OPGEN, INC. Patent applications |
Patent application number | Title | Published |
20150284777 | METHODS OF IDENTIFYING AN ORGANISM - This disclosure features methods of identifying an organism. In certain embodiments, the invention provides methods of distinguishing virulent and non-virulent strains of organisms, such as | 10-08-2015 |
20150218619 | DEVICES AND METHODS FOR IMMOBILIZING NUCLEIC ACIDS - The present invention generally relates to devices and methods for immobilizing nucleic acids on a substrate. In certain embodiments, devices of the invention include a voltage source, and a substrate coupled to the voltage source, in which hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids. | 08-06-2015 |
20140274750 | SEQUENCE ASSEMBLY USING OPTICAL MAPS - The invention generally relates to sequence assembly and particularly to ordering the alignment of contigs to reference maps. The invention provides systems and methods for assembling contigs by aligning those contigs to a reference map in descending order of placement confidence. Each placement decreases the number of possible placements for the remaining contigs, which otherwise would have been likely to match in numerous places. Contigs are thereby placed along the reference genome with confidence and thus can be assembled into a genome-scale sequence assembly. | 09-18-2014 |
20140272948 | HIERARCHICAL ASSEMBLY OF OPTICAL MAPS - The invention generally relates to optical maps and particularly to computationally tractable methods of assembling large numbers of single molecule maps by dividing the maps into smaller groups of maps within which all of the maps are similar to one another by some metric. For each group, all of the maps are assembled into contigs. The resulting contigs are then assembled into one or more genome assemblies. By dividing the maps into groups, a number of comparison operations required for assembly is reduced and, since each group of maps can be assembled into a contig in a discrete operation, the overall assembly operation can be parallelized. | 09-18-2014 |
20140127686 | METHODS OF IDENTIFYING AN ORGANISM - This disclosure features methods of identifying an organism. In certain embodiments, the invention provides methods of distinguishing virulent and non-virulent strains of | 05-08-2014 |
20130217009 | METHODS OF IDENTIFYING AN ORGANISM - This disclosure features methods of identifying an organism. In certain embodiments, the invention provides methods of distinguishing virulent and non-virulent strains of | 08-22-2013 |
20130029877 | METHODS FOR OPTIMIZING OPTICAL MAPPING CONDITIONS - The invention generally relates to methods and apparatuses for optimizing conditions for optical mapping. In certain embodiments, methods of the invention involve providing a substrate including a gradient of silanes in a first direction, introducing to the substrate, a gradient of enzyme activity in a second direction, contacting a plurality of enzymes and a plurality of nucleic acids to the substrate, and analyzing enzymatic activity and interaction of the nucleic acids with the substrate, thereby determining the optimal conditions for optical mapping of the nucleic acid. | 01-31-2013 |
20130029348 | METHODS OF ELONGATING NUCLEIC ACIDS - The invention generally relates to methods for elongating nucleic acid, such as DNA, on a charged substrate. In certain embodiments, methods of the invention involve contacting an applicator to a sample including a nucleic acid, and swabbing the applicator on a charged substrate, thereby elongating the nucleic acid on the substrate. | 01-31-2013 |
20130029347 | DEVICES AND METHODS FOR IMMOBILIZING NUCLEIC ACIDS - The present invention generally relates to devices and methods for immobilizing nucleic acids on a substrate. In certain embodiments, devices of the invention include a voltage source, and a substrate coupled to the voltage source, in which hydrophobicity of the substrate changes in response to an applied electric field and a surface of the substrate is coated with a substance that retains nucleic acids. | 01-31-2013 |
20130029323 | SYSTEMS, DEVICES, AND METHODS FOR AUTOMATED CHARACTERIZATION OF A NUCLEIC ACID MOLECULE - The invention generally relates to systems, cartridges, and methods for automated characterization of a nucleic acid molecule, in particular, optical mapping of DNA from an organism. In certain embodiments, the invention provides a cartridge for characterizing a nucleic acid molecule, the cartridge including a reaction chamber having a derivatized bottom surface, at least one reagent reservoir, and a pump, in which the reaction chamber, the reagent reservoir, and the pump are fluidically connected to each other. | 01-31-2013 |
20120183953 | GENOME ASSEMBLY - 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. | 07-19-2012 |
20120164133 | METHODS OF IDENTIFYING AN ORGANISM - 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. | 06-28-2012 |
20120045749 | METHODS OF CATEGORIZING AN ORGANISM - 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. | 02-23-2012 |
20110231102 | METHOD, SYSTEM AND SOFTWARE ARRANGEMENT FOR COMPARATIVE ANALYSIS AND PHYLOGENY WITH WHOLE-GENOME OPTICAL MAPS - 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. | 09-22-2011 |
20110177521 | METHODS AND KITS FOR ISOLATING NUCLEIC ACID FROM AN ORGANISM - 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. | 07-21-2011 |
20110086344 | METHODS OF CHARACTERIZING SMALL NUCLEIC ACID MOLECULES - 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. | 04-14-2011 |
20100028886 | METHODS OF DETERMINING PROPERTIES OF MOLECULES - 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. | 02-04-2010 |
20090317804 | METHODS OF DETERMINING ANTIBIOTIC RESISTANCE - 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. | 12-24-2009 |
20090208950 | METHODS OF IDENTIFYING AN ORGANISM FROM A HETEROGENEOUS SAMPLE - 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. | 08-20-2009 |
20090076735 | Method, system and software arrangement for comparative analysis and phylogeny with whole-genome optical maps - 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. | 03-19-2009 |