Patents by Inventor Paul Peluso

Paul Peluso 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: 20180023134
    Abstract: The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in an active loading of molecules and complexes into reaction sites with improved efficiency over loading by passive diffusion methods alone.
    Type: Application
    Filed: July 21, 2017
    Publication date: January 25, 2018
    Inventors: Jeremiah Hanes, Satwik Kamtekar, Yufeng Qian, Keith Bjornson, Thang Pham, David Rank, Paul Peluso, Erik Miller, Kristin Gleitsman, Leewin Chern, Steven Lin, Stephen Turner
  • 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
  • Publication number: 20160350478
    Abstract: Exemplary embodiments provide methods and systems for diploid genome assembly and haplotype sequence reconstruction. Aspects of the exemplary embodiment include generating a fused assembly graph from reads of both haplotypes, the fused assembly graph including identified primary contigs and associated contigs; generating haplotype-specific assembly graphs using phased reads and haplotype aware overlapping of the phased reads; merging the fused assembly graph and haplotype-specific assembly graphs to generate a merged assembly haplotype graph; removing cross-phasing edges from the merged assembly haplotype graph to generate a final haplotype-resolved assembly graph; and reconstructing haplotype-specific contigs from the final haplotype-resolved assembly graph resulting in haplotype-specific contigs.
    Type: Application
    Filed: May 23, 2016
    Publication date: December 1, 2016
    Inventors: Chen-Shan Chin, Paul Peluso, David Rank
  • 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: 8936926
    Abstract: Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.
    Type: Grant
    Filed: December 21, 2006
    Date of Patent: January 20, 2015
    Assignee: Pacific Biosciences of California
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoffrey Otto, Thang Pham, David Rank, Stephen Turner
  • 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
  • Publication number: 20140315756
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Application
    Filed: June 27, 2014
    Publication date: October 23, 2014
    Inventors: David R. Rank, Jeffrey Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto, Ronald L. Cicero
  • Patent number: 8802600
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Grant
    Filed: March 29, 2007
    Date of Patent: August 12, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jeffery Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto, Ron Cicero
  • Patent number: 8795961
    Abstract: Preparations, compositions and methods of sequencing nucleic acids are provided. The preparations, methods and compositions employ multiple priming sites on a target nucleic acid and typically utilize single molecule sequencing processes to identify sequence portions of the target which are then assembled to obtain the sequence of the target.
    Type: Grant
    Filed: September 3, 2009
    Date of Patent: August 5, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Paul Peluso
  • Patent number: 8772202
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Grant
    Filed: June 4, 2012
    Date of Patent: July 8, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jeffrey Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto, Ronald L. Cicero
  • Patent number: 8518643
    Abstract: The quality of information from single molecule analyses is improved by employing a method in which a single molecule reaction carried out within an optical confinement is monitored, the single molecule reaction is halted, and data from the optical confinement is obtained while the reaction is not occurring. Characteristic optical behavior observed while the reaction is halted is used to improve the quality of information obtained during the single molecule reaction, for example, by correcting the reaction data, excluding the reaction data, or providing a confidence level to the reaction data.
    Type: Grant
    Filed: February 1, 2011
    Date of Patent: August 27, 2013
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David Rank, Paul Peluso
  • 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: 8343746
    Abstract: Compositions that include DNA polymerases having increased residence times for nucleotide analogues, particularly modified recombinant ?29-type DNA polymerases with such increased residence times, are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA amplification are also provided. Compositions including ?-thiophosphate nucleotide analogues with four or more phosphate groups are described, as are methods for determining the sequence of nucleic acid molecules using such analogues.
    Type: Grant
    Filed: October 22, 2007
    Date of Patent: January 1, 2013
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Arek Bibillo, Paul Peluso
  • Patent number: 8323939
    Abstract: Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.
    Type: Grant
    Filed: October 26, 2007
    Date of Patent: December 4, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoffrey Otto, Thang Pham, David Rank, Stephen Turner
  • Publication number: 20120302459
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Application
    Filed: June 4, 2012
    Publication date: November 29, 2012
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jeffrey Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto, Ron Cicero
  • 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
  • Patent number: 8193123
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Grant
    Filed: October 26, 2007
    Date of Patent: June 5, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jeffery Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto, Ron Cicero
  • Patent number: 8137942
    Abstract: Reactive surfaces, substrates and methods of producing and using such substrates and surfaces are provided. The substrates and surfaces provide low density reactive groups preferably on an otherwise non-reactive surface for use in different applications including single molecule analyses.
    Type: Grant
    Filed: October 31, 2007
    Date of Patent: March 20, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Daniel Roitman, Paul Peluso, Mathieu Foquet
  • Patent number: 8133702
    Abstract: Engineered nucleotide compositions, having polymerase interacting components that improve the interactivity of the polymerase and the nucleotide, particularly for nucleic acid sequencing applications. Compositions include the interactive polymerases along with the nucleotide analogs. Kits, methods and systems are provided for analysis of nucleic acid synthesis reactions.
    Type: Grant
    Filed: May 25, 2011
    Date of Patent: March 13, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Paul Peluso, Arkadusz Bibillo
  • 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