Patents by Inventor John Lyle

John Lyle 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: 10294523
    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: September 23, 2015
    Date of Patent: May 21, 2019
    Assignee: Pacific Biosciences of California, Inc.
    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
  • Patent number: 10184148
    Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.
    Type: Grant
    Filed: April 5, 2017
    Date of Patent: January 22, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Patent number: 10150872
    Abstract: Multimeric protected fluorescent reagents and their methods of synthesis are provided. The reagents are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The reagents contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements. The reagents also contain coupling elements connect monomeric compounds into multimeric forms, thereby increasing brightness.
    Type: Grant
    Filed: February 4, 2016
    Date of Patent: December 11, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Frank Zheng, Jeremiah Hanes, Gene Shen, Louis Brogley, Stephen Yue, Yuri Lapin, John Lyle, Honey Osuna, Andrei Fedorov, Lubomir Sebo
  • Publication number: 20180346507
    Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.
    Type: Application
    Filed: April 30, 2018
    Publication date: December 6, 2018
    Inventors: Lubomir SEBO, Jeremiah HANES, Gene SHEN, Louis BROGLEY, Stephen YUE, Frank ZHENG, Yuri LAPIN, John LYLE, Honey OSUNA, Andrei FEDOROV
  • Publication number: 20180316547
    Abstract: A data system for delivering operational data relating to resource instances in a cloud network includes a plurality of different types of resource instances deployed in the cloud network for a plurality of tenants. Each of the resource instances includes an agent application configured to generate diagnostic log data and metric data for each of the resource instances. A server includes an interface, accessible by the plurality of tenants, configured to create a data service configuration for each of the plurality of tenants. The data service configuration configures storage, streaming and analytic data services for the diagnostic log data and the metric data generated by the resource instances corresponding to each of the plurality of tenants.
    Type: Application
    Filed: April 27, 2017
    Publication date: November 1, 2018
    Applicant: Microsoft Technology Licensing, LLC
    Inventors: Ashwin KAMATH GOVINDA, Jagadish Raghavendra Kulkarni, Andy Shen, Anatoliy Panasyuk, Shrirang Pradip Khisti, John Lyle Kemnetz, Vinicius Canaa Medeiros Ruela
  • Publication number: 20180250222
    Abstract: As people age, the microbiome of human skin changes through processes of selection due both to external and intrinsic factors. While human lifespan is finite determined by the inevitable decay of human cellular and genomic structures, the lifespan and aging of the microbiome is more ecological in nature, driven by selective pressures both connected and unconnected to human's own aging. Through the manipulation of the microbiome, using corollaries of processes used in ecosystem restoration, this invention includes ways, compositions and formulations to restore the microbiome of the skin allowing the skin to be in a more youthful and/or native state and prevent or reverse some of the undesirable appearances of aging. The invention described herein restores a putative ancestral microbiome function and thus protects the skin from damage caused by the UV rays present in sunshine.
    Type: Application
    Filed: February 27, 2018
    Publication date: September 6, 2018
    Inventors: John Lyle, Victor Fung
  • Publication number: 20180237757
    Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.
    Type: Application
    Filed: February 12, 2018
    Publication date: August 23, 2018
    Inventors: David R. Rank, Paul S. Peluso, David K. Hanzel, Geoff Otto, Thang Pham, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
  • Patent number: 10030264
    Abstract: Methods for performing analytical reactions and compositions for use in such methods, where the methods have reduced signal levels deriving from non-specific adsorption of detected reagents to other components of the analytical method, e.g., other reagents, solid phase components, vessels, etc.
    Type: Grant
    Filed: January 6, 2015
    Date of Patent: July 24, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, Stephen Yue, Lei Sun, Gene Shen, John Lyle
  • Patent number: 9957291
    Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.
    Type: Grant
    Filed: August 5, 2014
    Date of Patent: May 1, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lubomir Sebo, Jeremiah Hanes, Gene Shen, Louis Brogley, Stephen Yue, Frank Zheng, Yuri Lapin, John Lyle, Honey Osuna, Andrei Fedorov
  • Patent number: 9951321
    Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogs into active site regions and for coordinating with the nucleotide analogs in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.
    Type: Grant
    Filed: December 6, 2016
    Date of Patent: April 24, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
  • Patent number: 9944980
    Abstract: Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.
    Type: Grant
    Filed: October 31, 2007
    Date of Patent: April 17, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: David R. Rank, Jonas Korlach, Yue Xu, Stephen Turner, Jeffery Wegener, Daniel Roitman, John Lyle
  • Publication number: 20170313756
    Abstract: Provided herein are stable peptide analogs of the native alpha-melanocyte stimulating hormone (?-MSH) having selectivity for the melanocortin 1 receptor (MC1R). Also provided herein are pharmaceutical preparations of the ?-MSH peptide analogs, as well as methods of using these analogs in the treatment of medical and veterinary conditions involving MC1R.
    Type: Application
    Filed: July 10, 2017
    Publication date: November 2, 2017
    Applicant: Genzyme Corporation
    Inventors: Michael A. PERRICONE, John Lyle DZURIS, Timothy E. WEEDEN, James E. STEFANO, Clark Q. PAN, Andrea E. EDLING
  • Patent number: 9776717
    Abstract: An apparatus comprises a base vehicle, a takeoff and landing system, a rack system, a refueling system associated with the base vehicle, and a controller. The rack system comprises a group of racks with slots in which the slots receive unmanned aerial vehicles, provide refueling connections that facilitate refueling of the unmanned aerial vehicles located in the slots, and provide data connections that facilitate data transmission with the unmanned aerial vehicles located in the slots. The refueling system refuels an unmanned aerial vehicle located in a slot using a refueling connection in the refueling connections. The controller communicates with the unmanned aerial vehicle using a data connection and control the refueling of the unmanned aerial vehicles by the refueling system while the unmanned aerial vehicle is in the slot, enabling exchanging data with the unmanned aerial vehicle and the refueling of the unmanned aerial vehicle simultaneously.
    Type: Grant
    Filed: October 2, 2015
    Date of Patent: October 3, 2017
    Assignee: THE BOEING COMPANY
    Inventors: Charles B. Spinelli, John Lyle Vian
  • Publication number: 20170260579
    Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.
    Type: Application
    Filed: April 5, 2017
    Publication date: September 14, 2017
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Patent number: 9738698
    Abstract: Provided herein are stable peptide analogs of the native alpha-melanocyte stimulating hormone (?-MSH) having selectivity for the melanocortin 1 receptor (MC1R). Also provided herein are pharmaceutical preparations of the ?-MSH peptide analogs, as well as methods of using these analogs in the treatment of medical and veterinary conditions involving MC1R.
    Type: Grant
    Filed: August 19, 2015
    Date of Patent: August 22, 2017
    Assignee: GENZYME CORPORATION
    Inventors: Michael A. Perricone, John Lyle Dzuris, Timothy E. Weeden, James E. Stefano, Clark Q. Pan, Andrea E. Edling
  • Patent number: 9732382
    Abstract: Compositions, devices, systems and methods for reducing and/or preventing photo-induced damage of one or more reactants in an illuminated analytical reaction by addition of one or more photoprotective compounds to the reaction mixture and allowing the reaction to proceed for a period that is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: August 11, 2014
    Date of Patent: August 15, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Yue, Robert Weber, Xiangxu Kong, Andrei Fedorov, John Lyle
  • Patent number: 9715235
    Abstract: A method and apparatus for autonomously managing operation of an unmanned aerial vehicle. Sensor data is received by a computer system located onboard the unmanned aerial vehicle. The sensor data is processed by the computer system to generate information of interest related to at least one target, while the unmanned aerial vehicle is out of a communications range of a control station. A number of actions to be performed is identified by the computer system based on the information of interest related to the at least one target, while the unmanned aerial vehicle is out of the communications range of the control station.
    Type: Grant
    Filed: June 5, 2015
    Date of Patent: July 25, 2017
    Assignee: THE BOEING COMPANY
    Inventors: James Statelar McGrew, John Lyle Vian
  • Publication number: 20170152492
    Abstract: Compositions that include polymerases with features for improving entry of nucleotide analogues into active site regions and for coordinating with the nucleotide analogues in the active site region are provided. Methods of making the polymerases and of using the polymerases in sequencing and DNA replication and amplification as well as kinetic models of polymerase activity and computer-implemented methods of using the models are also provided.
    Type: Application
    Filed: December 6, 2016
    Publication date: June 1, 2017
    Inventors: David K. Hanzel, Geoff Otto, Paul S. Peluso, Thang Pham, David R. Rank, Fred Christians, Arekadiusz Bibillo, Insil Park, Sonya Clark, John Lyle
  • Patent number: D819889
    Type: Grant
    Filed: April 6, 2017
    Date of Patent: June 5, 2018
    Inventor: John Lyles
  • Patent number: D835845
    Type: Grant
    Filed: February 16, 2017
    Date of Patent: December 11, 2018
    Inventors: Donald Graves, John Lyles