Patents by Inventor Xiaoxu Li

Xiaoxu Li 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
  • Publication number: 20210381043
    Abstract: This invention provides a process for sequencing single-stranded DNA by employing a nanopore and modified nucleotides.
    Type: Application
    Filed: August 18, 2021
    Publication date: December 9, 2021
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li
  • Publication number: 20210285041
    Abstract: Disclosed herein, inter alia, are nucleotide analogues, and methods of use thereof, having cleavable orthogonal linkers.
    Type: Application
    Filed: March 28, 2018
    Publication date: September 16, 2021
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Xiaoxu Li, Xin Chen, Shiv Kumar, James Russo, Minchen Chien
  • Patent number: 11098353
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Grant
    Filed: December 20, 2019
    Date of Patent: August 24, 2021
    Assignee: 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: 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: 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
  • 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: 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: 20190136308
    Abstract: This invention provides a process for sequencing single-stranded DNA employing modified nucleotides.
    Type: Application
    Filed: May 24, 2018
    Publication date: May 9, 2019
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaoxu Li
  • 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: 10214988
    Abstract: A method for abandonment of a subsea well includes: setting a packer of a lower cementing tool against a bore of an inner casing hung from a subsea wellhead; fastening a pressure control assembly (PCA) to the subsea wellhead; hanging an upper cementing tool from the PCA and stabbing the upper cementing tool into a polished bore receptacle of the lower cementing tool; perforating a wall of the inner casing below the packer; perforating the inner casing wall above the packer by operating a perforator of the upper cementing tool; mixing a resin and a hardener to form a sealant; and pumping a fluid train through bores of the cementing tools and into an inner annulus formed between the inner casing and an outer casing hung from the subsea wellhead. The fluid train includes the sealant followed by a cement slurry.
    Type: Grant
    Filed: June 17, 2016
    Date of Patent: February 26, 2019
    Assignee: CSI TECHNOLOGIES LLC
    Inventors: Fred Sabins, David Brown, Jeffrey Watters, Jorge Esteban Leal, Larry Watters, Xiaoxu Li
  • 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
  • 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
  • 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