Patents by Inventor Harmen J. Bussemaker

Harmen J. Bussemaker 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).

  • Method for identifying aQTL regions whose genotype modulates transcription factor activity
    Patent number: 8483970
    Abstract: The disclosed subject matter is directed to genetic linkage methods for identifying genetic determinants of transcription factor activity. An inferred transcription factor activity profile is generated based on a nucleotide sequence-specific mathematical model of gene expression regulation. Genetic linkage analysis is performed to identify at least one genetic determinant linked to a specific transcription factor segregant based on the inferred transcription factor profile.
    Type: Grant
    Filed: September 29, 2009
    Date of Patent: July 9, 2013
    Assignee: The Trustees of Columbia University in the city of New York
    Inventors: Harmen J. Bussemaker, Eunjee Lee
  • System and method for quantifying the sequence specificity of nucleotide binding factors
    Patent number: 8219323
    Abstract: Systems and methods for determining free energy parameters for predicting binding affinities of nucleotide sequences are provided. The disclosed subject matter obtains phenotypic measurements for nucleotide sequences (for example a DNA sequence or RNA sequence), links the phenotypic measurements to the nucleotide sequences to obtain linked pairs of phenotypic measurements and nucleotide sequences, estimates a relationship between the phenotypic measurements and the nucleotide sequences using the linked pairs, and obtains sequence specific affinity parameters from the estimated relationship.
    Type: Grant
    Filed: May 16, 2007
    Date of Patent: July 10, 2012
    Assignee: The Trustees of Columbia University in the City of New York
    Inventors: Harmen J. Bussemaker, Barrett C. Foat, Ronald G. Tepper
  • Method for Identifying Genetic Determinants of Transcription Factor Activity
    Publication number: 20100153018
    Abstract: The disclosed subject matter is directed to genetic linkage methods for identifying genetic determinants of transcription factor activity. An inferred transcription factor activity profile is generated based on a nucleotide sequence-specific mathematical model of gene expression regulation. Genetic linkage analysis is performed to identify at least one genetic determinant linked to a specific transcription factor segregant based on the inferred transcription factor profile.
    Type: Application
    Filed: September 29, 2009
    Publication date: June 17, 2010
    Inventors: Harmen J. Bussemaker, Eunjee Lee
  • System and method for quantifying the sequence specificity of nucleotide binding factors
    Publication number: 20080102460
    Abstract: Systems and methods for determining free energy parameters for predicting binding affinities of nucleotide sequences are provided. The disclosed subject matter obtains phenotypic measurements for nucleotide sequences (for example a DNA sequence or RNA sequence), links the phenotypic measurements to the nucleotide sequences to obtain linked pairs of phenotypic measurements and nucleotide sequences, estimates a relationship between the phenotypic measurements and the nucleotide sequences using the linked pairs, and obtains sequence specific affinity parameters from the estimated relationship.
    Type: Application
    Filed: May 16, 2007
    Publication date: May 1, 2008
    Inventors: Harmen J. Bussemaker, Barrett C. Foat, Ronald G. Tepper