Patents Assigned to Nabsys, Inc.
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Patent number: 9051609Abstract: Methods for sequencing a biopolymer by forming local ternary complexes along the length of the double-stranded biopolymer target molecule using one or more probes and obtaining information about the location of the probe(s) using a detector. These methods offer particular advantage when implemented with nanopore (including micropore) detection systems.Type: GrantFiled: August 20, 2012Date of Patent: June 9, 2015Assignee: NABsys, Inc.Inventors: John Oliver, Barrett Bready, Peter Goldstein, Franco Preparata
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Patent number: 8926813Abstract: Devices and methods for detecting the length of analytes, and/or sequencing analytes are provided in which two or more electrical signals are obtained as an analyte traverses a fluidic channel. Detection of the relative position of probes hybridized to a biopolymer and/or the length of the analyte (e.g., a biopolymer) does not rely on the absolute time between detection events of a given electrical signal to determine a distance associated with the biopolymer. Instead, multiple signals are obtained as functions of time) corresponding to a plurality of detector volumes at known locations along a fluidic channel through which the biopolymer passes, and the distances are determined from the multiple signals.Type: GrantFiled: August 6, 2012Date of Patent: January 6, 2015Assignee: Nabsys, Inc.Inventor: John S. Oliver
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Publication number: 20140349304Abstract: Assay methods and apparatus for the analysis of biopolymers are disclosed. The assays employ nicking endonucleases to enable the generation of flaps on target biomolecules which are detected in nanopore or fluidic channel devices. Identification of flap locations enables a map of the target biomolecule to be derived.Type: ApplicationFiled: March 6, 2014Publication date: November 27, 2014Applicant: NABsys, Inc.Inventor: John S. Oliver
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Patent number: 8882980Abstract: Devices and methods for detecting an analyte are provided. Devices for voltage sensing of analytes may comprise a fluidic channel defined in a substrate, a pair of sensing electrodes disposed in a fluidic channel for sensing voltage therein, and a pair of electromotive electrodes for applying potential along the fluidic channel. The pair of sensing electrodes may include a first and second sensing electrode disposed at two discrete locations along the length of the fluidic channel and the pair of electromotive electrodes may be disposed at a first end and a second end of the fluidic channel. The fluidic channel may include a nanochannel or a microchannel.Type: GrantFiled: September 3, 2009Date of Patent: November 11, 2014Assignee: NABsys, Inc.Inventors: Xinsheng Ling, Barrett Bready, John S. Oliver, Maryam Jouzi, Leo Petrossian
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Patent number: 8859201Abstract: A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.Type: GrantFiled: November 9, 2011Date of Patent: October 14, 2014Assignee: NABsys, Inc.Inventor: Peter H. Goldstein
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Publication number: 20140278137Abstract: Techniques for assembly of genetic maps including de novo assembly of distance maps using multiple alignment consensus construction. Multiple map alignment can be performed on a defined bundle of fragment maps corresponding to biomolecule fragments to determine consensus events and corresponding locations. Fragment maps in the bundle can be removed when there is no overhang from the consensus events. When the subset of fragment maps in the bundle is less than a predetermined threshold, one or more additional fragment maps can be added based on fragment signatures, a consensus alignment score, and a pairwise alignment score. Techniques for multiple alignment can include generating a graph with edges and vertices representing each pairwise relation. An ordered set of sets of events best representing a multiple alignment reflecting all pairwise alignments can be generated by repeatedly randomly removing edges and combining vertices to identify a min cut of the graph.Type: ApplicationFiled: March 14, 2014Publication date: September 18, 2014Applicant: NABSYS, INC.Inventors: Peter Goldstein, William Heaton, Franco Preparata, Eli Upfal
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Publication number: 20140272954Abstract: Embodiments of the present invention relate to a method for producing patterns of sequence specific markers on a chromosomal segment. By comparing these patterns to those produced on a reference chromosome, various genetic abnormalities can be detected.Type: ApplicationFiled: March 7, 2014Publication date: September 18, 2014Applicant: NABsys, Inc.Inventors: Stan Rose, Ulrich Broeckel
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Publication number: 20140248183Abstract: Devices for detecting an analyte are provided. Devices for voltage sensing of analytes may comprise a plurality of fluidic channels defined in a substrate, each channel having a pair of sensing electrodes disposed in or adjacent to the fluidic channel and defining a detection volume for sensing voltage therein. At least one pair of electromotive electrodes for applying potential along at least one fluidic channel is provided as well.Type: ApplicationFiled: March 5, 2014Publication date: September 4, 2014Applicant: NABsys, Inc.Inventors: John S. Oliver, Jing Tang
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Publication number: 20140212874Abstract: Methods for enhancing the binding of oligonucleotide probes to DNA and RNA are disclosed. The methods make use of thermodynamic and kinetic effects to reduce probe mismatches and failure of complementary probes to bind to DNA and RNA templates. Mapping and sequencing of the probed DNA and RNA samples are contemplated herein.Type: ApplicationFiled: January 16, 2014Publication date: July 31, 2014Applicant: NABsys, Inc.Inventor: John S. Oliver
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Patent number: 8715933Abstract: Assay methods and apparatus for the analysis of biopolymers are disclosed. The assays employ nicking endonucleases to enable the generation of flaps on target biomolecules which are detected in nanopore or fluidic channel devices. Identification of flap locations enables a map of the target biomolecule to be derived.Type: GrantFiled: September 27, 2010Date of Patent: May 6, 2014Assignee: Nabsys, Inc.Inventor: John S. Oliver
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Publication number: 20140087390Abstract: A protocol and system for determining sites at which proteins directly bind to DNA or RNA, modify other proteins including histones, or bind to other proteins as well as determining sites at which DNA or RNA is modified is described herein. A simplified, highly accurate method for studying protein interactions with DNA or RNA and sites of DNA or RNA modification using nanodetector systems is provided.Type: ApplicationFiled: September 25, 2013Publication date: March 27, 2014Applicant: NABsys, Inc.Inventors: John S. Oliver, John Thompson
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Publication number: 20130026038Abstract: Devices and methods for detecting the length of analytes, and/or sequencing analytes are provided in which two or more electrical signals are obtained as an analyte traverses a fluidic channel. Detection of the relative position of probes hybridized to a biopolymer and/or the length of the analyte (e.g., a biopolymer) does not rely on the absolute time between detection events of a given electrical signal to determine a distance associated with the biopolymer. Instead, multiple signals are obtained as functions of time) corresponding to a plurality of detector volumes at known locations along a fluidic channel through which the biopolymer passes, and the distances are determined from the multiple signals.Type: ApplicationFiled: August 6, 2012Publication date: January 31, 2013Applicant: NABsys, Inc.Inventor: John S. Oliver
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Publication number: 20130011934Abstract: Methods for sequencing a biopolymer by forming local ternary complexes along the length of the double-stranded biopolymer target molecule using one or more probes and obtaining information about the location of the probe(s) using a detector. These methods offer particular advantage when implemented with nanopore (including micropore) detection systems.Type: ApplicationFiled: August 20, 2012Publication date: January 10, 2013Applicant: NABsys, Inc.Inventors: John Oliver, Barrett Bready, Peter Goldstein, Franco Preparata
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Patent number: 8278047Abstract: Methods for sequencing a biopolymer by forming local ternary complexes along the length of the double-stranded biopolymer target molecule using one or more probes and obtaining information about the location of the probe(s) using a detector. These methods offer particular advantage when implemented with nanopore (including micropore) detection systems.Type: GrantFiled: October 1, 2008Date of Patent: October 2, 2012Assignee: Nabsys, Inc.Inventors: John Oliver, Barrett Bready, Peter Goldstein, Franco Preparata
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Patent number: 8262879Abstract: Devices and methods for detecting the length of analytes and/or sequencing analytes are provided in which two or more electrical signals are obtained as an analyte traverses a fluidic channel. Detection of the relative position of probes hybridized to a biopolymer and/or the length of the analyte (e.g., a biopolymer) does not rely on the absolute time between detection events of a given electrical signal to determine a distance associated with the biopolymer. Instead, multiple signals are obtained (e.g., as functions of time) corresponding to a plurality of detector volumes at known locations along a fluidic channel through which the biopolymer passes, and the distances are determined from the multiple signals.Type: GrantFiled: September 3, 2009Date of Patent: September 11, 2012Assignee: Nabsys, Inc.Inventor: John S. Oliver
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Publication number: 20120214162Abstract: Assay methods for preparing a biomolecule analyte includes hybridizing a sequence specific oligonucleotide probe to a biomolecule template and reacting the resulting analyte with a binding moiety.Type: ApplicationFiled: February 10, 2012Publication date: August 23, 2012Applicant: NABSYS, INC.Inventor: John S. Oliver
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Patent number: 8246799Abstract: Devices and methods for detecting the length of analytes and/or sequencing analytes are provided in which two or more electrical signals are obtained as an analyte traverses a nanopore or fluidic channel. Detection of the relative position of probes hybridized to a biomolecule and/or the length of the analyte (e.g., a biomolecule) rely on detection events to determine a distance associated with the biomolecule. Multiple signals may be obtained (e.g., as functions of time) corresponding to a plurality of detector volumes at known locations along a fluidic channel through which the biomolecule passes, and the distances may be determined from the multiple signals.Type: GrantFiled: May 28, 2010Date of Patent: August 21, 2012Assignee: Nabsys, Inc.Inventors: John S. Oliver, Petre Ianakiev
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Publication number: 20120074925Abstract: Assay methods and apparatus for the analysis of biopolymers are disclosed. The assays employ nicking endonucleases to enable the generation of flaps on target biomolecules which are detected in nanopore or fluidic channel devices. Identification of flap locations enables a map of the target biomolecule to be derived.Type: ApplicationFiled: September 27, 2010Publication date: March 29, 2012Applicant: NABsys, Inc.Inventor: John S. Oliver
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Publication number: 20100096268Abstract: Devices and methods for detecting an analyte are provided. Devices for voltage sensing of analytes may comprise a fluidic channel defined in a substrate, a pair of sensing electrodes disposed in a fluidic channel for sensing voltage therein, and a pair of electromotive electrodes for applying potential along the fluidic channel. The pair of sensing electrodes may include a first and second sensing electrode disposed at two discrete locations along the length of the fluidic channel and the pair of electromotive electrodes may be disposed at a first end and a second end of the fluidic channel. The fluidic channel may include a nanochannel or a microchannel.Type: ApplicationFiled: September 3, 2009Publication date: April 22, 2010Applicant: NABsys, Inc.Inventors: Xinsheng Ling, Barrett Bready, John S. Oliver, Maryam Jouzi, Leo Petrossian
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Publication number: 20100078325Abstract: Devices and methods for detecting the length of analytes and/or sequencing analytes are provided in which two or more electrical signals are obtained as an analyte traverses a fluidic channel. Detection of the relative position of probes hybridized to a biopolymer and/or the length of the analyte (e.g., a biopolymer) does not rely on the absolute time between detection events of a given electrical signal to determine a distance associated with the biopolymer. Instead, multiple signals are obtained (e.g., as functions of time) corresponding to a plurality of detector volumes at known locations along a fluidic channel through which the biopolymer passes, and the distances are determined from the multiple signals.Type: ApplicationFiled: September 3, 2009Publication date: April 1, 2010Applicant: NABsys, Inc.Inventor: John S. Oliver