Recent Patents in Bioinformatics, December 2010 — January 2011
US Patent 7,881,874. Method and system for comparative genomics. Inventors: Gad Landau, Laxmi Priya Parida, Oren Weimann. Assignee: International Business Machines
The patent describes a method to represent the similarity between at least two genomes that includes detecting common gene clusters and representing them in a PQ tree.
US Patent 7,881,873. Systems and methods for statistical genomic DNA based analysis and evaluation. Inventors: Shreeram Akilesh, Kevin Mills, Derry Charles Roopenian, Daniel Shaffer. Assignee: The Jackson Laboratory
Describes methods to perform statistical analysis of genomic data from experimental samples to determine which sequences "have a basis of variation in an experimental sample when compared to a control sample, and additionally provide a quantitative measure of this variation." The abstracts states that the method can also be used to select DNA sequences that contain genes with copy number and/or fold changes.
US Patent 7,873,499. Methods of populating data structures for use in evolutionary simulations. Inventors: Sergey Selifonov, P.C. Willem. Assignee: Codexis
This patent covers computer code to populate data structures for use in evolutionary modeling. In particular, the program provides methods of populating a data structure with "a plurality of character strings." According to the abstract, the method involves initially encoding two or more biological molecules into character strings, selecting at least two substrings, concatenating them to form one or more product strings, and then optionally repeating the process using one or more product strings as an initial character string.
US Patent 7,873,477. Method and system using systematically varied data libraries. Inventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy Minshull, Jon Ness, Robin Emig. Assignee: Codexis Mayflower Holdings
Describes a method for providing biological results in the form of systematically varied libraries of sequences. The approach involves sending a set of instructions from a server to a client that describes one or more "diversity generation operations" available for execution at the server system. The client responds with sequence characteristics of one or more biological molecules and requests that at least one "operation" be performed. The server analyzes the sequence data and provides a set of oligonucleotides corresponding to the sequences that can be reassembled into new recombinant nucleic acids.
US Patent 7,869,960. Method and apparatus for detecting bio-complexes using rule-based templates. Inventors: Jae Hun Choi , Jong Min Park, Seon Hee Park. Assignee: Electronics and Telecommunications Research Institute
Describes a method for detecting protein bio-complexes using a rule-based template in large interaction networks.
US Patent 7,869,957. Methods and systems to identify operational reaction pathways. Inventors: Bernhard Palsson, Markus Covert, Markus Herrgard. Assignee: The Regents of the University of California
This patent describes a method of refining a biosystem reaction network comprised of providing a mathematical representation of a biosystem, determining the differences between the observed and in silico behavior of the system under similar conditions, and then repeating the process with a modified version of the model system.
US Patent 7,869,956. Computerized system and method for documenting and presenting mutation observations. Inventor: Mark Hoffman. Assignee: Cerner Innovation
Describes a computing environment for documenting genetic mutation information. The system includes modules for disassembling and assembling the data and storing it as discrete elements, which include a patient identification value, a reference sequence identification value, and a starting and ending point value within the reference sequence, among others.