Patents by Inventor Kevin L. Gunderson

Kevin L. Gunderson 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: 20210214701
    Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.
    Type: Application
    Filed: March 25, 2021
    Publication date: July 15, 2021
    Applicant: Encodia, Inc.
    Inventors: Kevin DESAI, Kevin L. GUNDERSON, Robert C. JAMES, Lei SHI, Stephen VERESPY, III
  • Patent number: 11060135
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Grant
    Filed: August 30, 2018
    Date of Patent: July 13, 2021
    Assignee: Illumina, Inc.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20210208150
    Abstract: The present disclosure relates to methods and kits for forming a stable complex comprising a binding agent and a target (e.g., a macromolecule). In some embodiments, the target comprises a peptide, a polypeptide, or a protein to be analyzed. In some embodiments, the present disclosure relates to formation of a stable complex comprising a binding agent and a target (e.g., a macromolecule) to be analyzed in a method which employs barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels. Provided herein is also a programmable system for information transfer comprising one or more adaptor molecules.
    Type: Application
    Filed: January 14, 2021
    Publication date: July 8, 2021
    Applicant: Encodia, Inc.
    Inventors: Kevin L. GUNDERSON, Norihito MURANAKA
  • Patent number: 11041196
    Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.
    Type: Grant
    Filed: June 12, 2019
    Date of Patent: June 22, 2021
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 11021504
    Abstract: Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.
    Type: Grant
    Filed: May 16, 2019
    Date of Patent: June 1, 2021
    Assignee: Illumina, Inc.
    Inventors: Frank J Steemers, Kevin L Gunderson, Kerri York, Ryan Christopher Smith
  • Publication number: 20210129107
    Abstract: The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.
    Type: Application
    Filed: November 16, 2020
    Publication date: May 6, 2021
    Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
  • Publication number: 20210108258
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Application
    Filed: December 7, 2020
    Publication date: April 15, 2021
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Patent number: 10968448
    Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.
    Type: Grant
    Filed: January 7, 2020
    Date of Patent: April 6, 2021
    Assignee: Illumina, Inc.
    Inventors: Frank J. Steemers, Jeffrey S. Fisher, Kevin L. Gunderson, Sasan Amini, Christian Gloeckner
  • Patent number: 10961576
    Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.
    Type: Grant
    Filed: December 9, 2019
    Date of Patent: March 30, 2021
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
  • Patent number: 10960377
    Abstract: Provided herein are methods and compositions for placing single target molecules on a patterned substrate.
    Type: Grant
    Filed: June 6, 2019
    Date of Patent: March 30, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Kevin L. Gunderson, Jingwei Bai, Boyan Boyanov
  • Publication number: 20210047635
    Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
    Type: Application
    Filed: September 2, 2020
    Publication date: February 18, 2021
    Inventors: Christian Gloeckner, Amirali Kia, Molly He, Trina Faye Osothprarop, Frank J. Steemers, Kevin L. Gunderson, Sasan Amini, Jerome Jendrisak
  • Patent number: 10870099
    Abstract: The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.
    Type: Grant
    Filed: February 21, 2013
    Date of Patent: December 22, 2020
    Assignee: Illumina, Inc.
    Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
  • Publication number: 20200370103
    Abstract: This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.
    Type: Application
    Filed: August 5, 2020
    Publication date: November 26, 2020
    Applicant: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Frank J. Steemers
  • Publication number: 20200348257
    Abstract: A kit includes an array of charge sensors attached to a solid-phase substrate , wherein individual charge sensors in the array respectively comprise a channel and a polymerase and are located at different addressable locations on the solid-phase substrate; and a liquid comprising a plurality of different nucleic acids, each of the different nucleic acids including a unique label to be detected by a charge sensor of the array.
    Type: Application
    Filed: March 20, 2020
    Publication date: November 5, 2020
    Inventors: Boyan BOYANOV, Jeffrey G. MANDELL, Jingwei BAI, Kevin L. GUNDERSON, Cheng-Yao CHEN, Michel PERBOST
  • Patent number: 10815478
    Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
    Type: Grant
    Filed: November 5, 2015
    Date of Patent: October 27, 2020
    Assignee: Illumina, Inc.
    Inventors: Christian Gloeckner, Amirali Kia, Molly He, Trina Faye Osothprarop, Frank J. Steemers, Kevin L. Gunderson, Sasan Amini, Jerome Jendrisak
  • Publication number: 20200318182
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods.
    Type: Application
    Filed: April 10, 2020
    Publication date: October 8, 2020
    Inventors: Kevin L. Gunderson, Jingwei Bai, Matthew William Kellinger, John M. Beierle, Jonathan Mark Boutell, Roberto Rigatti, Maria Candelaria Rogert Bacigalupo, Boyan Boyanov, Klaus Maisinger
  • Publication number: 20200318180
    Abstract: A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. A permanent tether can include a head region anchored to the polymerase, a tail region, and an elongated body disposed therebetween that occurs in the aperture of the nanopore. A first moiety can be disposed on the elongated body that binds to the elongated tag of a first nucleotide upon which the polymerase is acting. A reporter region can be disposed on the elongated body that indicates when the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide.
    Type: Application
    Filed: May 8, 2020
    Publication date: October 8, 2020
    Applicant: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Jeffrey G. Mandell
  • Publication number: 20200318167
    Abstract: Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.
    Type: Application
    Filed: March 27, 2020
    Publication date: October 8, 2020
    Inventors: Boyan Boyanov, Liangliang Qiang, Kevin L. Gunderson, Kay Klausing, Lea Pickering, Cyril Delattre, Tarun Khurana
  • Patent number: 10787704
    Abstract: The present disclosure provides a method for sequencing nucleic acids. The method can include polymerase catalyzed incorporation of nucleotides into a nascent nucleic acid strand against a nucleic acid template, wherein the polymerase is attached to a charge sensor that detects nucleotide incorporation events. One or more non-natural nucleotide types that each produce a unique signatures at the charge sensor can be used to uniquely identify different nucleotides in the template nucleic acid.
    Type: Grant
    Filed: May 11, 2016
    Date of Patent: September 29, 2020
    Assignees: ILLUMINA, INC., THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Kevin L Gunderson, Jingwei Bai, Cheng-Yao Chen, Jeffrey G Mandell, Sergio Peisajovich, Philip G Collins, Gregory A Weiss, Boyan Boyanov
  • Publication number: 20200224267
    Abstract: A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.
    Type: Application
    Filed: April 1, 2020
    Publication date: July 16, 2020
    Inventors: Robert C. Kain, Tarun Khurana, Kevin L. Gunderson, Yir-Shyuan Wu