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).

  • Publication number: 20190144919
    Abstract: 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: Application
    Filed: December 6, 2018
    Publication date: May 16, 2019
    Inventors: Alicia Jackson, Dagmar Beyerlein, Sonya Clark, Richard P. Rava
  • Publication number: 20180237757
    Abstract: 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: Application
    Filed: February 12, 2018
    Publication date: August 23, 2018
    Inventors: 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: 9951321
    Abstract: 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: Grant
    Filed: December 6, 2016
    Date of Patent: April 24, 2018
    Assignee: 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: 20170152492
    Abstract: 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: Application
    Filed: December 6, 2016
    Publication date: June 1, 2017
    Inventors: 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: 9556479
    Abstract: 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: Grant
    Filed: November 11, 2014
    Date of Patent: January 31, 2017
    Assignee: 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: 9127259
    Abstract: 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: Grant
    Filed: March 30, 2009
    Date of Patent: September 8, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Keith Bjornson, Sonya Clark, Insil Park, Fred Christians
  • Publication number: 20150184239
    Abstract: 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: Application
    Filed: November 11, 2014
    Publication date: July 2, 2015
    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: 8921086
    Abstract: 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: Grant
    Filed: December 21, 2006
    Date of Patent: December 30, 2014
    Assignee: 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: 8911972
    Abstract: 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: Grant
    Filed: December 14, 2010
    Date of Patent: December 16, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Mark Chaisson, Sonya Clark, Christopher Silk, John Lyle, Lei Jia, Keith Bjornson
  • Patent number: 8420366
    Abstract: 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: Grant
    Filed: September 30, 2010
    Date of Patent: April 16, 2013
    Assignee: 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: 8257954
    Abstract: 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: Grant
    Filed: March 30, 2009
    Date of Patent: September 4, 2012
    Assignee: 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: 20120034602
    Abstract: 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: Application
    Filed: July 5, 2011
    Publication date: February 9, 2012
    Applicant: 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
  • Publication number: 20110189659
    Abstract: 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: Application
    Filed: September 30, 2010
    Publication date: August 4, 2011
    Applicant: 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: 20110160077
    Abstract: 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: Application
    Filed: December 14, 2010
    Publication date: June 30, 2011
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Mark Chaisson, Sonya Clark, Christopher Silk, John Lyle, Lei Jia, Keith Bjornson
  • Publication number: 20110059505
    Abstract: 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: Application
    Filed: June 8, 2010
    Publication date: March 10, 2011
    Inventors: David K. Hanzel, Geoff Otto, Devon Murphy, Paul Peluso, Thang Pham, David R. Rank, Paul Mitsis, Fred Christians, Arek Bibillo, Insil Park, Sonya Clark, John Lyle
  • Publication number: 20100112645
    Abstract: 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: Application
    Filed: March 30, 2009
    Publication date: May 6, 2010
    Applicant: 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: 20100093555
    Abstract: 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: Application
    Filed: March 30, 2009
    Publication date: April 15, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Keith Bjornson, Sonya Clark, Insil Park, Fred Christians
  • Publication number: 20090176233
    Abstract: Methods of screening for and selecting for improved polymerases suitable for single molecule sequencing are provided.
    Type: Application
    Filed: December 5, 2008
    Publication date: July 9, 2009
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Sonya Clark, Homero L. Rey, Fred Christians, Jonas Korlach
  • Patent number: D773740
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: December 6, 2016
    Assignee: Virginia Commonwealth University
    Inventors: Sonya Clark, Jordana Kron, John Reavey-Cantwell
  • Patent number: D774700
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: December 20, 2016
    Assignee: Virginia Commonwealth University
    Inventors: Sonya Clark, Jordana Kron, John Reavey-Cantwell