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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

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.