Patents by Inventor Zach Serber
Zach Serber 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).
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Publication number: 20220356497Abstract: The disclosure relates to the biosynthesis of terpenoids, such as, for example, geraniol and derivatives thereof, using genetic engineering. In particular, the disclosure relates to the biosynthesis of nepetalactol, nepetalactone, dihydronepetalactone, and derivatives thereof. The disclosure provides recombinant cells genetically engineered to produce high levels of nepetalactol, nepetalactone and/or dihydronepetalactone. The disclosure also provides methods of producing nepetalactol, nepetalactone and dihydronepetalactone using cell-based systems as well as cell-free systems.Type: ApplicationFiled: June 26, 2020Publication date: November 10, 2022Inventors: Stefan DE KOK, Warren LAU, Fern MCSORLEY, Hermann-Josef MEYER, Zach SERBER, Grayson WAWRZYN
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Patent number: 11193150Abstract: The present disclosure provides isolated nepetalactone oxidoreductase polypeptides (NORs), nepetalactol synthases (NEPSs), and related polynucleotides, engineered host cells, and cultures, as well as methods for producing NORs and NEPSs, and for using them to produce nepetalactol, nepetalactone, and dihydronepetalactone. The present disclosure also provides methods for engineering cells (e.g., microbial cells) to produce nepetalactone from a fermentation substrate such as glucose, as well as engineered cells having this capability and related cultures and methods for producing nepetalactone.Type: GrantFiled: May 29, 2020Date of Patent: December 7, 2021Assignee: ZYMERGEN INC.Inventors: Grayson Wawrzyn, Christine Roche, Patrick J. Westfall, Warren Lau, Savita Ganesan, Fern R. McSorley, Zach Serber
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Publication number: 20210102193Abstract: 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: December 18, 2020Publication date: April 8, 2021Inventors: 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: 10968445Abstract: 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: GrantFiled: October 15, 2020Date of Patent: April 6, 2021Assignee: 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: 20210024918Abstract: 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: October 15, 2020Publication date: January 28, 2021Inventors: 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: 10883101Abstract: 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: May 29, 2020Date of Patent: January 5, 2021Assignee: 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: 20200370058Abstract: The present disclosure provides a HTP genomic engineering platform for improving Escherichia coli. 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.Type: ApplicationFiled: June 6, 2018Publication date: November 26, 2020Inventors: Matthew Davis, Christy Wisnewski, Patrick Westfall, Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Michael Flashman, Robert Haushalter, Stacy-Anne Morgan, Michael Blaisse, Prabha Ramakrishnan, Kyle Rothschild-Mancinelli, Youngnyun Kim
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Publication number: 20200362376Abstract: The present disclosure provides isolated nepetalactone oxidoreductase polypeptides (NORs), nepetalactol synthases (NEPSs), and related polynucleotides, engineered host cells, and cultures, as well as methods for producing NORs and NEPSs, and for using them to produce nepetalactol, nepetalactone, and dihydronepetalactone. The present disclosure also provides methods for engineering cells (e.g., microbial cells) to produce nepetalactone from a fermentation substrate such as glucose, as well as engineered cells having this capability and related cultures and methods for producing nepetalactone.Type: ApplicationFiled: May 29, 2020Publication date: November 19, 2020Applicant: Zymergen Inc.Inventors: Grayson Wawrzyn, Christine Roche, Patrick J. Westfall, Warren Lau, Savita Ganesan, Fern R. McSorley, Zach Serber
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Patent number: 10808243Abstract: 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: April 2, 2020Date of Patent: October 20, 2020Assignee: 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: 20200291392Abstract: 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: May 29, 2020Publication date: September 17, 2020Inventors: 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: 10745694Abstract: 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: November 27, 2019Date of Patent: August 18, 2020Assignee: 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: 20200239897Abstract: Provided are native promoters comprising polynucleotides isolated from Corynebacterium glutamicum, and mutant promoters derived therefrom, which may be used to regulate, i.e., either increase or decrease, on-pathway and/or off-pathway gene expression. Also provided are promoter ladders comprising a plurality of the promoters having incrementally increasing promoter activity. Also provided are host cells and recombinant vectors comprising the promoters, and methods of expressing ancillary genes of interest and producing biomolecules using the host cells.Type: ApplicationFiled: June 7, 2018Publication date: July 30, 2020Inventors: Zach Serber, Katherine G. Gora, Shawn P. Manchester, Peter Enyeart, Alexander Shearer
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Publication number: 20200239873Abstract: 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: April 2, 2020Publication date: July 30, 2020Inventors: 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: 10696991Abstract: The present disclosure provides isolated nepetalactone oxidoreductase polypeptides (NORs), nepetalactol synthases (NEPSs), and related polynucleotides, engineered host cells, and cultures, as well as methods for producing NORs and NEPSs, and for using them to produce nepetalactol, nepetalactone, and dihydronepetalactone. The present disclosure also provides methods for engineering cells (e.g., microbial cells) to produce nepetalactone from a fermentation substrate such as glucose, as well as engineered cells having this capability and related cultures and methods for producing nepetalactone.Type: GrantFiled: August 7, 2019Date of Patent: June 30, 2020Assignee: Zymergen Inc.Inventors: Grayson Wawrzyn, Christine Roche, Patrick J. Westfall, Warren Lau, Savita Ganesan, Fern R. McSorley, Zach Serber
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Publication number: 20200149035Abstract: 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: November 27, 2019Publication date: May 14, 2020Inventors: 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: 10647980Abstract: 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: July 1, 2019Date of Patent: May 12, 2020Assignee: 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: 20200048628Abstract: 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: October 28, 2019Publication date: February 13, 2020Inventors: 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: 20190390237Abstract: The present disclosure provides isolated nepetalactone oxidoreductase polypeptides (NORs), nepetalactol synthases (NEPSs), and related polynucleotides, engineered host cells, and cultures, as well as methods for producing NORs and NEPSs, and for using them to produce nepetalactol, nepetalactone, and dihydronepetalactone. The present disclosure also provides methods for engineering cells (e.g., microbial cells) to produce nepetalactone from a fermentation substrate such as glucose, as well as engineered cells having this capability and related cultures and methods for producing nepetalactone.Type: ApplicationFiled: August 7, 2019Publication date: December 26, 2019Inventors: Grayson Wawrzyn, Christine Roche, Patrick J. Westfall, Warren Lau, Savita Ganesan, Fern R. McSorley, Zach Serber
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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