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In Print: Bioinformatics Tool-Related Papers of Note, June 2003


Horn D, Axel I. Novel clustering algorithm for microarray expression data in a truncated SVD space. [Bioinformatics. 2003 Jun 12; 19(9):1110-5]: Describes a clustering method that compresses dimensions via singular-value decomposition before applying a clustering algorithm. Available at

Hudek A, Cheung J, Boright A, Scherer, S. Genescript: DNA sequence annotation pipeline. [Bioinformatics 2003 19 (9): 1177-1178]: Software for annotating DNA sequence. Available at

Krishnamurthy L. et al. Pathways database system: an integrated system for biological pathways. [Bioinformatics. 2003 19(8): 930-937]: Describes an integrated system of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data. Available upon request ([email protected]).

Michaud D, Marsh A, Dhurjati P. eXPatGen: generating dynamic expression patterns for the systematic evaluation of analytical methods. [Bioinformatics 2003 19 (9): 1140-1146]: An on-line simulator to generate dynamic gene expression patterns typical of microarray experiments in order to evaluate analysis methods. Available at:

Smith L, Yeganova L, Wilbur WJ. Hidden Markov models and optimized sequence alignments. [Comput Biol Chem. 2003 Feb;27(1):77-84]: A version of the Needleman-Wunsch algorithm for sequence alignment in which the mutation matrix is allowed to vary under the control of a hidden Markov process.

Thompson, JD, Thierry, JC, Poch, O. RASCAL: rapid scanning and correction of multiple sequence alignments. [Bioinformatics 2003 19 (9): 1155-1161]: Multiple sequence alignment software that combines a number of recently developed methods into a two-step refinement process. Available at

Troyanskaya O, et al. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). [Proc. Natl. Acad. Sci. 2003 100 (14): 8348–8353 (epub ahead of print)]: Describes MAGIC (Multisource Association of Genes by Integration of Clusters), a framework that uses formal Bayesian reasoning to integrate heterogeneous types of high-throughput biological data for gene function prediction.

Zhang K, Sun F, Waterman MS, Chen T. Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data. [Am J Hum Genet. 2003 Jun 10 (epub ahead of print)]: Describes two algorithms to find a haplotype block partition with a fixed number of tag SNPs that can cover the maximal percentage of the whole genome.

Also note: the July 1 issue of Nucleic Acids Research is devoted to web-based bioinformatics software. The issue, which describes 131 packages, from AMIGene to XplorMed, is available at

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