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Recent Patents in Bioinformatics, Nov.- Dec. 2006, and 2006 Patent Leaders

US Patent 7,152,070. System and method for integrating and accessing multiple data sources within a data warehouse architecture. Inventors: Charles Musick, Terence Critchlow, Madhaven Ganesh, Tom Slezak, Krzysztof Fidelis. Assignee: The Regents of the University of California.
Covers a system and method for integrating data sources in a data warehouse. The method includes four types of metadata — abstract concepts, databases, transformations, and mappings — and a mediator generator that automatically generates data-management computer code based on the metadata. The resulting code defines a translation library that provides a data representation for domain-specific knowledge and a mediator class that defines methods to enter information into the data warehouse. According to the inventors, the method can be applied to a number of application areas, including protein sequence and structure analysis and functional genomics and proteomics.

US Patent 7,149,631. Alternative splicing and nonsense-mediated decay: computational methods and gene regulation. Inventors: Steven Brenner, Richard Green, Benjamin Lewis. Assignee: The Regents of the University of California.
Covers computational methods identify alternate splice forms of gene transcripts and isoforms that are subject to nonsense-mediated decay. According to the patent abstract, these methods were used to identify “thousands of human genes that generate alternative splice forms, and to demonstrate that about a third of these are subject to NMD.” According to the inventors, the high prevalence of NMD-targeted transcripts “indicates a systemic way of regulating gene expression — by shunting gene expression to nonproductive splice variants.”

US Patent 7,146,384. System and method for data analysis, manipulation, and visualization. Inventor: Reyad Sawafta. Assignee: TransTech Pharma.
Protects systems and methods for data analysis, including data retrieval, dynamic scripting and execution, mining, storing, and visualization. One embodiment of the invention “provides various views of assay data derived from a molecular discovery process,” according to the patent abstract.

US Patent 7,146,278. Method of selecting marker molecules for prediction of molecular activity. Inventor: William Egan, Steven Dixon. Assignee: Accelrys.
Protects a method that predicts properties of a candidate molecule by first classifying a set of reference molecules as either possessing or not possessing at least one property, and then selecting a subset of the molecules to predict whether the candidate molecule possesses at least one property.

US Patent 7,142,989. Computer software to computer-design optimum oligonucleic acid sequence candidate from nucleic acid base sequences analyzed and method thereof. Inventors: Yoshiaki Aoki, Mitsuyoshi Ishikawa. Assignee: Kabushikigaisha Dynacom.
Protects a software program that designs “an optimum oligonucleic acid base sequence candidate from nucleic acid base sequences being analyzed,” according to the patent abstract. The program includes a first command to receive specifications of tolerated ranges of double-chain bond temperature, base sequence length, and GC content, and then stores the information. A second command then determines whether a sequence in each length falls within respective tolerated ranges based on the items received by the first command.


Bioinformatics Patent Leaders in 2006*
US Patent No.
Affymetrix (7)
System, method, and computer software for genotyping analysis and identification of allelic imbalance
Computer software products for nucleic acid hybridization analysis
Method, system, and computer software
Method and system for providing a probe array chip design database
Methods, computer software products, and systems for correlating gene lists
Methods for selecting nucleic acid probes
Computer software for automated annotation of biological sequences
Hitachi/Hitachi Software Engineering (4)
Method and device for assembling nucleic acid base sequences
Method for displaying gene experiment data
Method and apparatus for displaying gene expression patterns
Method of displaying gene data, and recording medium
Regents of the University of California (4)
Methods for classifying high-dimensional biological data
Alternative splicing and nonsense-mediated decay: computational methods and gene regulation
System and method for integrating and accessing multiple data sources within a data warehouse architecture
Method for the evolutionary design of biochemical reaction networks
Accelrys (3)
Molecular docking technique for screening of combinatorial libraries
Prediction of molecular polar surface area and bioabsorption.
Method of selecting marker molecules for prediction of molecular activity
Applera (2)
Methods for searching polynucleotide probe targets in databases
Auto-analysis framework for sequence evaluation.
BioDiscovery (2)
Automated DNA array image segmentation and analysis
System and method for automatically processing microarrays
Gene Logic (2)
Methods and systems for efficient comparison, identification, processing, and importing of gene expression data
Computer methods and systems for displaying information relating to gene expression data
IBM (2)
System and method for molecular dynamic simulation
Method and apparatus for data mining to discover associations and covariances associated with data
Maxygen (2)
Methods for making character strings, polynucleotides and polypeptides having desired characteristics
Methods for making character strings, polynucleotides and polypeptides having desired characteristics
Rosetta Inpharmatics (2)
Computer systems and methods for identifying genes and determining pathways associated with traits
Computer systems and computer programs for determining protein activity levels using gene expression
SRI International (2)
Data relationship model
Biopolymer sequence comparison
University of Texas System (2)
Statistical methods for analyzing biological sequences
Computer-based method for creating collections of sequences from a dataset of sequence identifiers corresponding to natural complex biopolymer sequences and linked to corresponding annotations
*As of Dec. 21, 2006

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