Patents by Inventor David R. Liu

David R. Liu 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).

  • Publication number: 20250136960
    Abstract: Described herein are compositions, vectors, cells, methods, and kits that provide cell data recorder systems for recording cell states. The cell data recorder systems allow for the recording of both the presence and duration of one or more stimuli in a programmable, reproducible, and multiplexable manner. These cell data recorder systems employ a nucleic acid programmable DNA binding protein, such as a Cas9 nuclease, or a fusion protein comprising a nucleic acid programmable DNA binding domain and a nucleic acid editing domain to introduce recordable changes in the genome of a cell or in a plasmid within the cell.
    Type: Application
    Filed: August 7, 2024
    Publication date: May 1, 2025
    Inventors: David R. Liu, Weixin Tang
  • Patent number: 12281303
    Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.
    Type: Grant
    Filed: May 31, 2023
    Date of Patent: April 22, 2025
    Assignees: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, James William Nelson
  • Patent number: 12281338
    Abstract: Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids or the modification of nucleic acids or proteins, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of nucleic acid programmable DNA binding proteins e.g., GeoCas9 or variants thereof, and effector domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing or protein modification are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a GeoCas9 and effector domains, are provided.
    Type: Grant
    Filed: October 29, 2019
    Date of Patent: April 22, 2025
    Assignees: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Yongjoo Kim
  • Publication number: 20250115901
    Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.
    Type: Application
    Filed: April 25, 2024
    Publication date: April 10, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, James William Nelson
  • Publication number: 20250109177
    Abstract: Aspects of the disclosure relate to compositions and methods for targeted protein degradation. In some embodiments, the disclosure relates to methods of evolving protein degrons to interact with certain small molecule inducers (e.g., VS-777, PT-179, or PK-1016). In some embodiments, the disclosure relates to compositions (e.g., peptides, nucleic acids encoding the protein degrons, etc.) used for targeted protein degradation. In some embodiments, the disclosure relates to methods of degrading a target polypeptide in a cell.
    Type: Application
    Filed: December 12, 2024
    Publication date: April 3, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College, The Brigham and Women's Hospital, Inc.
    Inventors: David R. Liu, Amit Choudhary, Jaron August McClure Mercer, Stephan DeCarlo, Praveen Tiwari, Praveen Kokkonda, Veronika Shoba, Arghya Deb, Sreekanth Vedagopuram
  • Publication number: 20250109165
    Abstract: Provided herein are compounds of Formula (I-A), (I-B), or (I-C), and pharmaceutically acceptable salts, solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers, isotopically enriched forms, prodrugs, or mixtures thereof, and compositions thereof. Also provided are methods and kits involving the inventive compounds or compositions for treating and/or preventing diseases and/or conditions (e.g., neurological disease (e.g., Alzheimer's disease, multiple sclerosis, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis), metabolic disorder (e.g., obesity, diabetes, X-linked adrenoleukodystrophy (X-ALD)), proliferative disease (e.g., cancers), hepatic disease (e.g., liver cirrhosis), conditions associated with autophagy (e.g., neurodegenerative disease, infection, cancer, conditions associated with aging, heart disease), conditions associated with aging, conditions associated with modulating the mPTP, cardiovascular conditions (e.g.
    Type: Application
    Filed: December 9, 2024
    Publication date: April 3, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Alexander A. Peterson
  • Publication number: 20250100365
    Abstract: Embodiments of the present disclosure relate to youth electric recreational vehicles. In some embodiments, a youth recreational vehicle, comprises: one or more front ground engaging members, one or more rear ground engaging members, and a frame supported by the one or more front ground engaging members and the one or more rear ground engaging members. In addition, the youth recreational vehicle comprises a seat supported by the frame and configured to support at least one rider and an electric powertrain. The electric powertrain is configured to drive at least one of: (i) the one or more front ground engaging members and (ii) the one or more rear ground engaging members. The electric powertrain comprises: a controller, at least one electric motor, and at least one battery pack.
    Type: Application
    Filed: December 6, 2024
    Publication date: March 27, 2025
    Inventors: Austin R. Bartz, Chiao George Liu, Scott D. Taylor, Kyle J. Schounard, William B. Rodriguez, Yassin M. Kelay, David F. Buehler, John M. Nutter, Lindsay SB Edwards, Joseph A. Wegleitner
  • Publication number: 20250101395
    Abstract: The present disclosure provides Cas protein variants comprising one or more amino acid substitutions relative to wild-type Cas14a1. Fusion proteins comprising the Cas protein variants described herein are also provided by the present disclosure. Further provided herein are methods for modifying a target nucleic acid using the Cas proteins and fusion proteins provided herein. The present disclosure also provides guide RNAs, complexes, polynucleotides, systems, cells, kits, and pharmaceutical compositions.
    Type: Application
    Filed: December 6, 2024
    Publication date: March 27, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Aditya Raguram
  • Publication number: 20250103397
    Abstract: Techniques for quality of service (QoS) support for input/output devices and other agents are described. In embodiments, a processing device includes execution circuitry to execute a plurality of software threads; hardware to control monitoring or allocating, among the plurality of software threads, one or more shared resources; and configuration storage to enable the monitoring or allocating of the one or more shared resources among the plurality of software threads and one or more channels through which one or more devices are to be connected to the one or more shared resources.
    Type: Application
    Filed: December 30, 2023
    Publication date: March 27, 2025
    Applicant: Intel Corporation
    Inventors: Andrew J. Herdrich, Daniel Joe, Filip Schmole, Philip Abraham, Stephen R. Van Doren, Priya Autee, Rajesh M. Sankaran, Anthony Luck, Philip Lantz, Eric Wehage, Edwin Verplanke, James Coleman, Scott Oehrlein, David M. Lee, Lee Albion, David Harriman, Vinit Mathew Abraham, Yi-Feng Liu, Manjula Peddireddy, Robert G. Blankenship
  • Publication number: 20250100123
    Abstract: An oscillating power tool includes an outer housing having a head portion and a handle portion extending therefrom, an inner housing within the outer housing, a first annular gap between the inner housing and the head portion of the outer housing, and a motor and a drive mechanism having an output shaft that oscillates and defines an output axis. The output shaft extends through an opening in the head portion and defines a second annular gap between the output shaft and the outer housing. The oscillating power tool also includes an over-travel limit member in the first annular gap. In response to relative movement between the inner housing and the outer housing, the over-travel limit member prevents contact between them. The over-travel limit member limits lateral movement of the inner housing relative to the outer housing in a direction transverse to the output axis.
    Type: Application
    Filed: December 10, 2024
    Publication date: March 27, 2025
    Inventors: Jeffrey S. HOLLY, Jacob N. ZIMMERMAN, James C. SITTER, David A. BIERDEMAN, Andrew R. SCHAUER, You Gen LIU
  • Publication number: 20250092382
    Abstract: The disclosure provides adenosine deaminases that are capable of deaminating adenosine in DNA. The disclosure also provides fusion proteins comprising a Cas9 (e.g., a Cas9 nickase) domain and adenosine deaminases that deaminate adenosine in DNA. In some embodiments, the fusion proteins further comprise a nuclear localization sequence (NLS), and/or an inhibitor of base repair, such as, a nuclease dead inosine specific nuclease (dISN).
    Type: Application
    Filed: April 19, 2024
    Publication date: March 20, 2025
    Applicant: President and Fellows of Harvard College
    Inventors: David R. Liu, Nicole Gaudelli
  • Publication number: 20250092374
    Abstract: Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for engineering Cas9 and Cas9 variants that have increased activity on target sequences that do not contain the canonical PAM sequence. In some embodiments, fusion proteins comprising such Cas9 variants and nucleic acid editing domains, e.g., deaminase domains, are provided.
    Type: Application
    Filed: June 3, 2024
    Publication date: March 20, 2025
    Applicant: President and Fellows of Harvard College
    Inventors: David R. Liu, Johnny Hao Hu
  • Publication number: 20250094398
    Abstract: Techniques for a unified relational database framework for hybrid vector search are provided. In one technique, multiple documents are accessed and a vector table and a text table are generated. For each accessed document, data within the document is converted to plaintext, multiple chunks are generated based on the plaintext, an embedding model generates a vector for each of the chunks, the vectors are stored in the vector table along with a document identifier that identifies the accessed document, tokens are generated based on the plaintext, the tokens are stored in the text table along with the document identifier. Such processing may be performed in a database system in response to a single database statement to create a hybrid index. In response to receiving a hybrid query, a vector query and a text query are generated and executed and the respective results may be combined.
    Type: Application
    Filed: September 13, 2024
    Publication date: March 20, 2025
    Inventors: Aleksandra Czarlinska, Saurabh Naresh Netravalkar, Denis B. Mukhin, Harichandan Roy, Zhen Hua Liu, Sebastian de la Hoz Luna, Beda Christoph Hammerschmidt, George R. Krupka, Bo Xia, David Chih-Wei Jiang
  • Publication number: 20250090687
    Abstract: The present disclosure provides zinc finger domain-containing proteins comprising optimized ?-, ?-, and linker motifs, and fusion proteins comprising said zinc finger domain-containing proteins fused to an effector domain. The present disclosure also provides double-stranded DNA deaminase A (DddA) variants and fusion proteins comprising said DddA variants fused to a programmable DNA binding protein (e.g., any of the zinc finger domain-containing proteins disclosed herein, a TALE protein, or a CRISPR/Cas9 protein). Methods for editing DNA (including genomic DNA and mitochondrial DNA) using the fusion proteins described herein are also provided by the present disclosure. The present disclosure further provides polynucleotides, vectors, cells, kits, and pharmaceutical compositions comprising the zinc finger domain-containing proteins, DddA variants, and fusion proteins described herein.
    Type: Application
    Filed: November 22, 2024
    Publication date: March 20, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Julian Wills
  • Publication number: 20250084400
    Abstract: Disclosed herein are compositions, methods, kits, and systems relating to efficient delivery of cargos (e.g., therapeutic cargos) into cells, for instance, for in vivo delivery. The present disclosure provides lipid-containing particles (e.g., virus-like particles) for delivering therapeutic cargos. The present disclosure also provides polynucleotides encoding the lipid-containing particles provided herein, which may be useful for producing said lipid-containing particles. Also provided are methods for editing nucleic acid molecules in cells using the lipid-containing particles provided herein, as well as cells and kits comprising the lipid-containing particles.
    Type: Application
    Filed: November 22, 2024
    Publication date: March 13, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Thomas J. Cahill, III, Philip DeSouza, Aditya Raguram, Samagya Banskota, Meirui An
  • Publication number: 20250084399
    Abstract: Disclosed herein are compositions, methods, kits, and systems relating to efficient delivery of cargos (e.g., therapeutic cargos) into cells, for instance, for in vivo delivery. The present disclosure provides lipid-containing particles (e.g., virus-like particles) for delivering therapeutic cargos. The present disclosure also provides polynucleotides encoding the lipid-containing particles provided herein, which may be useful for producing said lipid-containing particles. Also provided are methods for editing nucleic acid molecules in cells using the lipid-containing particles provided herein, as well as cells and kits comprising the lipid-containing particles.
    Type: Application
    Filed: November 22, 2024
    Publication date: March 13, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Thomas J. Cahill, III, Philip DeSouza, Aditya Raguram, Samagya Banskota, Meirui An
  • Publication number: 20250064981
    Abstract: Nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods are described herein for delivering a base editor (or “nucleobase editor”) to cells, e.g., via AAV vectors. In particular, the disclosure provides compositions, methods, and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors containing size-minimized regulatory components that enable, e.g., the packaging of base editors. Provided herein are methods and compositions for delivering base editor proteins to a cell or tissue in a single recombinant AAV (rAAV) vector. Contemplated herein are improved methods and compositions for delivering these base editors in vivo, in a single rAAV particle. Further provided herein are base editors and compositions and cells comprising these base editors.
    Type: Application
    Filed: October 25, 2024
    Publication date: February 27, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Jonathan Ma Levy, Jessie Rose Davis, Tony P. Huang, Isaac Witte
  • Publication number: 20250064979
    Abstract: The present disclosure provides virus-like particles (VLPs) for delivering prime editors, and systems comprising such prime editor (PE) VLPs. The present disclosure also provides polynucleotides encoding the PE-VLPs described herein, which may be useful for producing said PE-VLPs. Also provided herein are methods for editing the genome of a target cell by introducing the presently described PE-VLPs into the target cell. The present disclosure also provides fusion proteins that make up a component of the PE-VLPs described herein, as well as polynucleotides, vectors, cells, and kits.
    Type: Application
    Filed: December 2, 2022
    Publication date: February 27, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Aditya Raguram, Samagya Banskota, Meirui An
  • Publication number: 20250059244
    Abstract: Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. The disclosure provides fusion proteins of nucleic acid programmable DNA binding proteins (napDNAbp), e.g., Cas9 or variants thereof, and nucleic acid editing proteins such as cytidine deaminase domains (e.g., novel cytidine deaminases generated by ancestral sequence reconstruction), and adenosine deaminases that deaminate adenine in DNA. Aspects of the disclosure relate to fusion proteins (e.g., base editors) that have improved expression and/or localize efficiently to the nucleus. In some embodiments, base editors are codon optimized for expression in mammalian cells. In some embodiments, base editors include multiple nuclear localization sequences (e.g., bipartite NLSs), e.g., at least two NLSs.
    Type: Application
    Filed: July 31, 2024
    Publication date: February 20, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Luke W. Koblan, Christopher Gerard Wilson, Jordan Leigh Doman
  • Patent number: 12215365
    Abstract: Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins of Cas9 and nucleic acid editing enzymes or enzyme domains, e.g., deaminase domains, are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of Cas9 and nucleic acid editing enzymes or domains, are provided.
    Type: Grant
    Filed: August 20, 2021
    Date of Patent: February 4, 2025
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, Alexis Christine Komor