Patents by Inventor James J. Russo

James J. Russo 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).

  • Patent number: 11266673
    Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing a nucleic acid.
    Type: Grant
    Filed: May 23, 2017
    Date of Patent: March 8, 2022
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Xin Chen, Xiaoxu Li, Zengmin Li, Min-Kang Hsieh, Minchen Chien, Shundi Shi, Jianyi Ren, Cheng Guo, Shiv Kumar, James J. Russo, Chuanjuan Tao, Steffen Jockusch, Sergey Kalachikov
  • Patent number: 11225687
    Abstract: This invention provides nucleoside polyphosphate analogues each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs. This invention also provides nucleotide polymerases with one or more attached and/or conjugated noble metal nanoparticles, wherein the noble metal nanoparticles are surface-enhanced Raman spectroscopy (SERS) substrates thereby creating a region of enhanced sensitivity for surface enhanced Raman spectroscopy (SERS) within or adjacent to the polymerase. This invention also provides a surface with regions of enhanced sensitivity for surface enhanced Raman spectroscopy comprising interspersed rough or nanostructured noble metal surface. This invention also provides methods for determining the sequence of a single stranded DNA or RNA polynucleotide using one or more of nucleoside polyphosphate analogues, polymerase with noble metal nanoparticles, and surface with noble metal.
    Type: Grant
    Filed: April 4, 2017
    Date of Patent: January 18, 2022
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, James J. Russo, Steffen Jockusch, Zengmin Li, Xiaoxu Li, Sergey Kalachikov, Irina Morozova
  • Patent number: 11085076
    Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.
    Type: Grant
    Filed: September 28, 2016
    Date of Patent: August 10, 2021
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Xiaoxu Li, Xin Chen, Zengmin Li, Shiv Kumar, Shundi Shi, Cheng Guo, Jianyi Ren, Min-Kang Hsieh, Minchen Chien, Chuanjuan Tao, Ece Erturk, Sergey Kalachikov, James J. Russo
  • Publication number: 20210199641
    Abstract: The present application discloses novel and inventive methods, apparatuses, and the required molecules to detect compounds (analytes) utilizing antibodies or other protein-binding molecules and nanopore-detectable tags using specially designed nanopores, coupled with ionic current readout, to provide a single molecule electronic detection solution, offering unique opportunities for multiplexing and quantitation.
    Type: Application
    Filed: January 22, 2021
    Publication date: July 1, 2021
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, James J. Russo, Sergey Kalachikov, Chuanjuan Tao, Shiv Kumar, Irina Morozova, Xiaoxu Li
  • Publication number: 20210139976
    Abstract: The invention provides various orthogonal nucleotide analogues and methods for using combinations of said various orthogonal nucleotide analogues for sequencing by synthesis.
    Type: Application
    Filed: March 14, 2019
    Publication date: May 13, 2021
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Xiaoxu Li, Shiv Kumar, Xin Chen, James J. Russo, Minchen Chien, Steffen Jockusch, Chuanjuan Tao, Xuanting Wang, Sergey Kalachikov, Irina Morozova, Shundi Shi
  • Publication number: 20200283833
    Abstract: This invention provides methods of using labeled nucleotide polyphosphate analogues to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, nucleotides and primer-conjugated nanopore proteins for use in such methods, and processes for producing such nucleotides and primer-conjugated nanopore proteins.
    Type: Application
    Filed: May 22, 2020
    Publication date: September 10, 2020
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Youngjin Cho, Shiv Kumar, Sergey Kalachikov, Chuanjuan Tao, Minchen Chien, James J. Russo
  • Patent number: 10732183
    Abstract: This invention provides methods for detecting the presence of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention also provides methods for determining the quantity of each of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention further provides methods for detecting interaction of at least two predetermined compounds using at least one tag moiety and at least one nanopore.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: August 4, 2020
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Shiv Kumar, Chuanjuan Tao, Sergey Kalachikov, James J. Russo
  • Patent number: 10662463
    Abstract: This invention provides methods of using labeled nucleotide polyphosphate analogues to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, nucleotides and primer-conjugated nanopore proteins for use in such methods, and processes for producing such nucleotides and primer-conjugated nanopore proteins.
    Type: Grant
    Filed: March 22, 2016
    Date of Patent: May 26, 2020
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Youngjin Cho, Shiv Kumar, Sergey Kalachikov, Chuanjuan Tao, Minchen Chien, James J. Russo
  • Patent number: 10648026
    Abstract: This invention provides nucleoside polyphosphate analogs each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs; and methods for determining the sequence of a single-stranded DNA or RNA using said nucleoside polyphosphate analogs. This invention also provides methods for detecting the interaction of a plurality of predetermined compounds, at least one of which having attached thereto a tag comprising a plurality of Raman-scattering moieties.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: May 12, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, Mirkó Palla, James J. Russo
  • Publication number: 20200115745
    Abstract: This disclosure is related to a method of sequencing a single-stranded DNA using deoxynucleotide polyphosphate analogues and translocation of tags from incorporated deoxynucleotide polyphosphate analogues through a nanopore.
    Type: Application
    Filed: October 15, 2019
    Publication date: April 16, 2020
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue JU, Shiv KUMAR, Zengmin LI, Chuanjuan TAO, Minchen CHIEN, James J. RUSSO, Sergey KALACHIKOV, Ken SHEPARD, Jacob Karl ROSENSTEIN
  • Publication number: 20200069717
    Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of thereof in the sequencing a nucleic acid.
    Type: Application
    Filed: May 23, 2017
    Publication date: March 5, 2020
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Xin Chen, Xiaoxu Li, Zengmin Li, Min-Kang Hsieh, Minchen Chien, Shundi Shi, Jianyi Ren, Cheng Guo, Shiv Kumar, James J. Russo, Chuanjuan Tao, Steffen Jockusch, Sergey Kalachikov
  • Publication number: 20200063194
    Abstract: The subject invention provides a method of determining whether a cytosine at a predefined position within a single strand of a double-stranded DNA of known sequence is hydroxymethylated. The invention also provides a method of determining whether a cytosine at a predefined position within a single strand of a double-stranded DNA of known sequence is unmethylated. The invention further provides a method of determining whether a cytosine at a predefined position within a single strand of a double-stranded DNA of known sequence is methylated but not hydroxymethylated. The invention also provides a method of determining whether a cytosine present at a predefined position within a single strand of a double-stranded DNA of known sequence, and within a CpG site, is unmethylated.
    Type: Application
    Filed: April 3, 2018
    Publication date: February 27, 2020
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Timothy H. Bestor, James J. Russo, Steffen Jockusch, Xiaoxu Li
  • Patent number: 10443096
    Abstract: This disclosure is related to a method of sequencing a single-stranded DNA using deoxynucleotide polyphosphate analogues and translocation of tags from incorporated deoxynucleotide polyphosphate analogues through a nanopore.
    Type: Grant
    Filed: December 16, 2011
    Date of Patent: October 15, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, Zengmin Li, Chuanjuan Tao, Minchen Chien, James J. Russo, Sergey Kalachikov, Ken Shepard, Jacob Karl Rosenstein
  • Publication number: 20190309008
    Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
    Type: Application
    Filed: April 1, 2019
    Publication date: October 10, 2019
    Applicants: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK, Government of The United States of America, as Represented by The Secretary of Commerce
    Inventors: Jingyue JU, Shiv KUMAR, Chuanjuan TAO, Minchen CHIEN, James J. RUSSO, John J. KASIANOWICZ, Joseph W.F. ROBERTSON
  • Patent number: 10337049
    Abstract: The present invention provides a method of determining whether cytosine residues present at a predetermined positions within a single strand of a double stranded DNA of known sequence are methylated as well as compounds for carrying out this method.
    Type: Grant
    Filed: December 17, 2015
    Date of Patent: July 2, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Timothy H. Bestor, Jingyue Ju, Xiaoxu Li, James J. Russo
  • Publication number: 20190153527
    Abstract: This invention provides nucleotide analogues each of which comprises a tag comprising one or more Forster resonance energy transfer (FRET) acceptor fluorophores, a nucleotide polymerase having one or more FRET donor fluorophores, and methods for sequencing single-stranded
    Type: Application
    Filed: April 4, 2017
    Publication date: May 23, 2019
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, James J. Russo, Steffen Jockusch, Zengmin Li, Xiaoxu Li, Sergey M. Kalachikov, Irina Morozova
  • Publication number: 20190112650
    Abstract: This invention provides nucleoside polyphosphate analogues each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs. This invention also provides nucleotide polymerases with one or more attached and/or conjugated noble metal nanoparticles, wherein the noble metal nanoparticles are surface-enhanced Raman spectroscopy (SERS) substrates thereby creating a region of enhanced sensitivity for surface enhanced Raman spectroscopy (SERS) within or adjacent to the polymerase. This invention also provides a surface with regions of enhanced sensitivity for surface enhanced Raman spectroscopy comprising interspersed rough or nanostructured noble metal surface. This invention also provides methods for determining the sequence of a single stranded DNA or RNA polynucleotide using one or more of nucleoside polyphosphate analogues, polymerase with noble metal nanoparticles, and surface with noble metal.
    Type: Application
    Filed: April 4, 2017
    Publication date: April 18, 2019
    Applicant: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, James J. Russo, Steffen Jockusch, Zengmin Li, Xiaoxu Li, Sergey Kalachikov, Irina Morozova
  • Patent number: 10246479
    Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
    Type: Grant
    Filed: April 8, 2013
    Date of Patent: April 2, 2019
    Assignees: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK, THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY OF COMMERCE
    Inventors: Jingyue Ju, Shiv Kumar, Chuanjuan Tao, Minchen Chien, James J. Russo, John J. Kasianowicz, Joseph W. F. Robertson
  • Publication number: 20180327828
    Abstract: This disclosure is related to a method for determining the identity of a nucleotide residue of a single-stranded DNA or RNA, or sequencing DNA or RNA, in a solution using an ion-sensing field effect transistor and reversible nucleotide terminators.
    Type: Application
    Filed: November 18, 2016
    Publication date: November 15, 2018
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Xiaoxu Li, Zengmin Li, Shiv Kumar, Xin Chen, Cheng Guo, Shundi Shi, Jianyi Ren, Chuanjuan Tao, Minchen Chien, James J. Russo, Lin Yu
  • Publication number: 20180274024
    Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.
    Type: Application
    Filed: September 28, 2016
    Publication date: September 27, 2018
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Xiaoxu Li, Xin Chen, Zengmin Li, Shiv Kumar, Shundi Shi, Cheng Guo, Jianyi Ren, Min-Kang Hsieh, Minchen Chien, Chuanjuan Tao, Ece Erturk, Sergey Kalachikov, James J. Russo