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IP Update: Recent Patents in Bioinformatics, November — December 2011

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US Patent 8,078,407. System and method for identifying disease-influencing genes. Inventor: Stephen J. Brown. Assignee: Health Hero Network

Describes a method for using behavior and psychological information to identify disease-influencing genes. It involves creating a database of information about the environments of individuals who are known to be at risk for certain diseases. This information can be combined with existing genotype data and used to find genes that are linked with disease as well as drug candidates and targets. The approach also includes data-mining techniques that are used to classify individuals based on their environmental profiles and to further categorize them based on their disease progression; as well as to find genetic differences between the groups.


US Patents 8,073,633 and 8,073,632. Computational methods and systems for suggesting modulators of CYP450 as treatment options. Inventors: Mahalaxmi Gita Bangera, Roderick A. Hyde, Elizabeth A. Sweeney, Lowell L. Wood, Jr. Assignee: The Invention Science Fund I

These patent abstracts describe computational approaches to identify enzymes in the CYP450 family that influence drug metabolism as well as modulators of these enzymes that can be used as treatments and methods of communicating them to the user.


US Patent 8,073,629. Simulation system of function of biological organ. Inventors: Yasuhiro Kouchi, Takeo Saitou, Masayoshi Seike. Assignee: Sysmex

The patent abstract describes a mathematical model for simulating the functions of biological organs. The tool uses time series data that represents the organ's biological response to estimate its response at time points that were not measured. The method uses that information to generate a reference time series dataset of the organ's response and uses it to construct a virtual representation of its function.


US Patent 8,073,627. System for identification of pathogens. Inventors: David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke. Assignee: Ibis Biosciences

Describes a method that includes computational tools for determining the origins of unknown bioagents by comparing them to the molecular masses of known pathogens to determine proper courses of treatment.


US Patents 8,068,994 and 8,068,993. Method for analyzing biological networks. Inventor: Sorin Draghici. Assignee: Wayne State University

Describes statistical methods for predicting the significance of biological pathways in diseases. It involves calculating an "impact factor" for each pathway that incorporates parameters such as "the normalized fold change of the differentially expressed genes, the statistical significance of the set of pathway genes, and the topology of the signaling pathway," the patent's description states. The inventor also notes that the approach improves on current pathway analysis methods, which have "limitations" that result in false positives and negatives.


US Patent 8,065,089. Methods and systems for analysis of dynamic biological pathways. Inventor: Kayvan Najarian. Assignee: University of North Carolina, Charlotte

The patent abstract describes a computational method for predicting the expression value of genes in time-series microarray data. Its steps include "a nonlinear independent component analysis algorithm that extracts the major components covering all considered genes" and "an autoregressive exogenous model ... to quantitatively express the dynamic interactions of [the] components." The tool then uses this information to predict the "expression parameters" for individual genes.


US Patent 8,050,872. System and method for rapid searching of highly similar protein-coding sequences using bipartite graph matching. Inventors: Bing Sun, Jacob T. Schwartz, Ofer H. Gill, Bhubaneswar Mishra. Assignee: New York University

Describes a method, called the Clean Ordered Mer-Based Alignment Tool, or COMBAT, for use in comparative genomic analysis. It works by searching for similar genomic sequences using a "stable-marriage" procedure with "incomplete lists" as a filter.


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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.