Patents Examined by Christopher M. Gross
  • Systems and methods of epitope binning and antibody profiling
    Patent number: 10900975
    Abstract: Methods for antibody profiling and epitope mapping are provided herein. More particularly, methods for screening and mapping epitopes of candidate antibodies and protein target identification are provided herein.
    Type: Grant
    Filed: May 12, 2016
    Date of Patent: January 26, 2021
    Assignee: Arizona Board of Regents on behalf of Arizona State University
    Inventor: Stephen Albert Johnston
  • Method of isolating biochemical molecules on microarray substrate
    Patent number: 10883136
    Abstract: Provided is a method of isolating biochemical molecules on a microarray substrate, the method including providing a microarray substrate to which clusters of different kinds of biochemical molecules being classified by individual spot units are attached, the individual spots being regularly arranged thereon; obtaining location information of the individual spot in which a desired cluster among clusters of the biochemical molecules locates; locating an extraction tool for applying energy to isolate the desired cluster according to the location information; and isolating the desired cluster from the microarray substrate by applying energy in a contact or non-contact manner using the extraction tool.
    Type: Grant
    Filed: December 9, 2013
    Date of Patent: January 5, 2021
    Assignee: SNU R&DB FOUNDATION
    Inventors: Sunghoon Kwon, Taehoon Ryu, Yeongjae Choi, Yushin Jung, Hyoki Kim, Howon Lee
  • Arrays
    Patent number: 10870925
    Abstract: Protein arrays and their use to assay, in a parallel fashion, the protein products of highly homologous or related DNA coding sequences and described. By highly homologous or related it is meant those DNA coding sequences which share a common sequence and which differ only by one or more naturally occurring mutations such as single nucleotide polymorphisms, deletions or insertions, or those sequences which are considered to be haplotypes. Such highly homologous or related DNA coding sequences are generally naturally occurring variants of the same gene. Arrays according to the invention have two or more individual proteins deposited in a spatially defined pattern on a surface in a form whereby a property such as an activity or function of the proteins can be investigated or assayed in parallel by interrogation of the array.
    Type: Grant
    Filed: April 3, 2018
    Date of Patent: December 22, 2020
    Assignee: SENGENICS CORPORATION PTE LTD
    Inventors: Jonathan Mark Boutell, Benjamin Leslie James Godber, Darren James Hart, Jonathan Michael Blackburn
  • Lipid probes and uses thereof
    Patent number: 10859585
    Abstract: Disclosed herein are methods, compositions, probes, assays and kits for identifying a lipid binding protein as a drug binding target. Also disclosed herein are methods, compositions, and probes for mapping a ligand binding site on a lipid binding protein, identification of lipid binding proteins, generating drug-lipid binding protein profiles, high throughput drug screening, and identification of drugs as potential lipid binding protein ligands.
    Type: Grant
    Filed: December 28, 2018
    Date of Patent: December 8, 2020
    Assignee: The Scripps Research Institute
    Inventors: Benjamin F. Cravatt, Micah J. Niphakis, Kenneth Lum, Bruno Correia, Armand Cognetta, Jonathan Hulce
  • Nucleic acid-guided editing of exogenous polynucleotides in heterologous cells
    Patent number: 10858761
    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: February 22, 2020
    Date of Patent: December 8, 2020
    Assignee: Inscripta, Inc.
    Inventors: Richard Fox, Daniel Held
  • Fusion proteins comprising an engineered knottin peptide and uses thereof
    Patent number: 10844106
    Abstract: The present disclosure presents a general approach to engineering existing protein-protein interactions through domain addition and evolution. The disclosure teaches the creation of novel fusion proteins that include knottin peptides where a portion of the knottin peptide is replaced with a sequence that has been created for binding to a particular target. Such fusion proteins can also be bispecific or multi specific in that they can bind to and/or inhibit two or more receptors or receptor ligands. Knottins may be fused with an existing ligand (or receptor) as a general platform for increasing the affinity of a ligand-receptor interaction or for creating a multi specific protein. In addition, the fusion proteins may comprise a knottin peptide fused to another protein where the other protein facilitates proper expression and folding of the knottin.
    Type: Grant
    Filed: November 7, 2011
    Date of Patent: November 24, 2020
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Jennifer R. Cochran, Douglas S. Jones, Mihalis S. Kariolis, Ping-Chuan Tsai
  • Single cell analysis of transposase accessible chromatin
    Patent number: 10844372
    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: December 14, 2017
    Date of Patent: November 24, 2020
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Geoffrey McDermott, Francesca Meschi, Xinying Zheng
  • Microfluidic device for storage and well-defined arrangement of droplets
    Patent number: 10828641
    Abstract: The present invention relates to systems and methods for the arrangement of droplets in pre-determined locations. Many applications require the collection of time-resolved data. Examples include the screening of cells based on their growth characteristics or the observation of enzymatic reactions. The present invention provides a tool and related techniques which addresses this need, and which can be used in many other situations. The invention provides, in one aspect, a tool that allows for stable storage and indexing of individual droplets. The invention can interface not only with microfluidic/microscale equipment, but with macroscopic equipment to allow for the easy injection of liquids and extraction of sample droplets, etc.
    Type: Grant
    Filed: April 25, 2017
    Date of Patent: November 10, 2020
    Assignee: President and Fellows of Harvard College
    Inventors: Christian Boehm, Amy Rowat, Sarah Koester, Jeremy Agresti, David A. Weitz
  • Probe set for analyzing a DNA sample and method for using the same
    Patent number: 10822640
    Abstract: This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X?-A?-B?-Z?, wherein sequence A? is complementary to a genomic fragment and sequence B? is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.
    Type: Grant
    Filed: November 8, 2019
    Date of Patent: November 3, 2020
    Assignee: VANADIS DIAGNOSTICS
    Inventors: Carl Oscar Fredrik Dahl, Olof John Ericsson, Filip Karlsson, Fredrik Roos
  • Peptide libraries
    Patent number: 10822604
    Abstract: The invention relates to novel libraries of linear and cyclic peptides, and methods of generating and screening such libraries for biological, pharmaceutical and other uses.
    Type: Grant
    Filed: April 30, 2015
    Date of Patent: November 3, 2020
    Assignee: MORPHOSYS AG
    Inventors: Katja Siegers, Jan Van Den Brulle
  • Ligand discovery for T cell receptors
    Patent number: 10816554
    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: April 3, 2015
    Date of Patent: October 27, 2020
    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
  • Compositions and methods for therapeutics prescreening
    Patent number: 10815530
    Abstract: A theranostic composition and method for determining the cell-specific potency of drugs is provided. Further, compositions and methods useful for studying the therapeutic profile of one or more drugs within a cell microenvironment, including but not limited to a tumor, are provided.
    Type: Grant
    Filed: August 13, 2015
    Date of Patent: October 27, 2020
    Assignee: TECHNION RESEARCH & DEVELOPMENT FOUNDATION LIMITED
    Inventors: Avi Schroeder, Zvi Yaari
  • Enzyme coupled assay for quantification of protein and peptide binding by SAMDI mass spectrometry
    Patent number: 10782287
    Abstract: Disclosed herein are methods of using an immobilized substrate, immobilized ligand, and a fusion protein of an enzyme for the substrate and a receptor for the ligand, where the immobilized substrate can react to form an immobilized product that has a different mass than the immobilized substrate, and using this transformation to indirectly determine the binding of the receptor and the ligand. These methods can be used for high-throughput screening for possible modulators (e.g., inhibitors or activators) of the ligand-receptor interaction.
    Type: Grant
    Filed: February 23, 2016
    Date of Patent: September 22, 2020
    Assignee: NORTHWESTERN UNIVERSITY
    Inventors: Milan Mrksich, Patrick O'Kane
  • Methods for displaying cyclic peptides on bacteriophage particles
    Patent number: 10774323
    Abstract: The present invention relates to methods for displaying cyclic peptides on the surface of bacteriophage particles and collections thereof.
    Type: Grant
    Filed: December 21, 2015
    Date of Patent: September 15, 2020
    Assignee: LANTHIOPEP B.V.
    Inventors: Johannes Herbert Urban, Markus Andreas Moosmeier, Tjibbe Bosma, Josef Prassler
  • Automated instrumentation for production of T-cell receptor peptide libraries
    Patent number: 10774446
    Abstract: The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.
    Type: Grant
    Filed: June 18, 2020
    Date of Patent: September 15, 2020
    Assignee: Inscripta, Inc.
    Inventors: Stephen Federowicz, Deanna Church, Michael Graige
  • Automated instrumentation for production of peptide libraries
    Patent number: 10774324
    Abstract: The present disclosure methods for identifying binding partners using cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of peptides that bind to targets of interest. The engineered peptides are preferably expressed in the cells under conditions that provide both secretion and display of the engineered peptides on the cell surfaces, thus providing access of the engineered peptides to identify potential binding pairs. The cell libraries cab be engineered using an automated editing system that provides for one or more targeted edits per cell.
    Type: Grant
    Filed: October 31, 2019
    Date of Patent: September 15, 2020
    Assignee: Inscripta, Inc.
    Inventors: Stephen Federowicz, Deanna Church, Michael Graige
  • Production method for charged non-protein amino acid-containing peptide
    Patent number: 10745692
    Abstract: An object of the present invention is to provide a method of producing a peptide containing a charged non-proteinogenic amino acid in a cell-free translation system, and the like. The present invention provides a method of producing a peptide containing a charged non-proteinogenic amino acid. It includes a step of expressing a peptide in a cell-free translation system including (i) at least one tRNA to which a non-proteinogenic amino acid having a protecting-group-introduced charged group has been bound and (ii) a nucleic acid that encodes the peptide and contains at least one codon corresponding to an anticodon of the tRNA; and a step of removing the protecting group of the non-proteinogenic amino acid residue contained in the peptide.
    Type: Grant
    Filed: August 4, 2014
    Date of Patent: August 18, 2020
    Assignees: The University of Tokyo, PeptiDream Inc.
    Inventors: Hiroshi Murakami, Takashi Kawakami, Patrick Reid, Toru Sasaki
  • Method of predicting/optimizing hydrogen sulfide scavenging capacity and reduction of scale formation
    Patent number: 10745633
    Abstract: A method of optimizing a hydrogen sulfide scavenger blend that includes selecting a hydrogen sulfide scavenger blend comprising at least two hydrogen sulfide scavengers; determining a scavenging capacity for the blend; modifying at least one blend parameter based on the determined scavenging capacity; redetermining the scavenging capacity for the modified blend; and selecting an optimized blend from the blend and the modified blend is disclosed.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: August 18, 2020
    Assignee: Schlumberger Norge AS
    Inventors: Raquel Rodriguez Gonzalez, Anders Grinrod
  • Compositions and methods for quantitative assessment of DNA-protein complex density
    Patent number: 10732185
    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 DNA density of a histone modification at a genomic locus.
    Type: Grant
    Filed: February 3, 2015
    Date of Patent: August 4, 2020
    Assignee: THE UNIVERSITY OF CHICAGO
    Inventors: Alexander J. Ruthenburg, Adrian Grzybowski, Chen Zhonglei
  • Targeted sequencing and UID filtering
    Patent number: 10731212
    Abstract: Provided herein are methods, compositions, and kits for targeted sequencing of polynucleotides with high accuracy and low amplification and sequencing errors and bias.
    Type: Grant
    Filed: June 17, 2019
    Date of Patent: August 4, 2020
    Assignee: Roche Molecular Systems, Inc.
    Inventors: William Donahue, Francois Vigneault