Patents Examined by Christopher M. Gross
  • Methods and systems for screening using microcapillary arrays
    Patent number: 11085039
    Abstract: High-throughput methods for screening large populations of variant proteins are provided. The methods utilize large-scale arrays of microcapillaries, where each microcapillary comprises a solution containing a variant protein, an immobilized target molecule, and a reporter element. Immobilized target molecules may include any molecule of interest, including proteins, nucleic acids, carbohydrates, and other biomolecules. The association of a variant protein with a molecular target is assessed by measuring a signal from the reporter element. The contents of microcapillaries identified in the assays as containing variant proteins of interest can be isolated, and cells expressing the variant proteins of interest can be characterized. Also provided are systems for performing the disclosed screening methods.
    Type: Grant
    Filed: December 12, 2016
    Date of Patent: August 10, 2021
    Assignee: xCella Biosciences, Inc.
    Inventors: Jennifer R. Cochran, Bob Chen, Spencer Caleb Alford
  • Nucleic acid-guided editing of exogenous polynucleotides in heterologous cells
    Patent number: 11085131
    Abstract: The present disclosure provides shuttle vectors for editing exogenous polynucleotides in heterologous live cells, as well as automated methods, modules, and multi-module cell editing instruments and systems for performing the editing methods.
    Type: Grant
    Filed: April 15, 2021
    Date of Patent: August 10, 2021
    Assignee: Inscripta, Inc.
    Inventors: Richard Fox, Daniel Held
  • Oligonucleotide encoded chemical libraries
    Patent number: 11084037
    Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.
    Type: Grant
    Filed: September 24, 2018
    Date of Patent: August 10, 2021
    Assignee: Plexium, Inc.
    Inventors: Kandaswamy Vijayan, Andrew Boyd MacConnell, Joseph Franklin Rokicki
  • Methods of screening
    Patent number: 11085926
    Abstract: The invention provides a method of identifying a peptide interaction site on a target protein wherein the target protein modulates the phenotype of a mammalian cell, using mammalian encoded peptides (SEPs) such as short open reading frame (sORF) encoded peptides. The invention further provides a method for the identification of new therapeutic targets and protein interaction sites for use in drug discovery.
    Type: Grant
    Filed: December 22, 2016
    Date of Patent: August 10, 2021
    Assignee: Phoremost Limited
    Inventors: Bryn Shaun Hardwick, Grahame James McKenzie
  • Polypeptide library
    Patent number: 11085038
    Abstract: The invention relates to novel polypeptide libraries that are conformationally constrained in an anti-parallel, helix-turn-helix arrangement. The invention further relates to methods of generating and screening such libraries for biological, pharmaceutical and other uses.
    Type: Grant
    Filed: April 8, 2020
    Date of Patent: August 10, 2021
    Assignee: MORPHOSYS AG
    Inventors: Roger Müller, Andreas Bültmann, Josef Prassler, Markus Moosmeier
  • Peptide array quality control
    Patent number: 11067582
    Abstract: The present application provides arrays for use in immunosignaturing and quality control of such arrays. Also disclosed are peptide arrays and uses thereof for diagnostics, therapeutics and research.
    Type: Grant
    Filed: January 21, 2020
    Date of Patent: July 20, 2021
    Assignee: Arizona Board of Regents on Behalf of Arizona State University
    Inventors: Neal Woodbury, Stephen Johnston, Phillip Stafford
  • Methods of library construction for polynucleotide sequencing
    Patent number: 11014957
    Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.
    Type: Grant
    Filed: December 20, 2016
    Date of Patent: May 25, 2021
    Assignee: REALSEQ BIOSCIENCES, INC.
    Inventors: Sergei A. Kazakov, Sergio Barberan-Soler, Anne Dallas, Brian H. Johnston
  • Method for predicting the off-target biding of a peptide which binds to a target peptide presented by a major histocompatibility complex
    Patent number: 11017882
    Abstract: The invention provides a method for predicting whether a binding peptide, which binds to a target peptide presented by a Major Histocompatibility Complex (MHC) and is for administration to a subject, has the potential to cross react with another peptide in the subject in vivo. The method comprises the steps of identifying at least one binding motif in the target peptide to which the binding peptide binds; and searching for peptides that are present in the subject that comprise the at least one binding motif and that are not the target peptide. The presence of one or more such peptides indicates that the binding peptide has the potential to cross react in vivo.
    Type: Grant
    Filed: June 17, 2015
    Date of Patent: May 25, 2021
    Assignees: Immunocore Limited, Adaptimmune Limited
    Inventors: Brian John Cameron, Annelise Brigitte Vuidepot, Bent Karsten Jakobsen
  • Predicting metabolic side effects of transported drugs
    Patent number: 11004539
    Abstract: Provided are drug-transport metabolomics profile assessments and therapies.
    Type: Grant
    Filed: February 17, 2017
    Date of Patent: May 11, 2021
    Assignee: The Regents of the University of California
    Inventors: Sanjay K. Nigam, Henry C. Liu
  • Identifying antigen clusters for monitoring a global state of an immune system
    Patent number: 11002735
    Abstract: Method, system and an article of manufacture for clustering and thereby identifying predefined antigens reactive with undetermined immunoglobulins of sera derived from patient subjects in need of diagnosis of disease or monitoring of treatment.
    Type: Grant
    Filed: January 21, 2020
    Date of Patent: May 11, 2021
    Assignee: YEDA RESEARCH AND DEVELOPMENT CO. LTD.
    Inventors: Irun R. Cohen, Eytan Domany, Francisco Javier Quintana, Guy Hed, Gad Getz
  • Methods for generating bispecific shark variable antibody domains and use thereof
    Patent number: 11001640
    Abstract: The present invention provides a method for generating bispecific shark variable antibody domains (vNAR domains) and uses thereof. The present invention further provides fusion proteins comprising the inventive bispecific vNAR domains as well as polynucleotide libraries for use in the generation of the inventive bi-specific vNARs. Furthermore, the invention provides pharmaceutical compositions comprising the inventive bispecific vNARs or fusion proteins comprising bi-specific vNAR domains for use in the treatment of pathological conditions in an individual. The invention also provides kits of parts comprising the bispecific vNAR domains or fusion proteins.
    Type: Grant
    Filed: October 21, 2015
    Date of Patent: May 11, 2021
    Assignee: Merck Patent GmbH
    Inventors: Stefan Becker, Bjoern Hock, Stefan Zielonka, Harald Kolmar, Martin Empting
  • Nucleic acid-guided editing of exogenous polynucleotides in heterologous cells
    Patent number: 10995424
    Abstract: The present disclosure provides shuttle vectors for editing exogenous polynucleotides in heterologous live cells, as well as automated methods, modules, and multi-module cell editing instruments and systems for performing the editing methods.
    Type: Grant
    Filed: November 17, 2020
    Date of Patent: May 4, 2021
    Assignee: Inscripta, Inc.
    Inventors: Richard Fox, Daniel Held
  • Functionalized surfaces and preparation thereof
    Patent number: 10987648
    Abstract: Compositions, devices, methods and systems are provided for differential functionalization of a surface of a structure to support biopolymer synthesis. Provided herein are processes which include use of lamps, lasers, and/or microcontact printing to add functional groups to surfaces for the efficient and uniform synthesis of oligonucleic acids.
    Type: Grant
    Filed: April 15, 2019
    Date of Patent: April 27, 2021
    Assignee: Twist Bioscience Corporation
    Inventors: Bill James Peck, Pierre Indermuhle, Eugene P. Marsh, Andres Fernandez, David Stern
  • Size selection of RNA using poly(A) polymerase
    Patent number: 10954542
    Abstract: This disclosure provides, among other things, a method for making a cDNA library. In some embodiments the method may comprise adding a polyA tail to the longer RNA fragments but not the shorter RNA fragments in a sample by incubating the population of RNA fragments with a polyA polymerase, wherein the reaction conditions used preferentially tail only the longer fragments but not the shorter fragments.
    Type: Grant
    Filed: May 20, 2020
    Date of Patent: March 23, 2021
    Assignee: BIOO SCIENTIFIC CORPORATION
    Inventor: Kevin Allen
  • Method for predicting the off-target biding of a peptide which binds to a target peptide presented by a major histocompatibility complex
    Patent number: 10937524
    Abstract: The invention provides a method for predicting whether a binding peptide, which binds to a target peptide presented by a Major Histocompatibility Complex (MHC) and is for administration to a subject, has the potential to cross react with another peptide in the subject in vivo. The method comprises the steps of identifying at least one binding motif in the target peptide to which the binding peptide binds; and searching for peptides that are present in the subject that comprise the at least one binding motif and that are not the target peptide. The presence of one or more such peptides indicates that the binding peptide has the potential to cross react in vivo.
    Type: Grant
    Filed: June 17, 2015
    Date of Patent: March 2, 2021
    Assignees: Immunocore Limited, Adaptimmune Limited
    Inventors: Brian John Cameron, Annelise Brigitte Vuidepot, Bent Karsten Jakobsen
  • Glycan arrays and method of use
    Patent number: 10935544
    Abstract: The invention relates to linkers and methods for generating arrays with linkers. The invention also relates to methods for identifying agents that bind to various types of molecules on the arrays and to defining the structural elements of the molecules on the arrays that bind to those agents. The arrays and methods provided herein may be used for epitope identification, drug discovery and as analytical tools. The invention provides useful glycans and epitope determinants that are useful in detecting, diagnosing, recurrence monitoring and preventing cancer.
    Type: Grant
    Filed: September 2, 2016
    Date of Patent: March 2, 2021
    Assignee: OBI PHARMA, INC.
    Inventors: Peiwen Yu, Wei-Chien Tang, Shu-Yi Lin, Cheng-Chi Wang
  • Single cell analysis of transposase accessible chromatin
    Patent number: 10927370
    Abstract: Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.
    Type: Grant
    Filed: May 22, 2019
    Date of Patent: February 23, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Geoffrey McDermott, Francesca Meschi, Xinying Zheng
  • De novo design of allosteric proteins
    Patent number: 10920217
    Abstract: Methods and compositions for making and isolating allosteric DNA binding proteins that bind to one or more allosteric effectors to induce a conformation change in the proteins are provided.
    Type: Grant
    Filed: July 2, 2019
    Date of Patent: February 16, 2021
    Assignee: President and Fellows of Harvard College
    Inventors: Srivatsan Raman, Noah D. Taylor, George M. Church
  • Method and device for detecting cellular targets in bodily sources using carbon nanotube thin film
    Patent number: 10919759
    Abstract: A device and method detect cellular targets in a bodily source by utilizing a biofunctional pad comprised of a thin film of carbon nanotubes (CNT's). When antibodies are absorbed by the CNT's, cellular targets having markers matching the antibodies may be detected in a bodily source placed upon the biofunctional pad by measuring the conductivity of the thin film using conductive contacts electrically coupled to the thin film, as the binding of the receptors in the cellular targets to the antibodies changes the free energy in the thin film. In many respects, the device functions as a Field Effect Transistor (FET) with the bodily source, e.g., blood, acting as a polyelectrolyte liquid gate electrode to create a varying electrostatic charge or capacitance in the thin film based upon the binding of cellular targets in the source to the antibodies present on the biofunctional pad.
    Type: Grant
    Filed: August 16, 2019
    Date of Patent: February 16, 2021
    Assignee: UNIVERSITY OF LOUISVILLE RESEARCH FOUNDATION, INC.
    Inventor: Balaji Panchapakesan
  • Methods, systems and compositions thereof for nucleic acid library quality control and quantification
    Patent number: 10913944
    Abstract: Methods, systems, kits and compositions are described for quality control and quantitation of nucleic acid libraries of double stranded nucleic acid libraries prior to massively parallel sequencing. Electrophoretic separation within a channel using a detectably labeled single stranded sizing ladder may be used to define the molecular weight range and amount of the double stranded nucleic acids.
    Type: Grant
    Filed: January 11, 2016
    Date of Patent: February 9, 2021
    Assignee: Life Technologies Corporation
    Inventors: Stephan Berosik, Jianbo Gao, Shiaw-Min Chen, H. Michael Wenz