Patents by Inventor Alex Chenchik

Alex Chenchik 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: 20230227889
    Abstract: Methods of preparing a plurality of sample-barcoded anchor-domain-flanked gene specific deoxyribonucleic acid (DNA) fragments from a template nucleic acid, e.g., ribonucleic acid (RNA), sample are provided. Aspects of the methods include employing a set of gene specific primer pairs, wherein each pair of gene specific primers is made up of a forward primer and a reverse primer, at least one of which includes a sample barcode domain. The methods find use in a variety of different applications, including high-throughput sequencing, e.g., expression profiling, applications, including of small biological samples, e.g., single-cells.
    Type: Application
    Filed: August 22, 2022
    Publication date: July 20, 2023
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov, Russell Paul Darst, IV, Donato Tedesco, Lester Kobzik
  • Patent number: 11655510
    Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.
    Type: Grant
    Filed: March 7, 2018
    Date of Patent: May 23, 2023
    Assignee: Cellecta, Inc.
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov
  • Publication number: 20220195493
    Abstract: Methods of preparing a plurality of sample-barcoded anchor-domain-flanked gene specific deoxyribonucleic acid (DNA) fragments from a template nucleic acid, e.g., ribonucleic acid (RNA), sample are provided. Aspects of the methods include employing a set of gene specific primer pairs, wherein each pair of gene specific primers is made up of a forward primer and a reverse primer, at least one of which includes a sample barcode domain. The methods find use in a variety of different applications, including high-throughput sequencing, e.g., expression profiling, applications, including of small biological samples, e.g., single-cells.
    Type: Application
    Filed: January 28, 2022
    Publication date: June 23, 2022
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov, Russell Paul Darst, IV, Donato Tedesco, Lester Kobzik
  • Publication number: 20220145285
    Abstract: Compartment-free single cell genetic analysis methods are provided. Aspects of the methods include: (a) combining a cellular sample with a plurality of distinct barcoded beads comprising barcoded reverse primers under conditions sufficient to produce a liquid composition comprising a plurality of separated cell/barcoded bead complexes; (b) hybridizing template binding domains of barcoded reverse primers to template nucleic acids of the cells to produce primed template nucleic acids; and (c) subjecting the primed template nucleic acids to primer extension reaction conditions sufficient to produce barcoded nucleic acids, e.g., for subsequent amplification and analysis, such as by Next Generation Sequencing (NGS) protocols. Also provided are compositions that find use in practicing embodiments of the methods.
    Type: Application
    Filed: August 12, 2020
    Publication date: May 12, 2022
    Inventors: Alex CHENCHIK, Russell Paul DARST, IV, Lester KOBZIK, Mikhail MAKHANOV, Donato TEDESCO
  • Patent number: 11274334
    Abstract: Methods of preparing a plurality of sample-barcoded anchor-domain-flanked gene specific deoxyribonucleic acid (DNA) fragments from a template nucleic acid, e.g., ribonucleic acid (RNA), sample are provided. Aspects of the methods include employing a set of gene specific primer pairs, wherein each pair of gene specific primers is made up of a forward primer and a reverse primer, at least one of which includes a sample barcode domain. The methods find use in a variety of different applications, including high-throughput sequencing, e.g., expression profiling, applications, including of small biological samples, e.g., single-cells.
    Type: Grant
    Filed: August 16, 2019
    Date of Patent: March 15, 2022
    Assignee: Cellecta, Inc.
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov, Russell Paul Darst, IV, Donato Tedesco, Lester Kobzik
  • Publication number: 20210301329
    Abstract: Single cell genetic analysis methods are provided. Aspects of the methods include: (a) producing a plurality of partitioned cell/barcoded bead complexes from a cellular sample and a plurality of distinct barcoded beads that include a plurality of barcoded reverse gene-specific primers; (b) hybridizing gene-specific template binding domains of the barcoded reverse gene-specific primers to template nucleic acids of the cells to produce primed template nucleic acids; and (c) subjecting the primed template nucleic acids to primer extension reaction conditions sufficient to produce barcoded nucleic acids, e.g., for subsequent amplification and analysis, such as by Next Generation Sequencing (NGS) protocols. Also provided are compositions that find use in practicing embodiments of the methods.
    Type: Application
    Filed: March 2, 2021
    Publication date: September 30, 2021
    Inventors: Alex Chenchik, Russell Paul Darst, IV, Lester Kobzik, Mikhail Makhanov, Donato Tedesco
  • Patent number: 10975440
    Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.
    Type: Grant
    Filed: April 19, 2016
    Date of Patent: April 13, 2021
    Assignee: Cellecta, Inc.
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov
  • Publication number: 20200063190
    Abstract: Methods of preparing a plurality of sample-barcoded anchor-domain-flanked gene specific deoxyribonucleic acid (DNA) fragments from a template nucleic acid, e.g., ribonucleic acid (RNA), sample are provided. Aspects of the methods include employing a set of gene specific primer pairs, wherein each pair of gene specific primers is made up of a forward primer and a reverse primer, at least one of which includes a sample barcode domain. The methods find use in a variety of different applications, including high-throughput sequencing, e.g., expression profiling, applications, including of small biological samples, e.g., single-cells.
    Type: Application
    Filed: August 16, 2019
    Publication date: February 27, 2020
    Inventors: Alex Chenchik, Costa Frangou, Mikhail Makhanov, Russell Paul Darst, IV, Donato Tedesco, Lester Kobzik
  • Patent number: 10196634
    Abstract: Methods of clonal analysis of functional genomic assays are provided. Aspects of the invention include transducing a population of target cells with a packaged viral effector library made up of a plurality of effector construct subsets, wherein each effector construct subset of the library includes a plurality of effector constructs having a common effector cassette linked to a distinct clonal barcode. Inclusion of distinct clonal barcodes in the effector construct subset allows for determination of the clonal representation of an effector construct subset in transduced target cells that exhibit a specific phenotype. Aspects of the invention further include compositions, e.g., libraries and components thereof, which find use in practicing the methods.
    Type: Grant
    Filed: June 6, 2016
    Date of Patent: February 5, 2019
    Assignee: Cellecta, Inc.
    Inventors: Alex Chenchik, Donato Tedesco, Mikhail Makhanov
  • Publication number: 20180245164
    Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.
    Type: Application
    Filed: March 7, 2018
    Publication date: August 30, 2018
    Inventor: Alex Chenchik
  • Publication number: 20160376664
    Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.
    Type: Application
    Filed: April 19, 2016
    Publication date: December 29, 2016
    Inventor: Alex Chenchik
  • Publication number: 20160340671
    Abstract: Methods of clonal analysis of functional genomic assays are provided. Aspects of the invention include transducing a population of target cells with a packaged viral effector library made up of a plurality of effector construct subsets, wherein each effector construct subset of the library includes a plurality of effector constructs having a common effector cassette linked to a distinct clonal barcode. Inclusion of distinct clonal barcodes in the effector construct subset allows for determination of the clonal representation of an effector construct subset in transduced target cells that exhibit a specific phenotype. Aspects of the invention further include compositions, e.g., libraries and components thereof, which find use in practicing the methods.
    Type: Application
    Filed: June 6, 2016
    Publication date: November 24, 2016
    Inventors: Alex Chenchik, Donato Tedesco, Mikhail Makhanov
  • Patent number: 9447411
    Abstract: Methods of obtaining a single cell expression profile from a target mammalian cell are provided. Aspects of the methods include contacting a cellular sample which includes the target mammalian cell with a packaged viral barcoded trans-splicing library including a plurality of barcoded trans-splicing constructs under transduction conditions, where a barcoded trans-splicing construct includes a trans-splicing element linked to a barcode element. The methods further include generating expression data from the resultant transduced target mammalian cell to obtain the single cell expression data from the target mammalian cell. Also provided are compositions, e.g., libraries and components thereof, which find use in practicing the methods.
    Type: Grant
    Filed: January 13, 2014
    Date of Patent: September 20, 2016
    Assignee: Cellecta, Inc.
    Inventor: Alex Chenchik
  • Patent number: 9429565
    Abstract: Methods of clonal analysis of functional genomic assays are provided. Aspects of the invention include transducing a population of target cells with a packaged viral effector library made up of a plurality of effector construct subsets, wherein each effector construct subset of the library includes a plurality of effector constructs having a common effector cassette linked to a distinct clonal barcode. Inclusion of distinct clonal barcodes in the effector construct subset allows for determination of the clonal representation of an effector construct subset in transduced target cells that exhibit a specific phenotype. Aspects of the invention further include compositions, e.g., libraries and components thereof, which find use in practicing the methods.
    Type: Grant
    Filed: May 8, 2013
    Date of Patent: August 30, 2016
    Assignee: Cellecta, Inc.
    Inventors: Alex Chenchik, Donato Tedesco, Mikhail Makhanov
  • Publication number: 20140206546
    Abstract: Methods of obtaining a single cell expression profile from a target mammalian cell are provided. Aspects of the methods include contacting a cellular sample which includes the target mammalian cell with a packaged viral barcoded trans-splicing library including a plurality of barcoded trans-splicing constructs under transduction conditions, where a barcoded trans-splicing construct includes a trans-splicing element linked to a barcode element. The methods further include generating expression data from the resultant transduced target mammalian cell to obtain the single cell expression data from the target mammalian cell. Also provided are compositions, e.g., libraries and components thereof, which find use in practicing the methods.
    Type: Application
    Filed: January 13, 2014
    Publication date: July 24, 2014
    Inventor: ALEX CHENCHIK
  • Publication number: 20100305002
    Abstract: This invention discloses reagents and methods for identifying peptides that modulate biological activities in cells, tissues, organs and organisms.
    Type: Application
    Filed: April 27, 2010
    Publication date: December 2, 2010
    Applicant: ROSWELL PARK CANCER INSTITUTE
    Inventors: Alex Chenchik, Andrei Gudkov, Andrei Komarov, Venkatesh Natarajan
  • Patent number: 7556919
    Abstract: Long oligonucleotide arrays, as well as methods for their preparation and use in hybridization assays, are provided. The subject arrays are characterized in that at least a portion of the probes of the array, and usually all of the probes of the array, are long oligonucleotides, e.g. oligonucleotides having a length of from about 50 to 120 nt. Each long oligonucleotide probe on the array is preferably chosen to exhibit substantially the same high target binding efficiency and substantially the same low non-specific binding under conditions in which the array is employed. The subject arrays find use in a number of different applications, e.g. differential gene expression analysis.
    Type: Grant
    Filed: November 9, 2004
    Date of Patent: July 7, 2009
    Assignee: Clontech Laboratories, Inc.
    Inventors: Alex Chenchik, Alexander Munishkin, Peter Simonenko
  • Publication number: 20070202505
    Abstract: The present invention provides methods for analysis of gene function using effector libraries.
    Type: Application
    Filed: September 8, 2003
    Publication date: August 30, 2007
    Inventor: Alex Chenchik
  • Patent number: 7041445
    Abstract: Long oligonucleotide arrays, as well as methods for their preparation and use in hybridization assays, are provided. The subject arrays are characterized in that at least a portion of the probes of the array, and usually all of the probes of the array, are long oligonucleotides, e.g. oligonucleotides having a length of from about 50 to 120 nt. Each long oligonucleotide probe on the array is preferably chosen to exhibit substantially the same high target binding efficiency and substantially the same low non-specific binding under conditions in which the array is employed. The subject arrays find use in a number of different applications, e.g. differential gene expression analysis.
    Type: Grant
    Filed: November 15, 1999
    Date of Patent: May 9, 2006
    Assignee: Clontech Laboratories, Inc.
    Inventors: Alex Chenchik, Alexander Munishkin, Peter Simonenko
  • Publication number: 20060068403
    Abstract: Long oligonucleotide arrays, as well as methods for their preparation and use in hybridization assays, are provided. The subject arrays are characterized in that at least a portion of the probes of the array, and usually all of the probes of the array, are long oligonucleotides, e.g. oligonucleotides having a length of from about 50 to 120 nt. Each long oligonucleotide probe on the array is preferably chosen to exhibit substantially the same high target binding efficiency and substantially the same low non-specific binding under conditions in which the array is employed. The subject arrays find use in a number of different applications, e.g. differential gene expression analysis.
    Type: Application
    Filed: November 9, 2004
    Publication date: March 30, 2006
    Inventors: Alex Chenchik, Alexander Munishkin, Peter Simonenko