Patents by Inventor Patrick Marks

Patrick Marks 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: 20190065678
    Abstract: Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.
    Type: Application
    Filed: August 31, 2017
    Publication date: February 28, 2019
    Inventors: Sofia Kyriazopoulou-Panagiotopoulou, Patrick Marks
  • Publication number: 20190065664
    Abstract: Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for events by calculating a plurality of event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.
    Type: Application
    Filed: December 14, 2017
    Publication date: February 28, 2019
    Inventors: Sofia Kyriazopoulou-Panagiotopoulou, Patrick Marks
  • Patent number: 10184764
    Abstract: A munition is rendered less sensitive to inadvertent initiations by providing a polymer liner on the entire inside surface of the munition. A thermoplastic liner may be fabricated totally within an empty inert munition casing by spraying a layer of electrostatically charged low melt thermoplastic material particles over substantially the entire inside surfaces of the munition casing, which casing is first electrically grounded. After thickening the particle layer through heat, further such layers may be then applied there over, until a desired cumulative thickness liner is fabricated.
    Type: Grant
    Filed: February 13, 2017
    Date of Patent: January 22, 2019
    Assignee: The United States of America as Represented by the Secretary of the Army
    Inventors: Patrick Mark, Daniel Lee Prillaman, Leon Moy
  • Publication number: 20180267534
    Abstract: A system and method for assisted EVA self-return is provided herein. The system estimates a crewmember's navigation state relative to a fixed location, for example on an accompanying orbiting spacecraft, and computes a guidance trajectory for returning the crewmember to that fixed location. The system may account for safety and clearance requirements while computing the guidance trajectory. According to at least one embodiment, the system provides a directional cue (e.g., a visual, auditory, or tactile cue) to a crewmember corresponding to the prescribed trajectory back to the fixed location. The system may be activated by the crewmember or remotely by another crewmember and/or system.
    Type: Application
    Filed: May 17, 2018
    Publication date: September 20, 2018
    Inventors: Kevin R. Duda, Richard W. Loffi, Patrick Mark Handley
  • Publication number: 20180265928
    Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
    Type: Application
    Filed: May 21, 2018
    Publication date: September 20, 2018
    Inventors: Michael Schnall-Levin, Mirna Jarosz, Christopher Hindson, Kevin Ness, Serge Saxonov, Benjamin Hindson, Xinying Zheng, Patrick Marks, John Stuelpnagel
  • Publication number: 20180267533
    Abstract: A system and method for assisted EVA self-return is provided herein. The system estimates a crewmember's navigation state relative to a fixed location, for example on an accompanying orbiting spacecraft, and computes a guidance trajectory for returning the crewmember to that fixed location. The system may account for safety and clearance requirements while computing the guidance trajectory. According to at least one embodiment, the system actuates the crewmember's safety jetpack to follow the prescribed trajectory to the fixed location.
    Type: Application
    Filed: May 17, 2018
    Publication date: September 20, 2018
    Inventors: Kevin R. Duda, Richard W. Loffi, Patrick Mark Handley
  • Patent number: 10023911
    Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof.
    Type: Grant
    Filed: October 13, 2015
    Date of Patent: July 17, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
  • Patent number: 9977427
    Abstract: A system and method for assisted EVA self-return is provided herein. The system estimates a crewmember's navigation state relative to a fixed location, for example on an accompanying orbiting spacecraft, and computes a guidance trajectory for returning the crewmember to that fixed location. The system may account for safety and clearance requirements while computing the guidance trajectory. According to at least one embodiment, the system actuates the crewmember's safety jetpack to follow the prescribed trajectory to the fixed location. In another embodiment, the system provides the crewmember with a directional cue (e.g., a visual, auditory, or tactile cue) corresponding to the prescribed trajectory back to the fixed location. The system may be activated by the crewmember or remotely by another crewmember and/or system.
    Type: Grant
    Filed: May 25, 2016
    Date of Patent: May 22, 2018
    Assignee: THE CHARLES STARK DRAPER LABORATORY, INC.
    Inventors: Kevin R. Duda, Richard W. Loffi, Patrick Mark Handley
  • Publication number: 20170235876
    Abstract: Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.
    Type: Application
    Filed: August 19, 2016
    Publication date: August 17, 2017
    Inventors: David Jaffe, Patrick Marks, Michael Schnall-Levin, Neil Weisenfeld
  • Publication number: 20170192425
    Abstract: A system and method for assisted EVA self-return is provided herein. The system estimates a crewmember's navigation state relative to a fixed location, for example on an accompanying orbiting spacecraft, and computes a guidance trajectory for returning the crewmember to that fixed location. The system may account for safety and clearance requirements while computing the guidance trajectory. According to at least one embodiment, the system actuates the crewmember's safety jetpack to follow the prescribed trajectory to the fixed location. In another embodiment, the system provides the crewmember with a directional cue (e.g., a visual, auditory, or tactile cue) corresponding to the prescribed trajectory back to the fixed location. The system may be activated by the crewmember or remotely by another crewmember and/or system.
    Type: Application
    Filed: May 25, 2016
    Publication date: July 6, 2017
    Inventors: Kevin R. Duda, Richard W. Loffi, Patrick Mark Handley
  • Publication number: 20170124473
    Abstract: A method for providing an interactive interface for live event outcome selection and prediction may include generating a set of cells for an event. The set of cells may be provided to a client device to present in a user interface. A selection of a cell may be received from the client device. The selected cell may be assigned to a user account. The method may generate a coordinate for each cell in the set, wherein each cell coordinate includes a plurality of dimensions, each dimension corresponding to a different entity of the event, and wherein each cell coordinate is unique for the set of cells. The method may comprise calculating, prior to the start of the event, a probability that an event result represented by a cell coordinate will occur; and presenting the probability in association with the cell on the user interface. Other embodiments are described and claimed.
    Type: Application
    Filed: October 30, 2015
    Publication date: May 4, 2017
    Inventors: Leonard Michael Lopez, Carlos Javier Carbonell Di Mola, Raymond Solebello, Christian J Soblotne, Patrick Mark Quinlivan
  • Publication number: 20160232291
    Abstract: Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.
    Type: Application
    Filed: February 9, 2016
    Publication date: August 11, 2016
    Inventors: Sofia Kyriazopoulou-Panagiotopoulou, Patrick Marks, Michael Schnall-Levin, Xinying Zheng, Mirna Jarosz, Serge Saxonov, Kristina Giorda, Patrice Mudivarti, Heather Ordonez, Jessica Terry, William Haynes Heaton
  • Publication number: 20160153038
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Application
    Filed: September 23, 2015
    Publication date: June 2, 2016
    Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
  • Publication number: 20160097093
    Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g.
    Type: Application
    Filed: October 13, 2015
    Publication date: April 7, 2016
    Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
  • Publication number: 20150376700
    Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
    Type: Application
    Filed: June 26, 2015
    Publication date: December 31, 2015
    Inventors: Michael Schnall-Levin, Mirna Jarosz, Christopher Hindson, Kevin Ness, Serge Saxonov, Benjamin Hindson, Grace X. Y. Zheng, Patrick Marks, John Stuelpnagel
  • Patent number: 9175343
    Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof.
    Type: Grant
    Filed: March 6, 2014
    Date of Patent: November 3, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
  • Patent number: 9175338
    Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
    Type: Grant
    Filed: November 12, 2010
    Date of Patent: November 3, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes, Joseph Puglisi
  • Publication number: 20140303016
    Abstract: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof.
    Type: Application
    Filed: March 6, 2014
    Publication date: October 9, 2014
    Applicant: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventors: Austin B. Tomaney, Kenneth Mark Maxham, David Holden, Kevin Hester, Devon Murphy, Patrick Marks
  • Patent number: 8803066
    Abstract: An imaging device suitable for detecting certain imaging particles and recording the detection of imaging particles, and as such can include certain recording devices such as a charge storage structure.
    Type: Grant
    Filed: July 24, 2012
    Date of Patent: August 12, 2014
    Assignee: Spansion LLC
    Inventors: Timothy Z. Hossain, Patrick Mark Clopton, Clayton Fullwood, Dan E. Posey
  • Patent number: 8748800
    Abstract: Systems and methods are described herein for detecting particles emitted by nuclear material. The systems comprise one or more semiconductor devices for detecting particles emitted from nuclear material. The semiconductor devices can comprise a charge storage element comprising several layers. A non-conductive charge storage layer enveloped on top and bottom by dielectric layers is mounted on a substrate. At least one top semiconductor layer can be placed on top of the top dielectric layer. A reactive material that reacts to particles, such as neutrons emitted from nuclear material, can be incorporated into the top semiconductor layer. When the reactive material reacts to a particle emitted from nuclear material, ions are generated that can alter the charge storage layer and enable detection of the particle.
    Type: Grant
    Filed: March 5, 2013
    Date of Patent: June 10, 2014
    Assignee: Spansion LLC
    Inventors: Timothy Z. Hossain, Patrick Mark Clopton, Christopher Foster, Christopher F. Lyons, Clayton Fulwood, Greg Alan Goodwin, Dan E. Posey