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).

  • Patent number: 11970448
    Abstract: Described herein are monomers capable of forming a biologically useful multimer when in contact with one, two, three or more other monomers in an aqueous media. In one aspect, such monomers may be capable of binding to another monomer in an aqueous media (e.g. in vivo) to form a multimer, (e.g. a dimer). Contemplated monomers may include a ligand moiety, a linker element, and a connector element that joins the ligand moiety and the linker element. In an aqueous media, such contemplated monomers may join together via each linker element and may thus be capable of modulating one or more biomolecules substantially simultaneously, e.g., modulate two or more binding domains on a protein or on different proteins.
    Type: Grant
    Filed: July 15, 2020
    Date of Patent: April 30, 2024
    Assignees: CORNELL UNIVERSITY, PURDUE RESEARCH FOUNDATION
    Inventors: Francis Barany, Maneesh Pingle, Donald E. Bergstrom, Sarah F. Giardina, Lee Daniel Arnold
  • Publication number: 20240000950
    Abstract: The present application is directed to a therapeutically useful compound, comprised of two monomers that are linked to each other through two or more reversible covalent bonds. Each monomer is a polyfunctionalized molecule comprising a bioorthogonal linker element and ligand or pharmacophore, wherein the linker and ligand/pharmacophore are covalently coupled to each other either directly or through an optional connector moiety.
    Type: Application
    Filed: August 4, 2021
    Publication date: January 4, 2024
    Inventors: Francis BARANY, Sarah F. GIARDINA, J. David Warren
  • Publication number: 20230295718
    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: October 7, 2022
    Publication date: September 21, 2023
    Inventors: FRANCIS BARANY, John William Efcavitch
  • Publication number: 20230285570
    Abstract: The present application is directed to a therapeutically useful monomer comprising a linker element and an E3 ubiquitin ligase binding moiety. The linker and the E3 ubiquitin ligase binding moiety are covalently coupled to each other either directly or through an optional connector moiety.
    Type: Application
    Filed: August 4, 2021
    Publication date: September 14, 2023
    Inventors: Francis BARANY, Sarah F. GIARDINA, Manny D. BACOLOD, Pradeep K. SINGH, J. David WARREN
  • Publication number: 20230287484
    Abstract: The present invention relates to methods for identifying and/or quantifying 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 or hydroxymethylated nucleotide bases, as well as markers to identify early cancer, monitor cancer treatment, and identify early cancer recurrence.
    Type: Application
    Filed: April 29, 2021
    Publication date: September 14, 2023
    Inventors: Francis BARANY, Manny D. BACOLOD, Jianmin HUANG, Philip B. FEINBERG, Aashiq H. MIRZA, Sarah F. GIARDINA
  • Publication number: 20230277553
    Abstract: The present application is directed to a therapeutic composition, comprising two precursor compounds (monomers) that are suitable for assembly via two or more reversible covalent bonds. The monomers are polyfunctionalized molecules comprising a bioorthogonal linker element and ligand or pharmacophore, wherein the linker and ligand/pharmacophore are covalently coupled to each other either directly or through an optional connector moiety.
    Type: Application
    Filed: August 4, 2021
    Publication date: September 7, 2023
    Inventors: Francis BARANY, Sarah F. GIARDANA, David J. WARREN
  • Patent number: 11486002
    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: July 29, 2019
    Date of Patent: November 1, 2022
    Assignee: CORNELL UNIVERSITY
    Inventors: Francis Barany, John William Efcavitch
  • Patent number: 11466311
    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: June 6, 2019
    Date of Patent: October 11, 2022
    Assignee: CORNELL UNIVERSITY
    Inventors: Francis Barany, John William Efcavitch, Cristian Ruiz Rueda, Jianmin Huang, Philip B. Feinberg
  • Publication number: 20220243263
    Abstract: The present invention relates to methods for identifying and/or quantifying 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: May 1, 2020
    Publication date: August 4, 2022
    Inventors: Francis BARANY, Manny D. BACOLOD, Jianmin HUANG, Aashiq H. MIRZA, Philip B. FEINBERG, Sarah F. GIARDINA
  • Publication number: 20220205050
    Abstract: The present application relates to methods for identifying and/or quantifying 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 or hydroxymethylated nucleotide bases, as well as markers to identify early cancer, monitor cancer treatment, and identify early cancer recurrence.
    Type: Application
    Filed: May 1, 2020
    Publication date: June 30, 2022
    Inventors: Francis BARANY, Manny D. BACOLOD, Jianmin HUANG, Philip FEINBERG, Aashiq MIRZA, Sarah GIARDINA
  • Publication number: 20220178916
    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: December 16, 2021
    Publication date: June 9, 2022
    Inventors: Francis BARANY, Eugene SPIER, Alain MIR
  • Publication number: 20220168742
    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, lncRNA, 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: February 14, 2022
    Publication date: June 2, 2022
    Inventor: Francis BARANY
  • Patent number: 11305282
    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: Grant
    Filed: March 29, 2018
    Date of Patent: April 19, 2022
    Assignee: CORNELL UNIVERSITY
    Inventor: Francis Barany
  • Patent number: 11209424
    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 ligation and/or polymerase reaction. In some embodiments, the ligation products formed in the 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: May 24, 2019
    Date of Patent: December 28, 2021
    Assignee: CORNELL UNIVERSITY
    Inventors: Francis Barany, Eugene Spier, Alain Mir
  • Patent number: 10912786
    Abstract: Described herein are silyl monomers capable of forming a biologically useful multimer when in contact with one, two, three or more other monomers in an aqueous media. Such multimer forming associations of monomers may be promoted by the proximal binding of the monomers to their target biomolecule(s). In one aspect, such monomers may be capable of binding to another monomer in an aqueous media (e.g. in vivo) to form a multimer, (e.g. a dimer). Contemplated monomers may include a ligand moiety, a linker element, and a connector element that joins the ligand moiety and the linker element. In an aqueous media, such contemplated monomers may join together via each linker element and may thus be capable of modulating one or more biomolecules substantially simultaneously, e.g., modulate two or more binding domains on a protein or on different proteins.
    Type: Grant
    Filed: August 25, 2016
    Date of Patent: February 9, 2021
    Assignees: Cornell University, Purdue Research Foundation
    Inventors: Francis Barany, Maneesh Pingle, Donald E. Bergstrom, Sarah F. Giardina, Lee Daniel Arnold
  • Patent number: 10870881
    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 19, 2018
    Date of Patent: December 22, 2020
    Assignees: CORNELL UNIVERSITY, UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL, NORTHEASTERN UNIVERSITY, BOARD OF SUPERVISORS OF LOUISIANA STATE UNIVERSITY AND AGRICULTURAL 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: 20200354319
    Abstract: Described herein are monomers capable of forming a biologically useful multimer when in contact with one, two, three or more other monomers in an aqueous media. In one aspect, such monomers may be capable of binding to another monomer in an aqueous media (e.g. in vivo) to form a multimer, (e.g. a dimer). Contemplated monomers may include a ligand moiety, a linker element, and a connector element that joins the ligand moiety and the linker element. In an aqueous media, such contemplated monomers may join together via each linker element and may thus be capable of modulating one or more biomolecules substantially simultaneously, e.g., modulate two or more binding domains on a protein or on different proteins.
    Type: Application
    Filed: July 15, 2020
    Publication date: November 12, 2020
    Inventors: Francis BARANY, Maneesh PINGLE, Donald E. BERGSTROM, Sarah F. GIARDINA, Lee Daniel ARNOLD
  • Patent number: 10830757
    Abstract: The present invention is directed to methods comprising 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, one or more nanotubes defined by the solid substrate and fluidically coupled to the bioreactor chamber 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 nanotubes have 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: Grant
    Filed: July 17, 2019
    Date of Patent: November 10, 2020
    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: 10829804
    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: Grant
    Filed: March 23, 2016
    Date of Patent: November 10, 2020
    Assignees: The University of North Carolina at Chapel Hill, Cornell University, Board of Supervisors of Louisiana State University and Agricultural and Mechanical College
    Inventors: Francis Barany, John William Efcavitch, Steven A. Soper, Sunggook Park
  • 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