Patents by Inventor Sonya Clark
Sonya Clark 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).
-
Patent number: 11932882Abstract: The application provides compositions including engineered reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.Type: GrantFiled: June 10, 2022Date of Patent: March 19, 2024Assignee: 10X GENOMICS, INC.Inventors: Sonya A. Clark, Derek Hunter Vallejo, Carolina Cuellar, Katherine Pfeiffer
-
Publication number: 20220403350Abstract: The application provides compositions including engineered reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.Type: ApplicationFiled: June 10, 2022Publication date: December 22, 2022Applicant: 10X Genomics, Inc.Inventors: Sonya A. CLARK, Derek Hunter Vallejo, Carolina Cuellar, Katherine Pfeiffer
-
Publication number: 20220275426Abstract: Provided herein, are matrices and methods for the stabilization of proteins and nucleic acids. The stabilized proteins and nucleic acids described herein can be in a sample taken from a subject and can be subsequently stabilized and stored on the matrix. An analyte of interest can be concentrated and eluted for analysis from this sample. The stabilized proteins and nucleic acids described herein can be components of a sample preparation reagent, and the reagent is stored on the matrix and hydration of the matrix with a sample can result in a reaction occurring.Type: ApplicationFiled: November 5, 2021Publication date: September 1, 2022Inventors: Alicia JACKSON, Dagmar BEYERLEIN, Sonya CLARK, Richard P. RAVA
-
Patent number: 11299720Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: GrantFiled: July 14, 2020Date of Patent: April 12, 2022Assignee: Pacific Biosciences of California, Inc.Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Publication number: 20210102181Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: ApplicationFiled: July 14, 2020Publication date: April 8, 2021Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 10717968Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: GrantFiled: February 12, 2018Date of Patent: July 21, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: David R. Rank, Paul S. Peluso, David K. Hanzel, Geoff Otto, Thang Pham, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Publication number: 20190144919Abstract: Provided herein, are matrices and methods for the stabilization of proteins and nucleic acids. The stabilized proteins and nucleic acids described herein can be in a sample taken from a subject and can be subsequently stabilized and stored on the matrix. An analyte of interest can be concentrated and eluted for analysis from this sample. The stabilized proteins and nucleic acids described herein can be components of a sample preparation reagent, and the reagent is stored on the matrix and hydration of the matrix with a sample can result in a reaction occurring.Type: ApplicationFiled: December 6, 2018Publication date: May 16, 2019Inventors: Alicia Jackson, Dagmar Beyerlein, Sonya Clark, Richard P. Rava
-
Publication number: 20180237757Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: ApplicationFiled: February 12, 2018Publication date: August 23, 2018Inventors: David R. Rank, Paul S. Peluso, David K. Hanzel, Geoff Otto, Thang Pham, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 9951321Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogs into active site regions and for coordinating with the nucleotide analogs in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: GrantFiled: December 6, 2016Date of Patent: April 24, 2018Assignee: Pacific Biosciences of California, Inc.Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Publication number: 20170152492Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: ApplicationFiled: December 6, 2016Publication date: June 1, 2017Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 9556479Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: GrantFiled: November 11, 2014Date of Patent: January 31, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: David K. Hanzel, Geoff Otto, Paul Peluso, Thang Pham, David R. Rank, Paul Mitsis, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 9127259Abstract: Provided are compositions comprising modified DNA polymerases that exhibit improved photostability compared to the parental polymerases from which they were derived. Provided are methods for generating enzymes, such as DNA polymerases, with the aforementioned phenotype. Provided are methods of using polymerases with increased resistance to photodamage to make a DNA or to sequence a DNA template.Type: GrantFiled: March 30, 2009Date of Patent: September 8, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Sonya Clark, Insil Park, Fred Christians
-
Publication number: 20150184239Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: ApplicationFiled: November 11, 2014Publication date: July 2, 2015Inventors: David K. Hanzel, Geoff Otto, Paul Peluso, Thang Pham, David R. Rank, Paul Mitsis, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 8921086Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.Type: GrantFiled: December 21, 2006Date of Patent: December 30, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: David K. Hanzel, Geoff Otto, Paul Peluso, Thang Pham, David R. Rank, Paul Mitsis, Fred Christians, Arek Bibillo, Insil Park, Sonya Clark, John Lyle
-
Patent number: 8911972Abstract: Systems and methods are provided for single-molecule sequencing of template nucleic acids in which the signal from a label attached to a polymerase enzyme is used to monitor conformational changes in the polymerase which occur while labeled nucleotides or nucleotide analogs are added to a growing nucleic acid chain which is complementary to the template nucleic acid. The signal indicative of the conformational state of the enzyme is used to determine with higher confidence when true nucleotide or nucleotide analog incorporation events occur, allowing for the improved quality of base calls and sequence determination.Type: GrantFiled: December 14, 2010Date of Patent: December 16, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: Mark Chaisson, Sonya Clark, Christopher Silk, John Lyle, Lei Jia, Keith Bjornson
-
Patent number: 8420366Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions and/or heterologous or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include reduced reaction rates at one or more steps of the polymerase kinetic cycle, increased closed polymerase/DNA complex stability, enhanced metal ion coordination, reduced exonuclease activity, decreased branching fractions, and the like. Polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog, are also provided. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: September 30, 2010Date of Patent: April 16, 2013Assignee: Pacific Biosciences of California, Inc.Inventors: Sonya Clark, Arek Bibillo, Paul Peluso, Fred Christians, Molly He, Insil Park, Harold Lee, Keith Bjornson, Lei Jia, Robin Emig
-
Patent number: 8257954Abstract: Provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are less than the branching fractions of the polymerases from which they were derived, or branching fractions that are less than about 25% for a phosphate-labeled nucleotide analog. Also provided are compositions comprising modified recombinant polymerases that exhibit closed polymerase/DNA complexes with increased stability relative to the parental polymerases. Also provided are compositions comprising modified recombinant polymerases that exhibit decreased rate constants relative to the parental polymerases. Provided are methods for generating polymerases with the aforementioned phenotypes. Provided are methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: March 30, 2009Date of Patent: September 4, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Sonya Clark, Arek Bibillo, Paul Peluso, Fred Christians, Molly He, Insil Park, Harold Lee, Keith Bjornson, Lei Jia, Robin Emig
-
Publication number: 20120034602Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: July 5, 2011Publication date: February 9, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Insil Park, Lei Jia, Arek Bibillo, Keith Bjornson, Molly He, Jeremiah Hanes, Harold Lee, Sonya Clark, Fred Christians, Paul Peluso, John Vieceli, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee
-
Patent number: D773740Type: GrantFiled: September 18, 2015Date of Patent: December 6, 2016Assignee: Virginia Commonwealth UniversityInventors: Sonya Clark, Jordana Kron, John Reavey-Cantwell
-
Patent number: D774700Type: GrantFiled: September 18, 2015Date of Patent: December 20, 2016Assignee: Virginia Commonwealth UniversityInventors: Sonya Clark, Jordana Kron, John Reavey-Cantwell