Patents by Inventor Bala Murali Venkatesan

Bala Murali Venkatesan 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: 20220243261
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: January 13, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220098653
    Abstract: Structured substrate including (a) a plurality of nanoparticles distributed on a solid support, (b) a gel material forming a layer in association with the plurality of nanoparticles, and (c) a library of target nucleic acids in the gel material.
    Type: Application
    Filed: December 10, 2021
    Publication date: March 31, 2022
    Inventors: M. Shane Bowen, Bala Murali Venkatesan, Hui Han, Sang Ryul Park
  • Patent number: 11254976
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: February 22, 2022
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20210402749
    Abstract: Embodiments of the present application relate to patterned polymer sheets and processes to prepare the same for sequencing applications. In particular, flexible micro- and nano-patterned polymer sheets are prepared and used as a template surface in sequencing reaction and new polish-free methods of forming isolated hydrogel plugs in nanowells are described.
    Type: Application
    Filed: June 8, 2021
    Publication date: December 30, 2021
    Inventors: Bala Murali Venkatesan, Kenny Chen, Steven M. Barnard
  • Publication number: 20210379585
    Abstract: A method of making a flowcell includes bonding a first surface of an organic solid support to a surface of a first inorganic solid support via a first bonding layer, wherein the organic solid support includes a plurality of elongated cutouts. The method further includes bonding a surface of a second inorganic solid support to a second surface of the organic solid support via a second bonding layer, so as to form the flowcell. The formed flowcell includes a plurality of channels defined by the surface of the first inorganic solid support, the surface of the second inorganic solid support, and walls of the elongated cutouts.
    Type: Application
    Filed: August 24, 2021
    Publication date: December 9, 2021
    Inventors: Jeffrey S. Fisher, John A. Moon, Bala Murali Venkatesan
  • Publication number: 20210379858
    Abstract: Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.
    Type: Application
    Filed: August 23, 2021
    Publication date: December 9, 2021
    Inventors: M. Shane Bowen, Bala Murali Venkatesan, Steven M. Barnard
  • Patent number: 11110452
    Abstract: A method of making a flowcell includes bonding a first surface of an organic solid support to a surface of a first inorganic solid support via a first bonding layer, wherein the organic solid support includes a plurality of elongated cutouts. The method further includes bonding a surface of a second inorganic solid support to a second surface of the organic solid support via a second bonding layer, so as to form the flowcell. The formed flowcell includes a plurality of channels defined by the surface of the first inorganic solid support, the surface of the second inorganic solid support, and walls of the elongated cutouts.
    Type: Grant
    Filed: July 3, 2018
    Date of Patent: September 7, 2021
    Assignee: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, John A. Moon, Bala Murali Venkatesan
  • Patent number: 11110683
    Abstract: Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.
    Type: Grant
    Filed: May 21, 2020
    Date of Patent: September 7, 2021
    Assignee: ILLUMINA, INC.
    Inventors: M. Shane Bowen, Bala Murali Venkatesan, Steven M. Barnard
  • Patent number: 11060135
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Grant
    Filed: August 30, 2018
    Date of Patent: July 13, 2021
    Assignee: Illumina, Inc.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20210130885
    Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.
    Type: Application
    Filed: January 11, 2021
    Publication date: May 6, 2021
    Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
  • Publication number: 20210108258
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Application
    Filed: December 7, 2020
    Publication date: April 15, 2021
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Patent number: 10913975
    Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.
    Type: Grant
    Filed: July 21, 2016
    Date of Patent: February 9, 2021
    Assignee: Illumina, Inc.
    Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
  • Patent number: 10807089
    Abstract: A fluidic device including an inorganic solid support attached to an organic solid support by a bonding layer, wherein the inorganic solid support has a rigid structure and wherein the bonding layer includes a material that absorbs radiation at a wavelength that is transmitted by the inorganic solid support or the organic solid support; and a channel formed by the inorganic solid support and the organic solid support, wherein the bonding layer that attaches the inorganic solid support to the organic solid support provides a seal against liquid flow. Methods for making fluidic devices, such as this, are also provided.
    Type: Grant
    Filed: February 22, 2018
    Date of Patent: October 20, 2020
    Assignee: ILLUMINA, INC.
    Inventors: Jeffrey S. Fisher, John A. Moon, Bala Murali Venkatesan
  • Publication number: 20200282693
    Abstract: Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.
    Type: Application
    Filed: May 21, 2020
    Publication date: September 10, 2020
    Inventors: M. Shane Bowen, Bala Murali Venkatesan, Steven M. Barnard
  • Patent number: 10682829
    Abstract: Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.
    Type: Grant
    Filed: December 17, 2014
    Date of Patent: June 16, 2020
    Assignee: ILLUMINA, INC.
    Inventors: M. Shane Bowen, Bala Murali Venkatesan, Steven M. Barnard
  • Publication number: 20200040386
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: August 19, 2019
    Publication date: February 6, 2020
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Patent number: 10385384
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 8, 2017
    Date of Patent: August 20, 2019
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20190178840
    Abstract: Provided herein are methods and devices for characterizing a biomolecule parameter by a nanopore-containing membrane, and also methods for making devices that can be used in the methods and devices provided herein. The nanopore membrane is a multilayer stack of conducting layers and dielectric layers, wherein an embedded conducting layer or conducting layer gates provides well-controlled and measurable electric fields in and around the nanopore through which the biomolecule translocates. In an aspect, the conducting layer is graphene.
    Type: Application
    Filed: August 31, 2018
    Publication date: June 13, 2019
    Inventors: Rashid BASHIR, Bala Murali VENKATESAN
  • Patent number: 10280454
    Abstract: A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.
    Type: Grant
    Filed: March 27, 2017
    Date of Patent: May 7, 2019
    Assignee: ILLUMINA, INC.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Patent number: 10175195
    Abstract: Provided herein are methods and devices for characterizing a biomolecule parameter by a nanopore-containing membrane, and also methods for making devices that can be used in the methods and devices provided herein. The nanopore membrane is a multilayer stack of conducting layers and dielectric layers, wherein an embedded conducting layer or conducting layer gates provides well-controlled and measurable electric fields in and around the nanopore through which the biomolecule translocates. In an aspect, the conducting layer is graphene.
    Type: Grant
    Filed: July 26, 2012
    Date of Patent: January 8, 2019
    Assignee: The Board of Trustees of the University of Illinois
    Inventors: Rashid Bashir, Bala Murali Venkatesan