Patents by Inventor Muhammad A. Sharaf

Muhammad A. Sharaf 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).

  • Patent number: 10196680
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: June 5, 2017
    Date of Patent: February 5, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20170275678
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: June 5, 2017
    Publication date: September 28, 2017
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Patent number: 9677126
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: August 19, 2016
    Date of Patent: June 13, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20160355877
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: August 19, 2016
    Publication date: December 8, 2016
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Patent number: 9434982
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: July 2, 2015
    Date of Patent: September 6, 2016
    Assignee: Applied Biosystems LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20150307925
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: July 2, 2015
    Publication date: October 29, 2015
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Patent number: 9074252
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: July 7, 2015
    Assignee: Applied Biosystems, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20140170656
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 19, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Muhammad A. SHARAF, Timothy WOUDENBERG, Khairuzzaman Bashar MULLAH
  • Patent number: 8637247
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: August 21, 2012
    Date of Patent: January 28, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: Muhammad Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20120316083
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: August 21, 2012
    Publication date: December 13, 2012
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Muhammad A. Sharaf, Timothy M. Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20110223596
    Abstract: The present invention generally relates to the detection of analytes, particularly biomolecules in samples. The invention also relates to compositions, methods, and kits for detecting the presence of analytes, typically in multiplex detection formats. The invention also relates to methods for determining the presence of at least one analyte in a sample, the methods employing employ single molecule detection techniques to individually detect at least one molecular complex or at least part of a molecular complex.
    Type: Application
    Filed: February 18, 2011
    Publication date: September 15, 2011
    Applicant: Life Technologies Corporation
    Inventors: Timothy M. WOUDENBERG, Dar Bahatt, Muhammad A. Sharaf, Timothy Z. Liu, Serguei Ermakov, Charles R. Connell, Jens J. Hyldig-Nielsen
  • Publication number: 20100291548
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Application
    Filed: March 12, 2007
    Publication date: November 18, 2010
    Applicant: Applera Corporation
    Inventors: Muhammad A. Sharaf, Timothy M. Woudenberg, Khairuzzaman Bashar Mullah
  • Publication number: 20100276580
    Abstract: Aspects of the present invention provide a method and apparatus of generating a calibration matrix for a spectral detector instrument. A calibration plate contains one or more dye mixtures in each well of the calibration plate at known absolute concentration. From the calibration plate, aspects of the present invention are used to prepare a concentration matrix based on the dyes used in the assay and the different dye mixtures used in the calibration plate. An excitation source exposes the calibration plate causing the spectral species in each of the wells to fluoresce. The emission spectra for the different dye mixtures of dyes as gathered by the spectral detector instrument at different points in the range of spectra is used to generate a spectral matrix. Bilinear calibration is performed on the concentration matrix and the spectral matrix as to determine a calibration matrix relating spectra directly to absolute concentrations.
    Type: Application
    Filed: November 3, 2009
    Publication date: November 4, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Muhammad A. Sharaf, Wanli Bi, Kenneth J. Livak
  • Publication number: 20100112572
    Abstract: The teachings herein generally relates to probes comprising fabricated coded molecular tags for detecting analytes. The teachings also relate to compositions, methods, and kits for fabricating coded molecular tags comprising a multiplicity or reporter groups in an ordered pattern.
    Type: Application
    Filed: July 21, 2009
    Publication date: May 6, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Timothy M. Woudenberg, Dar Bahatt, Muhammad A. Sharaf, Timothy Z. Liu, Serguei Ermakov, Charles R. Connell, Jens J. Hyldig-Nielsen, Benjamin Schroeder, Paolo Vatta
  • Publication number: 20100105886
    Abstract: The present teachings generally relate to probes and probes sets for detecting analytes. The teachings also relates to compositions, methods, and kits for assembling probes comprising at least one coded molecular tag.
    Type: Application
    Filed: July 21, 2009
    Publication date: April 29, 2010
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Timothy M. Woudenberg, Dar Bahatt, Muhammad A. Sharaf, Timothy Z. Liu, Serguei Ermakov, Charles R. Connell
  • Publication number: 20100096548
    Abstract: The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile.
    Type: Application
    Filed: December 22, 2009
    Publication date: April 22, 2010
    Applicant: Applied Biosystems, LLC
    Inventors: Muhammad A. Sharaf, Maria C. Roque-Biewer
  • Publication number: 20090280497
    Abstract: The present invention generally relates to the detection of analytes, particularly biomolecules in samples. The invention also relates to compositions, methods, and kits for detecting the presence of analytes, typically in multiplex detection formats. The invention also relates to methods for determining the presence of at least one analyte in a sample, the methods employing employ single molecule detection techniques to individually detect at least one molecular complex or at least part of a molecular complex.
    Type: Application
    Filed: June 26, 2009
    Publication date: November 12, 2009
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventors: Timothy M. Woudenberg, Dar Bahatt, Muhammad A. Sharaf, Timothy Z. Liu, Serguei Ermakov, Charles R. Connell, Jens J. Hyldig-Nielsen
  • Publication number: 20080001099
    Abstract: Aspects of the present invention provide a method and apparatus of generating a calibration matrix for a spectral detector instrument. A calibration plate contains one or more dye mixtures in each well of the calibration plate at known absolute concentration. From the calibration plate, aspects of the present invention are used to prepare a concentration matrix based on the dyes used in the assay and the different dye mixtures used in the calibration plate. An excitation source exposes the calibration plate causing the spectral species in each of the wells to fluoresce. The emission spectra for the different dye mixtures of dyes as gathered by the spectral detector instrument at different points in the range of spectra is used to generate a spectral matrix. Bilinear calibration is performed on the concentration matrix and the spectral matrix as to determine a calibration matrix relating spectra directly to absolute concentrations.
    Type: Application
    Filed: July 1, 2006
    Publication date: January 3, 2008
    Inventors: MUHAMMAD A. SHARAF, Wanli Bi, Kenneth J. Livak
  • Publication number: 20070249001
    Abstract: The present invention generally relates to the detection of analytes, particularly biomolecules in samples. The invention also relates to compositions, methods, and kits for detecting the presence of analytes, typically in multiplex detection formats. The invention also relates to methods for determining the presence of at least one analyte in a sample, the methods employing employ single molecule detection techniques to individually detect at least one molecular complex or at least part of a molecular complex.
    Type: Application
    Filed: March 23, 2007
    Publication date: October 25, 2007
    Applicant: Applera Corporation
    Inventors: Timothy Woudenberg, Dar Bahatt, Muhammad Sharaf, Timothy Liu, Serguei Ermakov, Charles Connell, Jens Hyldig-Nielsen
  • Patent number: 7198900
    Abstract: The present invention generally relates to the detection of analytes, particularly biomolecules in samples. The invention also relates to compositions, methods, and kits for detecting the presence of analytes, typically in multiplex detection formats. The invention also relates to methods for determining the presence of at least one analyte in a sample, the methods employing employ single molecule detection techniques to individually detect at least one molecular complex or at least part of a molecular complex.
    Type: Grant
    Filed: August 29, 2003
    Date of Patent: April 3, 2007
    Assignee: Applera Corporation
    Inventors: Timothy M. Woudenberg, Dar Bahatt, Muhammad A. Sharaf, Timothy Z. Liu, Serguei Ermakov, Charles R. Connell, Jens J. Hyldig-Nielsen