Patents by Inventor Austin B. Tomaney
Austin B. Tomaney 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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Patent number: 11844666Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: March 23, 2023Date of Patent: December 19, 2023Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Publication number: 20230268029Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: March 23, 2023Publication date: August 24, 2023Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Publication number: 20230268030Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: March 23, 2023Publication date: August 24, 2023Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Patent number: 10605737Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.Type: GrantFiled: April 6, 2017Date of Patent: March 31, 2020Assignee: APPLIED BIOSYSTEMS, LLCInventors: Austin B. Tomaney, Mark F. Oldham
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Patent number: 10294523Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: September 23, 2015Date of Patent: May 21, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
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Patent number: 10023911Abstract: 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.Type: GrantFiled: October 13, 2015Date of Patent: July 17, 2018Assignee: Pacific Biosciences of California, Inc.Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
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Publication number: 20170276609Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.Type: ApplicationFiled: April 6, 2017Publication date: September 28, 2017Applicant: APPLIED BIOSYSTEMS, LLCInventors: Austin B. TOMANEY, Mark F. OLDHAM
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Publication number: 20160153038Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: September 23, 2015Publication date: June 2, 2016Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
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Publication number: 20160097093Abstract: 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.Type: ApplicationFiled: October 13, 2015Publication date: April 7, 2016Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
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Patent number: 9175338Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: November 12, 2010Date of Patent: November 3, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes, Joseph Puglisi
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Patent number: 9175343Abstract: 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.Type: GrantFiled: March 6, 2014Date of Patent: November 3, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
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Publication number: 20150080270Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.Type: ApplicationFiled: August 22, 2014Publication date: March 19, 2015Inventors: Austin B. TOMANEY, Mark OLDHAM
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Publication number: 20140303016Abstract: 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.Type: ApplicationFiled: March 6, 2014Publication date: October 9, 2014Applicant: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
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Publication number: 20120319008Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.Type: ApplicationFiled: August 24, 2012Publication date: December 20, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Austin B. Tomaney, Mark F. Oldham
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Patent number: 8274650Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.Type: GrantFiled: May 6, 2010Date of Patent: September 25, 2012Assignee: Applied Biosystems, LLCInventors: Austin B. Tomaney, Mark F. Oldham
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Publication number: 20120214246Abstract: A system and method for measuring signals having a wide range of intensity components using detectors adapted for use in biological analysis devices. In certain biological analysis applications, signals emitted by a sample may have intensity components that vary over several orders of magnitude. Measurement of such a signal may yield an acceptable quality for one intensity component at the expense of another component. For example, a detector configured to measure a relatively weak intensity component may cause it to overflow when subjected to a relatively strong intensity component. The detector can be adapted to be operated at different configurations to allow measurements of different components of the signal, and the results can be combined to yield an accurate representation of the signal.Type: ApplicationFiled: January 30, 2012Publication date: August 23, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Mark F. Oldham, Austin B. Tomaney
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Patent number: 8182993Abstract: 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.Type: GrantFiled: June 5, 2008Date of Patent: May 22, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
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Publication number: 20120015825Abstract: Methods and systems for obtaining and processing optical signal data from analytical reactions, and in processing signal data from arrays of sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof are described. Defining and applying a 2-dimensional software mask allows for obtaining signal data from arrays with higher signal to noise than where the mask is not applied.Type: ApplicationFiled: June 30, 2011Publication date: January 19, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Cheng Frank Zhong, Austin B. Tomaney, Patrick Marks, Stuart George Johnson, James N. LaBrenz, Paul Lundquist
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Publication number: 20110192957Abstract: A system and method for measuring signals having a wide range of intensity components using detectors adapted for use in biological analysis devices. In certain biological analysis applications, signals emitted by a sample may have intensity components that vary over several orders of magnitude. Measurement of such a signal may yield an acceptable quality for one intensity component at the expense of another component. For example, a detector configured to measure a relatively weak intensity component may cause it to overflow when subjected to a relatively strong intensity component. The detector can be adapted to be operated at different configurations to allow measurements of different components of the signal, and the results can be combined to yield an accurate representation of the signal.Type: ApplicationFiled: September 27, 2010Publication date: August 11, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Mark F. Oldham, Austin B. Tomaney
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Publication number: 20110183320Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: November 12, 2010Publication date: July 28, 2011Applicant: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes, Joseph Puglisi