Patents by Inventor Ryan S. Senger

Ryan S. Senger 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).

  • Reverse engineering genome-scale metabolic network reconstructions for organisms with incomplete genome annotation and developing constraints using proton flux states and numerically-determined sub-systems
    Patent number: 8311790
    Abstract: A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was created using a new semi-automated reverse engineering algorithm. This invention includes algorithms and software that can reconstruct genome-scale metabolic networks for cell-types available through the Kyoto Encyclopedia of Genes and Genomes. This method can also be used to complete partial metabolic networks and cell signaling networks where adequate starting information base is available. The software may use a semi-automated approach which uses a priori knowledge of the cell-type from the user. Upon completion, the program output is a genome-scale stoichiometric matrix capable of cell growth in silico. The invention also includes methods for developing flux constraints and reducing the number of possible solutions to an under-determined system by applying specific proton flux states and identifying numerically-determined sub-systems.
    Type: Grant
    Filed: April 13, 2009
    Date of Patent: November 13, 2012
    Assignee: University of Delaware
    Inventors: Ryan S. Senger, Eleftherios Papoutsakis
  • REVERSE ENGINEERING GENOME-SCALE METABOLIC NETWORK RECONSTRUCTIONS FOR ORGANISMS WITH INCOMPLETE GENOME ANNOTATION AND DEVELOPING CONSTRAINTS USING PROTON FLUX STATES AND NUMERICALLY-DETERMINED SUB-SYSTEMS
    Publication number: 20090259451
    Abstract: A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was created using a new semi-automated reverse engineering algorithm. This invention includes algorithms and software that can reconstruct genome-scale metabolic networks for cell-types available through the Kyoto Encyclopedia of Genes and Genomes. This method can also be used to complete partial metabolic networks and cell signaling networks where adequate starting information base is available. The software may use a semi-automated approach which uses a priori knowledge of the cell-type from the user. Upon completion, the program output is a genome-scale stoichiometric matrix capable of cell growth in silico. The invention also includes methods for developing flux constraints and reducing the number of possible solutions to an under-determined system by applying specific proton flux states and identifying numerically-determined sub-systems.
    Type: Application
    Filed: April 13, 2009
    Publication date: October 15, 2009
    Applicant: University of Delaware
    Inventors: Ryan S. Senger, Eleftherios Papoutsakis