Patents by Inventor Jingyue Ju

Jingyue Ju 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: 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
  • Publication number: 20200248250
    Abstract: This disclosure provides chips, systems and methods for sequencing a nucleic acid sample. Tagged nucleotides arc provided into a reaction chamber comprising a nanopore in a membrane. An individual tagged nucleotide of the tagged nucleotides can contain a tag coupled to a nucleotide, which tag is detectable with the aid of the nanopore. Next, an individual tagged nucleotide of the tagged nucleotides can be incorporated into a growing strand complementary to a single stranded nucleic acid molecule derived from the nucleic acid sample. With the aid of the nanopore, a tag associated with the individual tagged nucleotide can be detected upon incorporation of the individual tagged nucleotide. The tag can be detected with the aid of the nanopore when the tag is released from the nucleotide.
    Type: Application
    Filed: January 6, 2020
    Publication date: August 6, 2020
    Applicants: The Trustees of Columbia University in the City of New York, Roche Sequencing Solutions, Inc.
    Inventors: Sergey Kalachikov, Jingyue Ju, Irina Morozova, Michael Dorwart
  • 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: 10718011
    Abstract: This invention provides methods of using labeled primers or probes for nucleic acid target detection and to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, and sets of oligonucleotide primers for use in such methods, as well as methods of quantitative PCR coupled with nanopore detection.
    Type: Grant
    Filed: February 12, 2015
    Date of Patent: July 21, 2020
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Chuanjuan Tao, Shiv Kumar, Minchen Chien, Jingyue Ju
  • Publication number: 20200208211
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Application
    Filed: December 20, 2019
    Publication date: July 2, 2020
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li
  • Patent number: 10689412
    Abstract: This invention provides a process of labeling a polynucleotide analogue to be detected by Raman and/or infrared spectroscopy detection.
    Type: Grant
    Filed: April 18, 2017
    Date of Patent: June 23, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Jian Wu, Zengmin Li
  • Patent number: 10669577
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: March 27, 2015
    Date of Patent: June 2, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10669582
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: March 8, 2018
    Date of Patent: June 2, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • 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: 10662472
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: May 26, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10648028
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: May 12, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • 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
  • Patent number: 10633700
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: April 28, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • 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
  • Patent number: 10577652
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: March 3, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • 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: 10570446
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: February 25, 2020
    Assignee: THE TRUSTEE OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10526647
    Abstract: This disclosure provides chips, systems and methods for sequencing a nucleic acid sample. Tagged nucleotides are provided into a reaction chamber comprising a nanopore in a membrane. An individual tagged nucleotide of the tagged nucleotides can contain a tag coupled to a nucleotide, which tag is detectable with the aid of the nanopore. Next, an individual tagged nucleotide of the tagged nucleotides can be incorporated into a growing strand complementary to a single stranded nucleic acid molecule derived from the nucleic acid sample. With the aid of the nanopore, a tag associated with the individual tagged nucleotide can be detected upon incorporation of the individual tagged nucleotide. The tag can be detected with the aid of the nanopore when the tag is released from the nucleotide.
    Type: Grant
    Filed: March 3, 2017
    Date of Patent: January 7, 2020
    Assignees: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK, ROCHE SEQUENCING SOLUTIONS, INC.
    Inventors: Sergey Kalachikov, Jingyue Ju, Irina Morozova, Michael Dorwart
  • Publication number: 20190390271
    Abstract: This invention provides a process for sequencing nucleic acids using 3? modified deoxynucleotide analogues or 3? modified deoxyinosine triphosphate analogues, and 3? modified dideoxynucleotide analogues having a detectable marker attached thereto.
    Type: Application
    Filed: April 15, 2019
    Publication date: December 26, 2019
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Jia Guo, Qinglin Meng, Zengmin Li, Huanyan Cao