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In Print: Bioinformatics Tool-Related Papers of Note, Oct. 2004

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Awad I, Rees C, Hernandez-Boussard T, Ball C, Sherlock G. Caryoscope: An Open Source Java application for viewing microarray data in a genomic context. [BMC Bioinformatics 2004, 5:151]: Discusses Caryoscope, an open source Java application for visualizing microarray data from array comparative genome hybridization experiments. Availability: http://dahlia.stanford.edu:8080/caryoscope/index.html.


Dowsey A, Dunn M, Yang G. ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis. [Proteomics. 2004 Oct 11 (epub ahead of print)]: Describes a grid-based system for analyzing 2D gels as part of the ProteomeGRID, which uses Condor cluster management and JPEG-LS lossless image compression for task farming.


Han K, Park B, Kim H, Hong J, Park J. HPID: The Human Protein Interaction Database. [Bioinformatics 2004 20(15):2466-2470]: Introduces the Human Protein Interaction Database, which was designed to provide human protein interaction information pre-computed from existing structural and experimental data; to predict potential interactions between proteins submitted by users; and to provide a depository for new human protein interaction data. Availability: http://www.hpid.org.


Jansen J, Hoefsloot H, Boelens H, van der Greef J, Smilde A. Analysis of longitudinal metabolomics data. [Bioinformatics 2004 20(15):2438-2446]: Describes a method for using weighted principal components analysis for analyzing metabolomics data. Availability: http://www-its.chem.uva.nl/research/pac/Software/pcaw.zip.


Liu Y, Zhao H. A computational approach for ordering signal transduction pathway components from genomics and proteomics data. [BMC Bioinformatics 2004, 5:158]: Describes an approach for predicting the order of signaling pathway components that is built on a score function that integrates protein-protein interaction data and microarray gene expression data.


Margolin A, Nemenman I, Basso K, Klein U, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. [arXiv pre-print archive: http://arXiv.org/abs/q-bio/0410037]: Describes ARACNE, an algorithm for reconstructing gene regulatory networks that can scale up to the complexity of mammalian cells, yet is general enough to address a much wider range of network deconvolution problems.


Morris C, Wood P, Griffiths S, Wilson K, Ashton A. MOLE: A data management application based on a protein production data model. [Proteins. 2004 Oct 1 (epub ahead of print)]: Describes MOLE (mining, organizing, and logging experiments), a data-management and target-tracking software package for molecular biologists and protein crystallographers. Availability: http://www.mole.ac.uk/.


Rees C, Demeter J, Matese J, Botstein D, Sherlock G. GeneXplorer: an interactive web application for microarray data visualization and analysis. [BMC Bioinformatics 2004, 5:141]: Describes GeneXplorer, a web application for microarray data visualization and analysis that uses HTML and JavaScript to display graphic and annotation information. Availability: http://search.cpan.org/dist/Microarray-GeneXplorer/.


Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. [RNA. 2004 Oct;10(10):1507-1517]: Describes RNA-hybrid, a program that predicts multiple potential binding sites of micro RNAs in large target RNAs by finding the energetically most favorable hybridization sites of a small RNA in a large RNA. Availability: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/.


Saunders N, Curmi P, Cavicchioli R. An online database for the detection of novel archaeal sequences in human ESTs. [Bioinformatics 2004 20(15):2361-2362]: Describes an automated screening system to detect foreign sequences of archaeal origin in human ESTs. Availability: http://psychro.bioinformatics.unsw.edu.au/pathogen/index.php.


Scott M, Thomas D, Hallett M. Predicting Subcellular Localization via Protein Motif Co-Occurrence. [Genome Res. 2004 Oct;14(10):1957-66]: Describes a Bayesian network localization predictor called PSLT that is based on the combinatorial presence of InterPro motifs and specific membrane domains in human proteins. The probabilistic framework generates a likelihood of localization to all organelles in order to predict multicompartmental proteins.


Tsai HH, Tsai CJ, Ma B, Nussinov R. In silico protein design by combinatorial assembly of protein building blocks. [Protein Sci. 2004 Oct;13(10):2753-2765]: Introduces a de novo algorithm for engineering new protein folds with low homology to existing proteins.


Underwood A, Green J. MOP-UP: an online tool for finding strain-specific primers or motifs in DNA or protein alignments. [Clin Microbiol Infect. 2004 Oct;10(10):948-50]: Presents MOP-UP, a web-based application for searching nucleic acid or amino-acid alignments for sequences or motifs that are unique to a subset of the members represented in the alignment. This has applications in the design of assays that aim to detect particular strains or species, according to the authors. Availability: http://www.hpa.org.uk/srmd/bioinformatics/tools/mop-ups.htm.


Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. [Proteins. 2004 Oct 8 (epub ahead of print)]: Presents a new scoring function, the template modeling score (TM-score), to assess the quality of protein structure templates and predicted full-length models. Availability: http://bioinformatics.buffalo.edu/TM-score.

 

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