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).
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Publication number: 20240124856Abstract: 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: ApplicationFiled: August 14, 2023Publication date: April 18, 2024Inventors: Arkadiusz Bibillo, Pranav Patel
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Publication number: 20240026316Abstract: 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: ApplicationFiled: July 7, 2023Publication date: January 25, 2024Inventors: Arkadiusz Bibillo, Pranav Patel
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Publication number: 20230366005Abstract: Methods, systems, and devices for sampling/isolating material from cells. An exemplary system may comprise a chip including an electrode array of sampling electrodes arranged along a surface of the chip. A cell-receiving area may be located adjacent the surface of the chip. The system also may comprise a tag array of tags supported by the chip and aligned with the electrode array. Each tag of the tag array may include an identifier that is unique to the tag within the tag array. Each tag may be configured to bind nucleic acids, or a capturing agent distinct from the tag may be aligned with each sampling electrode of the electrode array to capture a protein or other analyte of interest. The system further may comprise a control circuit configured to apply an individually controllable voltage to each sampling electrode of the electrode array and measure an electrical property of the sampling electrode.Type: ApplicationFiled: January 2, 2023Publication date: November 16, 2023Applicant: Bio-Rad Laboratories, Inc.Inventors: Arkadiusz BIBILLO, Pranav PATEL, Christopher REGGIARDO, Jonathan Petersen
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Patent number: 11802276Abstract: 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: GrantFiled: May 24, 2018Date of Patent: October 31, 2023Assignee: Roche Sequencing Solutions, Inc.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
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Patent number: 11746337Abstract: 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: GrantFiled: May 11, 2020Date of Patent: September 5, 2023Assignee: Roche Sequencing Solutions, Inc.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
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Patent number: 11739307Abstract: 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 ad cDNA and/or DNA libraries using modified reverse transcriptases.Type: GrantFiled: May 16, 2019Date of Patent: August 29, 2023Assignee: BIO-RAD LABORATORIES, INC.Inventors: Arkadiusz Bibillo, Pranav Patel
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Patent number: 11718836Abstract: 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: GrantFiled: February 5, 2021Date of Patent: August 8, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
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Publication number: 20230074210Abstract: 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: ApplicationFiled: October 26, 2022Publication date: March 9, 2023Inventors: Arkadiusz Bibillo, Randall W. Davis
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Patent number: 11542541Abstract: Methods, systems, and devices for sampling/isolating material from cells. An exemplary system may comprise a chip including an electrode array of sampling electrodes arranged along a surface of the chip. A cell-receiving area may be located adjacent the surface of the chip. The system also may comprise a tag array of tags supported by the chip and aligned with the electrode array. Each tag of the tag array may include an identifier that is unique to the tag within the tag array. Each tag may be configured to bind nucleic acids, or a capturing agent distinct from the tag may be aligned with each sampling electrode of the electrode array to capture a protein or other analyte of interest. The system further may comprise a control circuit configured to apply an individually controllable voltage to each sampling electrode of the electrode array and measure an electrical property of the sampling electrode.Type: GrantFiled: November 25, 2020Date of Patent: January 3, 2023Assignee: Bio-Rad Laboratories, Inc.Inventors: Arkadiusz Bibillo, Pranav Patel, Christopher Reggiardo, Jonathan Petersen
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Patent number: 11525124Abstract: 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: GrantFiled: May 11, 2020Date of Patent: December 13, 2022Assignee: Roche Sequencing Solutions, Inc.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
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Patent number: 11519026Abstract: 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: GrantFiled: January 31, 2019Date of Patent: December 6, 2022Assignee: Roche Sequencing Solutions, inc.Inventors: Arkadiusz Bibillo, Randall W. Davis
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Patent number: 11499190Abstract: 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: GrantFiled: May 29, 2020Date of Patent: November 15, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: Randall W. Davis, Roger J. A. Chen, Arkadiusz Bibillo, Daniel Korenblum
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Publication number: 20220235395Abstract: 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: ApplicationFiled: August 30, 2021Publication date: July 28, 2022Inventors: Arkadiusz Bibillo, Pranav Patel
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Patent number: 11104943Abstract: 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: GrantFiled: October 22, 2018Date of Patent: August 31, 2021Assignee: Bio-Rad Laboratories, Inc.Inventors: Arkadiusz Bibillo, Pranav Patel
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Publication number: 20210207109Abstract: 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 ad cDNA and/or DNA libraries using modified reverse transcriptases.Type: ApplicationFiled: May 16, 2019Publication date: July 8, 2021Inventors: Arkadiusz Bibillo, Pranav Patel
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Publication number: 20210189356Abstract: 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: ApplicationFiled: March 5, 2021Publication date: June 24, 2021Inventors: Aruna Ayer, Cleoma Renetta Arnold, Arkadiusz Bibillo, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin Alexander McGaw, Charles Wayan Schwab, Tyler O'Brien Shultz, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Daniel Wunderlich
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Publication number: 20210163904Abstract: 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: ApplicationFiled: February 5, 2021Publication date: June 3, 2021Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
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Publication number: 20210155975Abstract: Methods, systems, and devices for sampling/isolating material from cells. An exemplary system may comprise a chip including an electrode array of sampling electrodes arranged along a surface of the chip. A cell-receiving area may be located adjacent the surface of the chip. The system also may comprise a tag array of tags supported by the chip and aligned with the electrode array. Each tag of the tag array may include an identifier that is unique to the tag within the tag array. Each tag may be configured to bind nucleic acids, or a capturing agent distinct from the tag may be aligned with each sampling electrode of the electrode array to capture a protein or other analyte of interest. The system further may comprise a control circuit configured to apply an individually controllable voltage to each sampling electrode of the electrode array and measure an electrical property of the sampling electrode.Type: ApplicationFiled: November 25, 2020Publication date: May 27, 2021Applicant: Bio-Rad Laboratories, Inc.Inventors: Arkadiusz BIBILLO, Pranav PATEL, Christopher REGGIARDO, Jonathan PETERSEN
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Patent number: 10961520Abstract: 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: GrantFiled: February 26, 2020Date of Patent: March 30, 2021Assignees: Roche Molecular Systems, Inc., Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Cleoma Renetta Arnold, Arkadiusz Bibillo, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin Alexander McGaw, Charles Wayan Schwab, Tyler O'Brien Shultz, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Daniel Wunderlich
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Patent number: 10954557Abstract: 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: GrantFiled: October 23, 2018Date of Patent: March 23, 2021Assignee: Bio-Rad Laboratories, Inc.Inventors: Arkadiusz Bibillo, Pranav Patel