Patents by Inventor Timothy Woudenberg

Timothy Woudenberg 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: 20220154274
    Abstract: The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.
    Type: Application
    Filed: November 29, 2021
    Publication date: May 19, 2022
    Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
  • Publication number: 20210277445
    Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.
    Type: Application
    Filed: December 11, 2020
    Publication date: September 9, 2021
    Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
  • Patent number: 10865440
    Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.
    Type: Grant
    Filed: February 28, 2013
    Date of Patent: December 15, 2020
    Assignee: IntegenX, Inc.
    Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
  • Patent number: 10196680
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: June 5, 2017
    Date of Patent: February 5, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20180127818
    Abstract: The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.
    Type: Application
    Filed: July 3, 2017
    Publication date: May 10, 2018
    Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
  • Publication number: 20170275678
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: June 5, 2017
    Publication date: September 28, 2017
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Patent number: 9677126
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: August 19, 2016
    Date of Patent: June 13, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20160355877
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: August 19, 2016
    Publication date: December 8, 2016
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Publication number: 20160340726
    Abstract: The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.
    Type: Application
    Filed: August 8, 2016
    Publication date: November 24, 2016
    Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
  • Patent number: 9434982
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: July 2, 2015
    Date of Patent: September 6, 2016
    Assignee: Applied Biosystems LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Patent number: 9410889
    Abstract: The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.
    Type: Grant
    Filed: June 9, 2006
    Date of Patent: August 9, 2016
    Assignee: Applied Biosystem, LLC
    Inventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
  • Patent number: 9383295
    Abstract: Embodiments of the present invention provide improved microfluidic devices and related apparatus, systems, and methods. Methods are provided for reducing mixing times during use of microfluidic devices. Microfluidic devices and related methods of manufacturing are provided with increased manufacturing yield rates. Improved apparatus and related systems are provided for supplying controlled pressure to microfluidic devices. Methods and related microfluidic devices are provided for reducing dehydration of microfluidic devices during use. Microfluidic devices and related methods are provided with improved sample to reagent mixture ratio control. Microfluidic devices and systems are provided with improved resistance to compression fixture pressure induced failures. Methods and systems for conducting temperature controlled reactions using microfluidic devices are provided that reduce condensation levels within the microfluidic device.
    Type: Grant
    Filed: September 4, 2014
    Date of Patent: July 5, 2016
    Assignee: Fluidigm Corporation
    Inventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
  • Publication number: 20150307925
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: July 2, 2015
    Publication date: October 29, 2015
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Patent number: 9074252
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: July 7, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20150185118
    Abstract: Embodiments of the present invention provide improved microfluidic devices and related apparatus, systems, and methods. Methods are provided for reducing mixing times during use of microfluidic devices. Microfluidic devices and related methods of manufacturing are provided with increased manufacturing yield rates. Improved apparatus and related systems are provided for supplying controlled pressure to microfluidic devices. Methods and related microfluidic devices are provided for reducing dehydration of microfluidic devices during use. Microfluidic devices and related methods are provided with improved sample to reagent mixture ratio control. Microfluidic devices and systems are provided with improved resistance to compression fixture pressure induced failures. Methods and systems for conducting temperature controlled reactions using microfluidic devices are provided that reduce condensation levels within the microfluidic device.
    Type: Application
    Filed: September 4, 2014
    Publication date: July 2, 2015
    Inventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
  • Publication number: 20150024436
    Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.
    Type: Application
    Filed: February 28, 2013
    Publication date: January 22, 2015
    Applicant: INTEGENX INC,
    Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
  • Publication number: 20140170656
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 19, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Publication number: 20140045184
    Abstract: Embodiments of the present invention provide improved microfluidic devices and related apparatus, systems, and methods. Methods are provided for reducing mixing times during use of microfluidic devices. Microfluidic devices and related methods of manufacturing are provided with increased manufacturing yield rates. Improved apparatus and related systems are provided for supplying controlled pressure to microfluidic devices. Methods and related microfluidic devices are provided for reducing dehydration of microfluidic devices during use. Microfluidic devices and related methods are provided with improved sample to reagent mixture ratio control. Microfluidic devices and systems are provided with improved resistance to compression fixture pressure induced failures. Methods and systems for conducting temperature controlled reactions using microfluidic devices are provided that reduce condensation levels within the microfluidic device.
    Type: Application
    Filed: March 4, 2013
    Publication date: February 13, 2014
    Applicant: Fluidigm Corporation
    Inventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
  • Patent number: 8637247
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: August 21, 2012
    Date of Patent: January 28, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Muhammad Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Patent number: 8389960
    Abstract: Embodiments of the present invention provide improved microfluidic devices and related apparatus, systems, and methods. Methods are provided for reducing mixing times during use of microfluidic devices. Microfluidic devices and related methods of manufacturing are provided with increased manufacturing yield rates. Improved apparatus and related systems are provided for supplying controlled pressure to microfluidic devices. Methods and related microfluidic devices are provided for reducing dehydration of microfluidic devices during use. Microfluidic devices and related methods are provided with improved sample to reagent mixture ratio control. Microfluidic devices and systems are provided with improved resistance to compression fixture pressure induced failures. Methods and systems for conducting temperature controlled reactions using microfluidic devices are provided that reduce condensation levels within the microfluidic device.
    Type: Grant
    Filed: November 11, 2011
    Date of Patent: March 5, 2013
    Assignee: Fluidigm Corporation
    Inventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler