Patents by Inventor Mark S. Chee

Mark S. Chee 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: 20230136966
    Abstract: The present disclosure relates to methods and kits for analyzing a macromolecule. In some embodiments, the present disclosure relates to macromolecule analysis methods which employ barcoding and nucleic acid encoding of molecular recognition events. Also provided herein is a method and related kits for transferring information using a plurality of enzymes, including for performing a ligation, extension, and cleavage reaction with nucleic acid molecules associated with the macromolecule for analysis. In some embodiments, the macromolecule for analysis comprises a peptide, a polypeptide, or a protein.
    Type: Application
    Filed: August 16, 2021
    Publication date: May 4, 2023
    Applicant: Encodia, Inc.
    Inventor: Mark S. CHEE
  • Patent number: 11634709
    Abstract: Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing. Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids.
    Type: Grant
    Filed: August 26, 2021
    Date of Patent: April 25, 2023
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, Kevin L. Gunderson, Norihito Muranaka, Brian Tate Weinert
  • Patent number: 11634756
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: October 24, 2022
    Date of Patent: April 25, 2023
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20230107023
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: December 5, 2022
    Publication date: April 6, 2023
    Inventor: Mark S. Chee
  • Patent number: 11618918
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: June 2, 2022
    Date of Patent: April 4, 2023
    Assignee: Prognosys Biosciences, Inc.
    Inventors: Mark S. Chee, David A. Routenberg
  • Publication number: 20230054691
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Application
    Filed: August 9, 2022
    Publication date: February 23, 2023
    Applicant: Encodia, Inc.
    Inventors: Mark S. CHEE, Kevin L. Gunderson, Michael Phillip Weiner
  • Publication number: 20230040363
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: October 19, 2022
    Publication date: February 9, 2023
    Inventor: Mark S. Chee
  • Publication number: 20230042088
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: October 24, 2022
    Publication date: February 9, 2023
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11560587
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: August 1, 2022
    Date of Patent: January 24, 2023
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11549138
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: May 26, 2022
    Date of Patent: January 10, 2023
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11542543
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: March 11, 2022
    Date of Patent: January 3, 2023
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20220389491
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: August 1, 2022
    Publication date: December 8, 2022
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11519022
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: June 27, 2022
    Date of Patent: December 6, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11513126
    Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.
    Type: Grant
    Filed: October 31, 2018
    Date of Patent: November 29, 2022
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
  • Patent number: 11499187
    Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.
    Type: Grant
    Filed: October 21, 2019
    Date of Patent: November 15, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11499188
    Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.
    Type: Grant
    Filed: October 21, 2019
    Date of Patent: November 15, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 11479810
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: June 17, 2022
    Date of Patent: October 25, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20220333171
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 27, 2022
    Publication date: October 20, 2022
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20220325325
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 2, 2022
    Publication date: October 13, 2022
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. CHEE, David A. ROUTENBERG
  • Publication number: 20220315998
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 17, 2022
    Publication date: October 6, 2022
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee