Patents by Inventor Benjamin Flusberg

Benjamin Flusberg 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: 20190360997
    Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow, or kinetically observable kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 5:1 to 1:5. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.
    Type: Application
    Filed: April 8, 2019
    Publication date: November 28, 2019
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 10481144
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides devices having an array of nanopores. The devices comprise an upper fluidic region in fluidic contact with the nanopores. The upper fluidic region comprises and upper electrode. Below each nanopore, and in fluidic contact with each nanopore is a discrete fluidic region. There is no direct fluidic contact between these discrete fluidic regions. The devices have an advantage of lower levels of electrical cross-talk between nanopores in the array for improved nucleic acid sequencing.
    Type: Grant
    Filed: July 19, 2017
    Date of Patent: November 19, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 10473639
    Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow, or kinetically observable kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 5:1 to 1:5. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.
    Type: Grant
    Filed: April 8, 2019
    Date of Patent: November 12, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg
  • 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
  • Publication number: 20190133449
    Abstract: Analysis of live beings is facilitated. According to an example embodiment of the present invention, a light-directing arrangement such as an endoscope is mounted to a live being. Optics in the light-directing arrangement are implemented to pass source light (e.g., laser excitation light) into the live being, and to pass light from the live being for detection thereof. The light from the live being may include, for example, photons emitted in response to the laser excitation light (i.e., fluoresced). The detected light is then used to detect a characteristic of the live being.
    Type: Application
    Filed: September 24, 2018
    Publication date: May 9, 2019
    Inventors: Benjamin A. Flusberg, Eric David Cocker, Juergen Claus Jung, Mark J. Schnitzer
  • Patent number: 9993794
    Abstract: Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. For example, methods are presented for providing a surface comprising the plurality of array regions by exposing the surface to a solution comprising polymerase enzymes where each polymerase enzyme is bound to a binding structure having several functional moieties. The functional moieties of the binding structure react with the binding elements on the array regions such that the functional moieties on the binding structure react with other available binding sites in an array region, preventing other polymerase-binding structures from loading, and resulting in a single polymerase molecule bound to each of these regions.
    Type: Grant
    Filed: November 4, 2014
    Date of Patent: June 12, 2018
    Assignee: Paciic Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg, Lei Sun
  • Publication number: 20180074040
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides devices having an array of nanopores. The devices comprise an upper fluidic region in fluidic contact with the nanopores. The upper fluidic region comprises and upper electrode. Below each nanopore, and in fluidic contact with each nanopore is a discrete fluidic region. There is no direct fluidic contact between these discrete fluidic regions. The devices have an advantage of lower levels of electrical cross-talk between nanopores in the array for improved nucleic acid sequencing.
    Type: Application
    Filed: July 19, 2017
    Publication date: March 15, 2018
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 9772323
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides for using the signals from N monomeric units (n-mers) within the nanopore to provide sequence information. The invention includes substrates having arrays of nanopores with incorporated electronic circuits, for example, in semiconductor substrates. In some cases, the arrays of nanopores reside in discrete reservoirs.
    Type: Grant
    Filed: February 22, 2017
    Date of Patent: September 26, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 9746476
    Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.
    Type: Grant
    Filed: June 10, 2015
    Date of Patent: August 29, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener
  • 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: 20170168040
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides for using the signals from N monomeric units (n-mers) within the nanopore to provide sequence information. The invention includes substrates having arrays of nanopores with incorporated electronic circuits, for example, in semiconductor substrates. In some cases, the arrays of nanopores reside in discrete reservoirs.
    Type: Application
    Filed: February 22, 2017
    Publication date: June 15, 2017
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 9678056
    Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 10:1 to 1:10. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.
    Type: Grant
    Filed: December 1, 2016
    Date of Patent: June 13, 2017
    Assignee: Pacific Biosciense of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg
  • Publication number: 20170122929
    Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 10:1 to 1:10. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.
    Type: Application
    Filed: December 1, 2016
    Publication date: May 4, 2017
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 9636020
    Abstract: Analysis of live beings is facilitated. According to an example embodiment of the present invention, a light-directing arrangement such as an endoscope is mounted to a live being. Optics in the light-directing arrangement are implemented to pass source light (e.g., laser excitation light) into the live being, and to pass light from the live being for detection thereof. The light from the live being may include, for example, photons emitted in response to the laser excitation light (i.e., fluoresced). The detected light is then used to detect a characteristic of the live being.
    Type: Grant
    Filed: July 2, 2014
    Date of Patent: May 2, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Benjamin A. Flusberg, Eric David Cocker, Juergen Claus Jung, Mark Jacob Schnitzer
  • Patent number: 9546400
    Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. 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: September 13, 2013
    Date of Patent: January 17, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Benjamin Flusberg
  • Patent number: 9411149
    Abstract: Micro-optical imaging is facilitated. According to an example embodiment, a micro-optical probe arrangement includes a GRIN-type lens probe to direct light to and from a specimen. Compensation optics tailored to the probe and aberrations introduced by the lens are located in a light path through the lens, and compensate for the introduced aberrations. A light detector detects light from the specimen, as facilitated by the compensation optics, and generates data characterizing an image of the specimen.
    Type: Grant
    Filed: July 17, 2008
    Date of Patent: August 9, 2016
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Benjamin A. Flusberg, Mark Jacob Schnitzer, Tony H. Ko
  • 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
  • Publication number: 20150362503
    Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.
    Type: Application
    Filed: June 10, 2015
    Publication date: December 17, 2015
    Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener
  • 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