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Rosetta Inpharmatics, Agilent Technologies, Affymetrix, and The University of Chicago

Rosetta Inpharmatics of Seattle has received US Patent No. 7,130,746, “Computer systems and computer programs for determining protein activity levels using gene expression profiles.” The patent claims methods for determining the level of protein activity in a cell by: a) measuring cellular constituents in a cell where the activity of a specific protein is determined so that a diagnostic profile is obtained; b) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of the protein to obtain response profiles and interpolating the response profiles to generate response curves; and c) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure.

Agilent Technologies has received US Patent No. 7,132,236, “Composition and method for optimized hybridization using modified solutions.” The patent claims a composition, kit, and method for use with microarrays that allow a probe and target to hybridize at a temperature lower than their standard hybridization temperature. The kit includes a microarray, a chemical composition for use with the microarray, and a target for detection. The method provides the steps of adding to a probe and target the chemical component, heating the probe and target in the presence of the added component, and then allowing the biopolymers to hybridize.

Affymetrix has received US Patent No.7,133,780, “Computer software for automated annotation of biological sequences.” The patent claims methods, software products, and systems for automated high-throughout gene characterization. In one embodiment, hidden Markov models are used to characterize genes. Biological sequences are then classified according to their hit with different HM methods, and computer software and systems are provided for highly accurate and automated gene characterization. The methods, computer software, and system can be used to assign genes to families based upon protein structural similarity.

The University of Chicago has received US Patent No. 7,132,240, “Use of methylated nucleic acid segments for isolating centromere DNA.” The patent describes methods for the isolation of centromeres from potentially any organism. Using the methods, methylated centromere DNA may be isolated from potentially any centromere in an organism by preparing a sample of genomic DNA from a selected species, obtaining a plurality of methylated nucleic acid segments from the genomic DNA, and screening the methylated nucleic acid segments to identify a centromere nucleic acid sequence. The technique is amenable to mass screenings employing use of arrays comprising libraries of DNA from a target species, according to the patent’s abstract.

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