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Recent Patents in Bioinformatics, Oct. — Nov. 2006

US Patent 7,139,665. Computational method for designing enzymes for incorporation of non natural amino acids into proteins. Inventors: Deepshikha Datta, Pin Wang, Isaac Carrico, Stephen Mayo, David Tirrell. Assignee: California Institute of Technology.
Protects methods, reagents, and computational tools for designing non-natural substrate analogs for enzymes, especially for designing unnatural amino acid analogs for aminoacyl tRNA synthetases, such as the Phe tRNA synthetase.

US Patent 7,136,517. Image analysis process for measuring the signal on biochips. Inventors: Nicolas Ugolin, Mory Doukoure, Olivier Alibert, Sylvie Chevillard. Assignee: Commissariat a l'Energie Atomique.
Protects an image analysis process for measuring the signal on biochips that are organized into one or several blocks, with each block comprising a large number of spots. Each spot is composed of at least one probe. In the process, the spots appear in the form of a periodic and regular signal and this periodicity is used to identify the position of the blocks and the spots.

US Patent 7,134,995.  Animal genetic and health profile database management. Inventor: Jean Dodds. Assignee: Hemopet.
Covers a system, method, and apparatus for computerized management of databases relating to phenotypic health assessment and genomic mapping and genetic screening of animals. Users may input data relating to animal health, lifespan, and genetic background, and obtain reports relating to phenotypic health assessment of a particular animal subject or animal group, and genotypic characteristics of a particular subject or animal group to which the subject belongs.

US Patent 7,133,864. System and method for accessing biological data. Inventor: Chantal Roth. Assignee: Syngenta Participations.
Protects a system for searching a database of biological information. A search panel uses XML to send search requests to the database. A database graph generation module linked to the biological database generates a database graph representing the database schema. Once the database schema is known, another module creates joints between the database tables in order to most effectively join data from one table to another. An SQL statement incorporating the optimized joints is then used to search the biological database.

US Patent 7,133,781. Biopolymer sequence comparison. Inventors: Lawrence Toll, Patrick Lincoln, Peter Karp, Kemal Sonmez. Assignee: SRI International.
Covers methods, software, and systems for comparing biopolymer sequences. “The model includes at least two different characterizations of states of matching between segments of sequences at defined positions,” according to the patent abstract. Examples of states of matching include similarity and dissimilarity between objects, as well as similarity to a reference sequence or sequence profile. A topology of particular match states can be used to identify classes of sequences.

US Patent 7,133,780. Computer software for automated annotation of biological sequences. Inventors: Michael Siani-Rose, Ron Shigeta. Assignee: Affymetrix.
Protects 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 classified according to their hit with different HMM models using a curve analysis.

US Patent 7,130,746. Computer systems and computer programs for determining protein activity levels using gene expression profiles. Inventors: Stephen Friend, Roland Stoughton. Assignee: Rosetta Inpharmatics.
Covers methods for determining the level of protein activity in a cell by first measuring the abundance of cellular constituents in a cell. The method then measures the abundance of cellular constituents that occur in a cell in response to perturbations in the activity of certain proteins in order to obtain response profiles and interpolate the response profiles to generate response curves. Finally, the method determines 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. In alternative embodiments, the invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with those drugs.

US Patent 7,130,459. Reference database. Inventors: Norman Anderson, Leigh Anderson. Assignee: Large Scale Biology.
Covers methods for data acquisition and cataloging that are used to classify polypeptides into a reference index or database. The database can be used to identify previously unidentified samples, according to the patent abstract.

US Patent 7,127,379. Method for the evolutionary design of biochemical reaction networks. Inventors: Bernhard Palsson, Jeremy Edwards. Assignee: The Regents of the University of California.
Covers methods for achieving an optimal function of a biochemical reaction network. The methods “can be performed in silico using a reconstruction of a biochemical reaction network of a cell and iterative optimization procedures,” according to the patent abstract. The methods can also include laboratory culturing steps to confirm predictions made using the in silico methods. The invention includes computer systems and computer products, including computer-readable program code, for performing the in silico steps of the invention.

US Patent 7,127,354. Method of displaying gene data, and recording medium. Inventors: Yasuyuki Nozaki, Ryo Nakashige, Takuro Tamura. Assignee: Hitachi Software Engineering.
Protects a method of displaying gene data that is used to discover expression patterns specific to gene functions and to infer the function of a gene of which the function is unknown. “A threshold value representing the degree of similarity of expression patterns is established in advance, and genes having the same function and genes with similar expression patterns to them are extracted and displayed,” according to the patent abstract. Cluster analysis is performed on the extracted genes by re-selecting the experiment patterns for clustering.

US Patent 7,124,032. System and method for reconstructing pathways in large genetic networks from genetic perturbations. Inventor: Andreas Wagner. Assignee: Science & Technology Corporation @ UNM.
Protects a system and method for reconstructing pathways in large genetic networks from genetic perturbations. The method applies a recursive algorithm for determining the path between every gene pair in an arbitrarily large genetic network from large-scale gene perturbation data and reconstructs all direct and indirect regulatory gene interactions in the network. Genetic perturbation data is used to identify all genes accessible from a perturbed gene to generate an accessibility list for the gene. Graph theory mathematics is applied to the accessibility list, such as through a recursive algorithm performed on a desktop computer, to obtain an adjacency list for the gene that characterizes a genetic network.

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The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.