Patents by Inventor Erik Jedediah Dean

Erik Jedediah Dean 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: 20230078488
    Abstract: The present disclosure provides methods for predicting phenotypic performance of a host cell in industrial culture. Specifically, the present disclosure provides methods for predicting phenotypic performance of a host cell in industrial culture by determining the metabolite fingerprinting profile of a host cell in small lab-scale culture and applying said profile to a predictive model of phenotypic performance.
    Type: Application
    Filed: November 16, 2022
    Publication date: March 16, 2023
    Inventors: Erik Jedediah DEAN, Stephen LOK, Ana Belen IBANEZ ZAMORA, Ee-Been GOH, Stefan BAUER, Franklin LU
  • Publication number: 20220275361
    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 alga, 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 17, 2022
    Publication date: September 1, 2022
    Inventors: Zachariah 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: 20220230711
    Abstract: The present disclosure provides a microbe engineering platform that permits optimization of microbe fitness levels to optimize a microbe's suitability for industrial fermentation. The disclosed platform identifies an association between microbe properties and microbe fitness levels. The association between microbe properties and microbe fitness levels may be used to identify candidate microbes with desired fitness levels. The identified candidate microbes may be used to further optimize the industrial fermentation process.
    Type: Application
    Filed: December 6, 2021
    Publication date: July 21, 2022
    Applicant: ZYMERGEN INC.
    Inventors: WILLIAM SERBER, ERIK JEDEDIAH DEAN
  • Patent number: 11352621
    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: May 7, 2021
    Date of Patent: June 7, 2022
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 11312951
    Abstract: The present disclosure provides systems and methods for host cell improvement utilizing epistatic effects. The systems and methods described herein are host cell agnostic and therefore can be implemented across taxa. Furthermore, the disclosed systems and methods can be implemented to modulate or improve any host cell parameter of interest.
    Type: Grant
    Filed: May 12, 2021
    Date of Patent: April 26, 2022
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 11227670
    Abstract: The present disclosure provides a microbe engineering platform that permits optimization of microbe fitness levels to optimize a microbe's suitability for industrial fermentation. The disclosed platform identifies an association between microbe properties and microbe fitness levels. The association between microbe properties and microbe fitness levels may be used to identify candidate microbes with desired fitness levels. The identified candidate microbes may be used to further optimize the industrial fermentation process.
    Type: Grant
    Filed: May 4, 2018
    Date of Patent: January 18, 2022
    Assignee: ZYMERGEN INC.
    Inventors: William Serber, Erik Jedediah Dean
  • Patent number: 11208649
    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: May 5, 2021
    Date of Patent: December 28, 2021
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 11155807
    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: December 18, 2020
    Date of Patent: October 26, 2021
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 11155808
    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 22, 2021
    Date of Patent: October 26, 2021
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 20210324378
    Abstract: The present disclosure relates to methods of joining three or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro or in vivo. The method allows the joining of a large number of DNA fragments, in a deterministic fashion. It can be used to rapidly generate nucleic acid libraries that can be subsequently used in a variety of applications that include, for example, genome editing and pathway assembly. Kits for performing the method are also disclosed.
    Type: Application
    Filed: June 23, 2021
    Publication date: October 21, 2021
    Inventors: Erik Jedediah DEAN, Kedar PATEL, Aaron MILLER, Kunal MEHTA, Philip WEYMAN
  • Publication number: 20210284992
    Abstract: The present disclosure provides systems and methods for host cell improvement utilizing epistatic effects. The systems and methods described herein are host cell agnostic and therefore can be implemented across taxa. Furthermore, the disclosed systems and methods can be implemented to modulate or improve any host cell parameter of interest.
    Type: Application
    Filed: May 12, 2021
    Publication date: September 16, 2021
    Inventors: Zachariah 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: 20210261949
    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 5, 2021
    Publication date: August 26, 2021
    Inventors: Zachariah 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: 20210261950
    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 7, 2021
    Publication date: August 26, 2021
    Inventors: Zachariah 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: 11085040
    Abstract: The present disclosure provides systems and methods for host cell improvement utilizing epistatic effects. The systems and methods described herein are host cell agnostic and therefore can be implemented across taxa. Furthermore, the disclosed systems and methods can be implemented to modulate or improve any host cell parameter of interest.
    Type: Grant
    Filed: October 28, 2019
    Date of Patent: August 10, 2021
    Assignee: Zymergen Inc.
    Inventors: Zachariah 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: 20210222156
    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 22, 2021
    Publication date: July 22, 2021
    Inventors: Zachariah 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: 20210225455
    Abstract: Systems, methods and non-transitory computer-readable media identify a candidate biological sequence for enabling a function in a host cell. Embodiments access a predictive model that associates a plurality of biological sequences, such as enzymes, with one or more functions, such as reaction catalysis; predict, using the predictive model, that one or more candidate sequences of the plurality of biological sequences enable a desired function; and classify using a processor, candidate sequences that satisfy a confidence threshold as filtered candidate sequences.
    Type: Application
    Filed: August 14, 2019
    Publication date: July 22, 2021
    Applicant: Zymergen Inc.
    Inventors: Anupam Chowdhury, Alexander Glennon Shearer, Stepan Tymoshenko, Michelle L. Wynn, Erik Jedediah Dean
  • Patent number: 11066663
    Abstract: The present disclosure relates to methods of joining three or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro or in vivo. The method allows the joining of a large number of DNA fragments, in a deterministic fashion. It can be used to rapidly generate nucleic acid libraries that can be subsequently used in a variety of applications that include, for example, genome editing and pathway assembly. Kits for performing the method are also disclosed.
    Type: Grant
    Filed: October 31, 2019
    Date of Patent: July 20, 2021
    Assignee: Zymergen Inc.
    Inventors: Erik Jedediah Dean, Kedar Patel, Aaron Miller, Kunal Mehta, Philip Weyman
  • Publication number: 20210102193
    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: December 18, 2020
    Publication date: April 8, 2021
    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: 10968445
    Abstract: The present disclosure provides machine learning techniques for computationally predicting the phenotypic performance of combinations of genetic variations and for designing new improved host cells. The machine learning models and methods described herein are host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any host cell parameter of interest.
    Type: Grant
    Filed: October 15, 2020
    Date of Patent: April 6, 2021
    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: 20210024918
    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 15, 2020
    Publication date: January 28, 2021
    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