Patents Examined by Christopher M. Gross
  • Patent number: 11981910
    Abstract: Described are DNA molecules which can be transcribed into an mRNA harbouring novel UTR sequences combining the advantages of being extremely short and at the same time allowing for high translation efficiencies of RNA molecules containing them. Further, described are vectors comprising such a DNA molecule and to host cells comprising such a vector. Moreover, described are corresponding RNA molecules containing such UTRs. Further, described is a pharmaceutical composition comprising the described RNA molecule and optionally a pharmaceutically acceptable carrier as well as to the use of the described UTRs for translating a coding region of an RNA molecule into a polypeptide or a protein encoded by said coding region.
    Type: Grant
    Filed: June 6, 2022
    Date of Patent: May 14, 2024
    Assignee: ethris GmbH
    Inventors: Christian Plank, Carsten Rudolph, Manish Kumar Aneja, Ludwig Weiss
  • Patent number: 11970693
    Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.
    Type: Grant
    Filed: February 14, 2020
    Date of Patent: April 30, 2024
    Assignee: NAUTILUS SUBSIDIARY, INC.
    Inventor: Parag Mallick
  • Patent number: 11965157
    Abstract: The present disclosure relates to methods for constructing polynucleotide libraries and/or polynucleotide sequencing. Related kits and devices are also disclosed. The present disclosure also relates to compositions, kits, devices, and methods for conducting genetic and genomic analysis, for example, by polynucleotide sequencing. In particular aspects, provided herein are compositions, kits, and methods for constructing libraries with improved ligation efficiency and conversion rate during sequencing. In certain embodiments, the compositions, kits, and methods herein are useful for analyzing polynucleotide fragments, such as circulating polynucleotide fragments in the body of a subject, including circulating tumor DNA.
    Type: Grant
    Filed: April 18, 2018
    Date of Patent: April 23, 2024
    Assignee: Singlera Genomics, Inc.
    Inventors: Jeffrey A Gole, Athurva Gore, Rui Liu
  • Patent number: 11965158
    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: March 2, 2021
    Date of Patent: April 23, 2024
    Assignee: Illumina, Inc.
    Inventors: Frank J. Steemers, Jeffrey S. Fisher, Kevin L. Gunderson, Sasan Amini, Christian Gloeckner
  • Patent number: 11964997
    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: March 12, 2021
    Date of Patent: April 23, 2024
    Assignee: RealSeq Biosciences, Inc.
    Inventors: Sergei A. Kazakov, Sergio Barberan-Soler, Anne Dallas, Brian H. Johnston
  • Patent number: 11965890
    Abstract: One aspect of the present invention describes materials and methods of quantitatively measuring the density or percent occupancy of DNA binding proteins such as histones, histone variants, histone post translational modifications and transcription factors in chromatin at given DNA loci. One embodiment measures a factor's average quantity at specific gene loci, and controls for a number of pitfalls concerning antibody quality and handling issues. Other embodiments include calibrating and quantifying chromatin immunoprecipitation assays, assessing an affinity reagent specificity, as well as required reagents and their formulation in kits. Another embodiment allows for the diagnosis of a condition or disease by measuring the density of a histone modification at a genomic locus.
    Type: Grant
    Filed: June 19, 2020
    Date of Patent: April 23, 2024
    Assignee: THE UNIVERSITY OF CHICAGO
    Inventors: Alexander J. Ruthenburg, Adrian Grzybowski, Zhonglei Chen
  • Patent number: 11959129
    Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.
    Type: Grant
    Filed: October 13, 2021
    Date of Patent: April 16, 2024
    Assignee: Enumera Molecular, Inc.
    Inventors: Matthew Sekedat, Jeffrey Buis, Ronald David Beaubien, Jr., Sharat Singh, Jeff Perry, Steven Lockton, Chandni Jain, Natalie Mae Jameson-Kiesling
  • Patent number: 11959076
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Grant
    Filed: August 11, 2023
    Date of Patent: April 16, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori
  • Patent number: 11959922
    Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.
    Type: Grant
    Filed: August 9, 2022
    Date of Patent: April 16, 2024
    Assignee: Encodia, Inc.
    Inventors: Mark S. Chee, Kevin L. Gunderson, Michael Phillip Weiner
  • Patent number: 11946041
    Abstract: The invention relates to a method for screening a library of peptide ligands, said library comprising a plurality of polypeptides covalently linked to a molecular scaffold at two or more amino acid residues, comprising the steps of displaying said library of peptide ligands in a genetic display system, wherein the polypeptide comprises two or more reactive groups which form a covalent linkage to the molecular scaffold, and at least one loop which comprises a sequence of amino acids subtended between two of said reactive groups; exposing the peptide ligands to one or more cells which display one or more target molecules on the cell surface; and screening the peptide ligands for binding against the target, and selecting the ligands which bind to the target.
    Type: Grant
    Filed: April 24, 2018
    Date of Patent: April 2, 2024
    Assignee: BicycleRD Limited
    Inventors: Liuhong Chen, Michael Skynner, Amy Brown, James Cooke, Rachid Lani
  • Patent number: 11932900
    Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.
    Type: Grant
    Filed: October 25, 2022
    Date of Patent: March 19, 2024
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
  • Patent number: 11932848
    Abstract: The present invention relates to genomic analysis. In particular, the present invention provides methods and compositions for mapping genomic interactions.
    Type: Grant
    Filed: August 18, 2022
    Date of Patent: March 19, 2024
    Assignee: University of Massachusetts
    Inventors: Job Dekker, Josee Dostie
  • Patent number: 11929151
    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: January 26, 2021
    Date of Patent: March 12, 2024
    Assignees: Immunocore Limited, Adaptimmune Limited
    Inventors: Brian John Cameron, Annelise Brigitte Vuidepot, Bent Karsten Jakobsen
  • Patent number: 11926820
    Abstract: This disclosure describes methods and compositions for protein and peptide sequencing.
    Type: Grant
    Filed: September 11, 2020
    Date of Patent: March 12, 2024
    Assignee: Google LLC
    Inventors: Annalisa Marie Pawlosky, Michael Gibbons, Shirley Jing Shao, Marc Berndl, Michelle Therese Hoerner Dimon, Ali Bashir, Lauren Schiff
  • Patent number: 11898270
    Abstract: Provided is a pig genome-wide specific sgRNA library, a preparation method therefor, and an application thereof. The sgRNA is targeted at a pig genome-wide protein-coding gene, lincRNA and/or miRNA. Specifically, an sgRNA construct has the following structure: AL-N20-AR, wherein AL is the left homology arm sequence located at the upstream of the coding sequence of a pig specific SgRNA, N20 is the coding sequence of the pig specific SgRNA, and AR is a right homology arm sequence located at the downstream of the coding sequence of the pig specific sgRNA. The sgRNA library can be used for screening functional genes of a pig or for preparing a kit.
    Type: Grant
    Filed: August 21, 2017
    Date of Patent: February 13, 2024
    Assignee: HUAZHONG AGRICULTURAL UNIVERSITY
    Inventors: Shuhong Zhao, Shengsong Xie, Changzhi Zhao, Xinyun Li, Xiangdong Liu, Xiaosong Han, Gaojuan Yang, Yang Gao, Yilong Chen, Xiaoyong Du, Yiliang Miao, Yunlong Ma, Xiaolei Liu
  • Patent number: 11898204
    Abstract: The invention is a novel method of separately sequencing each strand of a nucleic acid involving the use of an adaptor comprising a strand cleavage site or a strand synthesis termination site. The adaptor may also be self-priming at the strand cleavage site.
    Type: Grant
    Filed: February 28, 2019
    Date of Patent: February 13, 2024
    Assignees: Roche Sequencing Solutions, Inc., KAPA Biosystems, Inc.
    Inventors: Aruna Arcot, Daleen Badenhorst, Rui Chen, Toummy Guettouche, Ashley Hayes, Jenny A. Johnson, Severine Margeridon, Martin Ranik, Persis Wadia, Alexandra Hui Wang
  • Patent number: 11896944
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.
    Type: Grant
    Filed: January 31, 2018
    Date of Patent: February 13, 2024
    Assignee: Illumina, Inc.
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 11873482
    Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.
    Type: Grant
    Filed: April 27, 2023
    Date of Patent: January 16, 2024
    Assignee: 10x Genomics, Inc.
    Inventors: Hanyoup Kim, David Sukovich, Layla Katiraee, Augusto Manuel Tentori, Lauren Gutgesell, Janine Hensel, Seayar Mohabbat
  • Patent number: 11846639
    Abstract: Compositions and methods are provided for the identification of peptide sequences that are ligands for a T cell receptor (TCR) of interest, in a given MHC context.
    Type: Grant
    Filed: July 16, 2021
    Date of Patent: December 19, 2023
    Assignees: The Board of Trustees of the Leland Stanford Junior University, CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Michael Edward Birnbaum, Juan Luis Mendoza, Michael Thomas Bethune, David Baltimore, Kenan Christopher Garcia
  • Patent number: 11841371
    Abstract: The application relates to methods and systems for proteomics and spatial mapping of biomolecules using a next generation sequencing readout to decipher biomolecular and cellular interaction networks. Specifically, disclosed are antenna networks generated by conjugating DNA antennas to proteins. The antennas carry a unique antenna identifier (UAI) sequence that can provide spatial location of the network, as well as biomolecules by transfer of the UAI to reporter oligonucleotides associated with other antennas and biomolecules. The methods and systems are also applicable to single cells.
    Type: Grant
    Filed: March 13, 2019
    Date of Patent: December 12, 2023
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Aviv Regev, Jellert Gaublomme