Patents by Inventor Gene Shen

Gene Shen 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: 9499862
    Abstract: In various embodiments, the present invention provides fluorescent dyes that are linked to another species through an amino acid or peptide linker. In an exemplary embodiment, the dye is linked to a polyphosphate nucleic acid through an amino acid or peptide linker. These conjugates find use in single molecule DNA sequencing and other applications. In various embodiments, the dye moiety is a cyanine dye. Cyanine dyes that are highly charged, such as those including multiple sulfonate, alkylsulfonate, carboxylate and/or alkylcarboxylate moieties are examples of cyanine dyes of use in the compounds of the invention.
    Type: Grant
    Filed: March 25, 2015
    Date of Patent: November 22, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventor: Gene Shen
  • Publication number: 20160310926
    Abstract: The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution.
    Type: Application
    Filed: March 23, 2016
    Publication date: October 27, 2016
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Lei SUN, Natasha Popovich, Gene Shen, Thang Pham, Stephen Turner
  • Patent number: 9441270
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Grant
    Filed: September 17, 2014
    Date of Patent: September 13, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Yue, Gene Shen, Wei-Chuan (David) Sun
  • Publication number: 20160237279
    Abstract: Multimeric protected fluorescent reagents and their methods of synthesis are provided. The reagents are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The reagents contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements. The reagents also contain coupling elements connect monomeric compounds into multimeric forms, thereby increasing brightness.
    Type: Application
    Filed: February 4, 2016
    Publication date: August 18, 2016
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Frank ZHENG, Jeremiah HANES, Gene SHEN, Louis BROGLEY, Stephen YUE, Yuri LAPIN, John LYLE, Honey OSUNA, Andrei FEDOROV, Lubomir SEBO
  • Patent number: 9315864
    Abstract: Heteroaryl cyanine dyes bearing sulfonic acid substituents are of use in various assays, including single molecule nucleic acid sequencing. Exemplary heteroaryl cyanines dyes include or more reactive functional group, which is of use to covalently conjugate the cyanine dye to a carrier molecule. An exemplary carrier molecule is an analyte molecule or other molecule of interest, for example, a nucleotide oligophosphate.
    Type: Grant
    Filed: November 20, 2013
    Date of Patent: April 19, 2016
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Yue, Gene Shen, Wei-Chuan Sun
  • Publication number: 20150344950
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Application
    Filed: June 3, 2015
    Publication date: December 3, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventor: Gene SHEN
  • Patent number: 9200311
    Abstract: The present invention provides methods and compositions for performing illuminated reactions, particularly sequencing reactions, while mitigating and/or preventing photodamage to reactants that can result from prolonged illumination. In particular, the invention provides methods and compositions for incorporating photoprotective agents into conjugates comprising reporter molecules and nucleoside polyphosphates.
    Type: Grant
    Filed: July 1, 2013
    Date of Patent: December 1, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Geoffrey Otto, Gene Shen, Xiangxu Kong, Robin Emig
  • Patent number: 9176799
    Abstract: A server system performs error detection on a hop-by-hop basis at multiple compute nodes, thereby facilitating the detection of a compute node experiencing failure. The server system communicates a packet from an originating node (the originating node) to a destination node by separating the packet into multiple flow control digits (flits) and routing the flits using a series of hops over a set of intermediate nodes. The packet's final flit includes error detection information, such as checksum data. As each intermediate node receives the final flit, it performs error detection using the error detection information. The pattern of nodes that detect an error indicates which intermediate node has experienced a failure.
    Type: Grant
    Filed: December 31, 2012
    Date of Patent: November 3, 2015
    Assignee: Advanced Micro Devices, Inc.
    Inventors: Min Xu, Sean Lie, Gene Shen
  • Publication number: 20150307933
    Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.
    Type: Application
    Filed: November 3, 2014
    Publication date: October 29, 2015
    Inventors: Gene Shen, Lubomir Sebo, Stephen Yue, Wei-Chuan Sun, Louis Brogley, Anderi Fedorov
  • Publication number: 20150197794
    Abstract: In various embodiments, the present invention provides fluorescent dyes that are linked to another species through an amino acid or peptide linker. In an exemplary embodiment, the dye is linked to a polyphosphate nucleic acid through an amino acid or peptide linker. These conjugates find use in single molecule DNA sequencing and other applications. In various embodiments, the dye moiety is a cyanine dye. Cyanine dyes that are highly charged, such as those including multiple sulfonate, alkylsulfonate, carboxylate and/or alkylcarboxylate moieties are examples of cyanine dyes of use in the compounds of the invention.
    Type: Application
    Filed: March 25, 2015
    Publication date: July 16, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventor: Gene SHEN
  • Patent number: 9051263
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Grant
    Filed: August 25, 2011
    Date of Patent: June 9, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventor: Gene Shen
  • Publication number: 20150125854
    Abstract: Methods for performing analytical reactions and compositions for use in such methods, where the methods have reduced signal levels deriving from non-specific adsorption of detected reagents to other components of the analytical method, e.g., other reagents, solid phase components, vessels, etc.
    Type: Application
    Filed: January 6, 2015
    Publication date: May 7, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Andrei FEDOROV, Stephen YUE, Lei SUN, Gene SHEN, John LYLE
  • Patent number: 8993737
    Abstract: In various embodiments, the present invention provides fluorescent dyes that are linked to another species through an amino acid or peptide linker. In an exemplary embodiment, the dye is linked to a polyphosphate nucleic acid through an amino acid or peptide linker. These conjugates find use in single molecule DNA sequencing and other applications. In various embodiments, the dye moiety is a cyanine dye. Cyanine dyes that are highly charged, such as those including multiple sulfonate, alkylsulfonate, carboxylate and/or alkylcarboxylate moieties are examples of cyanine dyes of use in the compounds of the invention.
    Type: Grant
    Filed: August 25, 2011
    Date of Patent: March 31, 2015
    Assignee: Pacific Biosciences, Inc.
    Inventor: Gene Shen
  • Publication number: 20150072894
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Application
    Filed: September 17, 2014
    Publication date: March 12, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Stephen YUE, Gene SHEN, Wei-Chuan (David) SUN
  • Publication number: 20150050659
    Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.
    Type: Application
    Filed: August 5, 2014
    Publication date: February 19, 2015
    Inventors: Lubomir SEBO, Jeremiah HANES, Gene SHEN, Louis BROGLEY, Stephen YUE, Frank ZHENG, Yuri LAPIN, John LYLE, Honey OSUNA, Andrei FEDOROV
  • Patent number: 8956816
    Abstract: Methods for performing analytical reactions and compositions for use in such methods, where the methods have reduced signal levels deriving from non-specific adsorption of detected reagents to other components of the analytical method, e.g., other reagents, solid phase components, vessels, etc.
    Type: Grant
    Filed: June 4, 2013
    Date of Patent: February 17, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, Stephen Yue, Lei Sun, Gene Shen, John Lyle
  • Patent number: 8927212
    Abstract: FRET-labeled compounds are provided for use in analytical reactions. In certain embodiments, FRET-labeled nucleotide analogs are used in place of naturally occurring nucleoside triphosphates or other analogs in analytical reactions comprising nucleic acids, for example, template-directed nucleic acid synthesis, DNA sequencing, RNA sequencing, single-base identification, hybridization, binding assays, and other analytical reactions.
    Type: Grant
    Filed: March 30, 2010
    Date of Patent: January 6, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Xiangxu Kong, Gene Shen
  • Patent number: 8906612
    Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.
    Type: Grant
    Filed: August 25, 2011
    Date of Patent: December 9, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Lubomir Sebo, Stephen Yue, Wei-Chuan Sun, Louis Brogley, Andrei Fedorov
  • Patent number: 8889886
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Grant
    Filed: August 25, 2011
    Date of Patent: November 18, 2014
    Assignee: Pacific Biosciences, Inc.
    Inventors: Stephen Yue, Gene Shen, David Sun
  • Publication number: 20140189443
    Abstract: A server system performs error detection on a hop-by-hop basis at multiple compute nodes, thereby facilitating the detection of a compute node experiencing failure. The server system communicates a packet from an originating node (the originating node) to a destination node by separating the packet into multiple flow control digits (flits) and routing the flits using a series of hops over a set of intermediate nodes. The packet's final flit includes error detection information, such as checksum data. As each intermediate node receives the final flit, it performs error detection using the error detection information. The pattern of nodes that detect an error indicates which intermediate node has experienced a failure.
    Type: Application
    Filed: December 31, 2012
    Publication date: July 3, 2014
    Applicant: Advanced Micro Devices, Inc.
    Inventors: Min Xu, Sean Lie, Gene Shen