Patents by Inventor Rupali Patwardhan

Rupali Patwardhan 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).

  • SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS
    Publication number: 20230348896
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: October 27, 2022
    Publication date: November 2, 2023
    Applicant: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Error detection in sequence tag directed sequencing reads
    Patent number: 11505795
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: February 28, 2020
    Date of Patent: November 22, 2022
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS
    Publication number: 20200332283
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: February 28, 2020
    Publication date: October 22, 2020
    Applicant: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Error detection in sequence tag directed subassemblies of short sequencing reads
    Patent number: 10577601
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: May 12, 2017
    Date of Patent: March 3, 2020
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Sequence tag directed subassembly of short sequencing reads into long sequencing reads
    Patent number: 10227585
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: May 6, 2016
    Date of Patent: March 12, 2019
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Methods for retrieval of sequence-verified DNA constructs
    Patent number: 9809904
    Abstract: In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.
    Type: Grant
    Filed: April 23, 2012
    Date of Patent: November 7, 2017
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jay Shendure, Jerrod Schwartz, Jacob Kitzman, Rupali Patwardhan, Joseph Hiatt
  • ERROR DETECTION IN SEQUENCE TAG DIRECTED SUBASSEMBLIES OF SHORT SEQUENCING READS
    Publication number: 20170247687
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: May 12, 2017
    Publication date: August 31, 2017
    Applicant: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS
    Publication number: 20160244748
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: May 6, 2016
    Publication date: August 25, 2016
    Applicant: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS
    Publication number: 20150133344
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: September 5, 2014
    Publication date: May 14, 2015
    Applicant: UNIVERSITY OF WASHINGTON
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Error detection in sequence tag directed subassemblies of short sequencing reads
    Patent number: 8865410
    Abstract: The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: February 6, 2013
    Date of Patent: October 21, 2014
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Sequence tag directed subassembly of short sequencing reads into long sequencing reads
    Patent number: 8846347
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: February 5, 2013
    Date of Patent: September 30, 2014
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Sequence tag directed subassembly of short sequencing reads into long sequencing reads
    Patent number: 8383345
    Abstract: The invention provides methods for preparing DNA sequencing libraries for assembling short read sequencing data into longer contiguous sequences and providing for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. The methods generally comprise incorporating adaptor or vector sequences into at least one member of a target fragment library, amplifying the population of target fragment library members to produce a plurality of copies of amplified DNA molecules, fragmenting the plurality of amplified DNA molecules, incorporating additional adaptor sequences, and amplifying a region of at least one of the plurality of amplified DNA molecules. At least one resulting amplicon comprises a sequence identical to or complementary to at least a portion of a sequence tag and a sequence identical to or complementary to a portion of a target fragment library member.
    Type: Grant
    Filed: September 14, 2009
    Date of Patent: February 26, 2013
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • METHODS FOR RETRIEVAL OF SEQUENCE-VERIFIED DNA CONSTRUCTS
    Publication number: 20120283110
    Abstract: In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.
    Type: Application
    Filed: April 23, 2012
    Publication date: November 8, 2012
    Inventors: Jay Shendure, Jerrod Schwartz, Jacob Kitzman, Rupali Patwardhan, Joseph Hiatt
  • SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS
    Publication number: 20100069263
    Abstract: The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Application
    Filed: September 14, 2009
    Publication date: March 18, 2010
    Applicant: WASHINGTON, UNIVERSITY OF
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner