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BioInform s Patent Roundup: Recent Patents in Bioinformatics: Jan 10, 2005


US Patent 6,839,635. Method and system for analyzing biological response signal data. Inventors: Douglas Bassett, Stewart Buskirk, Andrey Bondarenko. Assignee: Rosetta Inpharmatics.

Protects systems, methods, and computer program products for analysis of biological response data. Biological datasets are selected from an active biological viewer window on a computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in the destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. The patent also protects methods and computer programs for displaying hierarchical cluster trees from biological signal profiles in a hyperbolic display fashion, and for precomputing correlation data between biological signal profile data when the experiments are added to a biological response database, thereby eliminating the need for real time computation of correlation coefficients by a user computer.

US Patent 6,839,454. System and method for automatically identifying sub-grids in a microarray. Inventor: James Park. Assignee: BioDiscovery.

Covers a digital image-processing-based system and method for quantitatively processing nucleic acid species expressed in a microarray. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a computer that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray’s sub-grids. The computer identifies the position of each of the sub-grids by identifying regions in the digital image that each contains one of the sub-grids, identifying rows and columns in each region where nucleic acid species are expressed to form a set of candidate sub-grids in each region, selecting for each region a probable sub-grid from the set of candidate sub-grids in each region, and comparing the positions of the probable sub-grids from each region to finalize the sub-grid positions.

US Patent 6,836,733. Biological sequence pattern probe. Inventors: Eric Olson, Jeff Kozlowski, Assignee: VizX Labs.

Covers a method and apparatus for determining biological sequence sites of interest using client-server computer architecture. In the method, one or more users use a computer client to select a biological sequence database of interest, and determine the search parameters that control the specificity of results to be returned. The remote computer client submits the search request to a central computer server, which processes the search request. Once the server has received and processed the request, results are returned to one or more remote clients and viewed according to the previously selected search parameters.

US Patent 6,834,239. Method, system, and computer program product for determining properties of combinatorial library products from features of library building blocks. Inventors: Victor Lobanov, Dimitris Agrafiotis, Raymond Salemme. Assignee: None.

Covers a computational method for determining properties of combinatorial library products from features of library building blocks using a supervised machine-learning approach.

US Patent 6,834,237. Method and system for classifying a biological sample. Inventors: Lars Noergaard, Morten Albrechtsen, Ole Ingemann Olsen, Niels Harrit, Rasmus Bro-Joergensen. Assignee: Medicometrics.

Protects a method of training a classification system for characterizing a biological sample, a diagnostic classification system, and a method of characterizing a condition in an animal or a human being by using parameters obtained from the sample. The invention relates to classification based on physical parameters obtained from luminescence spectroscopy on light emitted from the sample. Each sample gives rise to a unique spectrofluorometric set of physical parameters, which can be analyzed to classify samples into two or more classes based on the fluorescence spectra, such as classifying with respect to presence/absence of a specific disease, group of diseases or risk of later attaining a specific disease or a body condition, or concentration of a specific compound or medicine.

US Patent 6,832,163. Methods of identifying heterogeneous features in an image of an array. Inventors: Glenda Delenstarr. Assignee: Agilent Technologies.

Protects methods for identifying heterogeneous features, including heterogeneous background regions, in an image of an array, such as a nucleic acid array. The methods are based an algorithm that employs a different dispersity measure depending on whether the signal features are weaker or stronger. The patent also covers computer-readable storage media that include an algorithm capable of performing the methods.

US Patent 6,832,162. Methods of ab initio prediction of alpha helices, beta sheets, and polypeptide tertiary structures. Inventors: Christodoulos Floudas, John Klepeis. Assignee: The Trustees of Princeton University.

Covers a four-stage ab initio approach for predicting the tertiary structure of polypeptides. The methods of the invention combine the classical and modern views of protein folding, while using free energy calculations and integer linear optimization to predict helical and beta-sheet structures, according to the inventors.

US Patent 6,826,296. Method and system for providing a probe array chip design database. Inventors: David Balaban, Earl Hubbell, Michael Mittmann, Gloria Cheung, Josie Dai. Assignee: Affymetrix.

Protects a method for organizing information related to the design of polymer probe array chips, including oligonucleotide array chips. The patent describes a database model that organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is translatable into database languages such as SQL and scales to store information about large numbers of chips with complex designs.


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