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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Mar 8, 2004


US Patent 6,697,739. Test for linkage and association in general pedigrees: the pedigree disequilibrium test. Inventors: Eden Martin, Norman Kaplan. Assignees: Duke University, US Department of Health and Human Services.

Provides a statistical method for analyzing linkage disequilibrium between at least one marker locus and a disease or trait locus of interest.

US Patent 6,692,916. Systems and methods for characterizing a biological condition or agent using precision gene expression profiles. Inventors: Michael Bevilacqua, Danute Bankaitis-Davis, John Cheronis, Victor Tryon. Assignee: Source Precision Medicine.

Covers methods for evaluating the biological condition of a subject using a calibrated profile data set of a subject’s RNA or protein. The biological condition may be a naturally occurring physiological state or may be the response to treatment of the subject with one or more agents.

US Patent 6,691,110. System and method for discovering patterns with noise. Inventors: Wei Wang, Jiong Yang, Philip Shi-lung Yu. Assignee: International Business Machines.

Covers a method for determining patterns in a data sequence based on a compatibility matrix that provides a probability between an actual occurrence of an item and an observed occurrence of that or another item between each item in the data sequence. Candidate patterns are generated, which are checked against the data sequence to determine a match value based on the compatibility matrix, and significant matches are determined based on candidate patterns having the match value above a certain threshold.

US Patent 6,691,109. Method and apparatus for high-performance sequence comparison. Inventors: Robert Bjornson, Nicholas Carriero, Andrew Sherman, Stephan Weston, James Wing. Assignee: TurboWorx.

Protects a computer-implemented method for performing remote sequence comparison in which multiple query sequences are searched against one or more sequence databases. The method partitions the query sequences and partitions the sequence databases into smaller subsets, assigning searching tasks to members of a group of computers working in parallel.

US Patent 6,691,045. Method for determining discrete quantitative structure-activity relationships. Inventor: Paul Labute. Assignee: Chemical Computing Group.

Protects a method for developing a quantitative structure-activity relationship that uses a training set of chemical compounds with molecular descriptors consisting of a number of multidimensional vectors with an activity class for each of the vectors. The method partitions the multidimensional vectors into interdependent groups, transforms the descriptors to lessen the interdependence of the groups, and estimates a probability distribution of the descriptors and for the activity classes.

US Patent 6,691,042. Methods for generating differential profiles by combining data obtained in separate measurements. Inventors: Lee Weng, Hongyue Dai. Assignee: Rosetta Inpharmatics.

Provides methods for generating differential expression profiles by combining expression data obtained in separate microarray measurements. The invention also relates to methods for determination and removal or reduction of systematic measurement biases between different microarrays.

US Patent 6,689,563. System and methods for sequencing by hybridization. Inventors: Franco Preparata, Eliezer Upfal. Assignee: Brown University Research Foundation.

Protects systems and methods related to “gapped” nucleic acid probes, their use in sequencing by hybridization to determine the sequence of nucleic acid sequences, and computer systems capable of analyzing data generated using gapped probes in sequencing by hybridization.

US Patent 6,687,692. Method and apparatus for providing an expression data-mining database. Inventors: David Balaban, Elina Khurgin. Assignee: Affymetrix.

Covers a system and method for organizing expression information “in a way that facilitates data mining,” according to the inventors. The database model may organize information relating to sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results, and scales to permit mining of expression or concentration information collected from large numbers of samples.

US Patent 6,681,198. Unified data acquisition system. Inventors: William Buote, Kenneth Rapp, Burleigh Hutchins. Assignee: VelQuest.

Covers a system for securing and validating the management and reporting of laboratory data, in which data capture and data access are denied absent appropriate electronic verification of the equipment and the user.


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The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.