Patents by Inventor Patrick Hsu

Patrick Hsu 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).

  • COMPOSITIONS AND METHODS OF A NUCLEASE CHAIN REACTION FOR NUCLEIC ACID DETECTION
    Publication number: 20240141412
    Abstract: Described herein are nucleic acid detection compositions and systems comprising an internal nuclease chain reaction (NCR) for signal amplification and methods of using these NCR-containing compositions and systems.
    Type: Application
    Filed: May 18, 2021
    Publication date: May 2, 2024
    Inventors: David Savage, Patrick Hsu, Noam Prywes, Emeric J. Charles, Gavin J. Knott, John James Desmarais, Shineui Kim, Eli Dugan, Maria Lukarska, Sita S. Chandrasekaran, Nicholas C. Lammers, Tina Y. Liu, Amanda Mok, Liana Lareau, Brittney Wai-Ling Thornton
  • SYSTEMS AND METHODS FOR AN ACCELERATED AND ENHANCED TUNING OF A MODEL BASED ON PRIOR MODEL TUNING DATA
    Publication number: 20240127124
    Abstract: Disclosed examples including generating a joint model based on first and second subject models, the first and second subject models selected based on a relationship between the first and second subject models; selecting the joint model from a plurality of joint models after a determination that entropy data points of the joint model satisfy a threshold, the entropy data points based on multiple tuning trials of the joint model; and providing tuning data associated with the joint model to a tuning session of a target model.
    Type: Application
    Filed: December 27, 2023
    Publication date: April 18, 2024
    Inventors: Michael McCourt, Ben Hsu, Patrick Hayes, Scott Clark
  • SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS
    Publication number: 20240035007
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems.
    Type: Application
    Filed: December 27, 2022
    Publication date: February 1, 2024
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, University of Tokyo, President and Fellows of Harvard College
    Inventors: Silvana KONERMANN, Alexandro TREVINO, Mark BRIGHAM, Fei RAN, Patrick HSU, Chie-yu LIN, Osamu NUREKI, Hiroshi NISHIMASU, Ryuichiro ISHITANI, Feng ZHANG
  • OPTIMIZED CRISPR-CAS DOUBLE NICKASE SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20230374550
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.
    Type: Application
    Filed: February 6, 2023
    Publication date: November 23, 2023
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng ZHANG, Patrick HSU, Chie-yu LIN, Fei RAN
  • ACTIVATORS OF TYPE III CAS PROTEINS
    Publication number: 20230357761
    Abstract: Described herein are compositions and systems comprising activators of type III accessory nucleases and methods of using these compositions and systems.
    Type: Application
    Filed: September 20, 2021
    Publication date: November 9, 2023
    Inventors: Jennifer Doudna, Patrick Hsu, David Savage, Tina Y. Liu, Shrutee Jakhanwal, Noam Prywes, Gavin J. Knott, Brittney Wai-Ling Thornton, Dylan C.J. Smock, Emeric J. Charles, Shineui Kim
  • COMPOSITIONS AND METHODS OF ISOTHERMAL NUCLEIC ACID AMPLIFICATION AND DETECTION
    Publication number: 20230313282
    Abstract: Described herein are nucleic acid detection compositions and systems comprising isothermal loop mediated signal amplification (LAMP) and methods of using these LAMP-based compositions and systems.
    Type: Application
    Filed: July 22, 2021
    Publication date: October 5, 2023
    Inventors: Patrick HSU, David SAVAGE, Noam PRYWES, Maria LUKARSKA, Shreeya AGRAWAL, Sita CHANDRASEKARAN, Alison FANTON
  • Protected guide RNAS (pgRNAS)
    Patent number: 11624078
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems, wherein the guide sequence is modified by secondary structure to increase the specificity of the CRISPR-Cas system and whereby the secondary structure can protect against exonuclease activity and allow for 5? additions to the guide sequence.
    Type: Grant
    Filed: April 9, 2020
    Date of Patent: April 11, 2023
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Feng Zhang, Omar O. Abudayyeh, James E. Dahlman, Patrick Hsu, David A. Scott
  • Systems, methods and compositions for sequence manipulation with optimized functional CRISPR-Cas systems
    Patent number: 11597919
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems.
    Type: Grant
    Filed: October 3, 2019
    Date of Patent: March 7, 2023
    Assignees: THE BROAD INSTITUTE INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE, UNIVERSITY OF TOKYO
    Inventors: Silvana Konermann, Alexandro Trevino, Mark Brigham, Fei Ran, Patrick Hsu, Chie-yu Lin, Osamu Nureki, Hiroshi Nishimasu, Ryuichiro Ishitani, Feng Zhang
  • Optimized CRISPR-Cas double nickase systems, methods and compositions for sequence manipulation
    Patent number: 11597949
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.
    Type: Grant
    Filed: April 9, 2020
    Date of Patent: March 7, 2023
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Feng Zhang, Patrick Hsu, Chie-Yu Lin, Fei Ran
  • PROTECTED GUIDE RNAS (PGRNAS)
    Publication number: 20220010339
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems, wherein the guide sequence is modified by secondary structure to increase the specificity of the CRISPR-Cas system and whereby the secondary structure can protect against exonuclease activity and allow for 5? additions to the guide sequence.
    Type: Application
    Filed: September 29, 2021
    Publication date: January 13, 2022
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng ZHANG, Omar O. ABUDAYYEH, James E. DAHLMAN, Patrick HSU, David A. SCOTT
  • METHODS, MODELS, SYSTEMS, AND APPARATUS FOR IDENTIFYING TARGET SEQUENCES FOR CAS ENZYMES FOR CRISPR-CAS SYSTEMS FOR TARGET SEQUENCES AND CONVEYING RESULTS THEREOF
    Publication number: 20210366572
    Abstract: Disclosed are thermodynamic and multiplication methods concerning CRISPR-Cas systems, and apparatus therefor.
    Type: Application
    Filed: February 23, 2021
    Publication date: November 25, 2021
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng Zhang, Yinqing Li, David Arthur Scott, Joshua Asher Weinstein, Patrick Hsu
  • Methods, models, systems, and apparatus for identifying target sequences for Cas enzymes or CRISPR-Cas systems for target sequences and conveying results thereof
    Patent number: 10930367
    Abstract: Disclosed are thermodynamic and multiplication methods concerning CRISPR-Cas systems, and apparatus therefor.
    Type: Grant
    Filed: June 12, 2015
    Date of Patent: February 23, 2021
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Feng Zhang, Yinqing Li, David Arthur Scott, Joshua Asher Weinstein, Patrick Hsu
  • OPTIMIZED CRISPR-CAS DOUBLE NICKASE SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20200377912
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.
    Type: Application
    Filed: April 9, 2020
    Publication date: December 3, 2020
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng ZHANG, Patrick HSU, Chie-Yu LIN, Fei RAN
  • PROTECTED GUIDE RNAS (PGRNAS)
    Publication number: 20200362369
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems, wherein the guide sequence is modified by secondary structure to increase the specificity of the CRISPR-Cas system and whereby the secondary structure can protect against exonuclease activity and allow for 5? additions to the guide sequence.
    Type: Application
    Filed: April 9, 2020
    Publication date: November 19, 2020
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng ZHANG, Omar O. ABUDAYYEH, James E. DAHLMAN, Patrick HSU, David A. SCOTT
  • Optimized CRISPR-Cas double nickase systems, methods and compositions for sequence manipulation
    Patent number: 10711285
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.
    Type: Grant
    Filed: December 17, 2015
    Date of Patent: July 14, 2020
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Feng Zhang, Patrick Hsu, Chie-yu Lin, Fei Ran
  • Protected guide RNAS (PGRNAS)
    Patent number: 10696986
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems, wherein the guide sequence is modified by secondary structure to increase the specificity of the CRISPR-Cas system and whereby the secondary structure can protect against exonuclease activity and allow for 5? additions to the guide sequence.
    Type: Grant
    Filed: June 12, 2017
    Date of Patent: June 30, 2020
    Assignees: THE BOARD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Feng Zhang, Omar O. Abudayyeh, James E. Dahlman, Patrick Hsu, David A. Scott
  • SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS
    Publication number: 20200115687
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems.
    Type: Application
    Filed: October 3, 2019
    Publication date: April 16, 2020
    Inventors: Silvana KONERMANN, Alexandro TREVINO, Mark BRIGHAM, Fei RAN, Patrick HSU, Chie-yu LIN, Osamu NUREKI, Hiroshi NISHIMASU, Ryuichiro ISHITANI, Feng ZHANG
  • CRISPR-CAS COMPONENT SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20200080094
    Abstract: The invention provides for systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for selecting specific cells by introducing precise mutations utilizing the CRISPR/Cas system.
    Type: Application
    Filed: August 7, 2019
    Publication date: March 12, 2020
    Inventors: Feng Zhang, Le Cong, David Benjamin Turitz Cox, Patrick Hsu, Shuailiang Lin, Fei Ran, Randall Jeffrey Platt, Neville Espi Sanjana
  • CRISPR-CAS COMPONENT SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20200063147
    Abstract: The invention provides for systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for selecting specific cells by introducing precise mutations utilizing the CRISPR/Cas system.
    Type: Application
    Filed: August 5, 2019
    Publication date: February 27, 2020
    Inventors: Feng Zhang, Le Cong, David Benjamin Turitz Cox, Patrick Hsu, Shuailiang Lin, Fei Ran, Randall Jeffrey Platt, Neville Espi Sanjana
  • Systems, methods and compositions for sequence manipulation with optimized functional CRISPR-Cas systems
    Patent number: 10550372
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems.
    Type: Grant
    Filed: June 10, 2016
    Date of Patent: February 4, 2020
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, University of Tokyo, President and Fellows of Harvard College
    Inventors: Silvana Konermann, Alexandro Trevino, Mark Brigham, Fei Ran, Patrick Hsu, Chie-yu Lin, Osamu Nureki, Hiroshi Nishimasu, Ryuichiro Ishitani, Feng Zhang