Patents by Inventor Geoffrey Nilsen

Geoffrey Nilsen 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: 20110004413
    Abstract: Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.
    Type: Application
    Filed: April 29, 2010
    Publication date: January 6, 2011
    Inventors: Paolo Carnevali, Jonathan M. Baccash, Igor Nazarenko, Aaron L. Halpern, Geoffrey Nilsen, Bruce Martin, Radoje Drmanac
  • Publication number: 20040229224
    Abstract: The invention provides methods of analyzing genes for differential relative allelic expression patterns. Haplotype blocks throughout the genomes of individuals are analyzed to identify haplotype patterns that are associated with specific differential relative allelic expression patterns. Haplotype blocks that contain associated haplotype patterns may be further investigated to identify genes or variants of genes involved in differential relative allelic expression patterns.
    Type: Application
    Filed: May 13, 2003
    Publication date: November 18, 2004
    Applicant: Perlegen Sciences, Inc.
    Inventors: Kelly A. Frazer, David R. Cox, Heng Tao, Krishna Pant, Geoffrey Nilsen