Patents by Inventor Molly He

Molly He 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: 20190144839
    Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.
    Type: Application
    Filed: November 28, 2018
    Publication date: May 16, 2019
    Applicant: Illumina, Inc.
    Inventors: Erin Bomati, Michael Previte, Matthew William Kellinger, Cheng-Yao Chen, Molly He
  • Publication number: 20190136303
    Abstract: A method for enriching or amplifying a target nucleic acid including providing a system having a guide nucleic acid, and a Cas or Argonaute protein or a variant thereof. The guide nucleic acid contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.
    Type: Application
    Filed: May 10, 2017
    Publication date: May 9, 2019
    Inventors: Jeffrey G. Mandell, Molly He
  • Publication number: 20190112730
    Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.
    Type: Application
    Filed: October 11, 2018
    Publication date: April 18, 2019
    Applicant: Illumina, Inc.
    Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
  • Patent number: 10233493
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: March 19, 2019
    Assignee: Illumina, Inc.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20190048332
    Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
    Type: Application
    Filed: October 29, 2018
    Publication date: February 14, 2019
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
  • Publication number: 20190040382
    Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
    Type: Application
    Filed: October 16, 2015
    Publication date: February 7, 2019
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
  • Publication number: 20190002973
    Abstract: A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.
    Type: Application
    Filed: September 10, 2018
    Publication date: January 3, 2019
    Applicant: Illumina, Inc.
    Inventors: Michael Previte, Molly He, Rigo Pantoja, Cheng-Yao Chen, Chunhong Zhou
  • Patent number: 10150954
    Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogs, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.
    Type: Grant
    Filed: June 1, 2017
    Date of Patent: December 11, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Erin Bomati, Michael Previte, Matthew William Kellinger, Cheng-Yao Chen, Molly He
  • Publication number: 20180298356
    Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
    Type: Application
    Filed: June 28, 2018
    Publication date: October 18, 2018
    Applicant: ILLUMINA, INC.
    Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
  • Patent number: 10100355
    Abstract: Embodiments provided herein relate to methods and compositions for obtaining nucleic acid sequence information. Some embodiments provided herein include methods and compositions for preparing nucleic acid libraries. In some embodiments, such nucleic acid libraries are useful for targeted nucleic acid sequencing.
    Type: Grant
    Filed: December 5, 2014
    Date of Patent: October 16, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Rigo Pantoja, Marie Hu, Erin Bomati, Molly He
  • Patent number: 10035992
    Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
    Type: Grant
    Filed: October 12, 2017
    Date of Patent: July 31, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
  • Publication number: 20180171311
    Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
    Type: Application
    Filed: October 12, 2017
    Publication date: June 21, 2018
    Applicant: ILLUMINA, INC.
    Inventors: Christian GLOECKNER, Amirali KIA, Erin BOMATI, Molly HE, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
  • Publication number: 20180155783
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Application
    Filed: December 22, 2017
    Publication date: June 7, 2018
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20180142378
    Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.
    Type: Application
    Filed: May 9, 2016
    Publication date: May 24, 2018
    Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
  • Publication number: 20180016571
    Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
    Type: Application
    Filed: November 5, 2015
    Publication date: January 18, 2018
    Inventors: Christian Gloeckner, Amirali Kia, Molly He, Trina Faye Osothprarop, Frank J. Steemers, Kevin L. Gunderson, Sasan Amini, Jerome Jendrisak
  • Patent number: 9862998
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Grant
    Filed: April 19, 2016
    Date of Patent: January 9, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Publication number: 20170355970
    Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.
    Type: Application
    Filed: August 22, 2017
    Publication date: December 14, 2017
    Applicant: Illumina, Inc.
    Inventors: Cheng-Yao Chen, Erin Bomati, Molly He
  • Publication number: 20170321195
    Abstract: Presented herein are methods and compositions for thermostable DNA polymerases that may be used to improve the PCR process and to improve the results obtained when using a thermostable DNA polymerase in other recombinant techniques such as DNA sequencing, nick-translation, and reverse transcription.
    Type: Application
    Filed: November 13, 2015
    Publication date: November 9, 2017
    Applicant: Illumina, Inc.
    Inventors: Misha Golynskiy, Molly He, Michael Previte, BeiBei Wang, Sergio Peisajovich
  • Publication number: 20170298327
    Abstract: Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3? sugar hydroxyl, as well as methods and kits using the same.
    Type: Application
    Filed: June 1, 2017
    Publication date: October 19, 2017
    Applicant: Illumina, Inc.
    Inventors: Erin Bomati, Michael Previte, Matthew William Kellinger, Cheng-Yao Chen, Molly He
  • Patent number: 9790476
    Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
    Type: Grant
    Filed: April 15, 2015
    Date of Patent: October 17, 2017
    Assignee: ILLUMINA, INC.
    Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan