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Recent Patents in Bioinformatics, May — June 2006

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US Patent 7,068,830. Method and system for providing a probe array chip design database. Inventors: David Balaban, Earl Hubbell, Michael Mittman, Gloria Cheung, Josie Dai. Assignee: Affymetrix.

Protects a method for "organizing information relating to the design of polymer probe array chips including oligonucleotide array chips," according to the patent abstract. A database model 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 permit storage of information about large numbers of chips with complex designs.


US Patent 7,065,453. Molecular docking technique for screening of combinatorial libraries. Inventors: David Diller, Kenneth Merz. Assignee: Accelrys.

Protects a high-throughput molecular docking method for screening combinatorial libraries to identify binding ligands. The method relies on a pre-docking conformational search to generate multiple solution conformations of a ligand and includes the steps of generating a binding site image of the protein; matching "hot spots" of the binding site image to atoms in "at least one solution conformation of the multiple solution conformations of the ligand to obtain at least one ligand position relative to the protein in a ligand-protein complex formation;" and optimizing the ligand position while allowing translation, orientation, and rotatable bonds of the ligand to vary, while holding the protein fixed.


US Patent 7,065,451. Computer-based method for creating collections of sequences from a dataset of sequence identifiers corresponding to natural complex biopolymer sequences and linked to corresponding annotations. Inventors: Harold Garner, Amit Kulkarni. Assignee: Board of Regents, The University of Texas System.

Protects computer-based systems and methods for the design, comparison, and analysis of genetic and proteomic databases. In a particular embodiment, the systems and methods have been implemented in a computer tool called ARROGANT, package for providing annotation to large gene and protein collections. ARROGANT "takes in a large collection of sequence identifiers and associates it with other information collected from many sources like sequence annotations, pathways, homology, polymorphisms, artifacts, etc.," according to the patent abstract.


US Patent 7,062,384. Methods for classifying high-dimensional biological data. Inventors: David Rocke, Danh Nguyen. Assignee: The Regents of the University of California.

Protects methods of classifying biological samples based on high-dimensional data obtained from the samples. The methods "are especially useful for prediction of a class to which the sample belongs under circumstances in which the data are statistically under-determined," including microarray data, according to the patent abstract. The invention relies on a dimension-reduction step followed by a logistic determination step and is applicable for binary and multi-class classifications.


US Patent 7,062,076. Artificial intelligence system for genetic analysis. Inventors: Glenn Osborne, Simon Chin, Paul McDonald, Scott Schneider. Assignee: Iris Biotechnologies.

Protects an artificial intelligence system for the acquisition and analysis of nucleic acid array hybridization information. The system is divided into at least one central data processing facility and one or more user facilities, linked by encrypted network connections or similar links. Each user facility may include an optical scanning system to collect hybridization signals from a nucleic acid array, an image processing system to convert the optical data into a set of hybridization parameters, a connection to a data network, and a user interface to display, manipulate, search, and analyze hybridization information. This system reads data from a DNA microarray or a proteomics chip, "analyzes test results based on maintained parameters, evaluates patient risk for various ailments, recommends methods of treatment, presents information to medical and/or private individuals, and notifies test participants when new treatment becomes available," according to the patent abstract.


US Patent 7,058,650. Methods for establishing a pathways database and performing pathway searches. Inventors: Yonghong Yang, John Tillinghast. Christopher Piercy.

Covers a computerized storage and retrieval system for biological information organized as a protein pathways database, as well as methods "for performing pathway searches on nodes (proteins or other molecules), modes (interactions), and nodes-and-modes." The protein pathways database is a relational database that integrates protein sequence, genomic sequence, gene-expression, protein interactions, protein-protein association and pathway data and can be searched using a query pathway to predict homologous or orthologous nodes, modes, and pathways.


US Patent 7,058,616. Method and system for predicting resistance of a disease to a therapeutic agent using a neural network. Inventors: Brendan Larder, Dechao Wang. Assignee: Virco Bvba.

Protects a method and system for predicting the resistance of a disease to a therapeutic agent. The method uses a trained neural network to interpret genotypic information obtained from the disease. The neural network is trained using a database of known or determined genotypic mutations that are correlated with phenotypic therapeutic agent resistance. The invention also provides methods for predicting the probability of a patient developing a genetic disease using a trained neural network.


US Patent 7,058,517. Methods for obtaining and using haplotype data. Inventors: Rex Denton, Richard Judson, Gualberto Ruano, Claiborne Stephens, Andreas Windemuth, Chuanbo Xu. Assignee: Genaissance Pharmaceuticals (now Clinical Data).

Covers methods, computer programs, and databases for analyzing gene haplotype information. These include methods for finding and measuring the frequency of haplotypes in the general population; for finding correlations between an individual's haplotypes or genotypes and a clinical outcome; for predicting an individual's haplotypes from the individual's genotype for a gene; and for predicting an individual's clinical response to a treatment based on the individual's genotype or haplotype.


US Patent 7,058,515. Methods for making character strings, polynucleotides and polypeptides having desired characteristics. Inventors: Sergey Selifonov, Willem Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip Patten, Jeremy Minshull, Lorraine Giver. Assignee: Maxygen.

Covers "in silico nucleic acid recombination methods" and related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods.

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In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.