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IP Update: Apr 22, 2011

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Recent Patents in Bioinformatics, March — April 2011

US Patent 7,930,156. Method and apparatus for supporting analysis of gene interaction network, and computer product. Inventors: Koji Maruhashi, Hiroshi Yamakawa, Yoshio Nakao. Assignee: Fujitsu.

Describes a method and a tool for analyzing gene interaction networks. According to the scientists, the system provides detailed information for each "analysis subject partial network," including the number of nodes and the number of edges for each disease. The scientists wrote that based on the information, a user can designate a disease, and a network diagram "indicating a partial network related to the designated disease" is created and displayed.


US Patent 7,930,107. Methods of generating variant proteins with increased host string content. Inventors: Gregory Alan Lazar, John R. Desjarlais, Philip W. Hammond. Assignee: Xencor.

The patent describes novel methods used to generate variant proteins with increased host string content and provides a description of proteins that are engineered using these methods.


US Patent 7,917,306. Methods and systems for generating cell lineage tree of multiple cell samples. Inventors: Dan Frumkin, Adam Wasserstrom, Shai Kaplan, Uriel Feige, Ehud Y. Shapiro. Assignee: Yeda Research and Developement.

Describes a method of generating a cell lineage tree. The method involves determining at least one genotypic marker for each cell and computationally clustering data representing the marker to create the tree.


US Patent 7,917,303. Method for identifying combinations of motifs that do not mutate simultaneously in a set of viral polypeptide sequences comprising a putative drug binding site. Inventors: Anne Vanet, Michaela Muller-Trutwin, Thomas Valere, Sophie Brouillet, Emmanuelle Ollivier, Laurent Marsan. Assignee: Centre National de la Recherche Scientifique.

The patent describes methods for identifying a motif or a combination of motifs that predetermine mutations in a set of sequences. This process involves aligning a set of motif sequences represented by a single-character code and then comparing them to a reference sequence.


US Patent 7,917,302. Determination of optimal local sequence alignment similarity score. Inventors: Torbjorn Rognes. Assignees: Torbjorn Rognes and Erling Christen Seeberg

The patent describes an implementation of the Smith-Waterman sequence alignment algorithm that uses parallel processing to achieve an eight-fold speed-up.


US Patent 7,917,300. Method and program for predicting gene network. Inventors: Shuichi Onami, Koji Kyoda. Assignees: Japan Science and Technology Agency and Keio University

Describes a method of predicting gene networks by using indirect causal relationships to supplement a network comprised of direct causal relationships.


US Patent 7,917,299. Method and apparatus for performing similarity searching on a data stream with respect to a query string. Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster. Assignee: Washington University

Describes a method for performing similarity searching on a biosequence data stream.


US Patent 7,912,652. System and method for mutation detection and identification using mixed-base frequencies. Inventor: Jon M. Sorenson, Assignee: Applied Biosystems (Life Technologies)

The patent describes methods of evaluating sequence information to characterize putative heterozygous indel mutations. According to the abstract, the methods "utilize sequence and trace information to identify mixed-base presence resulting from allelic differences. These methods may be applied to identify and resolve single nucleotide polymorphisms, insertions, deletions, and other mutational events."


The Scan

Test of the China Initiative

According to Science, the upcoming trial of Harvard University chemist Charles Lieber will test the US China Initiative.

Collaborative Approach

A virologist who spotted the Omicron variant of SARS-CoV-2 tells the Associated Press that its detection was aided by scientific sharing.

Genes of a Guide Dog

Wired reports on a study aimed at uncovering genes involved in being a successful guide dog.

PLOS Papers on RNAs in Metastatic Prostate Cancer, Ebola Field Lab, Embryonic RNA Editing

In PLOS this week: circRNA-mediated ceRNA network points to prostate cancer biomarkers, Ebola testing at frontline field laboratory, and more.