Patents Assigned to OPGEN, INC.
  • GENOME ASSEMBLY
    Publication number: 20120183953
    Abstract: The invention generally relates to methods for assembling sequence contigs. In certain embodiments, methods of the invention involve converting sequence contigs into maps, generating a plurality of single molecule restriction maps, aligning single molecule restriction maps to ends of the maps of the sequence contigs, thereby producing extended sequence contigs, and aligning extended sequence contigs.
    Type: Application
    Filed: April 28, 2011
    Publication date: July 19, 2012
    Applicant: OpGen, Inc.
    Inventors: Nianqing XIAO, John K. HENKHAUS, Bin ZHU, Deacon SWEENEY, Thomas ANANTHARAMAN, Ryan PTASHKIN
  • METHODS OF IDENTIFYING AN ORGANISM
    Publication number: 20120164133
    Abstract: This disclosure features methods of identifying an organism. The methods include: (a) obtaining a nucleic acid sample from an organism; (b) imaging said nucleic acid; (c) obtaining a restriction map of said nucleic acid; and (d) correlating the restriction map of said nucleic acid with a restriction map database, thereby identifying the organism.
    Type: Application
    Filed: May 14, 2008
    Publication date: June 28, 2012
    Applicant: OPGEN INC.
    Inventor: Adam M. Briska
  • METHODS OF CATEGORIZING AN ORGANISM
    Publication number: 20120045749
    Abstract: The invention generally relates to methods of identifying and categorizing organisms and more specifically methods of generating and using patterns of chromosomal variation in order to classify organisms.
    Type: Application
    Filed: January 29, 2010
    Publication date: February 23, 2012
    Applicant: OPGEN, INC.
    Inventor: Colin William Dykes
  • METHOD, SYSTEM AND SOFTWARE ARRANGEMENT FOR COMPARATIVE ANALYSIS AND PHYLOGENY WITH WHOLE-GENOME OPTICAL MAPS
    Publication number: 20110231102
    Abstract: The present invention provides a method for organizing genomic information from multiple organisms. In one embodiment of the invention, phylogenetic trees can be constructed for the organisms. The method of the present invention is termed CAPO, Comparative Analysis and Phylogeny with Optical-Maps. Optical maps of organisms are obtained and phylogeny between the organisms is determined by optical map comparison and bipartite graph matching between the organisms, as, for example, computed by a stable marriage algorithm.
    Type: Application
    Filed: December 14, 2010
    Publication date: September 22, 2011
    Applicant: OPGEN, INC.
    Inventors: Adam Briska, Jacob Schwartz, Bing Sun, Bhubaneswar Mishra
  • METHODS AND KITS FOR ISOLATING NUCLEIC ACID FROM AN ORGANISM
    Publication number: 20110177521
    Abstract: The invention generally relates to methods and kits for isolating nucleic acids from an organism. In certain embodiments, methods of the invention involve contacting a plurality of lytic enzymes to an organism, thereby lysing a cell wall of the organism to release the nucleic acid, and introducing at least one agent to separate the nucleic acid from the lysed cells, thereby isolating the nucleic acid.
    Type: Application
    Filed: January 19, 2010
    Publication date: July 21, 2011
    Applicant: OpGen, Inc.
    Inventor: John Kevin Henkhaus
  • METHODS OF CHARACTERIZING SMALL NUCLEIC ACID MOLECULES
    Publication number: 20110086344
    Abstract: The invention generally relates to methods of characterizing small nucleic acid molecules, such as plasmids or nucleic acid molecules obtained from a virus. In certain embodiments, the invention provides a method of characterizing a small circular nucleic acid molecule, the method including performing rolling circle amplification on a small circular nucleic acid molecule, thereby producing a concatamer, and generating an optical map of the concatamer, thereby characterizing the small circular nucleic acid molecule.
    Type: Application
    Filed: October 8, 2009
    Publication date: April 14, 2011
    Applicant: OPGEN, INC.
    Inventors: Ronald W. Lennox, Colin W. Dykes
  • METHODS OF DETERMINING PROPERTIES OF MOLECULES
    Publication number: 20100028886
    Abstract: This disclosure features, inter alia, methods for determining at least one property of a nucleic acid. The methods include: (a) fixing the nucleic acid on a planar surface; (b) digesting the nucleic acid into fragments with at least one enzyme; (c) imaging the nucleic acid; and (d) analyzing the imaged nucleic acid to determine the property of the nucleic acid, wherein no internal nucleic acid standard is added during the method.
    Type: Application
    Filed: May 13, 2009
    Publication date: February 4, 2010
    Applicant: OPGEN, INC.
    Inventor: Adam M. Briska
  • METHODS OF DETERMINING ANTIBIOTIC RESISTANCE
    Publication number: 20090317804
    Abstract: This disclosure relates to methods of determining an antibiotic resistance profile of a bacterium, and methods of treating a patient with a therapeutically effective antibiotic. The methods include comparing the restriction map of the nucleic acid with a restriction map database, and determining antibiotic resistance of the bacterium by matching regions of the nucleic acid to corresponding regions in the database.
    Type: Application
    Filed: May 14, 2008
    Publication date: December 24, 2009
    Applicant: OPGEN INC.
    Inventor: Adam M. BRISKA
  • METHODS OF IDENTIFYING AN ORGANISM FROM A HETEROGENEOUS SAMPLE
    Publication number: 20090208950
    Abstract: This disclosure features methods of identifying at least one organism from a heterogeneous sample. The methods include: (a) obtaining a nucleic acid from at least one organism in a heterogeneous sample; (b) imaging said nucleic acid; (c) obtaining a restriction map of said nucleic acid; and (d) correlating the restriction map of said nucleic acid with a restriction map database, thereby identifying at least one organism in the heterogeneous sample.
    Type: Application
    Filed: October 24, 2008
    Publication date: August 20, 2009
    Applicant: OPGEN, INC.
    Inventor: Adam M. Briska
  • Method, system and software arrangement for comparative analysis and phylogeny with whole-genome optical maps
    Publication number: 20090076735
    Abstract: The present invention provides a method for organizing genomic information from multiple organisms. In one embodiment of the invention, phylogenetic trees can be constructed for the organisms. The method of the present invention is termed CAPO, Comparative Analysis and Phylogeny with Optical-Maps. Optical maps of organisms are obtained and phylogeny between the organisms is determined by optical map comparison and bipartite graph matching between the organisms, as, for example, computed by a stable marriage algorithm.
    Type: Application
    Filed: August 15, 2008
    Publication date: March 19, 2009
    Applicants: OpGen, Inc., New York University
    Inventors: Adam Briska, Jacob Schwartz, Bing Sun, Bhubaneswar Mishra