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).

  • Synthesis of cleavable fluorescent nucleotides as reversible terminators for DNA sequencing by synthesis
    Patent number: 10144961
    Abstract: This invention provides novel azido linkers for deoxynucleotide analogs having a detectable marker attached thereto.
    Type: Grant
    Filed: May 16, 2017
    Date of Patent: December 4, 2018
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Huanyan Cao, Zengmin Li, Qinglin Meng, Jia Guo, Shenglong Zhang, Lin Yu
  • ION SENSOR DNA AND RNA SEQUENCING BY SYNTHESIS USING NUCLEOTIDE REVERSIBLE TERMINATORS
    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
  • DESIGN AND SYNTHESIS OF NOVEL DISULFIDE LINKER BASED NUCLEOTIDES AS REVERSIBLE TERMINATORS FOR DNA SEQUENCING BY SYNTHESIS
    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
  • MASSIVE PARALLEL METHOD FOR DECODING DNA AND RNA
    Publication number: 20180201642
    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: Application
    Filed: March 8, 2018
    Publication date: July 19, 2018
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators
    Patent number: 10000801
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: June 19, 2018
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li
  • PORE-FORMING PROTEIN CONJUGATE COMPOSITIONS AND METHODS
    Publication number: 20180135121
    Abstract: The present disclosure relates to compositions and methods based on a fast, efficient chemical reaction for conjugating a pore-forming protein, such as ?-hemolysin, to a biomolecule, such as antibodies, receptors, and enzymes, such as DNA polymerase, and the use of such pore-forming conjugates in nanopore devices and methods.
    Type: Application
    Filed: January 11, 2018
    Publication date: May 17, 2018
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Zengmin Li, Sergey Kalachikov, Carl Fuller
  • POLYMER TAGGED NUCLEOTIDES FOR SINGLE MOLECULE ELECTRONIC SNP ASSAY
    Publication number: 20180112257
    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: March 22, 2016
    Publication date: April 26, 2018
    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
  • NUCLEIC ACID SEQUENCING BY NANOPORE DETECTION OF TAG MOLECULES
    Publication number: 20180073071
    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 compositions, methods, and systems for sequencing nucleic acids using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.
    Type: Application
    Filed: September 22, 2017
    Publication date: March 15, 2018
    Applicants: The Trustees of Columbia University in the City of New York, Genia Technologies, Inc.
    Inventors: Jingyue JU, Randall DAVIS, Roger CHEN
  • Pyrosequencing methods and related compositions
    Patent number: 9909177
    Abstract: This invention provides methods for pyrosequencing and compositions comprising 3?-O-modified deoxynucleoside triphosphates.
    Type: Grant
    Filed: September 10, 2015
    Date of Patent: March 6, 2018
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Jian Wu, Dae H. Kim
  • Pore-forming protein conjugate compositions and methods
    Patent number: 9890426
    Abstract: The present disclosure relates to compositions and methods based on a fast, efficient chemical reaction for conjugating a pore-forming protein, such as ?-hemolysin, to a biomolecule, such as antibodies, receptors, and enzymes, such as DNA polymerase, and the use of such pore-forming protein conjugates in nanopore devices and methods.
    Type: Grant
    Filed: February 22, 2017
    Date of Patent: February 13, 2018
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, Sergey Kalachikov, Carl Fuller
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9868985
    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 analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: July 12, 2017
    Date of Patent: January 16, 2018
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • DESIGN AND SYNTHESIS OF CLEAVABLE FLUORESCENT NUCLEOTIDES AS REVERSIBLE TERMINATORS FOR DNA SEQUENCING BY SYNTHESIS
    Publication number: 20170321267
    Abstract: This invention provides novel azido linkers for deoxynucleotide analogues having a detectable marker attached thereto.
    Type: Application
    Filed: May 16, 2017
    Publication date: November 9, 2017
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Huanyan Cao, Zengmin Li, Qinglin Meng, Jia Guo, Shenglong Zhang, Lin Yu
  • MASSIVE PARALLEL METHOD FOR DECODING DNA AND RNA
    Publication number: 20170313737
    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: Application
    Filed: July 12, 2017
    Publication date: November 2, 2017
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • DNA SEQUENCING BY SYNTHESIS USING RAMA AND IFRARED SPECTROSCOPY DETECTION
    Publication number: 20170283451
    Abstract: This invention provides a process of labeling a polynucleotide analogue to be detected by Raman and/or infrared spectroscopy detection.
    Type: Application
    Filed: April 18, 2017
    Publication date: October 5, 2017
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue JU, Jian WU, Zengmin LI
  • NUCLEIC ACID SEQUENCES USING TAGS
    Publication number: 20170241948
    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: Application
    Filed: March 3, 2017
    Publication date: August 24, 2017
    Applicants: The Trustees of Columbia University in the City of New York, Genia Technologies, Inc.
    Inventors: Sergey Kalachikov, Jingyue Ju, Irina Morozova, Michael Dorwart
  • Universal methylation profiling methods
    Patent number: 9738922
    Abstract: This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.
    Type: Grant
    Filed: December 19, 2014
    Date of Patent: August 22, 2017
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Timothy H. Bestor, John R. Edwards, Jingyue Ju, Xiaoxu Li
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9725480
    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 analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: May 27, 2016
    Date of Patent: August 8, 2017
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9718852
    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 analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: December 15, 2016
    Date of Patent: August 1, 2017
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9719139
    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 analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: December 15, 2016
    Date of Patent: August 1, 2017
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Massive parallel method for decoding DNA and RNA
    Patent number: 9708358
    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 analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: December 15, 2016
    Date of Patent: July 18, 2017
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki