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).
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Publication number: 20220154274Abstract: 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: ApplicationFiled: November 29, 2021Publication date: May 19, 2022Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
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Publication number: 20210277445Abstract: 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: ApplicationFiled: December 11, 2020Publication date: September 9, 2021Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
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Patent number: 10865440Abstract: 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: GrantFiled: February 28, 2013Date of Patent: December 15, 2020Assignee: IntegenX, Inc.Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
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Patent number: 10196680Abstract: 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: GrantFiled: June 5, 2017Date of Patent: February 5, 2019Assignee: APPLIED BIOSYSTEMS, LLCInventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Publication number: 20180127818Abstract: 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: ApplicationFiled: July 3, 2017Publication date: May 10, 2018Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
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Publication number: 20170275678Abstract: 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: ApplicationFiled: June 5, 2017Publication date: September 28, 2017Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Patent number: 9677126Abstract: 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: GrantFiled: August 19, 2016Date of Patent: June 13, 2017Assignee: APPLIED BIOSYSTEMS, LLCInventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Publication number: 20160355877Abstract: 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: ApplicationFiled: August 19, 2016Publication date: December 8, 2016Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
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Publication number: 20160340726Abstract: 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: ApplicationFiled: August 8, 2016Publication date: November 24, 2016Inventors: Eric S. NORDMAN, Mark F. OLDHAM, Timothy WOUDENBERG
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Patent number: 9434982Abstract: 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: GrantFiled: July 2, 2015Date of Patent: September 6, 2016Assignee: Applied Biosystems LLCInventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Patent number: 9410889Abstract: 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: GrantFiled: June 9, 2006Date of Patent: August 9, 2016Assignee: Applied Biosystem, LLCInventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
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Patent number: 9383295Abstract: 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: GrantFiled: September 4, 2014Date of Patent: July 5, 2016Assignee: Fluidigm CorporationInventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
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Publication number: 20150307925Abstract: 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: ApplicationFiled: July 2, 2015Publication date: October 29, 2015Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
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Patent number: 9074252Abstract: 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: GrantFiled: December 20, 2013Date of Patent: July 7, 2015Assignee: Applied Biosystems, LLCInventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Publication number: 20150185118Abstract: 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: ApplicationFiled: September 4, 2014Publication date: July 2, 2015Inventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
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Publication number: 20150024436Abstract: 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: ApplicationFiled: February 28, 2013Publication date: January 22, 2015Applicant: INTEGENX INC,Inventors: David Eberhart, Yuan Li, James Ogg, Ezra Van Gelder, Stephen J. Williams, Timothy Woudenberg, Dean S. Burgi, William D. Nielsen
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Publication number: 20140170656Abstract: 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: ApplicationFiled: December 20, 2013Publication date: June 19, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
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Publication number: 20140045184Abstract: 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: ApplicationFiled: March 4, 2013Publication date: February 13, 2014Applicant: Fluidigm CorporationInventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler
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Patent number: 8637247Abstract: 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: GrantFiled: August 21, 2012Date of Patent: January 28, 2014Assignee: Applied Biosystems, LLCInventors: Muhammad Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Patent number: 8389960Abstract: 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: GrantFiled: November 11, 2011Date of Patent: March 5, 2013Assignee: Fluidigm CorporationInventors: Martin Pieprzyk, Geoff Facer, Timothy Woudenberg, Brian Fowler