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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

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.