Patents Assigned to Zymergen, Inc.
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Patent number: 10544390Abstract: 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: GrantFiled: June 28, 2017Date of Patent: January 28, 2020Assignee: Zymergen Inc.Inventors: Shawn Manchester, Alexander Neckelmann
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Patent number: 10544411Abstract: 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: GrantFiled: June 29, 2017Date of Patent: January 28, 2020Assignee: Zymergen Inc.Inventors: Shawn Manchester, Jeffrey Mellin
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Publication number: 20190392919Abstract: Systems and methods for predicting the viability of producing target molecules in a host organism are provided. A starting metabolite set for the host and a reaction set are obtained. Included in a filtered reaction set are reactions that are indicated as catalyzed by one or more corresponding catalysts that are themselves indicated as likely available to catalyze the reactions in the host organism. In each processing step, pursuant to the reactions of the filtered reaction set, data representing the starting metabolites and metabolites generated in previous processing steps is processed, to generate data representing one or more viable target molecules.Type: ApplicationFiled: August 12, 2019Publication date: December 26, 2019Applicant: Zymergen Inc.Inventors: Erik Jedediah Dean, Alexander G. Shearer, Michelle L. Wynn
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Patent number: 10457933Abstract: 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: GrantFiled: March 16, 2018Date of Patent: October 29, 2019Assignee: 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
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Publication number: 20190316117Abstract: 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: ApplicationFiled: July 1, 2019Publication date: October 17, 2019Applicant: 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
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Patent number: 10336999Abstract: The disclosure provides compositions and methods for producing natural products in microorganisms that are otherwise unexpressed, poorly expressed or poorly transcribed. In particular aspects, the disclosure provides compositions and methods for activating a silent gene or gene cluster with a bacteriophage and/or Streptomyces Antibiotic Regulatory Protein (SARP) transcription factor.Type: GrantFiled: May 27, 2016Date of Patent: July 2, 2019Assignee: Zymergen Inc.Inventors: Oliver Liu, Jeffrey Hoon Kim
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Patent number: 10336998Abstract: 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: GrantFiled: March 16, 2018Date of Patent: July 2, 2019Assignee: 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
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Publication number: 20190194647Abstract: 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: ApplicationFiled: June 29, 2017Publication date: June 27, 2019Applicant: Zymergen Inc.Inventors: Shawn Manchester, Jeffrey Mellin
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Patent number: 10318526Abstract: Systems and methods for enabling construction of complex Boolean chemical substructure queries in a structured graphical user interface are provided. The chemical substructures (molecules) may be represented graphically in standard molecular notation, and may be arranged horizontally and vertically on the interface, along with Boolean logical operators. Boolean logical operators of a first type may logically associate molecules arranged in horizontal fashion to form row queries, whereas Boolean logical operators of a different, second type may logically associate the row queries to form a composite query to be applied to a database of molecules. The operators of the first type may comprise disjunctive operators, whereas the operators of the second type may comprise conjunctive operators.Type: GrantFiled: July 5, 2016Date of Patent: June 11, 2019Assignee: Zymergen Inc.Inventors: Jed Dean, Adam Safir, Gregory Michael Werner
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Patent number: 10233419Abstract: Disclosed are apparatuses, systems, and methods for performing electroporation.Type: GrantFiled: June 30, 2016Date of Patent: March 19, 2019Assignee: Zymergen Inc.Inventors: John Cesarek, Travis Lee, Richard Hansen
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Patent number: 10047358Abstract: 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: GrantFiled: March 16, 2018Date of Patent: August 14, 2018Assignee: 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
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Patent number: 9988624Abstract: 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: GrantFiled: December 30, 2016Date of Patent: June 5, 2018Assignee: 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
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Publication number: 20180011899Abstract: Systems and methods for enabling construction of complex Boolean chemical substructure queries in a structured graphical user interface are provided. The chemical substructures (molecules) may be represented graphically in standard molecular notation, and may be arranged horizontally and vertically on the interface, along with Boolean logical operators. Boolean logical operators of a first type may logically associate molecules arranged in horizontal fashion to form row queries, whereas Boolean logical operators of a different, second type may logically associate the row queries to form a composite query to be applied to a database of molecules. The operators of the first type may comprise disjunctive operators, whereas the operators of the second type may comprise conjunctive operators.Type: ApplicationFiled: July 5, 2016Publication date: January 11, 2018Applicant: Zymergen, Inc.Inventors: Jed Dean, Adam Safir, Gregory Michael Werner
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Publication number: 20170316353Abstract: The generation of a factory order to control production of nucleotide sequences by a gene manufacturing system includes receiving an expression indicating an operation on sequence operands, each representing at least one nucleotide sequence part, evaluating the expression to a sequence specification, wherein the sequence specification comprises a data structure including one or more first-level operations and one or more second-level operations, and generating the factory order based upon execution of the one or more first-level operations and the one or more second-level operations. In a recursive manner, the one or more first-level operations operate on at least one first-level sequence operand, the value of which is resolved by execution of one or more of the second-level operations. The factory order may then be provided to the gene manufacturing system to assemble the sequence parts into nucleotide sequences represented by the sequence specification.Type: ApplicationFiled: April 27, 2016Publication date: November 2, 2017Applicant: Zymergen, Inc.Inventors: Barbara Frewen, Aaron Kimball