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).

  • Methods for stable complex formation and related kits
    Patent number: 11169157
    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: Grant
    Filed: January 14, 2021
    Date of Patent: November 9, 2021
    Assignee: ENCODIA, INC.
    Inventors: Kevin L. Gunderson, Norihito Muranaka
  • Preserving genomic connectivity information in fragmented genomic DNA samples
    Patent number: 11149310
    Abstract: A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.
    Type: Grant
    Filed: March 18, 2019
    Date of Patent: October 19, 2021
    Assignee: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, Frank J. Steemers, Sasan Amini, Kevin L. Gunderson
  • MACROMOLECULE ANALYSIS EMPLOYING NUCLEIC ACID ENCODING
    Publication number: 20210302431
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Application
    Filed: March 10, 2021
    Publication date: September 30, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. GUNDERSON, Michael Phillip Weiner
  • FUNCTIONALIZATION AND PURIFICATION OF MOLECULES BY REVERSIBLE GROUP EXCHANGE
    Publication number: 20210277043
    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: Application
    Filed: May 26, 2021
    Publication date: September 9, 2021
    Applicant: Illumina, Inc.
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
  • METHODS AND COMPOSITIONS USING ONE-SIDED TRANSPOSITION
    Publication number: 20210277388
    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: Application
    Filed: March 2, 2021
    Publication date: September 9, 2021
    Inventors: Frank J. Steemers, Jeffrey S. Fisher, Kevin L. Gunderson, Sasan Amini, Christian Gloeckner
  • HYBRID NANOPORE SENSORS
    Publication number: 20210269877
    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: Application
    Filed: March 1, 2021
    Publication date: September 2, 2021
    Inventors: BOYAN BOYANOV, JEFFREY G MANDELL, KEVIN L GUNDERSON, JINGWEI BAI, LIANGLIANG QIANG, BRADLEY BAAS
  • PROXIMITY INTERACTION ANALYSIS
    Publication number: 20210254047
    Abstract: The present disclosure relates to methods for assessing identity and spatial relationship between a polypeptide and a moiety in a sample. In some embodiments, both the polypeptide and the moiety are parts of a larger polypeptide, and the present methods can be used assess identity and spatial relationship between the polypeptide and the moiety in the same polypeptide or protein. In other embodiments, the polypeptide and the moiety belong to different molecules, and the present methods can be used assess identity and spatial relationship between the polypeptide and the moiety different molecules, e.g., in a protein-protein complex, a protein-DNA complex or a protein-KNA complex.
    Type: Application
    Filed: September 4, 2019
    Publication date: August 19, 2021
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. GUNDERSON
  • MODIFIED CLEAVASES, USES THEREOF AND RELATED KITS
    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
  • Microarray fabrication system and method
    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
  • METHODS FOR STABLE COMPLEX FORMATION AND RELATED KITS
    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
  • Compositions and methods for polynucleotide sequencing
    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
  • Functionalization and purification of molecules by reversible group exchange
    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
  • COMPOSITIONS AND METHODS FOR THE AMPLIFICATION OF NUCLEIC ACIDS
    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
  • MICROARRAY FABRICATION SYSTEM AND METHOD
    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
  • Methods and compositions using one-sided transposition
    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
  • Compositions and methods for single molecular placement on a substrate
    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
  • Hybrid nanopore sensors
    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
  • TRANSPOSASE COMPOSITIONS FOR REDUCTION OF INSERTION BIAS
    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
  • Compositions and methods for the amplification of nucleic acids
    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
  • METHODS AND COMPOSITIONS FOR WHOLE GENOME AMPLIFICATION AND GENOTYPING
    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