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).
-
Patent number: 11788080Abstract: 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: GrantFiled: June 27, 2022Date of Patent: October 17, 2023Assignee: Encodia, Inc.Inventors: Kevin Desai, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
-
Patent number: 11782062Abstract: 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: GrantFiled: February 8, 2023Date of Patent: October 10, 2023Assignee: 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: 11760772Abstract: 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: GrantFiled: May 26, 2021Date of Patent: September 19, 2023Assignee: Illumina, Inc.Inventors: Frank J. Steemers, Kevin L. Gunderson, Kerri York, Ryan Christopher Smith
-
Patent number: 11753677Abstract: The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.Type: GrantFiled: November 9, 2022Date of Patent: September 12, 2023Assignee: Encodia, Inc.Inventors: Mark S. Chee, Haibiao Gong, Kevin L. Gunderson
-
Publication number: 20230279386Abstract: 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.Type: ApplicationFiled: March 24, 2023Publication date: September 7, 2023Applicant: Encodia, Inc.Inventors: Mark S. CHEE, Kevin L. Gunderson, Norihito Muranaka, Brian Tate Weinert
-
Publication number: 20230272457Abstract: 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: ApplicationFiled: March 6, 2023Publication date: August 31, 2023Inventors: Boyan Boyanov, Liangliang Qiang, Kevin L. Gunderson, Kay Klausing, Lea Pickering, Cyril Delattre, Tarun Khurana
-
Patent number: 11732301Abstract: 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: GrantFiled: March 1, 2021Date of Patent: August 22, 2023Assignee: Illumina, Inc.Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
-
Publication number: 20230257727Abstract: 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: ApplicationFiled: January 18, 2023Publication date: August 17, 2023Applicant: Encodia, Inc.Inventors: Kevin DESAI, Kevin L. GUNDERSON, Robert C. JAMES, Lei SHI, Stephen VERESPY, III
-
Publication number: 20230236198Abstract: 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: ApplicationFiled: February 8, 2023Publication date: July 27, 2023Applicant: Encodia, Inc.Inventors: Mark S. CHEE, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
-
Publication number: 20230220589Abstract: The present disclosure relates to a binder that specifically binds to an N-terminally modified polypeptide through interaction with a modified N-terminal amino acid. Also provided herein is a method and related kits for treating a polypeptide using or comprising the binder and/or modified cleavase. In some embodiments, 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 polypeptide for analysis.Type: ApplicationFiled: September 29, 2021Publication date: July 13, 2023Applicant: Encodia, Inc.Inventors: Kevin L. GUNDERSON, Soumya GANGULY, Robert C. JAMES, Kenneth KUHN, Zachary MILES, Lei SHI, Stephen VERESPY, III, Aaron WISE, Zongxiang ZHOU
-
Patent number: 11697847Abstract: 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: GrantFiled: April 1, 2020Date of Patent: July 11, 2023Assignee: ILLUMINA, INC.Inventors: Robert C. Kain, Tarun Khurana, Kevin L. Gunderson, Yir-Shyuan Wu
-
Patent number: 11692223Abstract: The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods, including methods for modifying immobilized capture primers comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of template nucleic acids under conditions sufficient for hybridization to produce one or more immobilized template nucleic acids, and b) extending one or more immobilized capture primers to produce one or more immobilized extension products complementary to the one or more template nucleic acid.Type: GrantFiled: April 10, 2020Date of Patent: July 4, 2023Assignee: Illumina Cambridge LimitedInventors: 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: 20230203562Abstract: Provided herein are high-throughput, population-wide serotyping and antibody profiling assays. Disclosed variants of a Digital Serotyping assay employ next generation sequencing to measure the “serotyping profile” of barcoded subject serum antibodies tested against a range of DNA-tagged pathogen-derived antigens. The disclosed assay setup enables multiplexing in both the sample and antigen dimensions, generating a large multi-dimensional serotyping data set for more comprehensive serotyping profiling of large populations across a large number of antigens and possible pathogens. Moreover, the ability to easily scale and multiplex the number of peptide epitopes allows rapid updating of the assay content to monitor the ever-changing spectrum of pathogens. Additional applications of this technology include cancer immunology and autoimmune conditions (e.g., neoantigen or autoimmune profiling), screening for toxins, antibody therapeutics development, biosecurity, and veterinary medicine.Type: ApplicationFiled: December 27, 2022Publication date: June 29, 2023Applicant: Encodia, Inc.Inventors: Eric OKERBERG, Kevin L. GUNDERSON, Norihito MURANAKA, Jongbum KIM, Byung Joon LIM, Lei SHI, Soumya GANGULY, Devin SULLIVAN
-
Publication number: 20230183680Abstract: Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom.Type: ApplicationFiled: January 12, 2023Publication date: June 15, 2023Inventors: Frank J. Steemers, Sasan Amini, Kevin L. Gunderson, Natasha Pignatelli, Igor Goryshin
-
Publication number: 20230168254Abstract: 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: ApplicationFiled: August 11, 2022Publication date: June 1, 2023Applicant: Encodia, Inc.Inventors: Mark S. Chee, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
-
Publication number: 20230143290Abstract: The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.Type: ApplicationFiled: November 9, 2022Publication date: May 11, 2023Applicant: Encodia, Inc.Inventors: Mark S. CHEE, Haibiao GONG, Kevin L. GUNDERSON
-
Patent number: 11634709Abstract: 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: GrantFiled: August 26, 2021Date of Patent: April 25, 2023Assignee: Encodia, Inc.Inventors: Mark S. Chee, Kevin L. Gunderson, Norihito Muranaka, Brian Tate Weinert
-
Patent number: 11634707Abstract: Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.Type: GrantFiled: February 10, 2016Date of Patent: April 25, 2023Assignee: ILLUMINA, INC.Inventors: Kevin L Gunderson, Frank J Steemers, Jeffrey S Fisher, Roberto Rigatti
-
Patent number: 11629373Abstract: 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: GrantFiled: March 27, 2020Date of Patent: April 18, 2023Assignee: Illumina, Inc.Inventors: Boyan Boyanov, Liangliang Qiang, Kevin L. Gunderson, Kay Klausing, Lea Pickering, Cyril Delattre, Tarun Khurana
-
Patent number: 11591641Abstract: 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: GrantFiled: August 5, 2020Date of Patent: February 28, 2023Assignee: Illumina, Inc.Inventors: Kevin L. Gunderson, Frank J. Steemers