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IP Update: Jul 22, 2011

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Recent Patents in Bioinformatics, June — July 2011

US Patent 7,983,887. Fast computational methods for predicting protein structure from primary amino acid sequence. Inventors: Pratul Kumar Argawal. Assignee: UT-Battelle

Describes a method that uses the primary amino acid sequence of a protein, energy minimization, molecular dynamics, and protein vibrational modes to predict the three-dimensional structure of a protein as well as to determine possible intermediates in the protein folding pathway. The abstract notes that unlike other approaches, the method does not depend on the size of the protein and has applications in the design of novel drugs and protein engineering.


US Patent 7,983,848. Computerized method and system for inferring genetic findings for a patient. Inventors: Mark A. Hoffman, David P. McCallie. Assignee: Cerner Innovation

Describes an approach for inferring genetic findings for a patient in a computing environment. The inferred findings are calculated using genetic findings for family members of the patient, linkage analysis, haplotype analysis, semantic test results for the person, and/or population genetics information.


US Patent 7,979,446. Computer-implemented biological sequence identifier system and method. Inventors: Anthony P. Malanoski, Baochuan Lin, Joel M. Schnur, David A Stenger. Assignee: The United States of America as represented by the Secretary of the Navy

This patent describes a method of submitting reference sequences to a taxonomic database to produce taxonomic results and reporting a taxonomic identification based on these results. These reference sequences are the output of genetic database queries that return a score for each sequence.


US Patent 7,974,789. Genetic diagnosis using multiple sequence variant analysis. Inventors: Marc Zabeau, Patrick Stanssens, Yannick Gansemans. Assignee: Methexis Genomics

Describes an approach for defining a subset of variations that can be used as genetic markers to search for correlations with certain phenotypic traits. According to the investigators, the approach can be implemented in algorithms and programs that convert genotype data into constituent haplotypes. These tools can be used in genome-wide association studies, clinical in vitro diagnosis, plant and animal breeding, and identification of microorganisms.


US Patent 7,974,788. Gene discovery through comparisons of networks of structural and functional relationships among known genes and proteins. Inventors: Andrey Rzhetsky, Sergey Kalachikov, Michael O. Krauthammer, Carol Friedman, Pauline Kra.

This patent describes a natural language processing system for extracting and structuring information on genes and proteins found in genomics journal articles in a form that is appropriate for subsequent applications.


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.