Patents Represented by Attorney, Agent or Law Firm Lin Sun-Hoffman
  • Encoding and decoding reactions for determining target polynucleotides
    Patent number: 7604937
    Abstract: The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one label and at least one address primer is employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments universal bases and reduced libraries of probes can be employed for highly multiplexed analysis of target polynucleotides.
    Type: Grant
    Filed: March 24, 2005
    Date of Patent: October 20, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Qin Lao, Mark T. Reed
  • Encoding and decoding reactions for determining target molecules
    Patent number: 7601821
    Abstract: The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.
    Type: Grant
    Filed: March 24, 2005
    Date of Patent: October 13, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Mark R. Andersen, Kenneth J. Livak, Adam Broomer, Caifu Chen
  • Methods, compositions, and kits comprising linker probes for quantifying polynucleotides
    Patent number: 7601495
    Abstract: The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3? target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3? target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.
    Type: Grant
    Filed: May 31, 2005
    Date of Patent: October 13, 2009
    Assignee: Applied Biosystems, LLC
    Inventors: Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Q. Lao, Neil A. Straus
  • Methods and kits for identifying target nucleotides in mixed populations
    Patent number: 7427479
    Abstract: Ligation-based methods and kits are disclosed for identifying at least two target nucleotides in a mixed population sample, that is a sample that contains or potentially contains target nucleic acid sequences from more than one source. Typically, two ligation reaction compositions are formed, ligation products generated, and the ligation products or their surrogates are analyzed to identify target nucleotides in the mixed population sample. In certain embodiments, the target nucleic acid sequences, the ligation products, or both are amplified. In certain embodiments, multiplex amplification and/or ligation reactions are performed.
    Type: Grant
    Filed: April 29, 2005
    Date of Patent: September 23, 2008
    Assignee: Applera Corporation
    Inventors: Achim E. Karger, Elena V. Bolchakova
  • Methods and kits for methylation detection
    Patent number: 7364855
    Abstract: Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.
    Type: Grant
    Filed: May 2, 2005
    Date of Patent: April 29, 2008
    Assignee: Applera Corporation
    Inventors: Mark R. Andersen, Jer-Kang Chen, Michael W. Hunkapiller, Steven M. Menchen
  • Selective capture and enrichment of proteins expressed on the cell surface
    Patent number: 7348416
    Abstract: The present invention provides a method for enriching cell surface proteins by oxidizing glycosylated protein with periodate. The present invention further provides that the cell surface proteins are obtained from intact cells either from cell lines or from tissues. The present invention provides a method not only capable of obtaining increased quantities of the cell surface proteins, but also capable of obtaining a wide ranges of proteins that are not detectable by other means.
    Type: Grant
    Filed: November 19, 2004
    Date of Patent: March 25, 2008
    Assignee: Applera Corporation
    Inventors: Bruno Domon, Ian McCaffery, Terence Ryan
  • Isolated human dehydrogenases, nucleic acid molecules encoding these human dehydrogenases, and uses thereof
    Patent number: 7148331
    Abstract: The present invention provides amino acid sequences of polypeptides that are encoded by genes within the human genome, the dehydrogenase polypeptides of the present invention. The present invention specifically provides isolated polypeptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the dehydrogenase polypeptides, and methods of identifying modulators of the dehydrogenase polypeptides.
    Type: Grant
    Filed: August 25, 2004
    Date of Patent: December 12, 2006
    Assignee: Applera Corporation
    Inventors: Fangcheng Gong, Chunhua Yan, Valentina DiFrancesco, Ellen M. Beasley
  • Isolated human glutamate receptor DNA
    Patent number: 6830900
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the transporter peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the transporter peptides, and methods of identifying modulators of the transporter peptides.
    Type: Grant
    Filed: March 29, 2001
    Date of Patent: December 14, 2004
    Assignee: Applera Corporation
    Inventors: Chunhua Yan, Ming-Hui Wei, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human protease proteins, nucleic acid molecules encoding human protease proteins, and uses thereof
    Patent number: 6818429
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the protease peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the protease peptides, and methods of identifying modulators of the protease peptides.
    Type: Grant
    Filed: August 7, 2002
    Date of Patent: November 16, 2004
    Assignee: Applera Corporation
    Inventors: Weiniu Gan, Karen A. Ketchum, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human dehydrogenases, nucleic acid molecules encoding these human dehydrogenases, and uses thereof
    Patent number: 6797499
    Abstract: The present invention provides amino acid sequences of polypeptides that are encoded by genes within the human genome, the dehydrogenase polypeptides of the present invention. The present invention specifically provides isolated polypeptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the dehydrogenase polypeptides, and methods of identifying modulators of the dehydrogenase polypeptides.
    Type: Grant
    Filed: April 9, 2002
    Date of Patent: September 28, 2004
    Assignee: Applera Corporation
    Inventors: Fangcheng Gong, Chunhua Yan, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human drug-metabolizing proteins, nucleic acid molecules encoding human drug-metabolizing proteins, and uses thereof
    Patent number: 6730505
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the drug-metabolizing enzyme peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the drug-metabolizing enzyme peptides, and methods of identifying modulators of the drug-metabolizing enzyme peptides.
    Type: Grant
    Filed: June 6, 2002
    Date of Patent: May 4, 2004
    Assignee: Applera Corporation
    Inventors: Karl Guegler, Karen A. Ketchum, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human phosphatase proteins, nucleic acid molecules encoding human phosphatase proteins, and uses thereof
    Patent number: 6723547
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the phosphatase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the phosphatase peptides, and methods of identifying modulators of the phosphatase peptides.
    Type: Grant
    Filed: April 2, 2001
    Date of Patent: April 20, 2004
    Assignee: Applera Corporation
    Inventors: Ellen M. Beasley, Marion Webster, Valentina Di Francesco, Ming-Hui Wei
  • Isolated human UDP-glycosyltransferase proteins
    Patent number: 6713295
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the drug-metabolizing enzyme peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the drug-metabolizing enzyme peptides, and methods of identifying modulators of the drug-metabolizing enzyme peptides.
    Type: Grant
    Filed: February 1, 2002
    Date of Patent: March 30, 2004
    Assignee: Applera Corporation
    Inventors: Marion Webster, Ming-Hui Wei, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human phosphatase proteins, nucleic acid molecules encoding human phosphatase proteins, and uses thereof
    Patent number: 6692949
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the phosphatase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the phosphatase peptides, and methods of identifying modulators of the phosphatase peptides.
    Type: Grant
    Filed: February 24, 2003
    Date of Patent: February 17, 2004
    Assignee: Applera Corporation
    Inventors: Chunhua Yan, Weiniu Gan, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human lipase proteins, nucleic acid molecules encoding human lipase proteins, and uses thereof
    Patent number: 6638738
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the lipase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the lipase peptides, and methods of identifying modulators of the lipase peptides.
    Type: Grant
    Filed: March 20, 2001
    Date of Patent: October 28, 2003
    Assignee: Applera Corporation
    Inventors: Chunhua Yan, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human phospholipase proteins, nucleic acid molecules encoding human phospholipase proteins, and uses thereof
    Patent number: 6638747
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the phospholipase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the phospholipase peptides, and methods of identifying modulators of the phospholipase peptides.
    Type: Grant
    Filed: December 18, 2001
    Date of Patent: October 28, 2003
    Assignee: Applera Corporation
    Inventors: Ellen M Beasley, Chunhua Yan, Valentina Di Francesco
  • Isolated human protease proteins, nucleic acid molecules encoding human protease proteins, and uses thereof
    Patent number: 6620607
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the protease peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the protease peptides, and methods of identifying modulators of the protease peptides.
    Type: Grant
    Filed: June 4, 2002
    Date of Patent: September 16, 2003
    Assignee: Applera Corporation
    Inventors: Karl Guegler, Marion Webster, Chunhua Yan, Wei Shao, Karen A. Ketchum, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human transporter proteins, nucleic acid molecules encoding human transporter proteins, and uses thereof
    Patent number: 6562593
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the transporter peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the transporter peptides, and methods of identifying modulators of the transporter peptides.
    Type: Grant
    Filed: December 20, 2000
    Date of Patent: May 13, 2003
    Assignee: Applera Corporation
    Inventors: Gennady Merkulov, Karl Guegler, Marion Webster, Karen A. Ketchum, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human phosphatase proteins, nucleic acid molecules encoding human phophatase proteins, and uses thereof
    Patent number: 6551809
    Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the phosphatase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the phosphatase peptides, and methods of identifying modulators of the phosphatase peptides.
    Type: Grant
    Filed: March 20, 2001
    Date of Patent: April 22, 2003
    Assignee: Applera Corporation
    Inventors: Chunhua Yan, Weiniu Gan, Valentina Di Francesco, Ellen M. Beasley
  • Isolated human dehydrogenase proteins, nucleic acid molecules encoding these human dehydrogenase proteins, and uses thereof
    Patent number: 6544764
    Abstract: The present invention provides amino acid sequences of polypeptides that are encoded by genes within the human genome, the dehydrogenase polypeptides of the present invention. The present invention specifically provides isolated polypeptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the dehydrogenase polypeptides, and methods of identifying modulators of the dehydrogenase polypeptides.
    Type: Grant
    Filed: June 8, 2001
    Date of Patent: April 8, 2003
    Assignee: Applera Corporation
    Inventors: Chunhua Yan, Zhenya Li, Gennady V Merkulov, Valentina Di Francesco, Ellen Beasley