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Bioinformatics Tool-Related Papers of Note, September 2006

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Dolan ME, Holden CC, Beard MK, Bult CJ. Genomes as geography: using GIS technology to build interactive genome feature maps. [BMC Bioinformatics. 2006 Sep 19;7:416]: Describes the Genome Spatial Information System, an effort to apply concepts and methodologies developed for displaying geographic data for displaying genomes spatially. In contrast to the horizontally stacked data tracks used by current genome browsers, GenoSIS uses registered spatial layers composed of spatial objects for displaying diverse data.
 

 
Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT. miTarget: microRNA target gene prediction using a support vector machine. [BMC Bioinformatics. 2006 Sep 18;7:411]: Introduces miTarget, a support vector machine classifier for miRNA target gene prediction that uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features.
 

 
Krishnamurthy N, Brown D, Kirshner D, Sjolander K. PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification. [Genome Biol. 2006 Sep 14;7(9):R83]: Discusses PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 “books” for protein families and domains, with pre-calculated structural, functional, and evolutionary analyses. Availability: http://phylogenomics.berkeley.edu/phylofacts/.
 

 
La Rosa P, Viara E, Hupe P, et al. VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles. [Bioinformatics. 2006 Sep 1;22(17):2066-73]: Describes a graphical user interface developed for visualization and analysis of molecular profiles, including CGH arrays, transcriptome arrays, SNP arrays, loss of heterozygosity results, and chromatin immunoprecipitation arrays.
 

 
Lee SI, Pe'er D, Dudley AM, Church GM, Koller D. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. [Proc Natl Acad Sci USA. 2006 Sep 19;103(38):14062-7]: Describes a probabilistic method, called Geronemo, designed to identify the mechanism by which genetic changes perturb a regulatory network. Geronemo automatically constructs a set of co-regulated genes, whose regulation can involve both sequence variations and expression of regulators.
 

 
Lewis J, Ossowski S, Hicks J, Errami M, Garner HR. Text similarity: an alternative way to search MEDLINE. [Bioinformatics. 2006 Sep 15;22(18):2298-304]: Discusses a hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall. The system includes a low-sensitivity weighted keyword-based first-pass algorithm, followed by a sentence-alignment-based similarity algorithm to rank-order those results. Availability: http://invention.swmed.edu/.
 

 
Liang Z, Xu M, Teng M, Niu L. NetAlign: a web-based tool for comparison of protein interaction networks. [Bioinformatics. 2006 Sep 1;22(17):2175-7]: Introduces NetAlign, a web-based tool for comparative analysis of protein interaction networks. NetAlign compares a query network with a target network by combining interaction topology and sequence similarity to identify conserved network substructures, which may derive from a common ancestor. Availability: http://www1.ustc.edu.cn/lab/pcrystal/NetAlign.
 

 

Titulaer MK, Siccama I, Dekker LJ, et al. A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls. [BMC Bioinformatics 2006, 7:403]: Presents a database application for detecting significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The software architecture includes a graphical user interface written in Java; a MySQL database, which contains all metadata; an FTP server to store all raw mass spectrometry files and processed data; and the software package R, which is used for modular statistical calculations.

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