Patents by Inventor Jon Sorenson

Jon Sorenson 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: 20210104331
    Abstract: Systems and methods for reducing a number of test objects in a test object dataset are provided. A target model with a first computational complexity is applied to a subset of test objects from the test object dataset and a target object, thereby obtaining a subset of target results. A predictive model with a second computational complexity is trained using the subset of test objects and the subset of target results. The predictive model is applied to the plurality of test objects, thereby obtaining a plurality of predictive results. A portion of the test objects are eliminated from the plurality of test objects based at least in part on the plurality of predictive results. The method determines whether one or more predefined reduction criteria are satisfied. When the predefined reduction criteria are not satisfied, an additional subset of test objects and target results are obtained, and the method is repeated.
    Type: Application
    Filed: September 30, 2020
    Publication date: April 8, 2021
    Inventors: Venkatesh Mysore, Jon Sorenson, Greg Friedland, Tushita Gupta, Izhar Wallach
  • Patent number: 10793903
    Abstract: 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: Grant
    Filed: September 28, 2016
    Date of Patent: October 6, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Publication number: 20200149100
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Application
    Filed: October 21, 2019
    Publication date: May 14, 2020
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 10563255
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: June 23, 2017
    Date of Patent: February 18, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 10294523
    Abstract: 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: Grant
    Filed: September 23, 2015
    Date of Patent: May 21, 2019
    Assignee: 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
  • Patent number: 9951383
    Abstract: 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. Methods are provided that include linking forward and reverse strands of a double stranded segment to form circular template molecules, and obtaining sequence data from the circular template molecule to identify modified bases, for example including the use of bisulfite treatment. 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: Grant
    Filed: September 21, 2016
    Date of Patent: April 24, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Publication number: 20170342481
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Application
    Filed: June 23, 2017
    Publication date: November 30, 2017
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 9738929
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: December 19, 2016
    Date of Patent: August 22, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid, Cheryl Heiner, Kevin Travers
  • Publication number: 20170233802
    Abstract: 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: Application
    Filed: September 28, 2016
    Publication date: August 17, 2017
    Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Publication number: 20170121764
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Application
    Filed: December 19, 2016
    Publication date: May 4, 2017
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 9624533
    Abstract: Methods for multiplex ligation-dependent probe amplification include (a) providing a sample tissue to query different target nucleic acids, (b) providing different probe sets for each of the target nucleic acids, each probe set including a first locus specific probe having a first adapter sequence and a first target specific portion and a second locus specific probe having a second adapter sequence, and a second target specific portion adjacent to the first target specific portion, (c) hybridizing the probe sets to the target sequences to form hybridization complexes, (d) ligating the hybridization complexes to form ligated probes, (e) amplifying the ligated probes to form amplicons, the amplifying step being carried out with a first universal primer including a region complementary to the first adapter sequence and a second universal primer including a region complementary to the second adapter sequence, and (f) detecting the amplicons in a detection system by sequencing each of the amplicons.
    Type: Grant
    Filed: December 6, 2013
    Date of Patent: April 18, 2017
    Assignee: INVITAE CORPORATION
    Inventors: Eric Olivares, Jon Sorenson, Tom Landers
  • Publication number: 20170037464
    Abstract: 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. Methods are provided that include linking forward and reverse strands of a double stranded segment to form circular template molecules, and obtaining sequence data from the circular template molecule to identify modified bases, for example including the use of bisulfite treatment. 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: Application
    Filed: September 21, 2016
    Publication date: February 9, 2017
    Inventors: Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
  • Patent number: 9556480
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: May 11, 2015
    Date of Patent: January 31, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Publication number: 20160153038
    Abstract: 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: Application
    Filed: September 23, 2015
    Publication date: June 2, 2016
    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
  • Patent number: 9194772
    Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.
    Type: Grant
    Filed: September 10, 2009
    Date of Patent: November 24, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Linda Lee, Sam Woo, Congcong Ma, Richard Reel, Mark Oldham, David Cox, Benjamin Schroeder, Jon Sorenson, Willy Wiyatno
  • Patent number: 9175341
    Abstract: 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: Grant
    Filed: December 10, 2009
    Date of Patent: November 3, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Benjamin Flusberg, Stephen Turner, Jessica Lee, Lei Jia, Jonas Korlach, Jon Sorenson, Dale Webster, John Lyle, Kevin Travers, Jeremiah Hanes, Joseph Puglisi
  • Patent number: 9175338
    Abstract: 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: Grant
    Filed: November 12, 2010
    Date of Patent: November 3, 2015
    Assignee: 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
  • Publication number: 20150307934
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Application
    Filed: May 11, 2015
    Publication date: October 29, 2015
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 9057102
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: November 27, 2013
    Date of Patent: June 16, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 8986928
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.
    Type: Grant
    Filed: April 9, 2010
    Date of Patent: March 24, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg, Mathieu Foquet, Hans Callebaut, Robert Sebra, Bidhan Chaudhuri, Jon Sorenson, Keith Bjornson, Adrian Fehr, Jonas Korlach, Robin Emig