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

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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*
Organization
US Patent No.
Title
Affymetrix (7)
6,988,040
System, method, and computer software for genotyping analysis and identification of allelic imbalance
6,996,475
Computer software products for nucleic acid hybridization analysis
7,031,846
Method, system, and computer software
7,068,830
Method and system for providing a probe array chip design database
7,117,097
Methods, computer software products, and systems for correlating gene lists
7,117,095
Methods for selecting nucleic acid probes
7,133,780
Computer software for automated annotation of biological sequences
Hitachi/Hitachi Software Engineering (4)
7,085,651
Method and device for assembling nucleic acid base sequences
7,010,430
Method for displaying gene experiment data
7,031,847
Method and apparatus for displaying gene expression patterns
7,127,354
Method of displaying gene data, and recording medium
Regents of the University of California (4)
7,062,384
Methods for classifying high-dimensional biological data
7,149,631
Alternative splicing and nonsense-mediated decay: computational methods and gene regulation
7,152,070
System and method for integrating and accessing multiple data sources within a data warehouse architecture
7,127,379
Method for the evolutionary design of biochemical reaction networks
Accelrys (3)
7,065,453
Molecular docking technique for screening of combinatorial libraries
7,113,870
Prediction of molecular polar surface area and bioabsorption.
7,146,278
Method of selecting marker molecules for prediction of molecular activity
Applera (2)
7,085,652
Methods for searching polynucleotide probe targets in databases
7,110,890
Auto-analysis framework for sequence evaluation.
BioDiscovery (2)
6,990,221
Automated DNA array image segmentation and analysis
7,099,502
System and method for automatically processing microarrays
Gene Logic (2)
7,020,561
Methods and systems for efficient comparison, identification, processing, and importing of gene expression data
7,031,843
Computer methods and systems for displaying information relating to gene expression data
IBM (2)
7,096,167
System and method for molecular dynamic simulation
7,043,476
Method and apparatus for data mining to discover associations and covariances associated with data
Maxygen (2)
7,024,312
Methods for making character strings, polynucleotides and polypeptides having desired characteristics
7,058,515
Methods for making character strings, polynucleotides and polypeptides having desired characteristics
Rosetta Inpharmatics (2)
7,035,739
Computer systems and methods for identifying genes and determining pathways associated with traits
7,130,746
Computer systems and computer programs for determining protein activity levels using gene expression
SRI International (2)
7,039,238
Data relationship model
7,133,781
Biopolymer sequence comparison
University of Texas System (2)
7,016,786
Statistical methods for analyzing biological sequences
7,065,451
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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