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Recent Patents in Bioinformatics, October — November, 2008

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US Patent 7,454,293. Methods for enhanced detection and analysis of differentially expressed genes using gene chip microarrays. Inventors: Gordon Okimoto; Charles Boyd; Johann Urschitz. Assignee: University of Hawai'i.
 
Protects a method for detection and statistical analysis of differentially expressed genes in gene chip microarrays. The method first transforms gene expression data into an expression data matrix, then performs wavelet denoising of the expression data matrix values to enhance their signal-to-noise ratio, and then performs singular value decomposition of the wavelet-denoised expression data matrix “to concentrate most of the gene expression signal in primary matrix eigenarrays to enhance the separation of true gene expression values from background noise,” according to the patent abstract. “The transformation of gene chip data into an image data paradigm facilitates the use of powerful image data processing techniques, including a generalized logarithm (g-log) function to stabilize variance over intensity, and the WSVD combination of wavelet packet transform and denoising and SVD to clearly enhance separation of the truly changed genes from background noise.”
 

 
US Patent 7,451,047. System and method for programatic access to biological probe array data. Inventors: Luis Jevons; Derek Bernhart; Nga Yu Cheung; Conrad Sheppy. Assignee: Affymetrix.
 
Protects an application programming interface that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related to probe arrays, the patent abstract states.
 

 
US Patent 7,444,308. Data mining platform for bioinformatics and other knowledge discovery. Inventors: Isabelle Guyon; Edward Reiss; Rene Doursat; Jason Aaron Edward Weston. Assignee: Health Discovery Corporation.
 
Covers a data-mining platform that comprises several system modules, each formed from several components. Each module has an input data component, a data analysis engine for processing the input data, an output data component for outputting the results of the data analysis, and a web server to access and monitor the other modules within the unit and to provide communication to other units. Each module processes a different type of data, the patent abstract states. For example, a first module may process microarray data while a second module processes biomedical literature for information supporting relationships between genes, and diseases and gene functionality.
 

 
US Patent 7,444,243. Probabilistic method for determining nucleic acid coding features. Inventor: James McIninch. Assignee: Monsanto Technology.
 
Protects a computational method for gene prediction. Specifically, the invention relates to the probabilistic analysis of nucleic acid sequences to determine coding features, including state probabilities for each nucleotide in a nucleic acid sequence, coding strand, open reading frame extent, insertion and deletion location, exon location, and protein sequence.
 

 
US Patent 7,437,249. Methods and systems for detrending signal intensity data from chemical arrays.  Inventors: John Frederick Corson; Jayati Ghosh; Svetlana Shchegrova. Assignee: Agilent Technologies.
 
Protects methods, systems and computer-readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface-fitted to calculate a surface approximation, and the surface approximation is normalized and used to de-trend the signal intensity values from the features, according to the patent abstract.
 

 
US Patent 7,433,787. System, method, and computer program product using a database in a computing system to compile and compare metabolomic data obtained from a plurality of samples. Inventors: Thomas Henry Barrett; Corey Donald DeHaven; Danny Alexander. Assignee: Metabolon.
 
Protects a method for generating a visual display of metabolomic data compiled by a database and an associated processor. The database automatically receives a three-dimensional spectrometry data set for a group of samples and the processor manipulates the data sets to produce plots that are directly comparable to characteristic plots corresponding to several selected metabolites. The processor device may generate a visual display that indicates the presence of the selected metabolites across the group of samples. The method “enables a user to analyze a series of complex data sets in a visual display that may indicate the presence of the selected metabolites across the group of samples,” according to the patent abstract. “Furthermore, the visual display generated by embodiments of the present invention also expedites the subjective analysis of the spectrometry data sets.”
 

 
US Patent 7,430,475. Biological discovery using gene regulatory networks generated from multiple-disruption expression libraries. Inventors: Seiyo Imoto; Takao Goto; Satoru Miyano; Kosuke Tashiro; Michiel de Hoon; Christopher J. Savoie; Saturo Kuhara. Assignee: GNI.
 
Protects new inferential methods to analyze complex biological information, including gene networks. The new methods include modifications of Boolean inferential methods and the application of those methods to determining relationships between expressed genes in organisms, determining cause and effect relationships between expressed genes, and in some embodiments, for determining upstream effectors of regulated genes. Additional modifications of Bayesian methods include the use of heterogeneous variance and different curve-fitting methods, including spline functions, to improve estimation of graphs of networks of expressed genes; and the use of bootstrapping methods and the determination of edge effects to more accurately provide network information between expressed genes.

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