Patents Examined by Jeremy C Flinders
  • Synthetic nucleic acids having non-natural structures
    Patent number: 11377655
    Abstract: Nucleic acid compositions having nucleotide sequences that do not occur in nature are provided. Also provided are populations of different nucleic acids having universal adapters or universal primer binding sites. Methods of capturing, copying or amplifying nucleic acids of interest using universal adapters, universal primer binding sites and/or universal primers are also provided.
    Type: Grant
    Filed: July 16, 2020
    Date of Patent: July 5, 2022
    Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: Arnold Oliphant, James Yu
  • Articles for diagnosis of liver fibrosis
    Patent number: 11371097
    Abstract: Disclosed are methods and articles (e.g., gene arrays or antibodies) for determining the progression or regression of liver fibrosis, for the diagnosis of liver disease, and for screening compounds for hepatotoxicity and efficacy against liver fibrosis. Related therapeutic methods also are disclosed.
    Type: Grant
    Filed: January 29, 2016
    Date of Patent: June 28, 2022
    Assignee: The Government of the United States, as represented by the Secretary of the Army
    Inventors: Mohamed Diwan M. Abdulhameed, Gregory J. Tawa, Danielle L. Ippolito, John A. Lewis, Sven Anders Wallqvist, Jonathan D. Stallings, Matthew G. Permenter
  • Mirror nucleic acid replication system
    Patent number: 11371027
    Abstract: Provided is a method for replicating a mirror nucleic acid, comprising: reacting a mirror nucleic acid template, a mirror nucleic acid primer and mirror dNTPs/rNTPs in the presence of a mirror nucleic acid polymerase, so as to obtain the mirror nucleic acid.
    Type: Grant
    Filed: February 15, 2017
    Date of Patent: June 28, 2022
    Assignee: Tsinghua University
    Inventors: Ting Zhu, Lei Liu, Weiliang Xu, Zimou Wang, Wenjun Jiang, Jiaxing Wang, Linping Yu
  • Random RNA libraries, methods of generating same, and screening methods utilizing same
    Patent number: 11371041
    Abstract: This invention provides sets and libraries of short hairpin ribonucleic acid (shRNA) molecules comprising a double-stranded region of random sequence containing random mismatches, methods of generating same, sets and libraries of expression vectors for same, methods of generating same, and methods for identifying an RNA therapeutic or RNA molecule that has an ability to affect a biological parameter, for identifying a drug target for a disease or disorder of interest, and for identifying a variant of an RNA molecule that has an altered ability to affect a biological parameter of interest.
    Type: Grant
    Filed: April 15, 2019
    Date of Patent: June 28, 2022
    Assignee: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA
    Inventors: Robert B. Wilson, Yongping Wang
  • Spatially encoded biological assays
    Patent number: 11365442
    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: September 25, 2020
    Date of Patent: June 21, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Production and monitoring of metabolites in cells
    Patent number: 11365410
    Abstract: Methods of making and monitoring metabolites in cells are provided.
    Type: Grant
    Filed: April 12, 2016
    Date of Patent: June 21, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Jameson K. Rogers, George M. Church
  • Method for identifying antibiotic targets
    Patent number: 11359195
    Abstract: Disclosed are methods related to identifying an essential gene which serves as an antibiotic target in a bacterium.
    Type: Grant
    Filed: July 20, 2017
    Date of Patent: June 14, 2022
    Assignee: DISCUVA LIMITED
    Inventors: David Hugh Williams, Arthur Keith Turner
  • Method for preparing DNA library derived from FFPE tissue using endonuclease
    Patent number: 11359192
    Abstract: The present invention relates to a method of preparing a DNA library derived from FFPE tissue using endonucleases, and the majority of general clinical samples are FFPE tissues and in case of old FFPE tissues, DNA library preparation often fails and NGS analysis becomes difficult and therefore there is a desperate need to overcome these problems. S1 nucleases are enzymes which specifically cleave only single-stranded DNA and in almost all FFPEs, there is a nick in the dsDNA everywhere, which can be the target of S1 nucleases. In the process of extracting gDNA from FFPE tissues, since when S1 nucleases are treated and eluted under appropriate conditions during elution, a DNA fragment can be obtained with DNA having a size suitable for DNA library preparation together with the DNA extraction, the Covaris fragmentation process can be omitted and cost and time can be reduced.
    Type: Grant
    Filed: November 3, 2017
    Date of Patent: June 14, 2022
    Assignee: GenoPeaks Co., Ltd.
    Inventors: Se-Jin Jang, Sung-Min Chun, Chang Ohk Sung, Yu Jin Kim, Ji-Young Lee, Hye-Joon Jeon
  • Method for rapid differential diagnosis of infection using supercritical fluid chromatographic separation of microbial quorum sensing molecules
    Patent number: 11360062
    Abstract: A method for rapid differential diagnosis of infection using supercritical fluid chromatographic separation of quorum sensing molecules as biomarkers for infection agents.
    Type: Grant
    Filed: January 30, 2018
    Date of Patent: June 14, 2022
    Assignee: UNM Rainforest innovations
    Inventors: Aaron Neumann, Linnea K. Ista
  • Method for enriching biomolecules and for removing the biomolecules from a biological sample
    Patent number: 11352617
    Abstract: A method includes enriching biomolecules and removal of the biomolecules from a biological sample. In the presence of particles, an alginate solution and salts of divalent and/or polyvalent cations or an acid are added to a biological sample, and an alginate-gel-biomolecule-complex is formed on the particles. The complex is removed from the sample by separation of the particles, and from which subsequently the biomolecules or ingredients of the biomolecules are released. The biomolecules, which shall be enriched, include cell-free nucleic acids, viruses or subcellular microparticles.
    Type: Grant
    Filed: July 25, 2016
    Date of Patent: June 7, 2022
    Assignee: IST INNUSCREEN GMBH
    Inventor: Timo Hillebrand
  • Method for synthesis of polynucleotides using a diverse library of oligonucleotides
    Patent number: 11352619
    Abstract: A method for synthesizing a target double stranded (ds) polynucleotide by providing an oligonucleotide library within an array device that has a diversity of oligonucleotide library members, each of which has a different nucleotide sequence and is contained in a separate library containment in an aqueous solution. The library includes single stranded oligonucleotides and double stranded oligonucleotides with at least one overhang and covers at least 10,000 pairs of matching oligonucleotides. In a first step, transferring at least a first pair of matching oligonucleotides transferred from the library into a first reaction containment using a liquid handler and the matching oligonucleotides are assembled, thereby obtaining a first reaction product comprising at least one overhang.
    Type: Grant
    Filed: October 15, 2018
    Date of Patent: June 7, 2022
    Assignee: RIBBON BIOLABS GMBH
    Inventors: Harold Paul Vladar, Rodrigo Aparecido Fernandes Redondo
  • Methods of analyzing nucleic acids
    Patent number: 11339422
    Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).
    Type: Grant
    Filed: March 26, 2020
    Date of Patent: May 24, 2022
    Assignee: Illumina, Inc.
    Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
  • Modified variable domain molecules and methods for producing them
    Patent number: 11332522
    Abstract: The present disclosure provides an isolated, engineered or non-naturally occurring protein comprising an antibody light chain variable domain (VL) which may comprise at least one negatively charged amino acid positioned between residues 49 to 56 according to the numbering system of Kabat, the protein capable of binding specifically to an antigen.
    Type: Grant
    Filed: May 9, 2019
    Date of Patent: May 17, 2022
    Assignee: GARVAN INSTITUTE OF MEDICAL RESEARCH
    Inventors: Daniel Christ, Kip Dudgeon, Romain Rouet
  • Barcode-based nucleic acid sequence assembly
    Patent number: 11332738
    Abstract: Provided herein are methods, systems, and compositions for efficient nucleic acid assembly. Nucleic acid assembly may comprise assembly of variants comprising paired homology.
    Type: Grant
    Filed: June 19, 2020
    Date of Patent: May 17, 2022
    Assignee: Twist Bioscience Corporation
    Inventors: Rebecca Nugent, Siyuan Chen, Ross Kettleborough, Elian Lee, Nathan Raynard
  • Method for making a cDNA library
    Patent number: 11326160
    Abstract: This disclosure provides, among other things, a method for making a cDNA library. In some embodiments the method may comprise reverse transcribing mRNA to produce DNA:mRNA hybrids, treating the DNA:mRNA hybrids with RNAseH to produce mRNA fragments, and reverse transcribing the mRNA fragments.
    Type: Grant
    Filed: June 3, 2020
    Date of Patent: May 10, 2022
    Assignee: BIOO SCIENTIFIC CORPORATION
    Inventors: Kevin Allen, Adam Morris
  • Methods for treating breast cancer and for identifying breast cancer antigens
    Patent number: 11300574
    Abstract: Disclosed herein are isolated compositions including at least 2 of mutant peptides selected from the group consisting of SEQ ID NOS: 1-149, or polypeptides comprising the mutant peptides; wherein the composition comprises mutant peptides encoded by 2 or more genes. Also disclosed are methods for personalized treatment of breast cancer involving creating a peptide array of mutant peptides comprising the mutations in protein-encoding regions of the high-frequency cancer genes or the exome in a subject and screening the peptide array with a biological sample from the subject to detect antibodies in the biological sample that bind to the array, to detect antigenic targets for therapy in treating the subject.
    Type: Grant
    Filed: May 25, 2018
    Date of Patent: April 12, 2022
    Assignee: UNIVERSITY OF CONNECTICUT
    Inventors: David Han, Veneta Qendro
  • Detection and modification of gut microbial population
    Patent number: 11287419
    Abstract: Methods and systems for evaluating health/disease state of an individual are provided herein. In particular, the disclosure provides methods for measuring levels of one or more metabolites of interest in an individual and using these measurements to assess the individual's health. The disclosure also provides systems for carrying out the disclosed methods. For example, the disclosed systems may include a metabolite level evaluation module to determine the individual's heath based on the metabolite levels measured.
    Type: Grant
    Filed: June 9, 2021
    Date of Patent: March 29, 2022
    Assignee: IXCELA, INC.
    Inventors: Wayne R. Matson, Samantha A. Matson, Erika N. Ebbel-Angle, Srikant Sarangi
  • Detection and modification of gut microbial population
    Patent number: 11287418
    Abstract: Methods and systems for evaluating health/disease state of an individual are provided herein. In particular, the disclosure provides methods for measuring levels of one or more metabolites of interest in an individual and using these measurements to assess the individual's health. The disclosure also provides systems for carrying out the disclosed methods. For example, the disclosed systems may include a metabolite level evaluation module to determine the individual's health based on the metabolite levels measured.
    Type: Grant
    Filed: June 9, 2021
    Date of Patent: March 29, 2022
    Assignee: IXCELA, INC.
    Inventors: Wayne R. Matson, Samantha A. Matson, Erika N. Ebbel-Angle, Srikant Sarangi
  • Detection and modification of gut microbial population
    Patent number: 11287420
    Abstract: Methods and systems for evaluating heath/disease state of an individual are provided herein. In particular, the disclosure provides methods for measuring levels of one or more metabolites of interest in an individual and using these measurements to assess the individual's health. The disclosure also provides systems for carrying out the disclosed methods. For example, the disclosed systems may include a metabolite level evaluation module to determine the individual's heath based on the metabolite levels measured.
    Type: Grant
    Filed: June 9, 2021
    Date of Patent: March 29, 2022
    Assignee: IXCELA, INC.
    Inventors: Wayne R. Matson, Samantha A. Matson, Erika N. Ebbel-Angle, Srikant Sarangi
  • Detection and modification of gut microbial population
    Patent number: 11287417
    Abstract: Methods and systems for evaluating heath/disease state of an individual are provided herein. In particular, the disclosure provides methods for measuring levels of one or more metabolites of interest in an individual and using these measurements to assess the individual's health. The disclosure also provides systems for carrying out the disclosed methods. For example, the disclosed systems may include a metabolite level evaluation module to determine the individual's heath based on the metabolite levels measured.
    Type: Grant
    Filed: June 9, 2021
    Date of Patent: March 29, 2022
    Assignee: IXCELA, INC.
    Inventors: Wayne R. Matson, Samantha A. Matson, Erika N. Ebbel-Angle, Srikant Sarangi