Patents by Inventor Chen-Shan Chin

Chen-Shan Chin 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: 20180060484
    Abstract: Aspects of the present disclosure provide methods, systems, and computer program products for generating one or more extended contigs. Aspects of the exemplary embodiment include receiving input contigs for a genome; generating local assembly subgraphs including the ends of each contig; identifying subgraphs that unambiguously connect two contigs; and generating an extended contig in which the orientation and order of at least two contigs is determined. Extended contigs can include any number of linearly ordered and linked contigs.
    Type: Application
    Filed: August 21, 2017
    Publication date: March 1, 2018
    Inventor: Chen-Shan Chin
  • Publication number: 20170132361
    Abstract: Computer implemented methods for improving the assembly of sequence data are provided. in preferred embodiments, these methods increase the efficiency of assembly of sequence datasets from complex samples, such as genomes having repetitive regions.
    Type: Application
    Filed: October 25, 2016
    Publication date: May 11, 2017
    Inventors: Shoudan Liang, Chen-Shan Chin
  • 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: 20150302144
    Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.
    Type: Application
    Filed: May 19, 2015
    Publication date: October 22, 2015
    Inventors: Chen-Shan Chin, Stephen Turner
  • Publication number: 20150286775
    Abstract: Exemplary embodiments provide methods and systems for string graph assembly of polyploid genomes. Aspects of the exemplary embodiment include receiving a string graph generated from sequence reads of at least 0.5 kb in length; identifying unitigs in the string graph and generating a unitig graph; and identifying string bundles in the unitig graph by: determining a primary contig from each of the string bundles; and determining associated contigs that contain structural variations compared to the primary contig.
    Type: Application
    Filed: June 18, 2015
    Publication date: October 8, 2015
    Inventor: Chen-Shan Chin
  • Publication number: 20150169823
    Abstract: Exemplary embodiments provide methods and systems for string graph assembly of polyploid genomes. Aspects of the exemplary embodiment include receiving a string graph generated from sequence reads of at least 0.5 kb in length; identifying unitigs in the string graph and generating a unitig graph; identifying string bundles in the unitig graph; determining a primary contig from each of the string bundles; and determining associated contigs that contain structural variations compared to the primary contig.
    Type: Application
    Filed: December 18, 2014
    Publication date: June 18, 2015
    Inventor: Chen-Shan Chin
  • Publication number: 20140025312
    Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.
    Type: Application
    Filed: July 12, 2013
    Publication date: January 23, 2014
    Inventors: Chen-Shan Chin, Patrick Marks, David Alexander, Aaron Klammer, Stephen W. Turner
  • Patent number: 8370079
    Abstract: The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.
    Type: Grant
    Filed: November 20, 2009
    Date of Patent: February 5, 2013
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jon Sorenson, Susan Tang, Patrick Marks, Chen-Shan Chin
  • Publication number: 20110257889
    Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.
    Type: Application
    Filed: February 24, 2011
    Publication date: October 20, 2011
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Aaron Klammer, Susan Tang, Mark Chaisson, Jon Sorenson, Chen-Shan Chin
  • Publication number: 20100169026
    Abstract: The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.
    Type: Application
    Filed: November 20, 2009
    Publication date: July 1, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Jon Sorenson, Susan Tang, Patrick Marks, Chen-Shan Chin
  • Publication number: 20100129810
    Abstract: A system for performing quality control for nucleic acid sample sequencing is disclosed. The system has a set of solid supports, each support having attached thereto a plurality of nucleic acid sequences. The set has plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived. A method of preparing a quality control for performing nucleic acid sample sequencing and a method of validating a nucleic acid sequencing instrument are also disclosed.
    Type: Application
    Filed: September 8, 2009
    Publication date: May 27, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Douglas P. GREINER, Carmen GJERSTAD, Janet S. ZIEGLE, Lee W. JONES, Min-Yi SHEN, Chen-Shan CHIN, Heinz BREU