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Recent Patents in Bioinformatics, Oct. — Nov. 2007

US Patent 7,299,134. Method for correlating gene expression profiles with protein expression profiles. Inventors: William Rich, William Hutchens. Assignee: Bio-Rad Laboratories.
Covers methods for correlating gene and protein expression in a cell. The method first obtains two or more biological samples, then generates a gene expression profile for each sample and determines the nucleotide sequence of at least one mRNA in each gene expression profile. Next, the method predicts the amino acid sequence of the polypeptide encoded by the mRNA in each gene expression profile, predicts the mass of the polypeptide encoded by the mRNA, and generates a protein profile of polypeptides in each sample by mass spectrometry. Finally, the method determines the presence in each protein profile of a polypeptide with a mass that is the same as the predicted mass of the encoded polypeptide, “thereby identifying at least one protein that is expressed from a corresponding mRNA in each biological sample, thereby correlating gene expression with protein expression in two or more biological samples,” according to the patent claims.

US Patent 7,297,940. Method, apparatus, and program product for classifying ionized molecular fragments. Inventor: Marshall Bern. Assignee: Palo Alto Research Center.
Protects a method that classifies spectral peaks in dissociation spectrum data in order to improve the efficiency of molecular sequencing. According to the patent claims, the computer-controlled method first accesses dissociation spectrum data comprising spectral peaks that represent fragments of a “parent molecule.” The spectral peaks are associated with their respective peak intensities. The method represents the spectral peaks as vertices, assigns weighted edges to the vertices, and then applies a confidence-weighted classification to those vertices that are “responsive” to the weighted edges.

US Patent 7,289,911. System, methods, and computer program product for analyzing microarray data. Inventor: David Roth Rigney. Assignee: None.
Protects systems, methods, and a computer program for analyzing gene expression data. In particular, the patent relates to methods for analyzing data acquired with microarray technologies. The methods partition a set of genes into clusters, “based on the similarity of the genes' rates of messenger RNA synthesis,” according to the patent abstract. The invention also covers methods for annotating clusters with words or phrases that are extracted from documents associated with genes in the clusters, as well as methods for evaluating the quality of clustering “based on the extent to which documents associated with genes in a cluster collectively distinguish that cluster from all the other clusters, as well as the extent to which some words and phrases, present in documents associated with genes in the cluster, collectively distinguish that cluster from all the other clusters,” the patent abstract states.

US Patent 7,286,970. Computational model, method, and system for kinetically-tailoring multi-drug chemotherapy for individuals. Inventor: Shea Nicole Gardner. Assignee: The Regents of the University of California.
Covers a method and system for tailoring treatment regimens to individual patients with diseased cells that are resistant to such treatments. The method is based on a mathematical model that tracks the rates of population change of diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. “Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith,” the patent abstract states. A treatment regimen can then be selected from the available treatment options based on the efficacy value.

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