Patents by Inventor Arkadiusz Bibillo

Arkadiusz Bibillo 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: 20190177706
    Abstract: Described herein are polymerase variants that are exonuclease deficient. Some variants retain the strand displacement capability comparable to the wild-type or parental polymerase. Some variants have a strand displacement capability that is improved relative to the wild-type or parental polymerase. The variants may have an extension rate that is greater than the wild-type or parental polymerase. The variants may have a waiting time that is less than the wild-type or parental polymerase.
    Type: Application
    Filed: February 20, 2019
    Publication date: June 13, 2019
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
  • Patent number: 10308918
    Abstract: Described herein are variant pol6 polymerase having at least having at least two substitutions, wherein at least one of the substitutions is at position S366 of SEQ ID NO: 2. The disclosed polymerases may be coupled to alpha-hemolysin nanopores, and may be used in nanopore-based sequencing apparatuses.
    Type: Grant
    Filed: February 1, 2016
    Date of Patent: June 4, 2019
    Assignees: Roche Molecular Systems, Inc., Genia Technologies, Inc.
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Cleoma Renetta Arnold, Charles Wayan Schwab, Eileen Thai, Ilya Lederman, Colin Alexander McGaw, Tyler O'Brien Shultz, Barbara Eckert, Shawn Suko, Mara Boenitz-Dulat, Bigna Woersdoerfer, David Daniel Wunderlich
  • Publication number: 20190161794
    Abstract: Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.
    Type: Application
    Filed: January 31, 2019
    Publication date: May 30, 2019
    Inventors: Arkadiusz Bibillo, Randall W. Davis
  • Patent number: 10266813
    Abstract: Described herein are polymerase variants that are exonuclease deficient. Some variants retain the strand displacement capability comparable to the wild-type or parental polymerase. Some variants have a strand displacement capability that is improved relative to the wild-type or parental polymerase. The variants may have an extension rate that is greater than the wild-type or parental polymerase. The variants may have a waiting time that is less than the wild-type or parental polymerase.
    Type: Grant
    Filed: February 27, 2017
    Date of Patent: April 23, 2019
    Assignee: Genia Technologies, Inc.
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
  • Publication number: 20190071711
    Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules and cDNA and/or DNA libraries using modified reverse transcriptases.
    Type: Application
    Filed: October 22, 2018
    Publication date: March 7, 2019
    Inventors: Arkadiusz BIBILLO, Pranav PATEL
  • Publication number: 20190040454
    Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules and cDNA and/or DNA libraries using modified reverse transcriptases.
    Type: Application
    Filed: October 23, 2018
    Publication date: February 7, 2019
    Inventors: Arkadiusz Bibillo, Pranav Patel
  • Publication number: 20190040453
    Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules and cDNA and/or DNA libraries using modified reverse transcriptases.
    Type: Application
    Filed: October 23, 2018
    Publication date: February 7, 2019
    Inventors: Arkadiusz Bibillo, Pranav Patel
  • Publication number: 20180340157
    Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.
    Type: Application
    Filed: May 24, 2018
    Publication date: November 29, 2018
    Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS
  • Publication number: 20180030524
    Abstract: This disclosure provides chips, systems and methods for sequencing a nucleic acid sample. Tagged nucleotides are provided into a reaction chamber comprising a nanopore in a membrane. An individual tagged nucleotide of the tagged nucleotides can contain a tag coupled to a nucleotide, which tag is detectable with the aid of the nanopore. Next, an individual tagged nucleotide of the tagged nucleotides can be incorporated into a growing strand complementary to a single stranded nucleic acid molecule derived from the nucleic acid sample. With the aid of the nanopore, a tag associated with the individual tagged nucleotide can be detected upon incorporation of the individual tagged nucleotide. The tag can be detected with the aid of the nanopore when the tag is released from the nucleotide.
    Type: Application
    Filed: March 27, 2017
    Publication date: February 1, 2018
    Inventors: Randall Davis, Roger Chen, Arkadiusz Bibillo, Daniel Korenblum
  • Publication number: 20170267983
    Abstract: Described herein are polymerase variants that are exonuclease deficient. Some variants retain the strand displacement capability comparable to the wild-type or parental polymerase. Some variants have a strand displacement capability that is improved relative to the wild-type or parental polymerase. The variants may have an extension rate that is greater than the wild-type or parental polymerase. The variants may have a waiting time that is less than the wild-type or parental polymerase.
    Type: Application
    Filed: February 27, 2017
    Publication date: September 21, 2017
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
  • Patent number: 9605309
    Abstract: This disclosure provides chips, systems and methods for sequencing a nucleic acid sample. Tagged nucleotides are provided into a reaction chamber comprising a nanopore in a membrane. An individual tagged nucleotide of the tagged nucleotides can contain a tag coupled to a nucleotide, which tag is detectable with the aid of the nanopore. Next, an individual tagged nucleotide of the tagged nucleotides can be incorporated into a growing strand complementary to a single stranded nucleic acid molecule derived from the nucleic acid sample. With the aid of the nanopore, a tag associated with the individual tagged nucleotide can be detected upon incorporation of the individual tagged nucleotide. The tag can be detected with the aid of the nanopore when the tag is released from the nucleotide.
    Type: Grant
    Filed: November 6, 2013
    Date of Patent: March 28, 2017
    Assignee: Genia Technologies, Inc.
    Inventors: Randall Davis, Roger Chen, Arkadiusz Bibillo, Daniel Korenblum
  • Patent number: 9494554
    Abstract: The present disclosure provides devices, systems and methods for sequencing nucleic acid molecules. Nucleic acid molecules can be sequenced with a high accuracy (e.g., greater than 97% in a single pass) using a chip comprising an array of independently addressable nanopore sensors at a density of at least about 500 sites per 1 mm2. An individual nanopore sensor can include a nanopore in a membrane that is adjacent or in proximity to a sensing electrode.
    Type: Grant
    Filed: June 14, 2013
    Date of Patent: November 15, 2016
    Assignee: Genia Technologies, Inc.
    Inventors: Randall Davis, Roger Chen, Arkadiusz Bibillo, Kevin Deierling
  • Publication number: 20160222363
    Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365Q, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.
    Type: Application
    Filed: February 1, 2016
    Publication date: August 4, 2016
    Inventors: Aruna AYER, Arkadiusz BIBILLO, Cleoma Renetta ARNOLD, Charles Wayan SCHWAB, Eileen THAI, Ilya LEDERMAN, Colin Alexander MCGAW, Tyler O'Brien SHULTZ, Barbara ECKERT, Shawn SUKO, Mara BOENITZ-DULAT, Bigna WOERSDOERFER, David Daniel WUNDERLICH
  • Publication number: 20140134616
    Abstract: This disclosure provides chips, systems and methods for sequencing a nucleic acid sample. Tagged nucleotides are provided into a reaction chamber comprising a nanopore in a membrane. An individual tagged nucleotide of the tagged nucleotides can contain a tag coupled to a nucleotide, which tag is detectable with the aid of the nanopore. Next, an individual tagged nucleotide of the tagged nucleotides can be incorporated into a growing strand complementary to a single stranded nucleic acid molecule derived from the nucleic acid sample. With the aid of the nanopore, a tag associated with the individual tagged nucleotide can be detected upon incorporation of the individual tagged nucleotide. The tag can be detected with the aid of the nanopore when the tag is released from the nucleotide.
    Type: Application
    Filed: November 6, 2013
    Publication date: May 15, 2014
    Applicant: Genia Technologies, Inc.
    Inventors: Randall Davis, Roger Chen, Arkadiusz Bibillo, Daniel Korenblum, Michael Dorwart
  • Publication number: 20140034497
    Abstract: The present disclosure provides devices, systems and methods for sequencing nucleic acid molecules. Nucleic acid molecules can be sequenced with a high accuracy (e.g., greater than 97% in a single pass) using a chip comprising an array of independently addressable nanopore sensors at a density of at least about 500 sites per 1 mm2. An individual nanopore sensor can include a nanopore in a membrane that is adjacent or in proximity to a sensing electrode.
    Type: Application
    Filed: June 14, 2013
    Publication date: February 6, 2014
    Applicant: Genia Technologies, Inc.
    Inventors: Randall Davis, Roger Chen, Arkadiusz Bibillo, Kevin Deierling
  • Patent number: 8530164
    Abstract: Provided are methods for enhanced sequencing of nucleic acid templates. Also provided are reaction conditions that increase branching fractions during polymerization reactions. Also provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are higher than the branching fractions of the polymerases from which they were derived. Provided are compositions comprising modified recombinant polymerases that exhibit delayed translocation relative to the polymerases from which they were derived. Also provided are compositions comprising modified recombinant polymerases that exhibit increased nucleotide or nucleotide analog residence time at an active site of the polymerase. Provided are methods for generating polymerases with the aforementioned phenotypes and methods of using such polymerases to sequence a DNA template or make a DNA.
    Type: Grant
    Filed: September 4, 2009
    Date of Patent: September 10, 2013
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Pranav Patel, Jonas Korlach, Arkadiusz Bibillo, Keith Bjornson, Jeremiah Hanes
  • Publication number: 20100075332
    Abstract: Provided are methods for enhanced sequencing of nucleic acid templates. Also provided are reaction conditions that increase branching fractions during polymerization reactions. Also provided are compositions comprising modified recombinant polymerases that exhibit branching fractions that are higher than the branching fractions of the polymerases from which they were derived. Provided are compositions comprising modified recombinant polymerases that exhibit delayed translocation relative to the polymerases from which they were derived. Also provided are compositions comprising modified recombinant polymerases that exhibit increased nucleotide or nucleotide analog residence time at an active site of the polymerase. Provided are methods for generating polymerases with the aforementioned phenotypes and methods of using such polymerases to sequence a DNA template or make a DNA.
    Type: Application
    Filed: September 4, 2009
    Publication date: March 25, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Pranav Patel, Jonas Korlach, Arkadiusz Bibillo, Keith Bjornson, Jeremiah Hanes
  • Patent number: 7153672
    Abstract: The present invention relates to a method of preparing a cDNA molecule which includes: contacting an RNA molecule, in the presence of dNTPs, with a non-LTR retrotransposon protein or polypeptide having reverse transcriptase activity under conditions effective for production of a cDNA molecule complementary to the RNA molecule, the contacting being carried out in the absence of a target DNA molecule of the non-LTR retrotransposon protein or polypeptide; and isolating the cDNA molecule. The preferred non-LTR retrotransposon protein or polypeptide is an R2 protein or polypeptide.
    Type: Grant
    Filed: August 30, 2001
    Date of Patent: December 26, 2006
    Assignee: University of Rochester
    Inventors: Thomas H. Eickbush, Arkadiusz Bibillo
  • Publication number: 20060281079
    Abstract: The present invention relates to a method of preparing a cDNA molecule which includes: contacting an RNA molecule, in the presence of dNTPs, with a non-LTR retrotransposon protein or polypeptide having reverse transcriptase activity under conditions effective for production of a cDNA molecule complementary to the RNA molecule, said contacting being carried out in the absence of a target DNA molecule of the non-LTR retrotransporon protein or polypeptide; and isolating the cDNA molecule.
    Type: Application
    Filed: August 30, 2001
    Publication date: December 14, 2006
    Inventors: Thomas Eickbush, Arkadiusz Bibillo