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Recent Patents in Bioinformatics, Jan. 2006 — Feb. 2007

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US Patent 7,177,867. Method and apparatus for providing scalable resource discovery. Inventors: David Stringer-Calvert, Patrick Lincoln, Steven Dawson. Assignee: SRI International.
 
Covers a scalable method and architecture for locating desired resources within a network of server nodes, each of which provides access to a subset of a global resource set. In one aspect of the invention, each of the server nodes are assigned membership in at least two sets, an “announce” set and a “request” set. The invention provides means to perform distributed agent-based computing. As an example application for the system, the patent describes “large bioinformatic calculations involving publicly available databases of proteomic strings, certain Boyer-Moore fast string-matching or Blast agents, and certain other evaluation agents to choose among many matches.”
 

 
US Patent 7,177,864. Method and system for data processing for pattern detection. Inventor: Michael Ekhaus. Assignee: Gibraltar Analytics.
 
Protects a computerized method that finds association relationships between attributes recorded in data files. The computer receives one or more data file records, each record containing two or more of attributes of interest. The software defines at least two attribute k-patterns by reference to a subset of the attributes, where k is an integer and represents the number of attributes that are included in a k-pattern. Using an invertible mapping algorithm, the software maps each of the attribute k-patterns into an associated key and determines a distribution pattern for each of the attribute k-patterns. The software then inverts the mapping to decode from the keys to the associated attribute k-pattern, and, using the keys, associates the distribution patterns determined with each of the attribute k-patterns. According to the inventor, the approach is applicable to bioinformatics data analysis as well as other data analysis areas.
 

 
US Patent 7,177,766. Selection of sites for targeting by zinc finger proteins and methods of designing zinc finger proteins to bind to preselected sites. Inventors: Stephen Eisenberg, Casey Case, George Cox, Andrew Jamieson, Edward Rebar. Assignee: Sangamo Biosciences.
 
Protects methods for selecting optimum subsequences for targeting by a zinc finger protein. The methods use a database containing information about previously characterized zinc finger proteins. Some of the methods of target site selection identify target segments with a DNA motif, while others use a correspondence regime between different triplets of three bases and the three possible positions of a triplet within a nine-base site. The invention also protects methods of designing zinc finger proteins that bind to a preselected target site.
 

 
US Patent 7,177,452. Visualization of information with an established order. Inventors: Pak Chung Wong, Harlan Foote, James Thomas, Kwong-Kwok Wong. Assignee: Battelle Memorial Institute.
 
Protects a system including processors for accessing data that is “representative of a biopolymer sequence of monomer units,” according to the patent abstract. The processors establish a pattern corresponding to at least one fractal curve and generate output signals corresponding to a number of image elements that are each representative of one of the monomer units. The patent also covers a display device for visualizing the biopolymer sequence by displaying the image elements in accordance with the pattern.
 

 
US Patent 7,171,311. Methods of assigning treatment to breast cancer patients. Inventors: Hongyue Dai, Yudong He, Peter Linsley, Mao Mao, Christopher Roberts, Laura Johanna Van't Veer, Marc Van de Vijver, Rene Bernards, AAM Hart. Assignee: Rosetta Inpharmatics, Netherlands Cancer Institute.
 
Protects genetic markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis.
 

 
US Patent 7,146,380. Extracting information from input data using a semantic cognition network. Inventors: Arno Schaepe, Maria Athelogou, Ursula Benz, Christof Krug, Gerd Binning. Assignee: Definiens.
 
Protects a method for extracting information from input data that includes mapping the input data into a data object network. The method uses a semantic cognition network comprised of the data object network, a class object network, and a processing object network.

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