Patents by Inventor Paul Hardenbol

Paul Hardenbol 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).

  • POLYNUCLEOTIDE BARCODE GENERATION
    Publication number: 20160304860
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Application
    Filed: July 1, 2016
    Publication date: October 20, 2016
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • Processes and Systems for Preparation of Nucleic Acid Sequencing Libraries and Libraries Prepared Using Same
    Publication number: 20160257984
    Abstract: This disclosure provides methods for preparing a sequencing library including the steps of providing a template nucleic acid sequence, dNTPs, dUTP, a primer, a polymerase, a dUTP excising enzyme, and a plurality of beads including oligonucleotide adapter sequence segments; amplifying the template nucleic acid with the polymerase, dNTPs, dUTP and random hexamer to provide a complementary nucleic acid sequence including occasional dUTPs; and excising the incorporated dUTPs with the dUTP excising enzyme to provide nicks in the complementary nucleic acid sequence to provide a sequencing library.
    Type: Application
    Filed: January 7, 2016
    Publication date: September 8, 2016
    Inventors: Paul Hardenbol, Pranav Patel, Benjamin Hindson, Paul William Wyatt, Keith Bjornson, Indira Wu, Kamila Belhocine
  • Methods and systems for processing polynucleotides
    Patent number: 9410201
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Grant
    Filed: April 7, 2015
    Date of Patent: August 9, 2016
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol
  • Polynucleotide barcode generation
    Patent number: 9388465
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Grant
    Filed: February 7, 2014
    Date of Patent: July 12, 2016
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • NANOPORE-BASED NUCLEIC ACID ANALYSIS WITH MIXED FRET DETECTION
    Publication number: 20160076091
    Abstract: Various methods, systems and devices for optical detection and analysis of polymers, such as polynucleotides, using nanopores, e.g., for determining sequences of nucleic acids, are provided herein. In certain variations, methods and systems for determining a nucleotide sequence of a polynucleotide, which include measuring mixed FRET signals as a polynucleotide translocates through a nanopore and determining a nucleotide sequence of the polynucleotide from the mixed FRET signals, are provided.
    Type: Application
    Filed: May 23, 2014
    Publication date: March 17, 2016
    Applicant: Quantapore, Inc.
    Inventors: Martin HUBER, Bason E. CLANCY, Paul HARDENBOL
  • NUCLEIC ACID BINDING PROTEINS AND USES THEREOF
    Publication number: 20160024558
    Abstract: Compositions, systems and methods employing nucleic acid binding proteins for use in the regulation and/or modulation of nucleic acid based reactions, including transcription, translation, modification, digestion, and hybridization reactions. Such compositions are employed in controlling a variety of different reaction types involving nucleic acids.
    Type: Application
    Filed: July 22, 2015
    Publication date: January 28, 2016
    Inventors: Paul Hardenbol, Keith Bjornson
  • Methods of Analyzing Nucleic Acids from Individual Cells or Cell Populations
    Publication number: 20150376609
    Abstract: Methods, compositions and systems for analyzing individual cells or cell populations through the partitioned analysis of contents of individual cells or cell populations. Individual cells or cell populations are co-partitioned with processing reagents for accessing cellular contents, and for uniquely identifying the contents of a given cell or cell population, and subsequently analyzing the cell's contents and characterizing it as having derived from an individual cell or cell population, including analysis and characterization of the cell's nucleic acids through sequencing.
    Type: Application
    Filed: June 26, 2015
    Publication date: December 31, 2015
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov, Paul Hardenbol, Rajiv Bharadwaj, Grace Zheng, Phillip Belgrader
  • Methods and Systems for Processing Polynucleotides
    Publication number: 20150218633
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Application
    Filed: April 7, 2015
    Publication date: August 6, 2015
    Inventors: Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20150005200
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: January 1, 2015
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20150005199
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: January 1, 2015
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20140378350
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: December 25, 2014
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20140378345
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: December 25, 2014
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20140378322
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: December 25, 2014
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING
    Publication number: 20140378349
    Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.
    Type: Application
    Filed: June 26, 2014
    Publication date: December 25, 2014
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Donald Masquelier, Serge Saxonov, Landon Merrill, Andrew Price, Paul Hardenbol, Yuan Li
  • POLYNUCLEOTIDE BARCODE GENERATION
    Publication number: 20140235506
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Application
    Filed: April 11, 2014
    Publication date: August 21, 2014
    Applicant: 10X Technologies, Inc.
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • PARTITIONING AND PROCESSING OF ANALYTES AND OTHER SPECIES
    Publication number: 20140227684
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Application
    Filed: February 7, 2014
    Publication date: August 14, 2014
    Applicant: 10X Technologies, Inc.
    Inventors: Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol, Christopher Hindson, Donald Masquelier, Mima Jarosz, Michael Schnall-Levin
  • POLYNUCLEOTIDE BARCODE GENERATION
    Publication number: 20140228255
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.
    Type: Application
    Filed: February 7, 2014
    Publication date: August 14, 2014
    Applicant: 10X Technologies, Inc.
    Inventors: Benjamin Hindson, Mirna Jarosz, Paul Hardenbol, Michael Schnall-Levin, Kevin Ness, Serge Saxonov
  • Methods and Systems for Processing Polynucleotides
    Publication number: 20140206554
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Application
    Filed: December 12, 2013
    Publication date: July 24, 2014
    Applicant: 10X Technologies, Inc.
    Inventors: Benjamin Hindson, Serge Saxonov, Kevin Ness, Paul Hardenbol
  • Precircle probe nucleic acid amplification methods
    Patent number: 8383348
    Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.
    Type: Grant
    Filed: August 9, 2011
    Date of Patent: February 26, 2013
    Assignee: Board of Trustees of the Leland Stanford Junior University
    Inventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis
  • DIRECT MULTIPLEX CHARACTERIZATION OF GENOMIC DNA
    Publication number: 20120065091
    Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.
    Type: Application
    Filed: August 9, 2011
    Publication date: March 15, 2012
    Inventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis