Patents by Inventor Stephen Yue
Stephen Yue 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: 10787573Abstract: 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: GrantFiled: December 4, 2018Date of Patent: September 29, 2020Assignee: 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: 20200299319Abstract: 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: ApplicationFiled: January 31, 2020Publication date: September 24, 2020Applicant: Pacific Biosciences of California, Inc.Inventors: Lubomir SEBO, Honey OSUNA, Stephen YUE, Yuri LAPIN
-
Patent number: 10781483Abstract: 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: GrantFiled: November 21, 2016Date of Patent: September 22, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Lubomir Sebo, Gene Shen, Stephen Yue, Honey Osuna, Yuri Lapin, Louis Brogley, Andrei Fedorov
-
Publication number: 20200256798Abstract: The present invention provides heteroaryl functionalized cyanine dyes including a reactive functional moiety, or which are conjugated to a carrier molecule.Type: ApplicationFiled: September 19, 2019Publication date: August 13, 2020Inventors: Stephen Yue, Gene SHEN, Wei-Chuan (David) SUN
-
Patent number: 10736995Abstract: An intermixed particulate bioresorbable material including cathodic particles and anodic particles bound to each other, wherein the anodic and cathodic particles are made respectively of an anodic and a cathodic material, the anodic and cathodic materials forming a galvanic couple. The anodic and cathodic particles are present in a predetermined ratio and the anodic particles, cathodic particles and predetermined ratio are such that bioresorption of the bioresorbable material is promoted by galvanic corrosion between the anodic and cathodic materials. Also, a medical device, manufactured using the bioresorbable material and a method of manufacturing the bioresorbable material and the medical device.Type: GrantFiled: June 22, 2018Date of Patent: August 11, 2020Assignee: LES ENTREPRISES NANOSTENT INC.Inventors: Rosaire Mongrain, Olivier Francois Bertrand, Stephen Yue
-
Publication number: 20200232023Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.Type: ApplicationFiled: August 20, 2019Publication date: July 23, 2020Inventors: Stephen Yue, Gene SHEN, Wei-Chuan (David) SUN
-
Publication number: 20200224258Abstract: Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.Type: ApplicationFiled: December 9, 2019Publication date: July 16, 2020Inventors: Gene Shen, Natasha Popovich, Erik Miller, Satwik Kamtekar, Keith Bjornson, Jeremiah Hanes, Stephen Yue, Lubomir Sebo, Zhong Wang
-
Patent number: 10676788Abstract: 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: GrantFiled: May 19, 2017Date of Patent: June 9, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Gene Shen, Stephen Yue, Lubomir Sebo, Louis Brogley
-
Patent number: 10669299Abstract: 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: GrantFiled: November 21, 2016Date of Patent: June 2, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Lubomir Sebo, Honey Osuna, Stephen Yue, Yuri Lapin
-
Patent number: 10655168Abstract: Compositions comprising covalently modified and mutated biotin-binding proteins, particularly biotin-binding proteins having a negative charge at physiological pH, are provided. Methods of producing such proteins are also provided, as are methods of immobilizing, sequencing, and making nucleic acids employing such proteins.Type: GrantFiled: December 21, 2018Date of Patent: May 19, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Lubomir Sebo, Leewin Chern, Thomas Linsky, Jeremiah Hanes, Erik Miller, Ying Yang, Stephen Yue
-
Publication number: 20200087722Abstract: 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: ApplicationFiled: June 13, 2019Publication date: March 19, 2020Applicant: Pacific Biosciences of California, Inc.Inventors: Gene SHEN, Stephen YUE, Lubomir SEBO, Louis BROGLEY
-
Patent number: 10544449Abstract: Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.Type: GrantFiled: January 6, 2017Date of Patent: January 28, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Gene Shen, Natasha Popovich, Erik Miller, Satwik Kamtekar, Keith Bjornson, Jeremiah Hanes, Stephen Yue, Lubomir Sebo, Zhong Wang
-
Patent number: 10458915Abstract: The present invention provides heteroaryl functionalized cyanine dyes including a reactive functional moiety, or which are conjugated to a carrier molecule.Type: GrantFiled: May 20, 2013Date of Patent: October 29, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Yue, Gene Shen, Wei-Chuan Sun
-
Publication number: 20190322681Abstract: Biotin derivatives, methods of using the biotin derivatives and kits comprising the biotin derivatives.Type: ApplicationFiled: March 27, 2019Publication date: October 24, 2019Inventors: Lai-Qiang YING, Bruce BRANCHAUD, Yu-Zhong ZHANG, Stephen YUE
-
Publication number: 20190309171Abstract: 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: ApplicationFiled: December 4, 2018Publication date: October 10, 2019Applicant: 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
-
Patent number: 10435741Abstract: 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: GrantFiled: November 18, 2016Date of Patent: October 8, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Yue, Andrei Fedorov, Gene Shen, Sophia Wu
-
Patent number: 10392659Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.Type: GrantFiled: September 12, 2016Date of Patent: August 27, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Yue, Gene Shen, Wei-Chuan (David) Sun
-
Publication number: 20190249237Abstract: Compositions comprising covalently modified and mutated biotin-binding proteins, particularly biotin-binding proteins having a negative charge at physiological pH, are provided. Methods of producing such proteins are also provided, as are methods of immobilizing, sequencing, and making nucleic acids employing such proteins.Type: ApplicationFiled: December 21, 2018Publication date: August 15, 2019Inventors: Satwik Kamtekar, Lubomir Sebo, Leewin Chern, Thomas Linsky, Jeremiah Hanes, Erik Miller, Ying Yang, Stephen Yue
-
Publication number: 20190106742Abstract: 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: ApplicationFiled: October 25, 2018Publication date: April 11, 2019Inventors: Stephen Yue, Andrei Fedorov, Gene Shen, Sophia Wu
-
Patent number: 10150872Abstract: 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: GrantFiled: February 4, 2016Date of Patent: December 11, 2018Assignee: 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