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BioInform s IP Roundup: Recent Patents in Bioinformatics: Jul 4, 2005

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US Patent 6,912,469. Electronic hybridization assay and sequence analysis. Inventor: Kenneth Cool. Assignee: None.

Covers an electronic hybridization assay that implements a hybridization reaction on sequences representative of the sequences of molecules under examination to provide an output representative of a chemical hybridization reaction. The method implements a correlation algorithm where the correlation output provides information regarding the relationship between the molecules under examination.


US Patent 6,909,974. System and method for discovery of biological instruments. Inventors: Kai Yung, Sylvia Fang, John Rohrlich, Stephen Dodgen. Assignee: Applera.

Covers methods for integrating laboratory instrumentation and applications to provide a unified control and coordination architecture under a common interface. The system provides mechanisms for detecting various hardware and software components. The individual functionalities and input/output data types for each component are automatically recognized and incorporated into a centralized control system that provides live monitoring of the operational status of available components.


US Patent 6,909,971. Method for gene mapping from chromosome and phenotype data. Inventors: Hannu Toivonen, Päivi Onkamo, Kari Vasko, Vesa Ollikainen, Petteri Sevon, Heikki Mannila, Juha Kere. Assignee: Licentia Oy.

Protects a method for gene mapping from chromosome and phenotype data, which uses linkage disequilibrium between genetic markers. All marker patterns that satisfy a certain pattern-evaluation function are searched from the data, and each marker is scored by a marker score and the location of the gene is predicted as a function of the scores of all the markers in the data.


US Patent 6,909,970. Fast microarray expression data analysis method for network exploration. Inventors: Valery Kanevsky, Aditya Vailaya. Assignee: Agilent Technologies.

Protects a method for performing network reconstruction that includes the steps of selecting a predictor set of features, adding a complement to the predictor set based on a quality of prediction, checking to see if all of the features of the predictor set are repeated, and then removing one feature from the predictor set. The algorithm repeats the steps of adding a complement, checking the predictor set, and removing a feature until the features of the predictor set are repeated.


US Patent 6,907,350. Method, system and apparatus for handling information on chemical substances. Inventor: Renpei Nagashima. Assignee: Chugai Seiyaku.

Covers methods for constructing and sharing libraries of information on chemical substances as they interact with various biological systems. The invention provides databases to maintain these libraries, methods and systems to construct such databases, and methods and systems to enable a client to search through such databases for desired information.


US Patent 6,906,320. Mass spectrometry data analysis techniques. Inventors: Jeffrey Sachs, Matthew Wiener, Nathan Yates. Assignee: Merck & Co.

Covers mass spectrometry data analysis techniques for selectively identifying analytes differing in abundance between different sample sets. The techniques determine the statistical significance of changes to signals associated with mass-to-charge ratios between individual samples and sample sets. Based on the statistical significance, changes likely to indicate analyte level differences are identified. Based on intensities of the signals, ratios of analyte abundances can be determined.


US Patent 6,905,818. Method for the identification and characterization of interacting molecules by automated interaction mating. Inventors: Erich Wanker, David Bancroft, Hans Lehrach, Niels Wedemeyer, Elmar Maier, Sebastian Meier-Ewert. Assignee: Max-Planck-Gesellschaft zur Forderung der Wissenschaften.

Protects a method for identifying and characterizing interacting molecules. The method is designed to detect positive clones from among the large numbers of false positive clones isolated by conventional two-hybrid systems and relies on a combination of selection steps used to detect clones that express interacting molecules from false positive clones.


US Patent 6,904,423. Method and system for artificial intelligence directed lead discovery through multi-domain clustering. Inventors: Christodoulos Nicolaou, Brian Kelley, Ruth Nutt, Susan Bassett. Assignee: Bioreason.

Covers a system for analyzing chemical structure and activity information and providing conclusions about structure-to-activity relationships. The computer-implemented method learns new substructure descriptors based on an analysis of the input data. The computer may then apply each substructure descriptor as a filter to establish new groups of molecules that match the descriptor. From each new group of molecules, the computer may in turn generate one or more additional new groups of molecules in order to product a tree structure that reflects pharmacophoric information and establishes through lineage what effect on activity various chemical substructures are likely to have. The tree structure can then be applied as a multi-domain classifier, to help a chemist classify test compounds into structural subclasses.


US Patent 6,902,883. System for cell-based screening. Inventors: Terry Dunlay, Lansing Taylor. Assignee: None.

Protects an optical system for determining the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for specific biological activity. The invention includes a computerized method for processing, displaying, and storing the data.

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