Patents by Inventor Andrei Fedorov

Andrei Fedorov 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: 20190106742
    Abstract: Compositions, devices, systems and methods for increasing the signal to noise ratio (SNR) and/or enhancing photoprotection in an illuminated analytical reaction by addition of one or more signal detection assay (SDA)-enhancing agents to the reaction mixture.
    Type: Application
    Filed: October 25, 2018
    Publication date: April 11, 2019
    Inventors: Stephen Yue, Andrei Fedorov, Gene Shen, Sophia Wu
  • 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
  • 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
  • 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: 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: 9702001
    Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.
    Type: Grant
    Filed: November 3, 2014
    Date of Patent: July 11, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Lubomir Sebo, Stephen Yue, Wei-Chuan Sun, Louis Brogley, Andrei Fedorov
  • Publication number: 20170145494
    Abstract: Compositions, devices, systems and methods for increasing the signal to noise ratio (SNR) and/or enhancing photoprotection in an illuminated analytical reaction by addition of one or more signal detection assay (SDA)-enhancing agents to the reaction mixture.
    Type: Application
    Filed: November 18, 2016
    Publication date: May 25, 2017
    Inventors: Stephen Yue, Andrei Fedorov, Gene Shen, Sophia Wu
  • Publication number: 20170145496
    Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs 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 analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
    Type: Application
    Filed: November 21, 2016
    Publication date: May 25, 2017
    Inventors: Lubomir SEBO, Gene SHEN, Stephen YUE, Honey OSUNA, Yuri LAPIN, Louis BROGLEY, Andrei FEDOROV
  • Patent number: 9650671
    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: March 9, 2015
    Date of Patent: May 16, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Patent number: 9637782
    Abstract: Mitigation of photo-induced damage in excitation illuminated reactions and analyses utilizing such reactions results in an enhanced performance for the reactions and the analyses. There is provided a novel class of triplet-state quenchers for mitigating photo-induced damage which are both simple in structure and effective at preventing and/or reducing photo-induced damage to reaction components of excitation illuminated reaction mixtures. Also provided are methods of using the compounds of the invention, devices and kits incorporating the compounds of the invention.
    Type: Grant
    Filed: September 27, 2013
    Date of Patent: May 2, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Andrei Fedorov, Wei-Chuan Sun, Stephen Yue
  • Patent number: 9575207
    Abstract: An apparatus for providing a signal indicative of a property of an earth formation includes: a carrier conveyable through a borehole; a neutron source disposed on the carrier and configured to emit neutrons into the earth formation; a radiation detector disposed on the carrier and configured to detect radiation from the earth formation due to interaction of emitted neutrons with the earth formation and to provide the signal indicative of the property; and a neutron shield configured to shield the radiation detector from emitted neutrons that did not interact with the earth formation; wherein the radiation detector shield includes a glass ceramic material having a plurality of nano-crystallites, each nano-crystallite in the plurality having a periodic crystal structure with a diameter or dimension that is less than 1000 nm that includes Li and/or Boron and a rare-earth element that have positions in the periodic crystal structure of each nano-crystallite.
    Type: Grant
    Filed: March 7, 2016
    Date of Patent: February 21, 2017
    Assignee: BAKER HUGHES INCORPORATED
    Inventors: Maxim Vasilyev, Valery Khabashesku, Mikhail Korjik, Andrei Fedorov
  • Publication number: 20160237279
    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: Application
    Filed: February 4, 2016
    Publication date: August 18, 2016
    Applicant: 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: 20160070022
    Abstract: An apparatus for estimating a property of an earth formation penetrated by a borehole includes: a carrier configured to be conveyed through the borehole and a gamma-ray detector disposed on the carrier and comprising a scintillation material. The scintillation material includes a barium silicate glass or glass ceramic transparent to light doped with Ce and containing ions of elements with atomic numbers greater than or equal to 55, and having a density greater than 4.5 g/cm3. The apparatus further includes a photodetector optically coupled to the scintillation material and configured to detect light photons emitted from the scintillation and to provide a signal correlated to the detected light photons and a processor configured to estimate the property using the signal.
    Type: Application
    Filed: November 4, 2015
    Publication date: March 10, 2016
    Applicant: BAKER HUGHES INCORPORATED
    Inventors: Valery N. Khabashesku, Maxim Vasilyev, Evgeniy Tretyak, Andrei Fedorov, Mikhail Korjik
  • Publication number: 20150203908
    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: March 9, 2015
    Publication date: July 23, 2015
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Publication number: 20150125854
    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: Application
    Filed: January 6, 2015
    Publication date: May 7, 2015
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Andrei FEDOROV, Stephen YUE, Lei SUN, Gene SHEN, John LYLE
  • Patent number: 8986930
    Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having monovalent cations that control the median pulse width for incorporated nucleotides are disclosed. The levels of alkali metals such as lithium, sodium, potassium, rubidium, and cesium in the polymerization are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.
    Type: Grant
    Filed: July 7, 2011
    Date of Patent: March 24, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Publication number: 20150079603
    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: Application
    Filed: August 11, 2014
    Publication date: March 19, 2015
    Inventors: Stephen Yue, Robert Weber, Xiangxu Kong, Andrei Fedorov, John Lyle