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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: May 17, 2004

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US Patent 6,735,530. Computational protein probing to identify binding sites. Inventor: Frank Guarnieri. Assignee: Sarnoff Corp.

Protects a computer-implemented method of analyzing a macromolecule for potential binding sites. The method comprises positioning a computer representation of a molecule or molecular fragment at a plurality of sampling sites of the macromolecule; repositioning the molecule or molecular fragment; accepting or rejecting each instance of the repositioned molecule or molecular fragment based on the Metropolis sampling criteria using the computed binding energy; repeating these steps; and outputting a list of unrejected instances of the molecule or molecular fragment.


US Patent 6,733,964. Computer-aided visualization and analysis system for sequence evaluation. Inventors: Mark Chee, Chunwei Wang, Luis Jevons, Derek Bernhart, Robert Lipshutz. Assignee: Affymetrix.

Describes a computer system for analyzing nucleic acid sequences by analyzing the fluorescence intensities of hybridized nucleic acid probes. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.


US Patent 6,731,781. System and method for automatically processing microarrays. Inventors: Soheil Shams, James Park, Yi-Xiong Zhou. Assignee: BioDiscovery.

Describes a digital image-processing-based system for quantitatively processing nucleic acid species expressed in a microarray. A preferred configuration includes memory for storing a digital image of the array and a processor that is used to detect a signal of a chemical material, segment the signal, and calculate a measure of the segmented signal. The processor identifies each of the sub-grids in the digital image, detecting in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal.


US Patent 6,730,023. Animal genetic and health profile database management. Inventor: W. Jean Dodds. Assignee: Hemopet.

Covers a database management system for phenotypic health assessment and genomic mapping and genetic screening of animals. Multiple remote users can access a computer network connected with a central database-processing resource; input data relating to animal health, lifespan, and genetic background; and obtain reports relating to phenotypic health assessment of a particular animal subject or animal group, and genotypic characteristics of a particular subject or animal group to which this subject belongs. The central computer database resource stores phenotypic data and genotypic data relating to animals and analyzes their relationship according to predetermined criteria.


US Patent 6,730,517. Automated process line. Inventors: Hubert Koster; Ping Yip, Jhobe Steadman, Dirk Reuter, Richard MacDonald. Assignee: Sequenom.

Protects a computer-based data analysis system and computer interface with integrated instrumentation for analysis of biopolymer samples, such as nucleic acids, proteins, peptides, and carbohydrates, to create an automated process line.


US Patent 6,728,642. Method of non-linear analysis of biological sequence data. Inventors: Karen Bloch, Gonzalo Arce. Assignee: E. I. du Pont de Nemours.

Protects a method of classifying biological elements into functional families that includes the steps of representing a characteristic numerically; performing a time-frequency transform on the numeric representation; and identifying biological elements of a common functional family by clusters of data having a common frequency characteristic in the time-frequency domain.


US Patent 6,727,100. Method of identifying candidate molecules. Inventors: Daniel Vitt, Stefan Busemann, Ulrich Dauer. Assignee: 4SC.

Protects a computer-implemented method for identifying candidate molecules expected to be biologically active. The method comprises the following steps: Creating a set of different molecules; assigning a descriptor representing a predetermined number of molecular properties to each molecule; mapping the set of molecules onto points of a two-dimensional grid such that the grid distance between grid points of two molecules is a measure for the similarity of the two molecule descriptors; forming a three-dimensional surface over the grid of molecules, with the surface representing the distribution of biological activity of the molecules; and selecting candidate molecules from the three-dimensional surface satisfying a predetermined criterion with respect to their biological activity.

 

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The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.