Patents by Inventor Jeffrey Mandell

Jeffrey Mandell 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: 20230295711
    Abstract: Provided herein are compositions and methods for sequencing using at least altering electrical characteristics of polymer bridges. In some examples, the bridges may span the space between first and second electrodes and may include first and second polymer chains that are hybridized to one another. A plurality of nucleotides may be coupled to corresponding labels. A polymerase may be coupled to the bridge and may add nucleotides to a first polynucleotide using at least a sequence of a second polynucleotide. The labels corresponding to those nucleotides respectively may alter hybridization between the first and second polymer chains. Detection circuitry may detect a sequence in which the polymerase adds the nucleotides to the first polynucleotide using at least changes in an electrical signal through the bridge, the changes being responsive to the respective alterations of hybridization using the labels corresponding to those nucleotides.
    Type: Application
    Filed: June 24, 2021
    Publication date: September 21, 2023
    Applicant: Illumina, Inc.
    Inventors: Jeffrey Mandell, Maria Candelaria Rogert Bacigalupo
  • Publication number: 20230175059
    Abstract: Provided herein are compositions and methods for electronically sequencing polynucleotides using partially double-stranded polymer bridges. The bridges may span the space between first and second electrodes. A plurality of nucleotides may be coupled to corresponding labels. A polymerase may add nucleotides to a first polynucleotide using at least a sequence of a second polynucleotide. The labels corresponding to those nucleotides respectively may hybridize to a portion of the bridge that is not double-stranded. Detection circuitry may detect a sequence in which the polymerase adds the nucleotides to the first polynucleotide using at least changes in an electrical signal through the bridge, the changes being responsive to the respective hybridizations between the non-double stranded portion of the bridge and the labels corresponding to those nucleotides.
    Type: Application
    Filed: May 3, 2021
    Publication date: June 8, 2023
    Applicant: Illumina, Inc.
    Inventor: Jeffrey Mandell
  • Publication number: 20230175055
    Abstract: In some examples, a device includes first and second electrodes separated from one another by a space; a particle coupled to the first electrode via a first plurality of bonds, and coupled to the second electrode via a second plurality of bonds; and a polymerase coupled to the particle. In some examples, a composition includes first and second electrodes separated from one another by a space; a fluid including a first electrically conductive label having a length at least as long as a length of the space; and detection circuitry to generate a first signal responsive to transient formation, using the first electrically conductive label, of a first electrically conductive bridge between the first and second electrodes.
    Type: Application
    Filed: May 6, 2021
    Publication date: June 8, 2023
    Applicant: Illumina, Inc.
    Inventors: Rico Otto, Hayden Black, Jeffrey Mandell
  • Publication number: 20230090867
    Abstract: Sequencing polynucleotides using nanopores is provided herein. A polynucleotide is disposed through a nanopore's aperture such that its 3? end is on the nanopore's first side and its 5? end is on the nanopore's second side. On the nanopore's first side, a duplex with the polynucleotide is formed that includes a 3? end. The duplex is extended on the first side of the nanopore by adding a nucleotide to the 3? end of the duplex. A first force is applied disposing the 3? end of the duplex within the aperture, and the nanopore inhibits translocation of the 3? end of the duplex to the second side of the nanopore. A value of an electrical property of the 3? end of the duplex and a single-stranded portion of the polynucleotide is measured. The nucleotide at the 3? end of the duplex is identified using the measured value.
    Type: Application
    Filed: September 19, 2022
    Publication date: March 23, 2023
    Applicant: ILLUMINA, INC.
    Inventors: Jeffrey Mandell, Jessica Killian
  • Patent number: 11578094
    Abstract: Provided is a method including detecting an incorporation of a labelled nucleotide into a nascent polynucleotide strand complementary to a template polynucleotide strand by a polymerase, wherein the polymerase is tethered to a solid support conductive channel by a tether and the labelled nucleotides is a compound of Formula I:
    Type: Grant
    Filed: November 30, 2020
    Date of Patent: February 14, 2023
    Assignees: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Jeffrey Mandell, Silvia Gravina, Sergio Peisajovich, Kaitlin Pugliese, Yin Nah Teo, Xiangyuan Yang, Maria Candelaria Rogert Bacigalupo
  • Patent number: 11542550
    Abstract: A labeled nucleotide includes a nucleotide, a linking molecule attached to a phosphate group of the nucleotide, and a redox-active charge tag attached to the linking molecule. The redox-active charge tag is to be oxidized or reduced by an electrically conductive channel when maintained in proximity of a sensing zone of the electrically conductive channel.
    Type: Grant
    Filed: February 13, 2019
    Date of Patent: January 3, 2023
    Assignee: Illumina, Inc.
    Inventors: Jeffrey Mandell, Steven Barnard, John Moon, Maria Candelaria Rogert Bacigalupo
  • Publication number: 20220162680
    Abstract: A method is provided that includes adding, using a polymerase coupled to a substrate, nucleotides in a solution to a first polynucleotide using at least a sequence of a second polynucleotide. The method includes separating, using labels respectively coupled to the nucleotides, quenchers from respective fluorophores. The method includes then detecting a sequence in which the polymerase adds the nucleotides to the first polynucleotide using at least fluorescence from the respective fluorophores.
    Type: Application
    Filed: October 21, 2021
    Publication date: May 26, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Jeffrey Mandell, Sergio Peisajovich, Seth McDonald, Kaitlin Pugliese
  • Publication number: 20220090193
    Abstract: Provided is a method including hybridizing a polynucleotide to a template, contacting a first template nucleotide 5-prime adjacent to a 5-prime-most nucleotide of the plurality of nucleotides that are complementary to the polynucleotide with a polymerase and a charge-tagged nucleotide, wherein the charge-tagged nucleotide is complementary to the first template nucleotide and includes a charge tag attached to a 5-prime polyphosphate of the charge-tagged nucleotide.
    Type: Application
    Filed: August 18, 2020
    Publication date: March 24, 2022
    Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Yannan ZHAO, Kaitlin PUGLIESE, Erin GARCIA, Ludovic VINCENT, Anmiv PRABHU, Silvia GRAVINA, Sergio PEISAJOVICH, Yin Nah TEO, Xiangyuan YANG, Jeffrey MANDELL, Jonathon STUTCHMAN
  • Publication number: 20210403993
    Abstract: The present disclosure relates to methods comprising (a) contacting a polymerase with a template polynucleotide and a plurality of free nucleotides, wherein the template polynucleotide is hybridized to a complementary polynucleotide comprising a 3? end overhung by a 5? terminal fragment of the template polynucleotide, and the plurality of free nucleotides comprise a compound Formula (I); wherein said contacting occurs under a complexation condition, the complexation condition effective to form a complex but not effective to form polymerization, wherein the complex comprises the polymerase, the template polynucleotide, the complementary polynucleotide, and one of the plurality of free nucleotides that is complementary to a first nucleotide of the 5? terminal fragment of the template polynucleotide; (b) detecting a signal from the fluorescent label; and (c) exposing the complex to a polymerization condition.
    Type: Application
    Filed: June 29, 2021
    Publication date: December 30, 2021
    Inventors: Kaitlin PUGLIESE, Sergio PEISAJOVICH, Jeffrey MANDELL, Seth MCDONALD
  • Publication number: 20210388425
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Application
    Filed: August 11, 2021
    Publication date: December 16, 2021
    Inventors: Brian K. Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Publication number: 20210179657
    Abstract: Provided is a method including detecting an incorporation of a labelled nucleotide into a nascent polynucleotide strand complementary to a template polynucleotide strand by a polymerase, wherein the polymerase is tethered to a solid support conductive channel by a tether and the labelled nucleotides is a compound of Formula I:
    Type: Application
    Filed: November 30, 2020
    Publication date: June 17, 2021
    Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Jeffrey MANDELL, Silvia GRAVINA, Sergio PEISAJOVICH, Kaitlin PUGLIESE, Yin Nah TEO, Xiangyuan YANG, Maria Candelaria Rogert BACIGALUPO
  • Patent number: 10851406
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Grant
    Filed: May 22, 2017
    Date of Patent: December 1, 2020
    Assignee: Ionian Technologies, LLC
    Inventors: Brian K Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Patent number: 10851131
    Abstract: Provided is a method including detecting an incorporation of a labelled nucleotide into a nascent polynucleotide strand complementary to a template polynucleotide strand by a polymerase, wherein the polymerase is tethered to a solid support conductive channel by a tether and the labelled nucleotides is a compound of Formula I:
    Type: Grant
    Filed: February 19, 2019
    Date of Patent: December 1, 2020
    Assignees: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Jeffrey Mandell, Silvia Gravina, Sergio Peisajovich, Kaitlin Pugliese, Yin Nah Teo, Xiangyuan Yang, Maria Candelaria Rogert Bacigalupo
  • Publication number: 20200157618
    Abstract: A labeled nucleotide includes a nucleotide, a linking molecule attached to a phosphate group of the nucleotide, and a redox-active charge tag attached to the linking molecule. The redox-active charge tag is to be oxidized or reduced by an electrically conductive channel when maintained in proximity of a sensing zone of the electrically conductive channel.
    Type: Application
    Filed: February 13, 2019
    Publication date: May 21, 2020
    Inventors: Jeffrey Mandell, Steven Barnard, John Moon, Maria Candelaria Rogert Bacigalupo
  • Publication number: 20200123193
    Abstract: Provided is a method including detecting an incorporation of a labelled nucleotide into a nascent polynucleotide strand complementary to a template polynucleotide strand by a polymerase, wherein the polymerase is tethered to a solid support conductive channel by a tether and the labelled nucleotides is a compound of Formula I:
    Type: Application
    Filed: February 19, 2019
    Publication date: April 23, 2020
    Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Jeffrey MANDELL, Silvia GRAVINA, Sergio PEISAJOVICH, Kaitlin PUGLIESE, Yin Nah TEO, Xiangyuan YANG
  • Publication number: 20190323072
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Application
    Filed: January 9, 2019
    Publication date: October 24, 2019
    Inventors: Brian K Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Publication number: 20180023130
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Application
    Filed: March 23, 2017
    Publication date: January 25, 2018
    Inventors: Brian K. Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Publication number: 20180023118
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Application
    Filed: May 22, 2017
    Publication date: January 25, 2018
    Inventors: Brian K Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell
  • Patent number: 9617586
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Grant
    Filed: July 14, 2008
    Date of Patent: April 11, 2017
    Assignee: Ionian Technologies, Inc.
    Inventors: Brian K. Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard B. Roth, Jeffrey Mandell
  • Patent number: 9562263
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Grant
    Filed: October 30, 2013
    Date of Patent: February 7, 2017
    Assignee: Ionian Technologies, Inc.
    Inventors: Brian K Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod Provins, Richard Roth, Jeffrey Mandell