Patents by Inventor John Vieceli
John Vieceli 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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Publication number: 20230151420Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: ApplicationFiled: July 29, 2022Publication date: May 18, 2023Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
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Patent number: 11447823Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: GrantFiled: April 9, 2020Date of Patent: September 20, 2022Assignee: Pacific Biosciences of California, Inc.Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
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Publication number: 20200347451Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: ApplicationFiled: April 9, 2020Publication date: November 5, 2020Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
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Patent number: 10655176Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: GrantFiled: October 8, 2018Date of Patent: May 19, 2020Assignee: OMNIOME, INC.Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
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Publication number: 20200080142Abstract: Disclosed is a system for determining the nucleotide sequence of polynucleotides. The system can comprise a light source, such as a laser or a LED, configured to generate light at a predetermined wavelength. A detector of the system can detect fluorescent emissions at a first wavelength and a second wavelength. A processor of the system identify the nucleotide as a first type if no fluorescent emission is detected by the at least one detector; identify the nucleotide as a second type if a fluorescent emission at the first wavelength of light is detected by the at least one detector; identify the nucleotide as a third type if a fluorescent emission at the second wavelength of light is detected by the at least one detector; and identify the nucleotide as a fourth type if fluorescent emissions at the first wavelength and the second wavelength of light are detected by the at least one detector.Type: ApplicationFiled: March 6, 2018Publication date: March 12, 2020Applicants: Illumina, Inc., Illumina Cambridge LimitedInventors: Robert LANGLOIS, John VIECELI, Xiaohai LIU
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Publication number: 20190338352Abstract: A method of determining nucleic acid sequences can include steps of (a) obtaining signal data from a nucleic acid sequencing procedure carried out on an array of nucleic acid features; (b) extracting signals from each nucleic acid feature to produce multiple extracted signal traces that each correlate signal characteristics with sequencing cycle for a particular nucleotide type at a particular nucleic acid feature; (c) comparing the series of signals for different nucleotide types at each of the features to distinguish a candidate base call from background signals for each cycle at each feature; (d) applying a baseline adjustment to each series of signals based on the extracted background signals; and (e) comparing the adjusted signal traces for different nucleotide types at each of the features, thereby distinguishing adjusted signals having characteristics of a base call from adjusted background signals for each cycle at each feature.Type: ApplicationFiled: March 21, 2019Publication date: November 7, 2019Applicant: Omniome, Inc.Inventors: Alex NEMIROSKI, Sean STROMBERG, John VIECELI
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Publication number: 20190169688Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: ApplicationFiled: October 8, 2018Publication date: June 6, 2019Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
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Patent number: 10161003Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: GrantFiled: March 15, 2018Date of Patent: December 25, 2018Assignee: Omniome, Inc.Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
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Publication number: 20180305749Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.Type: ApplicationFiled: March 15, 2018Publication date: October 25, 2018Inventors: Sean Stromberg, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
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Publication number: 20120034602Abstract: 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: July 5, 2011Publication date: February 9, 2012Applicant: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Insil Park, Lei Jia, Arek Bibillo, Keith Bjornson, Molly He, Jeremiah Hanes, Harold Lee, Sonya Clark, Fred Christians, Paul Peluso, John Vieceli, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee