Patents by Inventor Cole Trapnell

Cole Trapnell 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).

  • METHOD FOR SPATIALLY BARCODING CELLS IN TISSUE SLICES
    Publication number: 20220251632
    Abstract: Substrates and methods for spatially resolved analyses of tissue samples are provided, allowing the data from such analyses to be mapped back to the tissue's initial architecture. For analyses that have previously been conducted on bulk, homogenized samples or on dissociated cell components not directly traceable to their prior positions in the tissue sample, spatial resolution of this data can allow better characterization of cell-cell and cell-microenvironment relationships and interactions. This spatial context can aid in determining structure-function relationships in healthy and diseased tissues may thereby enhance the scientific understanding of tissue homeostasis, development, disease, and repair. The information determined using the methods of the disclosure can also be applied to enhancing diagnostics evaluation of diseased tissues.
    Type: Application
    Filed: July 22, 2020
    Publication date: August 11, 2022
    Applicant: University of Washington
    Inventors: Mary Regier, Kelly Rose Stevens, Sanjay Srivatsan, Cole Trapnell
  • HIGH-THROUGHPUT SINGLE-NUCLEI AND SINGLE-CELL LIBRARIES AND METHODS OF MAKING AND OF USING
    Publication number: 20220033805
    Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the method includes nuclear or cellular hashing which permits increased sample throughput and increased doublet detection at high collision rates. In one embodiment, the method includes normalization hashing which aids in estimating and removing technical noise in cell to cell variation and increases sensitivity and specificity.
    Type: Application
    Filed: March 2, 2020
    Publication date: February 3, 2022
    Inventors: Sanjay Srivatsan, Jose McFaline-Figueroa, Vijay Ramani, Junyue Cao, Gregory Booth, Jay Shendure, Cole Trapnell, Frank J. Steemers
  • High-throughput methodology for identifying RNA-protein interactions transcriptome-wide
    Patent number: 9797887
    Abstract: Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.
    Type: Grant
    Filed: June 9, 2015
    Date of Patent: October 24, 2017
    Assignees: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, PRESIDENT AND FELLOWS OF HARVARD COLLEGES
    Inventors: Brian D. Gregory, John Rinn, Fan Li, Cole Trapnell, Loyal A. Goff
  • HIGH-THROUGHPUT METHODOLOGY FOR IDENTIFYING RNA-PROTEIN INTERACTIONS TRANSCRIPTOME-WIDE
    Publication number: 20150355173
    Abstract: Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.
    Type: Application
    Filed: June 9, 2015
    Publication date: December 10, 2015
    Applicant: The Trustees of the University of Pennsylvania
    Inventors: Brian D. Gregory, John Rinn, Fan Li, Cole Trapnell, Loyal A. Goff
  • High-throughput methodology for identifying RNA-protein interactions transcriptome-wide
    Patent number: 9097708
    Abstract: Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.
    Type: Grant
    Filed: June 6, 2013
    Date of Patent: August 4, 2015
    Assignee: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA
    Inventors: Brian D. Gregory, John Rinn, Fan Li, Cole Trapnell, Loyal A. Goff
  • HIGH-THROUGHPUT METHODOLOGY FOR IDENTIFYING RNA-PROTEIN INTERACTIONS TRANSCRIPTOME-WIDE
    Publication number: 20130338009
    Abstract: Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.
    Type: Application
    Filed: June 6, 2013
    Publication date: December 19, 2013
    Inventors: Brian D. Gregory, John Rinn, Fan Li, Cole Trapnell, Loyal A. Goff