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

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Berman J, et al. The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. [BMC Bioinformatics 2004, 5:19]: Discusses the Tissue Microarray Data Exchange Specification, which allows tissue microarray data to be organized in an XML document annotated with common data elements.


Bickel D. HighProbability determines which alternative hypotheses are sufficiently probable: Genomic applications include detection of differential gene expression. [arXiv pre-print archive: http://arXiv.org/abs/ q-bio/0402049]: Describes software called HighProbability, which addresses the multiple testing problem in microarray analysis. Availability: http://www.davidbickel.com.


Comander J, et al. Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation. [BMC Genomics 2004, 5:17]: Presents an intensity-based variance estimation technique to improve the accuracy and precision of p-value estimates for differentially regulated genes. Availability: http://vessels.bwh.harvard.edu/software/papers/bmcg2004.


Cope L. A benchmark for Affymetrix GeneChip expression measures. [Bioinformatics 2004 20(3):323-331]: Discusses a graphical tool to evaluate summaries of Affymetrix probe-level data and determine how an expression measure performs in several important areas. Availability: http://affycomp.biostat.jhsph.edu.


Demir E, et al. An ontology for collaborative construction and analysis of cellular pathways. [Bioinformatics 2004 20(3):349-356]: Presents an ontology for the representation of cellular events, along with a software tool, PATIKA (pathway analysis tool for integration and knowledge acquisition). Availability: http://www.patika.org.


Hermjakob H, et al. The HUPO PSI’s Molecular Interaction format — a community standard for the representation of protein interaction data. [Nat. Biotechnol. 2004 22(2):177-83]: Proposes a community-standard data model for the representation and exchange of protein interaction data. Availability: http://psidev.sourceforge.net/mi/xml/doc/user/.


Hu Z, et al. VisANT: an online visualization and analysis tool for biological interaction data. [BMC Bioinformatics 2004, 5:17]: Introduces an open source application for integrating biomolecular interaction data. Availability: http://visant.bu.edu/.


Levenkova N, Gu Q, Rux J. Gene specific siRNA selector. [Bioinformatics 2004 20(3):430-432]: Presents an siRNA design tool that scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Availability: http://bioinfo.wistar.upenn.edu/siRNA/siRNA.htm.


Ludwig W et al. ARB: a software environment for sequence data. [Nucleic Acids Research 2004 32(4): 1363-1371]: Describes ARB, a project to develop a variety of interacting software tools for sequence database maintenance and analysis using a phylogenetic tree as a visualization framework.


Menconi G. Sublinear growth of information in DNA sequences. [arXiv pre-print archive: http://arXiv.org/abs/q-bio/0402046]: Introduces a method for analyzing complete genomes using an adaptive compression algorithm.


Nguyen T, et al. Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. [Bioinformatics 2004 20(3):439-443]: Presents a web-based software tool that acquires SNP allele frequencies from multiple data sources. Availability: https://mapgenetics.nimh.nih.gov/frequencyfinder/index.jsp.


Orlev N, Shamir R, Shiloh Y. PIVOT: Protein Interacions Visualization Tool. [Bioinformatics 2004 20(3):424-425]: Describes a visualization tool for protein-protein interactions. Availability: http://www.cs.tau.ac.il/~rshamir/pivot.


Petri A, Fleckner J, Matthiessen M. Array-A-Lizer: A serial DNA microarray quality analyzer. [BMC Bioinformatics 2004, 5:12]: Describes a software tool to analyze the hybridization quality of microarray experiments. Availability: http://madswichmann.dk/arrayalizer/.


Thompson J, Prigent V, Poch O. LEON: multiple alignment evaluation of neighbors. [Nucleic Acids Research 2004 32(4): 1298-1307]: Describes a method for predicting homology between proteins based on a multiple alignment of complete sequences.


Zhang B, et al. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. [BMC Bioinformatics 2004, 5:16]: Discusses a web-based tool that generates a tree-like structure to navigate the Gene Ontology for input gene sets. Availability: http://genereg.ornl.gov/gotm/.

 

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