Patents by Inventor Shawn Szyjka
Shawn Szyjka 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: 20230340539Abstract: The present disclosure provides methods for producing gene-edited cells free of gene-editing system molecules through the manipulation of prototrophy. Exemplary system molecules include those required for CRISPR editing techniques, such as plasmids and genes encoding Cas nucleases. The methods may employ constructs that temporarily disrupt prototrophy, the removal of which restores prototrophy. Also disclosed are gene-edited cells and populations of gene-edited cells comprising these constructs. The present methods and compositions may be used to achieve desired gene editing of a host cell in the absence of extraneous genetic material remaining from the genetic engineering technique itself.Type: ApplicationFiled: May 25, 2021Publication date: October 26, 2023Inventors: Colin Scott MAXWELL, Solomon Henry STONEBLOOM, Shawn SZYJKA
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Publication number: 20230265460Abstract: Provided herein are nucleic acid constructs comprising multiple guide RNAs interspersed with tRNA sequence at regular intervals as well as expression vectors and compositions comprising the same. Also provided herein are methods for assembling the nucleic acid constructs comprising multiple guide RNAs interspersed with tRNA sequence at regular intervals in a pooled and/or modular manner. Methods for using the nucleic acid constructs comprising multiple guide RNAs interspersed with tRNA sequence at regular intervals to facilitate multiplexed genomic editing of a host cell comprising said nucleic acid constructs are also provided herein.Type: ApplicationFiled: July 9, 2021Publication date: August 24, 2023Inventors: Solomon Henry STONEBLOOM, Colin Scott MAXWELL, Shawn SZYJKA
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Publication number: 20230074594Abstract: A CRISPR system is successfully used to modify the genomes of a gram-positive bacterium, such as a species of the Cornybacterium genus. Methods for modifying Corynebacterium species include single-nucleotide changes, creating gene deletions and/or insertions.Type: ApplicationFiled: August 3, 2022Publication date: March 9, 2023Inventors: Stephen BLASKOWSKI, Robert COATES, Kedar PATEL, Hendrik Marinus VAN ROSSUM, Shawn SZYJKA
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Publication number: 20220275361Abstract: 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: ApplicationFiled: May 17, 2022Publication date: September 1, 2022Inventors: Zachariah 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: 11352621Abstract: 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 7, 2021Date of Patent: June 7, 2022Assignee: 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
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Patent number: 11312951Abstract: 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: GrantFiled: May 12, 2021Date of Patent: April 26, 2022Assignee: 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
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Patent number: 11279940Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.Type: GrantFiled: May 27, 2021Date of Patent: March 22, 2022Assignee: Zymergen Inc.Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier
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Patent number: 11208649Abstract: 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 5, 2021Date of Patent: December 28, 2021Assignee: 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
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Patent number: 11155807Abstract: 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 18, 2020Date of Patent: October 26, 2021Assignee: 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
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Patent number: 11155808Abstract: 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 22, 2021Date of Patent: October 26, 2021Assignee: 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
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Patent number: 11130955Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa.Type: GrantFiled: August 15, 2019Date of Patent: September 28, 2021Assignee: Zymergen Inc.Inventors: Brian Chaikind, Hendrik M. Van Rossum, Aaron Miller, Paul Perkovich, Shawn Szyjka, Kedar Patel
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Publication number: 20210292774Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.Type: ApplicationFiled: May 27, 2021Publication date: September 23, 2021Inventors: Stephen BLASKOWSKI, Sara da Luz Areosa CLETO, Cameron COATES, Aaron MILLER, Sharon NADEMANEE, Melissa NETWAL, Kedar PATEL, Shawn SZYJKA, Philip WEYMAN, Solomon Henry STONEBLOOM, Colin Scott MAXWELL, Elizabeth Lauren MEIER
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Publication number: 20210284992Abstract: 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: ApplicationFiled: May 12, 2021Publication date: September 16, 2021Inventors: Zachariah 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: 20210285014Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.Type: ApplicationFiled: May 27, 2021Publication date: September 16, 2021Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier
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Publication number: 20210261949Abstract: 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 5, 2021Publication date: August 26, 2021Inventors: Zachariah 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: 20210261950Abstract: 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 7, 2021Publication date: August 26, 2021Inventors: Zachariah 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: 11085040Abstract: 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: GrantFiled: October 28, 2019Date of Patent: August 10, 2021Assignee: 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
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Publication number: 20210222156Abstract: 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: March 22, 2021Publication date: July 22, 2021Inventors: Zachariah 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: 11053515Abstract: The present invention relates to methods for editing the genome of a microbial host cell in one or more rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in a pooled and/or iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Compositions and kits for performing the methods are also disclosed.Type: GrantFiled: March 20, 2020Date of Patent: July 6, 2021Assignee: Zymergen Inc.Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier
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Patent number: 11053506Abstract: The present invention relates to methods for editing the genome of a microbial host cell in successive rounds of transformation. The method allows the introduction of genetic edits into the genome of a microbial host cell in an iterative fashion that does not require the use of functional counterselection following at least one round of transformation. It can be used to rapidly stack genetic edits in the genome of a microbial host cell. Kits for performing the methods are also disclosed.Type: GrantFiled: March 20, 2020Date of Patent: July 6, 2021Assignee: Zymergen Inc.Inventors: Stephen Blaskowski, Sara da Luz Areosa Cleto, Cameron Coates, Aaron Miller, Sharon Nademanee, Melissa Netwal, Kedar Patel, Shawn Szyjka, Philip Weyman, Solomon Henry Stonebloom, Colin Scott Maxwell, Elizabeth Lauren Meier