          Jeffrey Gabor

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-3

            File No. 333-245762

    Ladies and Gentlemen:

    Bionano Genomics, Inc. (the “Registrant”)
      hereby requests that the Securities and Exchange Commission take appropriate action to cause the above-referenced Registration Statement on Form S-3 to become effective at 4:00 p.m. Eastern Time on Tuesday, August 25, 2020, or as soon thereafter as
      is practicable.  The Registrant also hereby requests a copy of the written order verifying the effective date.

    If you have any questions regarding this request, please contact James Pennington of Cooley LLP at (858) 550-6029.

    Sincerely,

    Bionano Genomics, Inc.

            By:

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

            R. Erik Holmlin, Ph.D.

            President and Chief Executive Officer

            cc:

            James Pennington, Cooley LLP

United States securities and exchange commission logo
August 21, 2020
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-3
Filed August 14, 2020
File No. 333-245762
Dear Dr. Holmlin:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Jeffrey Gabor at 202-551-2544 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       James C. Pennington, Esq.

United States securities and exchange commission logo
May 19, 2020
R. Erik Holmlin, Ph.D.
Chief Executive Officer
Bionano Genomics, Inc
9540 Towne Centre Drive, Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc
Preliminary Proxy Statement on Schedule 14A
Filed May 13, 2020
File No. 001-38613
Dear Mr. Holmlin:
            We have completed our review of your filing.  We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence of action by the staff.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       James Pennington, Esq.

CORRESP
1
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      Oppenheimer & Co. Inc.

      85 Broad Street

      New York, New York 10004

      April 1, 2020

      VIA EDGAR

      United States Securities and Exchange Commission

      Division of Corporation Finance

      100 F Street, N.E.

      Washington, D.C. 20549

      Re:         Bionano Genomics, Inc.

      Registration Statement on Form S-1, as amended

      File No. 333-237074

      Ladies and Gentlemen:

      In accordance with the above-referenced Registration Statement, and pursuant to Rule 461 of the General Rules and Regulations of the Securities and Exchange Commission under the Securities Act of
        1933, as amended (the “Securities Act”), the undersigned, as the representative of the several underwriters (the “Representative”), hereby joins in the request of Bionano Genomics, Inc. that the effective date of the above-referenced Registration
        Statement be accelerated so that it will be declared effective at 4:00 p.m., Eastern Time, on April 1, 2020, or as soon thereafter as practicable.

      Pursuant to Rule 460 under the Securities Act, please be advised that there will be distributed to each underwriter or dealer, who is reasonably anticipated to be invited to participate in the
        distribution of the security, as many copies of the proposed form of preliminary prospectus as appears to be reasonable to secure adequate distribution of the preliminary prospectus.

      The undersigned, as the representative of the several underwriters, represents that the several underwriters have and will comply with the requirements of Rule 15c2-8 under the Securities
        Exchange Act of 1934, as amended.

               Very truly yours,

      OPPENHEIMER & CO. INC.

      As representative of the

      several Underwriters

              OPPENHEIMER & CO. INC.

              By:

              /s/ Peter Bennett

              Name:

              Peter Bennett

              Title:

              Managing Director, Head of Equity Capital Markets

CORRESP
1
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    April 1, 2020

    VIA EDGAR

    U.S. Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

            Attn:

            Mr. Jeffrey Gabor

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-1

            File No. 333-237074

            Acceleration Request

            Requested Date:

            Wednesday, April 1, 2020

            Requested Time:

            4:00 P.M. Eastern Time

    Ladies and Gentlemen:

    In accordance with Rule 461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests
      that the Securities and Exchange Commission (the “Commission”) take appropriate action to cause the above-referenced Registration Statement on Form S-1 (File No. 333-237074) (the “Registration Statement”) to become effective on April 1, 2020, at 4:00 P.M., Eastern Time, or as soon thereafter as is practicable, or at such later time as the Registrant or its legal counsel
      may orally request via telephone call to the staff. This request for acceleration is subject to your receiving a telephone call prior to such time from our legal counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes James
      Pennington of Cooley LLP to make such request on its behalf.

    Once the Registration Statement has been declared effective, please orally confirm that event with James Pennington of Cooley LLP, legal counsel to the Registrant, at (858) 550-6029.

            Very truly yours,

            Bionano Genomics, Inc.

          By:

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

            R. Erik Holmlin, Ph.D.

            President and Chief Executive Officer

            cc:

            James Pennington, Cooley LLP

            Ivan Blumenthal, Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.

            Cliff Silverman, Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.

CORRESP
1
filename1.htm

    March 17, 2020

    VIA EDGAR

    U.S. Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

            Attn:

            Jeffrey Gabor

            Re:

            Bionano Genomics, Inc. (the “Company”)

            Registration Statement on Form S-3

            Filed: March 11, 2020

            File No. 333-237070

    Ladies and Gentlemen:

    Pursuant to Rule 461 under the Securities Act of 1933, as amended, the Company hereby requests that the Securities and Exchange
      Commission (the “Commission”) take appropriate action to cause the above-referenced Registration Statement to become effective
      at 4:30 p.m. Eastern Time on March 19, 2020 or as soon thereafter as is practicable.

    If you have any questions regarding this request, please contact James Pennington of Cooley LLP at (858) 550-6029.

            Very truly yours,

            Bionano Genomics, Inc.

            By:

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

            R. Erik Holmlin, Ph.D.

            President and Chief Executive Officer

March 16, 2020
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9540 Towne Centre Drive, Suite 100
San Diego, California 92121
Re:Bionano Genomics, Inc.
Registration Statement on Form S-1
Filed March 11, 2020
File No. 333-237074
Dear Dr. Holmlin:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Jeffrey Gabor at 202-551-2544 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       James Pennington, Esq.

CORRESP
1
filename1.htm

    Oppenheimer & Co. Inc.

    85 Broad Street

    New York, New York 10004

      October 16, 2019

      VIA EDGAR

      United States Securities and Exchange Commission

        Division of Corporation Finance

        100 F Street, N.E.

        Washington, D.C. 20549

              Re:

                Bionano Genomics, Inc.

                Registration Statement on Form S-1, as amended

                File No. 333-233828

      Ladies and Gentlemen:

      In accordance with the above-referenced Registration Statement, and pursuant to Rule 461 of the General Rules and Regulations of the Securities and
        Exchange Commission under the Securities Act of 1933, as amended (the “Securities Act”), the undersigned, as the representative of the several underwriters (the “Representative”), hereby joins in the request of Bionano Genomics, Inc. that the
        effective date of the above-referenced Registration Statement be accelerated so that it will be declared effective at 8:00 a.m., Eastern Time, on Friday, October 18, 2019, or as soon thereafter as practicable.

      Pursuant to Rule 460 under the Securities Act, please be advised that there will be distributed to each underwriter or dealer, who is reasonably
        anticipated to be invited to participate in the distribution of the security, as many copies of the proposed form of preliminary prospectus as appears to be reasonable to secure adequate distribution of the preliminary prospectus.

      The undersigned, as the representative of the several underwriters, represents that the several underwriters have and will comply with the
        requirements of Rule 15c2-8 under the Securities Exchange Act of 1934, as amended.

              Very truly yours,

                OPPENHEIMER & CO. INC.

                As representative of the

                several Underwriters

                OPPENHEIMER & CO. INC.

              By:
              /s/ Peter Bennett

              Name:

                Peter Bennett

              Title:
              Managing Director, Head of Equity Capital Markets

CORRESP
1
filename1.htm

    October 16, 2019

    VIA EDGAR

    U.S. Securities and Exchange Commission

    Division of Corporation Finance

    100 F Street, N.E.

    Washington, D.C. 20549

            Attn:

            Mr. Michael Fay

            Re:

            Bionano Genomics, Inc.

            Registration Statement on Form S-1

            File No. 333-233828

            Acceleration Request

            Requested Date:

            Friday, October 18, 2019

            Requested Time:

            8:00 A.M. Eastern Time

    Ladies and Gentlemen:

    In accordance with Rule 461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests
      that the Securities and Exchange Commission (the “Commission”) take appropriate action to cause the above-referenced Registration Statement on Form S-1 (File No. 333-233828) (the “Registration Statement”) to become effective on October 18, 2019, at 8:00 A.M., Eastern Time, or as soon thereafter as is practicable, or at such later time as the Registrant or its legal
      counsel may orally request via telephone call to the staff. This request for acceleration is subject to your receiving a telephone call prior to such time from our legal counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes
      James Pennington of Cooley LLP to make such request on its behalf.

    Once the Registration Statement has been declared effective, please orally confirm that event with James Pennington of Cooley LLP, legal counsel to the Registrant, at (858) 550-6029.

            Very truly yours,

            Bionano Genomics, Inc.

            By:

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

            R. Erik Holmlin, Ph.D.

            President and Chief Executive Officer

            cc:

            James Pennington, Cooley LLP

            Ivan Blumenthal, Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.

            Cliff Silverman, Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.

September 3, 2019
R. Erik Holmlin
President and Chief Executive Officer
Bionano Genomics, Inc
9540 Towne Centre Drive, Suite 100
San Diego, CA 92121
Re:Bionano Genomics, Inc
Draft Registration Statement on Form S-1
Submitted August 20, 2019
CIK No. 0001411690
Dear Dr. Holmlin:
            This is to advise you that we do not intend to review your registration statement.
            We request that you publicly file your registration statement no later than 48 hours prior
to the requested effective date and time. Please refer to Rules 460 and 461 regarding requests for
acceleration. We remind you that the company and its management are responsible for the
accuracy and adequacy of their disclosures, notwithstanding any review, comments, action or
absence of action by the staff.
            Please contact Michael Fay at 202-551-3812 with any questions.
Sincerely,
Division of Corporation Finance
Office of Electronics and Machinery
cc:       James C. Pennington, Esq.

CORRESP
1
filename1.htm

CORRESP

 Via EDGAR

U.S. Securities and Exchange Commission

 Division of Corporation
Finance

 100 F Street, N.E.

 Washington, D.C. 20549

Attn: Ms. Heather Percival

Re:
 Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-230588

Acceleration Request

Requested Date:         Wednesday, April 17, 2019

Requested Time:        4:00 P.M. Eastern Time

Ladies and Gentlemen:

 In accordance with Rule
461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests that the Securities and Exchange Commission take appropriate action to cause the above-referenced Registration
Statement on Form S-1 (File No. 333-230588) (the “Registration Statement”) to become effective on April 17, 2019, at 4:00 P.M.,
Eastern Time, or as soon thereafter as is practicable.

 Once the Registration Statement has been declared effective, please orally confirm
that event with James Pennington of Cooley LLP, counsel to the Registrant, at (858) 550-6029.

 Very truly yours,

Bionano Genomics, Inc.

By:

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

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer

cc:
 Mike Ward, Bionano Genomics, Inc.

James Pennington, Cooley LLP

CORRESP
1
filename1.htm

CORRESP

 August 17, 2018

U.S. Securities and Exchange Commission

 Division of Corporation
Finance

 100 F Street, N.E.

 Washington, D.C. 20549

Re:

Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

 VIA EDGAR

 Ladies
and Gentlemen:

 Pursuant to Rule 461 of the General Rules and Regulations of the U.S. Securities and Exchange Commission under the Securities Act of 1933,
as amended, Roth Capital Partners, LLC, as representative of the underwriters, hereby requests acceleration of the effective date of the above-referenced Registration Statement so that it becomes effective at 4:30 PM, Eastern Time, on
August 20, 2018, or as soon thereafter as practicable, or at such other time as the Company or its outside counsel, Cooley LLP, request by telephone that such Registration Statement be declared effective. In addition, this request supersedes in
its entirety the Registrant’s prior request for acceleration submitted to the Commission on August 6, 2018.

 The following is supplemental
information supplied under Rule 418(a)(7) and Rule 460 under the Securities Act of 1933:

(i)
 Date of preliminary prospectus: August 17, 2018;

(ii)
 Dates of distribution: August 17, 2018 through the date hereof;

(iii)
 Number of prospective underwriters and selected dealers to whom the preliminary prospectus was furnished: 22;
and

(iv)
 Number of prospectuses so distributed: electronic 988, print 0.

The undersigned confirms that it has complied with and will continue to comply with, and it has been informed or will be informed by participating dealers
that they have complied with or will comply with, Rule 15c2-8 promulgated under the Securities Exchange Act of 1934, as amended, in connection with the above-referenced issue.

[Signature Page Follows]

ROTH CAPITAL PARTNERS, LLC

By:

 /s/ Aaron M. Gurewitz

Name:

Aaron M. Gurewitz

Title:

Head of Equity Capital Market

CORRESP
1
filename1.htm

CORRESP

 Via EDGAR

August 17, 2018

 U.S. Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

 Attn: Ms. Amanda Ravitz

Re:

Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

Acceleration Request

 Requested Date:

Monday, August 20, 2018

 Requested Time:

4:30 P.M. Eastern Time

 Ladies and Gentlemen:

In accordance with Rule 461 under the Securities Act of 1933, as amended, the undersigned registrant (the
“Registrant”) hereby requests that the Securities and Exchange Commission (the “Commission”) take appropriate action to cause the above-referenced Registration Statement on Form S-1 (File No. 333-225970) (the “Registration Statement”) to become effective on August 20, 2018, at 4:30 P.M., Eastern Time, or as soon
thereafter as is practicable, or at such later time as the Registrant or its counsel may orally request via telephone call to the staff. This request for acceleration is subject to your receiving a telephone call prior to such time from our legal
counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes James Pennington of Cooley LLP to make such request on its behalf. In addition, this request supersedes in its entirety the Registrant’s prior request for
acceleration submitted to the Commission on August 6, 2018.

 Once the Registration Statement has been declared effective, please
orally confirm that event with James Pennington of Cooley LLP, counsel to the Registrant, at (858) 550-6029.

Very truly yours,

Bionano Genomics, Inc.

By:

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

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer

cc:
 James Pennington, Cooley LLP

Angela Dowd, Loeb & Loeb LLP

CORRESP
1
filename1.htm

CORRESP

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with

Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

 James Pennington

 +1 858 550 6029

jpennington@cooley.com

VIA EDGAR

 August 17, 2018

 United
States Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 3030

 100 F Street, N.E.

Washington, D.C. 20549

Attn:
 Amanda Ravitz

 Heather Percival

Re:
 Bionano Genomics, Inc.

 Amendment No. 5 to Registration Statement on Form S-1

 Filed August 15, 2018

 CIK No. 0001411690

Dear Ms. Ravitz and Ms. Percival:

 On behalf of
Bionano Genomics, Inc. (“Bionano” or the “Company”), we are responding to the oral follow-up comments (the “Comments”) received from the
staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) on August 15, 2018, relating to the above referenced Amendment No. 5 to Registration Statement on Form S-1 (the “Amendment No. 5”) and the response letter from the Company to the Commission, dated August 16, 2018 (the “Response
Letter”).

 In response to the Comments, the Company has revised the Amendment No. 5 and is publicly filing via EDGAR an Amendment
No. 6 to Registration Statement on Form S-1 (the “Amendment No. 6”) with this response letter.

Set forth below are the Company’s responses to the Comments. Page references in the text of this response letter correspond to the page numbers of the
Amendment No. 6. Capitalized terms used in this letter but not otherwise defined herein shall have the meanings set forth in the Amendment No. 6.

Confidential Treatment Request

 Due to the commercially
sensitive nature of information contained herein, the Company hereby requests, pursuant to 17 C.F.R. § 200.83, that certain portions of this letter be maintained in confidence, not be made part of any public record and not be disclosed to any
person as they contain confidential information. The Company has filed a separate copy of this letter, marked to show the portions redacted from the version filed via EDGAR and for which the Company is requesting confidential treatment. In
accordance with 17 C.F.R. § 200.83(d)(1), if any person (including any governmental employee who is not an employee of the Commission) should request access to or an opportunity to inspect this letter, we request that we be immediately
notified of any such request, be furnished with a copy of all written materials pertaining to such request (including, but not limited to, the request itself) and be given at least ten business days advance notice of any intended release so that the
Company may, if deemed necessary or appropriate, pursue any remedies available to it. In such an event, we request that you telephone the undersigned rather than rely upon the U.S. mail for such notice. The address and telephone number for James
Pennington, the responsible representative, is c/o Cooley LLP, 4401 Eastgate Mall, San Diego, CA 92121, telephone number (858) 550-6029.

 [*] CERTAIN CONFIDENTIAL
INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED
AND FILED

 SEPARATELY WITH THE
COMMISSION PURSUANT TO 17 CFR §200.83

 Cooley LLP    4401 Eastgate
Mall    San Diego, CA    92121

 t: (858) 550-6000  f: (858) 550-6420  cooley.com

 United States Securities and Exchange Commission

August 17, 2018

 Page Two

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with

Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

Staff Comments and Company Responses

 Use of Proceeds,
page 53; Capital Resources, page 70

1.
 Please confirm that the revenue and cash projections in the response letter dated
August 16, 2018 account for the impact of the reduced amount of net proceeds, relative to the prior amendment to the registration statement, which will be available to spend on each of the purposes described in the prospectus
section titled “Use of Proceeds.” In addition, please disclose in the S-1 the basis for the company’s disclosure that it believes it will have sufficient cash for at least the next 18
months.

 Response: The Company respectfully acknowledges the Staff’s comment and hereby confirms that the revenue and
cash projections in the response letter dated August 16, 2018 account for the impact of the reduced amount of net proceeds which will be available to spend on each of the purposes described in the Amendment No. 6, relative to the prior
amendment to the registration statement. The Company also advises the Staff that it has revised pages 15 and 70 of the Amendment No. 6 to address the Staff’s request regarding disclosing the basis for the Company’s belief that it will
have sufficient cash for at least the next 18 months.

 Use of Proceeds, page 92

2.
 While the company’s strategies and objectives may not have changed in connection with the lower
net proceeds relative to the prior amendment to the registration statement, to what extent does the company anticipate that its ability to accomplish its strategies and objectives will be impacted by the lower net proceeds?

 Response: The Company respectfully acknowledges the Staff’s comment and reconfirms that the Company’s strategies and
objectives as disclosed in the Amendment No. 6 have not changed as a result of the lower net proceeds. [***]

 Destruction of this Unredacted
Letter Pursuant to Rule 418 Under the Securities Act of 1933, As Amended

 We further request, pursuant to Rule 418 under the Securities Act of 1933, as
amended, that this unredacted letter be destroyed promptly following the Staff’s completion of its review of such information.

*************************

[*] CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN
THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED AND FILED

SEPARATELY WITH THE COMMISSION PURSUANT TO 17 CFR
§200.83

 Cooley LLP    4401 Eastgate Mall    San Diego, CA    92121

t: (858) 550-6000  f: (858) 550-6420  cooley.com

 United States Securities and Exchange Commission

August 17, 2018

 Page Three

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with

Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

Please advise us if we can provide any further information or assistance to facilitate your review. Please direct any further comments or questions regarding
the Amendment No. 6 or this response letter to me at (858) 550-6029.

 Sincerely,

Cooley LLP

 /s/ James Pennington

James Pennington

 cc: R. Erik Holmlin, Ph.D., Bionano Genomics,
Inc.

 [*] CERTAIN CONFIDENTIAL
INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED
AND FILED

 SEPARATELY WITH THE
COMMISSION PURSUANT TO 17 CFR §200.83

 Cooley LLP    4401 Eastgate
Mall    San Diego, CA    92121

 t: (858) 550-6000  f: (858) 550-6420  cooley.com

CORRESP
1
filename1.htm

CORRESP

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with

Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

 James Pennington

 +1 858 550 6029

jpennington@cooley.com

VIA EDGAR

 August 16, 2018

 United
States Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 3030

 100 F Street, N.E.

Washington, D.C. 20549

Attn:

Amanda Ravitz

Heather Percival

Re:

 Bionano Genomics, Inc.

 Amendment
No. 5 to Registration Statement on Form S-1

 Filed August 15, 2018

CIK No. 0001411690

 Dear Ms. Ravitz and Ms. Percival:

On behalf of Bionano Genomics, Inc. (“Bionano” or the “Company”), we are responding to the oral comments (the
“Comments”) received from the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) on August 15, 2018, relating to the above referenced
Amendment No. 5 to Registration Statement on Form S-1 (the “Amendment No. 5”).

Set forth below are the Company’s responses to the Comments. Page references in the text of this response letter correspond to the page numbers of the
Amendment No. 5. Capitalized terms used in this letter but not otherwise defined herein shall have the meanings set forth in the Amendment No. 5.

Confidential Treatment Request

 Due to the commercially
sensitive nature of information contained herein, the Company hereby requests, pursuant to 17 C.F.R. § 200.83, that certain portions of this letter be maintained in confidence, not be made part of any public record and not be disclosed to any
person as they contain confidential information. The Company has filed a separate copy of this letter, marked to show the portions redacted from the version filed via EDGAR and for which the Company is requesting confidential treatment. In
accordance with 17 C.F.R. § 200.83(d)(1), if any person (including any governmental employee who is not an employee of the Commission) should request access to or an opportunity to inspect this letter, we request that we be immediately
notified of any such request, be furnished with a copy of all written materials pertaining to such request (including, but not limited to, the request itself) and be given at least ten business days advance notice of any intended release so that the
Company may, if deemed necessary or appropriate, pursue any remedies available to it. In such an event, we request that you telephone the undersigned rather than rely upon the U.S. mail for such notice. The address and telephone number for James
Pennington, the responsible representative, is c/o Cooley LLP, 4401 Eastgate Mall, San Diego, CA 92121, telephone number (858) 550-6029.

[*] CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN
THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION PURSUANT TO 17 CFR §200.83

 Cooley
LLP    4401 Eastgate Mall    San Diego, CA    92121

 t: (858) 550-6000 f: (858) 550-6420 cooley.com

 United States Securities and Exchange

Commission

 August 16, 2018

Page Two

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with

Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

 Staff Comments and Company Responses

Use of Proceeds, page 53; Capital Resources, page 70

1.
 Please explain the basis for the company’s continued expectation that the net proceeds from the
offering, together with cash generated from commercial sales and current cash and cash equivalents, will be sufficient to meet the company’s anticipated operating cash requirements for at least the next 18 months, taking into account the
significant decrease in the expected net proceeds from the offering relative to the prior amendment of the registration statement.

Response: The Company respectfully acknowledges the Staff’s comment and advises the Staff that it expects that the net proceeds from the
anticipated offering, together with cash generated from commercial sales and current cash on hand, will be sufficient to meet the Company’s cash requirements for at least the next 18 months. The Company believes this is the case despite the
decrease in expected net proceeds from the offering relative to the prior amendment of the registration statement filed on July 31, 2018 (the “Prior Amendment”).

[***]

2.
 Please explain the basis for the company’s continued expectation regarding its business plan and
the specific objectives it expects to pursue, taking into account the significant decrease in the expected net proceeds from the offering relative to the prior amendment of the registration statement.

Response: The Company respectfully acknowledges the Staff’s comment and advises the Staff that although the expected level of net proceeds from
the offering has decreased, the Company’s business plan has not changed. The specific objectives that the Company expects to pursue also have not changed as a result of the decrease in expected net proceeds from the offering. [***]

[***]

 Part II, Item 17.

3.
 Please revise the disclosure to reflect the Company’s applicable obligations with respect to
Item 512(a) of Regulation S-K, taking into account the warrants forming part of the units to be sold in the offering.

Response: The Company respectfully acknowledges the Staff’s comment and advises the Staff that the Company is aware of and will comply with its
applicable obligations in connection with Item 512(a) of Regulation S-K, taking into account the warrants forming part of the units to be sold in the offering.

[*] CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN
THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED AND FILED

SEPARATELY WITH THE COMMISSION PURSUANT TO 17 CFR
§200.83

 Cooley LLP    4401 Eastgate Mall    San Diego, CA    92121

 t: (858) 550-6000 f: (858) 550-6420 cooley.com

 United States Securities and Exchange

Commission

 August 16, 2018

Page Three

 * FOIA Confidential Treatment Request*

Confidential Treatment Requested by

Bionano Genomics, Inc. in connection with
Amendment No. 5 to Registration Statement

on Form S-1 filed August 15, 2018

 Destruction of this Unredacted Letter Pursuant to Rule 418 Under the Securities Act of 1933, As Amended

We further request, pursuant to Rule 418 under the Securities Act of 1933, as amended, that this unredacted letter be destroyed promptly following the
Staff’s completion of its review of such information.

 *************************

Please advise us if we can provide any further information or assistance to facilitate your review. Please direct any further comments or questions regarding
the Amendment No. 5 or this response letter to me at (858) 550-6029.

 Sincerely,

Cooley LLP

 /s/ James Pennington

James Pennington

 cc: R. Erik Holmlin, Ph.D., Bionano Genomics,
Inc.

 [*] CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN
THIS DOCUMENT, MARKED BY BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION PURSUANT TO 17 CFR §200.83

 Cooley
LLP    4401 Eastgate Mall    San Diego, CA    92121

 t: (858) 550-6000 f: (858) 550-6420 cooley.com

CORRESP
1
filename1.htm

CORRESP

 August 6, 2018

U.S. Securities and Exchange Commission

 Division of Corporation
Finance

 100 F Street, N.E.

 Washington, D.C. 20549

Re:
 Bionano Genomics, Inc.

 Registration Statement on Form S-1

 File No. 333-225970

 VIA EDGAR

 Ladies and
Gentlemen:

 Pursuant to Rule 461 of the General Rules and Regulations of the U.S. Securities and Exchange Commission under the Securities Act of 1933, as
amended, Roth Capital Partners, LLC, as representative of the underwriters (the “Representative”), hereby requests acceleration of the effective date of the above-referenced Registration Statement so that it becomes effective
at 4:30 PM, Eastern Time, on August 7, 2018, or as soon thereafter as practicable, or at such other time as the Company or its outside counsel, Cooley LLP, request by telephone that such Registration Statement be declared effective. In
addition, this request supersedes in its entirety the Representative’s prior request for acceleration submitted to the Commission on August 1, 2018.

The following is supplemental information supplied under Rule 418(a)(7) and Rule 460 under the Securities Act of 1933:

(i)
 Date of preliminary prospectus: July 31, 2018;

(ii)
 Dates of distribution: July 31, 2018 through the date hereof;

(iii)
 Number of prospective underwriters and selected dealers to whom the preliminary prospectus was furnished: 21;
and

(iv)
 Number of prospectuses so distributed: electronic 448, print 0.

The undersigned confirms that it has complied with and will continue to comply with, and it has been informed or will be informed by participating dealers
that they have complied with or will comply with, Rule 15c2-8 promulgated under the Securities Exchange Act of 1934, as amended, in connection with the above-referenced issue.

[Signature Page Follows]

ROTH CAPITAL PARTNERS, LLC

By:

/s/ Aaron M. Gurewitz

Name: Aaron M. Gurewitz

Title: Head of Equity Capital Markets

CORRESP
1
filename1.htm

CORRESP

 Via EDGAR

August 6, 2018

 U.S. Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

Attn:
 Ms. Amanda Ravitz

Re:
 Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

Acceleration Request

Requested Date:    Tuesday, August 7, 2018

Requested Time:   4:30 P.M. Eastern Time

Ladies and Gentlemen:

 In accordance with Rule
461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests that the Securities and Exchange Commission (the “Commission”) take appropriate action to
cause the above-referenced Registration Statement on Form S-1 (File No. 333-225970) (the “Registration Statement”) to become effective on
August 7, 2018, at 4:30 P.M., Eastern Time, or as soon thereafter as is practicable, or at such later time as the Registrant or its counsel may orally request via telephone call to the staff. This request for acceleration is subject to your
receiving a telephone call prior to such time from our legal counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes James Pennington of Cooley LLP to make such request on its behalf. In addition, this request supersedes in
its entirety the Registrant’s prior request for acceleration submitted to the Commission on August 1, 2018.

 Once the
Registration Statement has been declared effective, please orally confirm that event with James Pennington of Cooley LLP, counsel to the Registrant, at (858) 550-6029.

Very truly yours,

Bionano Genomics, Inc.

By:

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

 R. Erik Holmlin, Ph.D.

 President and Chief
Executive Officer

cc:
 Mike Ward, Bionano Genomics, Inc.

James Pennington, Cooley LLP

Angela Dowd, Loeb & Loeb LLP

CORRESP
1
filename1.htm

UW Acceleration Request

 August 1, 2018

U.S. Securities and Exchange Commission

 Division of Corporation
Finance

 100 F Street, N.E.

 Washington, D.C. 20549

Re:
Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

 VIA EDGAR

Ladies and Gentlemen:

 Pursuant to Rule 461 of the General
Rules and Regulations of the U.S. Securities and Exchange Commission under the Securities Act of 1933, as amended, Roth Capital Partners, LLC, as representative of the underwriters (the “Representative”), hereby requests
acceleration of the effective date of the above-referenced Registration Statement so that it becomes effective at 4:30 PM, Eastern Time, on August 2, 2018, or as soon thereafter as practicable, or at such
other time as the Company or its outside counsel, Cooley LLP, request by telephone that such Registration Statement be declared effective. In addition, this request supersedes in its entirety the Representative’s prior request for acceleration
submitted to the Commission on July 27, 2018.

 The following is supplemental information supplied under Rule 418(a)(7) and Rule 460 under the
Securities Act of 1933:

(i)
Date of preliminary prospectus: July 31, 2018;

(ii)
Dates of distribution: July 31, 2018 through the date hereof;

(iii)
Number of prospective underwriters and selected dealers to whom the preliminary prospectus was furnished: 21; and

(iv)
Number of prospectuses so distributed: electronic 448, print 0.

 The undersigned confirms that it has complied
with and will continue to comply with, and it has been informed or will be informed by participating dealers that they have complied with or will comply with, Rule 15c2-8 promulgated under the Securities
Exchange Act of 1934, as amended, in connection with the above-referenced issue.

 [Signature Page Follows]

ROTH CAPITAL PARTNERS, LLC

By:

/s/ Aaron M. Gurewitz

Name:

Aaron M. Gurewitz

Title:

Head of Equity Capital Markets

CORRESP
1
filename1.htm

CORRESP

 Via EDGAR

August 1, 2018

 U.S. Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

 Attn: Ms. Amanda Ravitz

Re:    Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

Acceleration Request

Requested Date:     Thursday, August 2, 2018

Requested Time:    4:30 P.M. Eastern Time

Ladies and Gentlemen:

 In accordance with Rule
461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests that the Securities and Exchange Commission (the “Commission”) take appropriate action to
cause the above-referenced Registration Statement on Form S-1 (File No. 333-225970) (the “Registration Statement”) to become effective on
August 2, 2018, at 4:30 P.M., Eastern Time, or as soon thereafter as is practicable, or at such later time as the Registrant or its counsel may orally request via telephone call to the staff. This request for acceleration is subject to your
receiving a telephone call prior to such time from our legal counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes James Pennington of Cooley LLP to make such request on its behalf. In addition, this request supersedes in
its entirety the Registrant’s prior request for acceleration submitted to the Commission on July 27, 2018.

 Once the
Registration Statement has been declared effective, please orally confirm that event with James Pennington of Cooley LLP, counsel to the Registrant, at (858) 550-6029.

Very truly yours,

Bionano Genomics, Inc.

By:

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

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer

cc:
Mike Ward, Bionano Genomics, Inc.

James Pennington, Cooley LLP

Angela Dowd, Loeb & Loeb LLP

CORRESP
1
filename1.htm

CORRESP

 VIA EDGAR

July 27, 2018

 U.S. Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

Attn:
Ms. Amanda Ravitz

Re:
Bionano Genomics, Inc.

 Registration Statement on Form
S-1

 File
No. 333-225970

 Ladies and Gentlemen:

Pursuant to Rule 461 of the General Rules and Regulations of the U.S. Securities and Exchange Commission under the Securities Act of 1933, as amended, Roth
Capital Partners, LLC, as representative of the underwriters, hereby requests acceleration of the effective date of the above-referenced Registration Statement so that it will become effective at 4:00 p.m., Eastern Time, on Tuesday, July 31,
2018, or as soon thereafter as practicable.

 The following is supplemental information supplied under Rule 418(a)(7) and Rule 460 under the Securities Act
of 1933:

(i)
Date of preliminary prospectus: July 19, 2018;

(ii)
Dates of distribution: July 19, 2018 through the date hereof;

(iii)
Number of prospective underwriters and selected dealers to whom the preliminary prospectus was furnished: 15; and

(iv)
Number of prospectuses so distributed: electronic 224, print 45.

 The undersigned confirms that it has
complied with and will continue to comply with, and it has been informed or will be informed by participating dealers that they have complied with or will comply with, Rule 15c2-8 promulgated under the
Securities Exchange Act of 1934, as amended, in connection with the above-referenced issue.

ROTH CAPITAL PARTNERS, LLC

By:

 /s/ Aaron M. Gurewitz

Name:

Aaron M. Gurewitz

Title:

Head of Equity Capital Market

CORRESP
1
filename1.htm

CORRESP

 Via EDGAR

July 27, 2018

 U.S. Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

Attn:
 Ms. Amanda Ravitz

Re:
 Bionano Genomics, Inc.

Registration Statement on Form S-1

File No. 333-225970

Acceleration Request

Requested Date:         Tuesday, July 31, 2018

Requested Time:        4:00 P.M. Eastern Time

Ladies and Gentlemen:

 In accordance with Rule
461 under the Securities Act of 1933, as amended, the undersigned registrant (the “Registrant”) hereby requests that the Securities and Exchange Commission take appropriate action to cause the above-referenced Registration
Statement on Form S-1 (File No. 333-225970) (the “Registration Statement”) to become effective on July 31, 2018, at 4:00 P.M., Eastern
Time, or as soon thereafter as is practicable, or at such later time as the Registrant or its counsel may orally request via telephone call to the staff. This request for acceleration is subject, however, to your receiving a telephone call prior to
such time from our legal counsel, Cooley LLP, confirming this request. The Registrant hereby authorizes James Pennington of Cooley LLP to make such request on its behalf.

Once the Registration Statement has been declared effective, please orally confirm that event with James Pennington of Cooley LLP, counsel to
the Registrant, at (858) 550-6029.

Very truly yours,

Bionano Genomics, Inc.

By:

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

R. Erik Holmlin, Ph.D.

President and Chief Executive Officer

cc:
 Mike Ward, Bionano Genomics, Inc.

James Pennington, Cooley LLP

Angela Dowd, Loeb & Loeb LLP

CORRESP
1
filename1.htm

CORRESP

James Pennington

VIA EDGAR

+1 858 550 6029

jpennington@cooley.com

 July 13, 2018

 United
States Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 3030

 100 F Street, N.E.

Washington, D.C. 20549

 Attn: Amanda Ravitz

Re:
Bionano Genomics, Inc.

 Registration Statement on Form
S-1

 Filed June 28, 2018

File No. 333-225970

Dear Ms. Ravitz:

 On behalf of Bionano Genomics, Inc.
(“Bionano” or the “Company”), we are responding to the comments (the “Comments”) of the staff (the “Staff”) of the Securities and Exchange Commission
(the “Commission”) contained in its letter, dated July 12, 2018 (the “Comment Letter”), relating to the above referenced Registration Statement on Form S-1
(the “Registration Statement”).

 In response to the Comments set forth in the Comment Letter, the Company has revised the
Registration Statement and is publicly filing via EDGAR an Amended Registration Statement on Form S-1 (the “Amended Registration Statement”) with this response letter.

For ease of reference, set forth below are the Company’s responses to the Comments. The numbering of the paragraphs below corresponds to the numbering of
the Comments, which for your convenience we have incorporated into this response letter. Page references in the text of this response letter correspond to the page numbers of the Amended Registration Statement. Capitalized terms used in this letter
but not otherwise defined herein shall have the meanings set forth in the Amended Registration Statement.

 Staff Comments and Company Responses

 Overview, page 1

1.
We note your response to prior comment 2. Please revise to disclose the amount of revenue received from each of the customers you mention.

Response: The Company respectfully acknowledges the Staff’s comment and has revised pages 1 and 66 of the Registration Statement.

Use of Proceeds, page 46

2.
Please expand your response to prior comment 5 to clarify why you will be unable to identify the amount to be used for each purpose disclosed. Otherwise, revise to provide the approximate amount
intended to be used for each purpose you disclose. Refer to Item 504 of Regulation S-K.

Cooley LLP    4401 Eastgate Mall    San Diego, CA    92121

t: (858) 550-6000 f: (858) 550-6420 cooley.com

United States Securities and Exchange

Commission

July 13, 2018

Page Two

 Response: The Company respectfully acknowledges the Staff’s comment and has revised page 46 of
the Registration Statement.

 Results of Operations, page 56

3.
It appears from your revisions in response to prior comment 7 that product volume decreased for the period ended March 31, 2018. If so, quantify and explain the reasons for the decrease.

 Response: The Company respectfully acknowledges the Staff’s comment and has revised page 56 of the Registration Statement
with respect to the financial information as of the interim period ended June 30, 2018.

 Government Regulation, page 84

4.
We note your response to prior comment 3. Please revise your disclosure to discuss the regulatory requirements regarding laboratory developed tests and how these regulatory requirements differ when the tests
are developed wholly or partly outside of the laboratory that offers them. Also address in your disclosure whether you have pursued or intend to pursue regulatory approval prior to sale to cytogenetics labs.

Response: The Company respectfully acknowledges the Staff’s comment and has revised page 86 of the Registration Statement.

*************************

 The Company respectfully requests
the Staff’s assistance in completing the review of the Amended Registration Statement as soon as possible. Please advise us if we can provide any further information or assistance to facilitate your review. Please direct any further comments or
questions regarding the Amended Registration Statement or this response letter to me at (858) 550-6029.

Sincerely,

 Cooley LLP

/s/ James Pennington

 James Pennington

cc: R. Erik Holmlin, Ph.D., Bionano Genomics, Inc.

Cooley LLP    4401 Eastgate Mall    San Diego, CA    92121

t: (858) 550-6000 f: (858) 550-6420 cooley.com

Mail Stop 3030

July 12, 2018

Via E -mail
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9640 Towne Centre Drive, Suite 100
San Diego, California 92121

Re: Bionano Genomics, Inc.
Registration Statement on Form S-1
Filed June 28, 2018
  File No. 333-225970

Dear Dr. Holmlin :

We have reviewed your registration statement  and have the following comments.  In
some of our comments, we may ask you to provide us with information so we may better
understand your disc losure.

Please respond to this letter by amending your registration statement and providing the
requested information .  If you do not believe our comments apply to your facts and
circumstances or do not believe an amendment is appropriate, please tell us why in your
response.

After reviewing any amendment to your registration statement and the information you
provide in response to these  comments, we may have additional comments.

Overview, page 1

1. We note your response to prior comment 2.   Please revise to disclose the amount of
revenue received from each of the customers you mention.

Use of Proceeds, page 46

2. Please expand your response to prior comment 5 to clarify why you will be unable to
identify the amount to be used for each purpose disclosed.  Otherwise, revise to provide
the approximate amount intended to be used for each purpos e you disclose.  Refer to Item
504 of Regulation S -K.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
July 12 , 2018
Page 2

 Results of Operations, page 56

3. It appears from your revision s in response to prior comment 7  that product volume
decreased for the period ended March 31, 2018.  If so, quantify and explain the reaso ns
for the decrease.

Government Regulation, page 84

4. We note your response to prior comment 3.  Please revise your disclosure to discuss the
regulatory requirements regarding laboratory developed tests and how these regulatory
requirements differ when the tests are developed wholly or partly outside of the
laboratory that offers them.  Also address in your disclosure whether you have pursued or
intend to pursue regulatory approval prior to sale to cytogenetics labs.

We remind you that the company an d its management are responsible for the accuracy
and adequacy of their disclosures, notwithstanding any review, comments, action or absence of
action by the staff.

Refer to Rules 460 and 461 regarding requests for  acceleration.  Please allow adequate
time for us to review any amendment prior to the requested effective date of the registration
statement.

You may contact Julie Sherman  at (202) 551 -3640 or Brian Cascio, Accounting Branch
Chief , at (202) 551 -3676 if you have questions regarding comments on the financial statements
and related matters.  Please contact Heather Percival  at (202) 551 -3498 or Geoff Kruczek, Senior
Attorney, at (202) 551 -3641 with any other questions.

Sincerely,

 /s/ Geoff Kruczek for

Amanda Ravitz
Assistant Director
Office of Electronics and Machinery

cc: James C. Pennington, Esq.
Cooley LLP

CORRESP
1
filename1.htm

CORRESP

 James Pennington

 +1 858 550 6029

jpennington@cooley.com

VIA EDGAR

 June 28, 2018

 United
States Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 3030

 100 F Street, N.E.

Washington, D.C. 20549

 Attn: Amanda Ravitz

Re:
Bionano Genomics, Inc.

 Amendment No. 1 to

Draft Registration Statement on Form S-1

Submitted June 12, 2018

CIK No. 0001411690

 Dear
Ms. Ravitz:

 On behalf of Bionano Genomics, Inc. (“Bionano” or the “Company”), we are responding to
the comments (the “Comments”) of the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) contained in its letter, dated June 26, 2018 (the
“Comment Letter”), relating to the above referenced confidential draft Registration Statement on Form S-1 (the “Amended DRS”).

In response to the Comments set forth in the Comment Letter, the Company has revised the Amended DRS and is publicly filing via EDGAR a revised Registration
Statement on Form S-1 (the “Registration Statement”) with this response letter.

 For
ease of reference, set forth below are the Company’s responses to the Comments. The numbering of the paragraphs below corresponds to the numbering of the Comments, which for your convenience we have incorporated into this response letter. Page
references in the text of this response letter correspond to the page numbers of the Registration Statement. Capitalized terms used in this letter but not otherwise defined herein shall have the meanings set forth in the Registration Statement.

Staff Comments and Company Responses

 Overview, page 1

1.
It appears from your response to comment 3 that your beliefs regarding cost-effectiveness of your products are based on your expectations rather than existing facts. If so, please revise to disclose the basis
of your beliefs. Also, tell us whether “small variations” and “large variations” are industry terms of art. In this regard, it is unclear whether sequencing systems could detect “large variations,” given the number of
base pairs you indicate in your response.

 Response: The Company respectfully advises the Staff that the following facts are the
basis for its belief that its products are cost-effective:

 Cooley
LLP    4401 Eastgate Mall    San Diego, CA    92121

 t: (858)
550-6000  f: (858) 550-6420  cooley.com

 United States Securities and Exchange

Commission

 June 28, 2018

Page Two

a) Saphyr provides a comprehensive list of large variations (greater than 500 base pairs each) across a whole human genome for approximately
$500.

 b) Illumina is broadly recognized throughout the industry for offering cost-effective products for the detection of variations less
than 1,000 base pairs. Those products provide such detection for $1,000 per whole human genome.

 In addition, the Company respectfully advises the Staff
that the terms “small variations” and “large variations” are not industry terms of art.

 Large variations, as the Company describes
them, include those that are between 500 base pairs and entire chromosomal arms (up to around 100 million base pairs). The sequencing systems that represent nearly the entire sequencing industry (Illumina’s systems) can reliably detect
only an extremely limited subset of large variations – specifically only those between 500 base pairs and 1,000 base pairs. The base pairs within the large variations detected by Illumina represent a very small fraction of the base pairs within
all large variations in a human genome.

2.
We note your response to comment 4. Please revise to disclose the significance to your business of each of the customers named in your disclosure.

Response: The Company respectfully advises the Staff that the purpose of the Company’s disclosure of the named customers is to (i) identify
notable examples of its customers that are well-known in the Company’s industry and (ii) reflect that the Company’s customer base is comprised of a broad range of types of companies and institutions. The Company respectfully submits
that the existing disclosure in the immediately preceding sentence discloses the significance of these customers to the Company’s business in that it states that the Company’s customers include “some of the world’s most prominent
clinical, translational research, basic research, academic and government institutions as well as leading pharmaceutical and diagnostic companies.”

3.
Please expand your revisions in response to comment 5 to clarify how the market data in your submission reflects the research use only designation of your product. Also, we note the revisions regarding
laboratory developed tests. Please tell us how regulatory approval of laboratory developed tests would impact your addressable market, and revise your disclosure to briefly describe any regulatory uncertainty regarding laboratory developed
tests.

 Response: The Company respectfully acknowledges the Staff’s comment with respect to the research use only
designation of its product. Accordingly, the Company has updated the references to the market data regarding high throughput sequencers on pages 1, 66 and 68 of the Registration Statement to clarify that this data is related to research use only
high throughput sequencers.

 With respect to the SECs comment as it relates to how regulatory approval of laboratory developed tests
(“LDTs”) will impact the Company’s addressable market, the Company does not believe that regulatory approval of LDTs would impact the addressable market, which is comprised of the 2,500 clinical cytogenics labs existing
worldwide. However, the Company respectfully acknowledges that regulatory uncertainty regarding LDTs could delay the Company’s ability to sell its products to this addressable market and has revised the risk factor disclosure on page 23 of the
Registration Statement accordingly.

 Cooley
LLP    4401 Eastgate Mall    San Diego, CA    92121

 t: (858)
550-6000  f: (858) 550-6420  cooley.com

 United States Securities and Exchange

Commission

 June 28, 2018

Page Three

Market Opportunity, page 2

4.
We note your response to comment 6. Please tell us whether any of the installed base of high throughput sequencers are marketed as other than research use only.

Response: The Company respectfully advises the Staff that the installed base of 6,000 high throughput sequencers are marketed for research use only,
and has updated the disclosure on pages 1, 66 and 68 of the Registration Statement accordingly.

 Use of Proceeds, page 46

5.
We note your response to comment 10 regarding possible “more specific determinations” about the use of proceeds. Please expand to clarify whether you intend to quantify the amount of proceeds to be
used for each of the purposes to which you refer.

 Response: The Company respectfully acknowledges the Staff’s comment and
advises the Staff that, prior to the completion of the offering, it does not anticipate being able to make specific determinations as to the amount of proceeds to be used for each of the purposes to which it refers.

Capitalization, page 48

6.
We note your response to comment 11 but also note that the amounts presented in the capitalization table do not sum up to $(20,522,150). Please correct the presentation in your next amendment.

 Response: The Company respectfully acknowledges the Staff’s comment and has revised the presentation in the capitalization
table on page 48 of the Registration Statement.

 Comparison of the Three Months Ended March 31, 2017 and 2018, page 56

7.
Please revise to clarify and quantify how changes in volume of instruments and consumables sold affected your results for the three months ended March 31, 2018 compared to the same period in
2017.

 Response: The Company respectfully acknowledges the Staff’s comment and will revise the next amendment of the
Registration Statement accordingly.

 Comparison of the Years Ended December 31, 2016 and 2017, page 57

8.
Please revise your disclosure in response to comment 12 to provide quantifications of revenue increases in volume and price as well as the growth rate in revenue from sales of instruments versus
consumables.

 Response: The Company respectfully acknowledges the Staff’s comment and has revised page 58 of the
Registration Statement.

 Cooley LLP    4401
Eastgate Mall    San Diego, CA    92121

 t: (858) 550-6000  f: (858)
550-6420  cooley.com

 United States Securities and Exchange

Commission

 June 28, 2018

Page Four

Principle Stockholders, page 109

9.
While we note your revisions in note 1 in response to comment 19, those revisions appear to refer only to who disclaims beneficial ownership rather than who has beneficial ownership. Please revise to identify
the natural persons who have or share voting and/or investment power over the referenced shares.

 Response: The Company
respectfully acknowledges the Staff’s comment and has revised page 110 of the Registration Statement.

 Note 2. Summary of Significant Accounting
Policies, page F-8

 Revenue Recognition, page F-10

10.
We note that your response to comment 22 appears to only address software upgrades and indicates that this is deemed incidental to the hardware. However, the disclosure on page 80 indicates that performance
enhancements will be delivered on a regular basis through software and hardware upgrades. Please revise further to disclose your accounting for hardware upgrades.

Response: The Company respectfully acknowledges the Staff’s comment and has revised page F-10 of the
Registration Statement.

 *************************

 The
Company respectfully requests the Staff’s assistance in completing the review of the Registration Statement as soon as possible. Please advise us if we can provide any further information or assistance to facilitate your review. Please direct
any further comments or questions regarding the Registration Statement or this response letter to me at (858) 550-6029.

Sincerely,

 Cooley LLP

/s/ James Pennington

 James Pennington

cc: R. Erik Holmlin, Ph.D., Bionano Genomics, Inc.

Cooley LLP    4401 Eastgate Mall    San Diego, CA    92121

t: (858) 550-6000  f: (858) 550-6420  cooley.com

Mail Stop 3030

June 26 , 2018

Via E -mail
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9640 Towne Centre Drive, Suite 100
San Diego, California 92121

Re: Bionano Genomics, Inc.
Amendment No. 1 to
Draft Registration Statement on Form S -1
Submitted June 12, 2018
  CIK No. 0001411690

Dear Dr. Holmlin :

We have reviewed your amended draft registration statement  and have the following
comments.  In some of our comments, we may ask you to provide us with i nformation so we
may better understand your disclosure.

Please respond to this letter by providing the requested information and either submitting
an amended draft registration statement or publicly filing your registration statement on
EDGAR.  If you do not believe our comments apply to your facts and circumstances or do not
believe an amendment is appropriate, please tell us why in your response.

After reviewing the information you provide in response to these  comments  and your
amended draft registration statement or filed registration statement,  we may have  additional
comments.

Overview,  page 1

1. It appears from your response to comment 3 that your beliefs  regarding cost -effectiveness
of your products are based on your expectations rather than existing facts.  If so, please
revise to disclose the basis of your beliefs.  Also, tell us wheth er “small variations” and
“large variations” are industry terms of art.  In this regard, it is unclear whether
sequencing systems could detect “large variations,” given the number of base pairs you
indicate in your response.

2. We note your response to comm ent 4.  Please revise to disclose the significance to your
business of each of the customers named in your disclosure.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 26, 2018
Page 2

3. Please expand your revisions in response to comment 5 to clarify how the market data in
your submission reflects the research use only designation of your product.  Also, we
note the revisions regarding laboratory developed tests.  Please tell us how regulatory
approval of laboratory developed tests would impact your addressable market, and revise
your disclosure to briefly describe any r egulatory uncertainty regarding laboratory
developed tests.

Market Opportunity, page 2

4. We note your response to comment 6.  Please tell us whether any of the installed base of
high throughput sequencers are marketed as other than research use only.

Use of Proceeds, page 46

5. We note your response to comment 10 regarding possible “more specific determinations”
about the use of proceeds.  Please expand to clarify whether you intend to quantify the
amount of proceeds to be used for each of the purposes to  which you refer.

Capitalization, page 48

6. We note your response to comment 11 but also note that the amounts presented in the
capitalization table do not sum up to $(20,522,150).  Please correct the presentation in
your next amendment.

Comparison of the Three Months Ended March 31, 2017 and 2018, page 56

7. Please revise to clarify and quantify how changes in volume of instruments and
consumables sold affected your results for the three months ended March 31, 2018
compared to the same period in 2017.

Comparison of the Years Ended December 31, 2016 and 2017 , page 57

8. Please revise your disclosure in response to comment 12 to provide quantifications of
revenue increases in volume and price as well as the growth rate in revenue from sales of
instruments v ersus consumables.

Principle Stockholders, page 109

9. While we note your revisions in note 1 in response to comment 19, those revisions appear
to refer only to who disclaims beneficial ownership rather than who has beneficial
ownership.  Please revise to  identify the natural persons who have or share voting and/or
investment po wer over the referenced shares.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 26, 2018
Page 3

 Note 2. Summary of Significant Accounting Policies, page F -8

Revenue Recognition, page F -10

10. We note that your response to comment 22 appears to on ly address software upgrades
and indicates that this is deemed incidental to the hardware.  However, the disclosure on
page 80 indicates that performance enhancements will be delivered on a regular basis
through software and hardware upgrades.  Please revi se further to disclose your
accounting for hardware upgrades.

You may contact Julie Sherman  at (202) 551 -3640 or Brian Cascio, Accounting Branch
Chief , at (202) 551 -3676  if you have questions regarding comments on the financial statements
and related matt ers.  Please contact Heather Percival  at (202) 551 -3498 or Geoff Kruczek, Senior
Attorney, at (202) 551 -3641  with any other questions.

Sincerely,

 /s/ Geoff Kruczek for

Amanda Ravitz
Assistant Director
Office of Electronics and Machinery

cc: James C.  Pennington, Esq.
Cooley LLP

Mail Stop 3030

June 5 , 2018

Via E -mail
R. Erik Holmlin, Ph.D.
President and Chief Executive Officer
Bionano Genomics, Inc.
9640 Towne Centre Drive, Suite 100
San Diego, California 92121

Re: Bionano Genomics, Inc.
Draft Registration Statement on Form S -1
Submitted May 14, 2018
  CIK No. 0001411690

Dear Dr. Holmlin:

We have reviewed your draft registration statement and have the following comments.  In
some of our comments, we may ask you to provide us with information so we may better
underst and your disclosure.

Please respond to this letter by providing any requested information and by publicly
filing your registration statement and non -public draft submission on EDGAR.  If you do not
believe our comments apply to your facts and circumstance s or do not believe revisions in
response to these comments are appropriate, please tell us why in your response.

After reviewing the information you provide in response to these comments and your
filed registration statement, we may have additional comments.

Cover Page

1. Please supplementally provide us with copies of all written communications, as defined
in Rule  405 under the Securities Act, that you , or anyone authorized to do so on your
behalf , present to potential investors in reliance on Section 5(d) of the Securities Act,
whether or not they retain copies of the communications.

2. We note your disclosure that  the closing of the offering is contingent on Nasdaq listing of
your common stock.  This contingency appears to create an offering that is other than a
firm commitment.  It is unclear whether the underwriters will be collecting funds prior to
the contingen cy being satisfied.  If so, please tell us whether the underwriters  will comply
with Rule 15c2 -4.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 2

 Overview, page 1

3. Please provide the basis for your beliefs regarding your product, including but not limited
to your belief that your product is cost -effec tive.  Also, given your extensive disclosure
regarding the attributes and functionality of your product relative to competing products,
please explain the reasons for your current level of sales and share of the market in which
you compete.

4. Please tell us the criteria you used to determine that the customers you highlight are
objectively representative of your business.  Include in your response whether any
unnamed customers also satisfy those criteria.

5. Please revise to disclose clearly and prominently the research use only designation of
your system and consumables.  Also revise to disclose how this designation impacts you r
addressable market.

Market Opportunity, page 2

6. Please tell us your basis for the addressable market calculations, given its res earch use
only designation, and provide a more detailed discussion of underlying assumptions used
in your calculations.  Please also provide your basis for the 15% figure on page 67.

Our Focus Areas, page 4

7. Please revise to clarify how you are addressin g these focus areas, including that you are
providing a system for research use only rather than the diagnosis or treatment of an y of
the diseases you mention.

Risk Factors, page 11

8. Please add risk factor disclosure for the exclusive forum provision disclosed on page 113.
Include as a separate risk factor a discussion of the risks associated with the provision
designating the U.S. federal district courts as the exclusive forum for re solving any
complaint asserting a cause of action arising under the Securities Act.

Provisions of our secured term loan facility…, page 14

9. Please expand your risk factor to include a brief description of the financial covenants
contained in your loan a greement.  Also, if the potential risk you discuss has actually
occurred, please revise to state so directly.  For example, please revise to address your
default and subsequent forbearance agreement from Western Alliance Bank for failing to
raise additiona l capital as of December 31, 2017 as described on page 58.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 3

 Use of Proceeds, page 46

10. Please disclose the amount of proceeds that you currently intend to use for each of the
purposes mentioned in the penultimate paragraph of this section.  Also, provide more
detail regarding your plan to expand your commercial capabilities and what research and
development activities you intend to fund.

Capitalization, page 48

11. Please explain to us how you calculated total capitalization in the table.

Comparison of th e Years Ended December 31, 2016 and 2017, page 56

12. Please quantify the amount of the increase in revenues attributable to changes in price
and increases in volume.  Also, provide the relative growth rate in revenue from sales of
instruments versus consumab les.

13. Please clarify your disclosure that you incurred higher manufacturing costs of your
instruments due to “the purchase quantities at lower volumes on a per -batch basis” given
you sold more instruments in the year ended December 31, 2017 compared to 20 16.

Loan facility, page 58

14. Please disclose the financing milestone that must be achieved in order to extend the
interest -only payments.

Note purchase agreement, page 58

15. Please file the note purchase agreement as an exhibit to your registration statement or
advise.

Business, page 65

Overview, page 65

16. Refer to the fourth paragraph.  Please revise to clarify your disclosure that your product is
being adopted as a “comple ment” to sequencers.  For example, do sequencers detect
variations that your product cannot detect?  Does your product function effectively only
when used with sequencers?

The Saphyr System’s Industry -Leading Sensitivity and Specificity, page 76

17. Please  tell us whether you commissioned any of the publications or studies cited in your
prospectus.

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 4

Certain Relationships and Related Party Transactions, page 105

18. Please disclose the conversion or net exercise rate for the securities identified in this
section, such as the February 2018 notes discussed on page F -26 and the number of
securities to be received upon conversion in connection with this transaction.

Principal Stockholders, page 108

19. Please revise your disclosure to identity the natural person or  persons who share voting
and investment control of the shares held by Praise Alliance International Limited and
Full Succeed International Limited.  Also, identify the natural person or persons with
whom Mr. Wang shares voting or investment control of the  shares held by LC Fund VI,
L.P. or advise.

Shares Eligible for Future Sale, page 114

20. We note you are not registering the shares issuable upon exercise of the underwriters’
warrants.  Please revise the disclosure in the second paragraph of this section regarding
the shares underlying the underwriters’ warrants accordingly or advise.

Financial Statements, page F -1

Note 2. Summary of Significant Accounting Policies, page F -8

Revenue Recognition, page F -10

21. We note your  discussion that the timing of revenue recognition on instrument sales is
based upon when delivery has occurred, the price is fixed or determinable, and
collectability is reasonably assured.  Please revise to disclose your accounting for
installation in di rect sales with customers.

22. We note your disclosure on page 79 that you designed the Saphyr system to
accommodate performance upgrades without the need for replacement of the entire
instrument and that performance enhancements will be delivered on a regul ar basis
through software and hardware upgrades.  Please revise to disclose your accounting for
these upgrades.

Note 8. Convertible Preferred Stock and Stockholders’ Deficit, page F -18

Common Stock, page F -21

23. We note the issuances of convertible preferr ed stock at prices significantly higher than
the exercise price of stock options granted.  Please explain to us how you considered the

R. Erik Holmlin, Ph.D.
Bionano Genomics, Inc.
June 5, 2018
Page 5

 convertible preferred stock issuances in the valuation of stock options granted in fiscal
2017.

We remind you that the  company and its management are responsible for the accuracy
and adequacy of their disclosures, notwithstanding any review, comments, action or absence of
action by the staff.

We also remind you that your registration statement must be on file no later than 48 hours
prior to the requested effective date and time.  Refer to Rules 460 and 461 regarding requests for
acceleration.  Please allow adequate time for us to review any ame ndment prior to the requested
effective date of the registration statement.

You may contact Julie Sherman at (202) 551 -3640 or Brian Cascio , Accounting Branch
Chief , at (202) 551 -3676 if you have questions regarding comments on the financial statemen ts
and related matters.  Please contact Heather Percival at (202) 551 -3498 or Geoff Kruczek, Senior
Attorney, at (202) 551 -3641 with any other questions.

Sincerely,

 /s/ Geoff Kruczek for

Amanda Ravitz
Assistant Director
Office of Electronics and Machi nery

cc: James C. Pennington, Esq.
Cooley LLP