Patents by Inventor David Rank

David Rank 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: 10783984
    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: Grant
    Filed: May 23, 2016
    Date of Patent: September 22, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Chen-Shan Chin, Paul Peluso, David Rank
  • 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
  • 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
  • Patent number: 8993230
    Abstract: The present invention provides methods, reagents and apparatus for conducting single molecule sequencing in an asynchronous manner. The subject methods and compositions are particularly useful for high throughput and multiplexed sequencing.
    Type: Grant
    Filed: December 4, 2008
    Date of Patent: March 31, 2015
    Assignee: Pacific Biosciences of Californ, Inc.
    Inventors: Paul S. Peluso, John S. Eid, David Rank
  • Patent number: 8975216
    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 30, 2006
    Date of Patent: March 10, 2015
    Assignee: Pacific BioSciences of California
    Inventors: David Rank, Jonas Korlach, Yue Xu, Stephen Turner, Jeffrey Wegener, Daniel Roitman, 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: 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: 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: 20110217698
    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: Application
    Filed: February 1, 2011
    Publication date: September 8, 2011
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Rank, Paul Peluso
  • Publication number: 20100260465
    Abstract: Isolated and/or recombinant enzymes that include surface binding domains, surfaces with active enzymes bound to them and methods of coupling enzymes to surfaces are provided. Enzymes can include large and/or multiple surface coupling domains for surface coupling.
    Type: Application
    Filed: December 21, 2006
    Publication date: October 14, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoff Otto, Thang Pham, David Rank, Stephen Turner
  • Publication number: 20100261247
    Abstract: Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.
    Type: Application
    Filed: December 21, 2006
    Publication date: October 14, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoffrey Otto, Thang Pham, David Rank, Stephen Turner
  • Publication number: 20100143900
    Abstract: The present invention provides methods, reagents and apparatus for conducting single molecule sequencing in an asynchronous manner. The subject methods and compositions are particularly useful for high throughput and multiplexed sequencing.
    Type: Application
    Filed: December 4, 2008
    Publication date: June 10, 2010
    Inventors: Paul S. Peluso, John S. Eid, David Rank
  • Patent number: 7681950
    Abstract: A seat assembly for a motorcycle includes a rider seat having a forward end and a rearward end, a mounting bracket pivotally coupling the forward end of the rider seat to a frame of a motorcycle, the rider seat being pivotable to raise the rearward end of the seat, and a support arm. The seat assembly further includes a rear seat support having a first end portion and a second end portion, the first end portion being pivotally coupled to the support arm and the second end portion supporting a rear seat. The rear seat support is pivotal from a first position in which the rear seat is hidden from view below the rider seat to a second position in which the rear seat can support a passenger. The seat assembly also includes a stop feature for supporting the second end portion relative to the support arm and a lock feature for inhibiting pivoting of the rear seat support.
    Type: Grant
    Filed: June 29, 2007
    Date of Patent: March 23, 2010
    Assignee: Harley-Davidson Motor Company Group, LLC
    Inventors: Douglas D. Clarkson, Francis Giunta, John B. Zapushek, Thomas Mandery, Brendon Smith, David Rank
  • Publication number: 20100068723
    Abstract: Methods and devices for the interfacing of microchips to various types of modules are disclosed. The technology disclosed can be used as sample preparation and analysis systems for various applications, such asDNA sequencing and genotyping, proteomics, pathogen detection, diagnostics and biodefense.
    Type: Application
    Filed: October 23, 2009
    Publication date: March 18, 2010
    Inventors: Stevan Bogdan Jovanovich, Iuliu Ioan Blaga, David Rank
  • Publication number: 20090001780
    Abstract: A seat assembly for a motorcycle includes a rider seat having a forward end and a rearward end, a mounting bracket pivotally coupling the forward end of the rider seat to a frame of a motorcycle, the rider seat being pivotable to raise the rearward end of the seat, and a support arm. The seat assembly further includes a rear seat support having a first end portion and a second end portion, the first end portion being pivotally coupled to the support arm and the second end portion supporting a rear seat. The rear seat support is pivotal from a first position in which the rear seat is hidden from view below the rider seat to a second position in which the rear seat can support a passenger. The seat assembly also includes a stop feature for supporting the second end portion relative to the support arm and a lock feature for inhibiting pivoting of the rear seat support.
    Type: Application
    Filed: June 29, 2007
    Publication date: January 1, 2009
    Applicant: HARLEY-DAVIDSON MOTOR COMPANY GROUP, INC.
    Inventors: Douglas D. Clarkson, Francis Giunta, John B. Zapushek, Thomas Mandery, Brendon Smith, David Rank
  • Publication number: 20080199932
    Abstract: Active surface coupled polymerases, surfaces that include such polymerases, and methods of making and using surface-attached polymerases are provided.
    Type: Application
    Filed: October 26, 2007
    Publication date: August 21, 2008
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Hanzel, Jonas Korlach, Paul Peluso, Geoffrey Otto, Thang Pham, David Rank, Stephen Turner
  • Publication number: 20080153100
    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: October 31, 2007
    Publication date: June 26, 2008
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Rank, Jonas Korlach, Yue Xu, Stephen Turner, Jeffery Wegener, Daniel Roitman, John Lyle
  • Publication number: 20080108082
    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: Application
    Filed: October 22, 2007
    Publication date: May 8, 2008
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: David Rank, Arek Bibillo, David Hanzel, Paul Peluso, Jeff Wegener
  • Publication number: 20080032301
    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: March 29, 2007
    Publication date: February 7, 2008
    Applicant: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: David Rank, Jeffery Wegener, Jonas Korlach, Daniel Roitman, Yue Xu, John Lyle, Stephen Turner, Paul Peluso, Geoff Otto
  • Publication number: 20080014576
    Abstract: Methods and devices for the interfacing of microchips to various types of modules are disclosed. The technology disclosed can be used as sample preparation and analysis systems for various applications, such as DNA sequencing and genotyping, proteomics, pathogen detection, diagnostics and biodefense.
    Type: Application
    Filed: February 2, 2007
    Publication date: January 17, 2008
    Applicant: Microchip Biotechnologies, Inc.
    Inventors: Stevan Jovanovich, Iuliu Blaga, David Rank