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Recent Patents in Bioinformatics, Feb. -- March 2006

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US Patent 7,020,561. Methods and systems for efficient comparison, identification, processing, and importing of gene expression data. Inventors: Kevin McLoughlin, Francois Collin, Victor Markowitz, Thodoros Topaloglou, Alexandros Athanasopoulos. Assignee: Gene Logic.

Covers systems and methods for analyzing gene expression, gene annotation, and sample information in a relational format. The methods include comparative differential expression analysis, expression pattern matching, and mapping of external attributes or identifiers to internal representations of gene fragments or samples.


US Patent 7,020,559. Methods for identifying and classifying organisms by mass spectrometry and database searching. Inventors: Plamen Demirev, Catherine Fenseleau. Assignee: University of Maryland.

Protects a method for rapid identification of biological materials based on the information contained in genome and protein sequence databases. In a preferred embodiment, the method uses mass spectrometry of intact or treated cells to determine the masses of a set of ions and correlates each ion in the set to a protein, along with the organismic source of the protein, by searching a database of protein molecular weights.


US Patent 7,016,786. Statistical methods for analyzing biological sequences. Inventors: Rama Ranganathan, Steve Lockless. Assignee: Board of Regents, the University of Texas System.

Covers statistical algorithms for identifying evolutionarily conserved amino acid positions within a family of proteins, and for identifying interacting amino acid positions within a protein sequence. The algorithms can also be used to analyze other polymer sequences such as polysaccharides, lipids, DNA, RNA, and DNA microarray data. The patent also describes algorithms for analyzing "the structural changes of perturbations to determine the mechanisms by which positions are coupled are also disclosed," according to the abstract.


US Patent 7,011,943. Method for detecting a designated genetic sequence in murine genomic DNA. Inventor: Timothy Hodge. Assignee: Transnetyx.

Protects a method for conducting transgenic and targeted mutagenesis screening of genomic DNA that includes a computer that receives instructions concerning the designated genetic sequence and other screening parameter selection from a remote user, and an automatic screening device that analyzes samples of genomic DNA for the designated sequence.


US Patent 7,010,431. Method for effecting computer implemented decision-support in the selection of the drug therapy of patients having a viral disease. Inventors: Charles Achim Bernard Boucher. Assignee: F. Hoffman-LaRoche.

Protects a computer-implemented decision-support method for selecting a drug therapy for patients with a viral disease. A rules database is provided and patient data is entered including genotype data on the viral genome of the viral disease. The rules database includes a number of associated rules for each available drug for treatment of the viral disease. Each rule indicates the suitability of the drug for treatment of a specific viral genotype. The patient data is entered into the rules database, and the database provides an output of drugs suitable for therapy. The drugs suitable for therapy are displayed in a ranking in accordance with their suitability indication.


US Patent 7,010,430. Method for displaying gene experiment data. Inventors: Ryo Nakashige, Yasuyuki Nozaki, Takuro Tamura, Tsunehiko Watanabe. Assignee: Hitachi Software Engineering.

Protects a visual display for comparing expression data of genes from two experiments based on expression data of one sample common to both experiments. In order to compare data of expression levels obtained from different experiments each using two types of samples, three types of expression levels are displayed in three dimensions as mediated by the data of the common sample used in both experiments. Specifically, expression level data for Samples A and B and expression level data for Samples A and C are combined and converted into single three-dimensional data and displayed as points inside a sphere.

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The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.