Patents by Inventor Shawn Manchester

Shawn Manchester has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20200291392
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: May 29, 2020
    Publication date: September 17, 2020
    Inventors: ZACH SERBER, ERIK JEDEDIAH DEAN, SHAWN MANCHESTER, KATHERINE GORA, MICHAEL FLASHMAN, ERIN SHELLMAN, AARON KIMBALL, SHAWN SZYJKA, BARBARA FREWEN, THOMAS TREYNOR, KENNETH S. BRUNO
  • Publication number: 20200263214
    Abstract: The disclosure relates to host cells having altered NADPH availability, allowing for increased production of compounds produced using NADPH, and methods of use thereof. NADPH availability is altered by one or more of: expressing an altered GAPDH, expressing a variant glutamate dehydrogenase (gdh), aspartate semialdehyde dehydrogenase (asd), dihydropicolinate reductase (dapB), and meso-diaminopimelate dehydrogenase (ddh), expressing a novel nicotinamide nucleotide transhydrogenase, expressing a novel threonine aldolase, and expressing or modulating the expression of a pyruvate carboxylase in the host cells.
    Type: Application
    Filed: May 18, 2018
    Publication date: August 20, 2020
    Inventors: Shawn Manchester, Benjamin Mason, Alexi Goranov
  • Patent number: 10745694
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: November 27, 2019
    Date of Patent: August 18, 2020
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20200239873
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: April 2, 2020
    Publication date: July 30, 2020
    Inventors: Zach SERBER, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20200149035
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: November 27, 2019
    Publication date: May 14, 2020
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Patent number: 10647980
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: July 1, 2019
    Date of Patent: May 12, 2020
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20200123496
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial hemoglobin gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial hemoglobin gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial hemoglobin genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Application
    Filed: December 20, 2019
    Publication date: April 23, 2020
    Inventors: Shawn Manchester, Alexander Neckelmann
  • Publication number: 20200123529
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial glucose permease gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial glucose permease gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial glucose permease genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Application
    Filed: December 20, 2019
    Publication date: April 23, 2020
    Inventors: Shawn Manchester, Jeffrey Mellin
  • Publication number: 20200048628
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: October 28, 2019
    Publication date: February 13, 2020
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Patent number: 10544411
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial glucose permease gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial glucose permease gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial glucose permease genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Grant
    Filed: June 29, 2017
    Date of Patent: January 28, 2020
    Assignee: Zymergen Inc.
    Inventors: Shawn Manchester, Jeffrey Mellin
  • Patent number: 10544390
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial hemoglobin gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial hemoglobin gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial hemoglobin genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Grant
    Filed: June 28, 2017
    Date of Patent: January 28, 2020
    Assignee: Zymergen Inc.
    Inventors: Shawn Manchester, Alexander Neckelmann
  • Patent number: 10457933
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: October 29, 2019
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20190316117
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: July 1, 2019
    Publication date: October 17, 2019
    Applicant: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Patent number: 10336998
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: July 2, 2019
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20190194647
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial glucose permease gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial glucose permease gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial glucose permease genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Application
    Filed: June 29, 2017
    Publication date: June 27, 2019
    Applicant: Zymergen Inc.
    Inventors: Shawn Manchester, Jeffrey Mellin
  • Publication number: 20190194599
    Abstract: The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial hemoglobin gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial hemoglobin gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial hemoglobin genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
    Type: Application
    Filed: June 28, 2017
    Publication date: June 27, 2019
    Inventors: Shawn Manchester, Alexander Neckelmann
  • Publication number: 20190194769
    Abstract: The present disclosure provides novel bacterial strains with altered expression or start codon modification of one or more RNA degradation/processing genes. The RNA degradation genes of the present disclosure are controlled by heterologous promoters. The present disclosure further describes methods for generating microbial strains comprising heterologous promoter sequences operably linked to RNA degradation/processing genes.
    Type: Application
    Filed: June 27, 2017
    Publication date: June 27, 2019
    Inventor: Shawn Manchester
  • Patent number: 10047358
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: August 14, 2018
    Assignee: Zymergen Inc.
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20180216099
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: March 16, 2018
    Publication date: August 2, 2018
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
  • Publication number: 20180216100
    Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.
    Type: Application
    Filed: March 16, 2018
    Publication date: August 2, 2018
    Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno