Patents by Inventor William F. Burkholder

William F. Burkholder 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: 20240043832
    Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules: amplifying the barcode-tagged molecules; fragmenting the amplified barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed.
    Type: Application
    Filed: October 2, 2023
    Publication date: February 8, 2024
    Inventors: Stephen R. QUAKE, William F. BURKHOLDER, Lewis Z. HONG
  • Patent number: 11859171
    Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of: assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules; amplifying the barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed.
    Type: Grant
    Filed: April 17, 2014
    Date of Patent: January 2, 2024
    Assignee: Agency for Science, Technology and Research
    Inventors: Stephen R. Quake, William F. Burkholder, Lewis Z. Hong
  • Publication number: 20160076023
    Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of: assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules; amplifying the barcode-tagged molecules; fragmenting the amplified barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed. Also disclosed are methods systems and software for assembling paired end sequence reads to produce extended reads.
    Type: Application
    Filed: April 17, 2014
    Publication date: March 17, 2016
    Applicant: Agency for Science, Technology and Research
    Inventors: Stephen R. Quake, William F. Burkholder, Lewis Z. Hong
  • Publication number: 20130011833
    Abstract: A method for identifying a target nucleic acid bound by an analyte in a sample comprising: (a) contacting said sample with a first probe comprising a first nucleic acid and a first analyte binding domain and a second probe comprising a second nucleic acid and second analyte binding domain, wherein said first and second probes can bind to said analyte, such that said first and second nucleic acid are in spatial proximity to form a complex with said target nucleic acid if said target nucleic acid is bound by said analyte in said sample; (b) incubating said sample with a ligase that can ligate said complex to form a ligated target nucleic acid template; (c) amplifying said target nucleic acid template if present in said sample, and (d) detecting the presence or absence of an amplified target nucleic acid template.
    Type: Application
    Filed: April 26, 2012
    Publication date: January 10, 2013
    Applicant: Agency for Science, Technology and Research
    Inventors: Stephen R. Quake, William F. Burkholder, Tze Howe Charn