Patents by Inventor Robin Emig
Robin Emig 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).
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Patent number: 11746338Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: March 3, 2021Date of Patent: September 5, 2023Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee, Molly He, Insil Park
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Publication number: 20210347860Abstract: The disclosure relates generally to the field of immune binding proteins and method for obtaining immune binding proteins from genomic or other sources. The disclosure also relates to anti-SARS-CoV-2 antibodies that have been obtained from subjects who became immune to this coronavirus, and to methods of using these anti-SARS-CoV-2 antibodies. Methods for neutralizing SARS-CoV-2 are disclosed, as well treatments for SARS-COV-2 using the anti-SARS-CoV-2 antibodies.Type: ApplicationFiled: May 9, 2021Publication date: November 11, 2021Applicant: Augmenta Bioworks, Inc.Inventors: Christopher J. Emig, Rosanna Man Wah Chau, Payam Shahi, Kim-Xuan Nguyen, YuShuan Lai, Robin Emig, John Beaber, Steven Henry, Marco Antonio Mena
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Publication number: 20210261928Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: March 3, 2021Publication date: August 26, 2021Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee, Molly He, Insil Park
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Patent number: 10975362Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: November 6, 2018Date of Patent: April 13, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee
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Publication number: 20190249153Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: November 6, 2018Publication date: August 15, 2019Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee, Molly He, Insil Park
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Patent number: 10167455Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: May 16, 2017Date of Patent: January 1, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee
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Patent number: 9996661Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.Type: GrantFiled: December 28, 2010Date of Patent: June 12, 2018Assignee: Codexis Mayflower Holdings, LLCInventors: Claes Gustafsson, Sridhar Govindarajan, Robin A. Emig, Richard John Fox, Ajoy K. Roy, Jeremy S. Minshull, S. Christopher Davis, Anthony R. Cox, Phillip A. Patten, Linda A. Castle, Daniel L. Siehl, Rebecca Lynne Gorton, Teddy Chen
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Publication number: 20170327801Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: May 16, 2017Publication date: November 16, 2017Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee
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Patent number: 9719073Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: March 9, 2015Date of Patent: August 1, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Insil Park, Lei Jia, Molly He, Jeremiah Hanes, Harold Lee, Fred Christians, Satwik Kamtekar, Erik Miller
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Patent number: 9587275Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: GrantFiled: September 8, 2015Date of Patent: March 7, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Lei Jia, Jeremiah Hanes, Lubomir Sebo
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Patent number: 9551028Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.Type: GrantFiled: November 25, 2014Date of Patent: January 24, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig, Stephen Turner
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Patent number: 9447464Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: GrantFiled: November 5, 2013Date of Patent: September 20, 2016Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Lei Jia, Jeremiah Hanes, Lubomir Sebo
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Publication number: 20160010150Abstract: Methods, Compositions, and Systems are provided for nucleic acid sequencing where the sequential incorporation of nucleotides uses two distinct chemical steps. A plurality of nucleotide analogs, each having a labeled leaving group at its 3? hydroxyl can be sequentially added to a growing strand in the presence of a selective cleaving activity that cleaves the 3? hydroxyl leaving group preferentially after it has been incorporated. The selective cleaving agent can comprise an exonuclease activity, and the exonuclease activity can be a polymerase-associated exonuclease activity. Nucleotide analogs having labels on both a cleavable polyphosphate portion and on a 3? hydroxyl leaving group can provide signals characteristic of nucleotide analog incorporation. Systems having illumination optics, collection optics, and substrates observe signals from the labels as they are being incorporated into a growing nucleic acid strand, allowing for the sequencing of template nucleic acids.Type: ApplicationFiled: September 8, 2015Publication date: January 14, 2016Inventors: Robin Emig, Lei Jia, Jeremiah Hanes, Lubomir Sebo
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Patent number: 9200311Abstract: The present invention provides methods and compositions for performing illuminated reactions, particularly sequencing reactions, while mitigating and/or preventing photodamage to reactants that can result from prolonged illumination. In particular, the invention provides methods and compositions for incorporating photoprotective agents into conjugates comprising reporter molecules and nucleoside polyphosphates.Type: GrantFiled: July 1, 2013Date of Patent: December 1, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Geoffrey Otto, Gene Shen, Xiangxu Kong, Robin Emig
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Publication number: 20150240221Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: ApplicationFiled: March 9, 2015Publication date: August 27, 2015Inventors: Robin Emig, Insil Park, Lei Jia, Arek Bibillo, Molly He, Jeremiah Hanes, Harold Lee, Fred Christians, Satwik Kamtekar, Erik Miller
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Publication number: 20150167071Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.Type: ApplicationFiled: November 25, 2014Publication date: June 18, 2015Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig, Stephen Turner
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Patent number: 8999676Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: July 5, 2011Date of Patent: April 7, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Lei Jia, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee
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Patent number: 8986928Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.Type: GrantFiled: April 9, 2010Date of Patent: March 24, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg, Mathieu Foquet, Hans Callebaut, Robert Sebra, Bidhan Chaudhuri, Jon Sorenson, Keith Bjornson, Adrian Fehr, Jonas Korlach, Robin Emig
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Patent number: 8921046Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.Type: GrantFiled: October 12, 2011Date of Patent: December 30, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: Keith Bjornson, Arek Bibillo, Fred Christians, Kevin Travers, Robin Emig, Stephen Turner
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Patent number: 8906831Abstract: Methods for non-random loading of single analyte molecules into array structures are provided. The methods allow for distribution of a population of target molecules into a plurality of size confined regions such as wells. Sizing moieties are linked to individual target molecules. The sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, such that only a selected number of sizing moieties will fit into the size confined regions. The confined regions and the sizing moieties or target molecules comprise a selected charge that allow for controlling the loading of the sizing moities.Type: GrantFiled: March 30, 2009Date of Patent: December 9, 2014Assignee: Pacific Biosciences of California, Inc.Inventors: John Eid, Stephen Turner, Ravi Dalal, Benjamin Flusberg, Jonas Korlach, Steven Lin, Adrian Fehr, Fred Christians, Robin Emig, Jeremy Gray, Robert Sebra, Lei Sun, Stephen Dudek