Patents by Inventor Francis Barany

Francis Barany 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: 20200038871
    Abstract: The present invention relates to methods, devices, instruments, processes, and systems for the highly specific, targeted molecular analysis of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, IncRNA, circulating tumor cells, or total blood cells. The technology enables highly sensitive identification and enumeration of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using spatial multiplexing and combined nuclease, ligation, polymerase, and sequencing reactions. Such technology may be used for non-invasive early detection of cancer, non-invasive cancer prognosis, and monitoring both treatment efficacy and disease recurrence of cancer.
    Type: Application
    Filed: March 29, 2018
    Publication date: February 6, 2020
    Inventor: Francis BARANY
  • Publication number: 20190346422
    Abstract: The present invention is directed to a device that comprises a biomolecular processor and one or more nanotubes. Each biomolecular processor comprises a bioreactor chamber defined by a solid substrate, a plurality of spaced support structures within said bioreactor chamber and attached to the solid substrate, and one or more capture molecules immobilized to some or all of said plurality of spaced support structures, said one or more capture molecules suitable to bind to a portion of a target nucleic acid molecule in a sample. The device also comprises one or more nanotubes defined by the solid substrate and fluidically coupled to the bioreactor chamber. Each of the one or more nanotubes has a passage extending between an input end proximate to the bioreactor chamber and an output end distal to the bioreactor chamber, and comprises one or more nanopores within the passage with each nanopore having a reduced diameter relative to the passage.
    Type: Application
    Filed: July 17, 2019
    Publication date: November 14, 2019
    Inventors: Steven A. Soper, Francis Barany, Sunggook Park, Michael Murphy, Collin J. McKinney, John William Efcavitch, Mateusz Hupert
  • Publication number: 20190346430
    Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction.
    Type: Application
    Filed: May 24, 2019
    Publication date: November 14, 2019
    Inventors: Francis BARANY, Eugene SPIER, Alain MIR
  • Publication number: 20190345552
    Abstract: The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism.
    Type: Application
    Filed: July 29, 2019
    Publication date: November 14, 2019
    Inventors: Francis Barany, John William Efcavitch
  • Publication number: 20190316187
    Abstract: The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.
    Type: Application
    Filed: June 6, 2019
    Publication date: October 17, 2019
    Inventors: Francis Barany, John William Efcavitch, Cristian Ruiz Rueda, Jianmin Huang, Philip B. Feinberg
  • Patent number: 10407722
    Abstract: The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism.
    Type: Grant
    Filed: June 8, 2015
    Date of Patent: September 10, 2019
    Assignee: Cornell University
    Inventors: Francis Barany, John William Efcavitch
  • Patent number: 10393726
    Abstract: The present invention is directed to a device that comprises a biomolecular processor and one or more nanotubes. Each biomolecular processor comprises a bioreactor chamber defined by a solid substrate, a plurality of spaced support structures within said bioreactor chamber and attached to the solid substrate, and one or more capture molecules immobilized to some or all of said plurality of spaced support structures, said one or more capture molecules suitable to bind to a portion of a target nucleic acid molecule in a sample. The device also comprises one or more nanotubes defined by the solid substrate and fluidically coupled to the bioreactor chamber.
    Type: Grant
    Filed: March 23, 2016
    Date of Patent: August 27, 2019
    Assignees: The University of North Carolina at Chapel Hill, Cornell University, Board of Supervisors of Louisiana State University and Agricultural and Mechanical College
    Inventors: Steven A. Soper, Francis Barany, Sunggook Park, Michael Murphy, Collin J. McKinney, John William Efcavitch, Mateusz Hupert
  • Patent number: 10344321
    Abstract: The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.
    Type: Grant
    Filed: October 8, 2015
    Date of Patent: July 9, 2019
    Assignee: Cornell University
    Inventors: Francis Barany, John William Efcavitch, Cristian Ruiz Rueda, Jianmin Huang, Philip B. Feinberg
  • Patent number: 10338062
    Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.
    Type: Grant
    Filed: February 6, 2017
    Date of Patent: July 2, 2019
    Assignee: Cornell University
    Inventors: Francis Barany, Eugene Spier, Alain Mir
  • Patent number: 10221447
    Abstract: The present invention is directed to methods for identifying the presence of one or more methylated or unmethylated target nucleotide sequences in a sample that involve coupled methylation sensitive restriction enzyme digestion-ligation and/or extension processes. In some embodiments, the ligation and primary extension products formed in the reaction processes of the present invention are subsequently amplified using a polymerase chain reaction. The ligation products or primary extension products are detected, and the presence of one or more methylated or unmethylated target nucleotide sequences in the sample is identified based on the detection.
    Type: Grant
    Filed: March 31, 2015
    Date of Patent: March 5, 2019
    Assignee: Cornell University
    Inventor: Francis Barany
  • Publication number: 20180346973
    Abstract: The present invention is directed methods for identifying, in a sample, one or more target nucleotide sequences differing from other nucleotide sequences in the sample by one or more nucleotides, one or more copy numbers, one or more transcript sequences, and/or one or more methylated residues, using ligation detection reactions, polymerase mediated extension reactions, and/or cleavage reactions. The present invention is also directed to methods for identifying, in a sample, one or more nucleotides in a target nucleotide sequence.
    Type: Application
    Filed: March 23, 2016
    Publication date: December 6, 2018
    Inventors: Francis Barany, John William Efcavitch, Steven A. Soper, Sunggook Park
  • Patent number: 10131938
    Abstract: The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The present invention further relates to an oligonucleotide array comprising of a support with the plurality of oligonucleotide probes immobilized on the support, a method of using the support to detect single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences, and a kit for such detection, which includes the support on which the oligonucleotides have been immobilized.
    Type: Grant
    Filed: July 7, 2017
    Date of Patent: November 20, 2018
    Assignee: Cornell Research Foundation, Inc.
    Inventors: Francis Barany, Monib Zirvi, Norman P. Gerry, Reyna Favis, Richard Kliman
  • Publication number: 20180265917
    Abstract: The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.
    Type: Application
    Filed: October 8, 2015
    Publication date: September 20, 2018
    Inventors: Francis BARANY, John William EFCAVITCH, Cristian RUIZ RUEDA, Jianmin HUANG, Philip B. FEINBERG
  • Publication number: 20180187257
    Abstract: The present invention relates to a device comprising a biomolecular processor. Each biomolecular processor has one or more bioreactor chambers defined by a solid substrate; a support structure within each bioreactor; a cleaving enzyme immobilized to the support structure and operatively positioned within the bioreactor chamber to cleave monomer or multimer units of a biopolymer molecule operatively engaged by the cleaving enzyme; and one or more time-of-flight channels formed in the solid substrate and fluidically coupled to said one or more bioreactor chambers. Each of the time-of-flight channels have two or more sensors including at least (i) a first sensor contacting the time-of-flight channel proximate to the input end of the channel and (ii) a second sensor contacting the time-of-flight channel proximate to the output end of channel. The present invention further relates to methods of sequencing and identifying biopolymer molecules using the device.
    Type: Application
    Filed: February 19, 2018
    Publication date: July 5, 2018
    Inventors: Steven A. SOPER, Francis BARANY, George GRILLS, Robin McCARLEY, Collin J. McKINNEY, Doral MOLDOVAN, Michael C. MURPHY, Dimitris NIKITOPOULOS, Sunggook PARK, Elizabeth J. PODLAHA-MURPHY
  • Patent number: 10011862
    Abstract: The present invention is directed to methods for identifying the presence of one or more methylated or unmethylated target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more methylated or unmethylated target nucleotide sequences in the sample is identified based on the detection.
    Type: Grant
    Filed: March 13, 2014
    Date of Patent: July 3, 2018
    Assignee: Cornell University
    Inventors: Francis Barany, Eugene Spier
  • Patent number: 9943603
    Abstract: The present invention is directed to a monomer useful in preparing therapeutic compounds. The monomer includes a diversity element which potentially binds to a target molecule with a dissociation constant of less than 300 ?M and a linker element connected to the diversity element. The linker element has a molecular weight less than 500 daltons, is connected, directly or indirectly through a connector, to said diversity element, and is capable of forming a reversible covalent bond or non-covalent interaction with a binding partner of the linker element. The monomers can be covalently or non-covalently linked together to form a therapeutic multimer or a precursor thereof. Also disclosed is a method of screening for therapeutic multimer precursors which bind to a target molecule associated with a condition and a method of screening for linker elements capable of binding to one another.
    Type: Grant
    Filed: July 29, 2014
    Date of Patent: April 17, 2018
    Assignees: Cornell University, Purdue Research Foundation
    Inventors: Francis Barany, Maneesh Pingle, Donald Bergstrom, Sarah Filippa Giardina
  • Publication number: 20180074039
    Abstract: The present invention is directed to a device that comprises a biomolecular processor and one or more nanotubes. Each biomolecular processor comprises a bioreactor chamber defined by a solid substrate, a plurality of spaced support structures within said bioreactor chamber and attached to the solid substrate, and one or more capture molecules immobilized to some or all of said plurality of spaced support structures, said one or more capture molecules suitable to bind to a portion of a target nucleic acid molecule in a sample. The device also comprises one or more nanotubes defined by the solid substrate and fluidically coupled to the bioreactor chamber.
    Type: Application
    Filed: March 23, 2016
    Publication date: March 15, 2018
    Inventors: Steven A. Soper, Francis Barany, Sunggook Park, Michael Murphy, Collin J. Mckinney, John William Efcavitch, Mateusz Hupert
  • Patent number: 9909173
    Abstract: The present invention relates to a device comprising a biomolecular processor. Each biomolecular processor has one or more bioreactor chambers defined by a solid substrate; a support structure within each bioreactor; a cleaving enzyme immobilized to the support structure and operatively positioned within the bioreactor chamber to cleave monomer or multimer units of a biopolymer molecule operatively engaged by the cleaving enzyme; and one or more time-of-flight channels formed in the solid substrate and fluidically coupled to said one or more bioreactor chambers. Each of the time-of-flight channels have two or more sensors including at least (i) a first sensor contacting the time-of-flight channel proximate to the input end of the channel and (ii) a second sensor contacting the time-of-flight channel proximate to the output end of channel. The present invention further relates to methods of sequencing and identifying biopolymer molecules using the device.
    Type: Grant
    Filed: February 10, 2014
    Date of Patent: March 6, 2018
    Assignees: Cornell University, University of North Carolina at Chapel Hill, Northeastern University, Board of Supervisors of Louisiana State University and Agriculture and Mechanical College
    Inventors: Steven A. Soper, Francis Barany, George Grills, Robin McCarley, Collin J. McKinney, Dorel Moldovan, Michael C. Murphy, Dimitris Nikitopoulos, Sunggook Park, Elizabeth J. Podlaha-Murphy
  • Publication number: 20180002744
    Abstract: The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The present invention further relates to an oligonucleotide array comprising of a support with the plurality of oligonucleotide probes immobilized on the support, a method of using the support to detect single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences, and a kit for such detection, which includes the support on which the oligonucleotides have been immobilized.
    Type: Application
    Filed: July 7, 2017
    Publication date: January 4, 2018
    Inventors: Francis BARANY, Monib ZIRVI, Norman P. GERRY, Reyna FAVIS, Richard KLIMAN
  • Patent number: 9771345
    Abstract: The present invention is directed to a monomer useful in preparing therapeutic compounds. The monomer includes one or more pharmacophores which potentially binds to a target molecule with a dissociation constant of less than 300 ?M and a linker element connected to the pharmacophore. The linker element has a molecular weight less than 500 daltons, is connected, directly or indirectly through a connector, to the pharmacophore.
    Type: Grant
    Filed: October 7, 2010
    Date of Patent: September 26, 2017
    Assignees: Cornell University, Purdue Research Foundation, BlinkBio, Inc.
    Inventors: Francis Barany, Maneesh Pingle, Sarah Filippa Giardina, Donald Bergstrom, Lee Daniel Arnold