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


Anders B, et al. GeneHopper: A Web-Based Search Engine to Link Gene-Expression Platforms through GenBank Accession Numbers. [Genome Biology 2003 4(5):R35]: A web-based search engine that links different expression resources based on UniGene clusters and HomoloGene orthologs. Available at:


Braun V, et al. ALES: Cell Lineage Analysis and Mapping of Developmental Events. [Bioinformatics 2003 19: 851-858]: Tools for visualizing, evaluating, and comparing cell lineages with the aim of identifying molecular and cellular events underlying development. Available at:


Brundege JM, Dubay C. Bioquery: An Object Framework for Building Queries to Biomedical Databases. [Bioinformatics 2003 19: 901-2]: An application for automating database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. Available at:


Brusic V, Petrovsky N. Bioinformatics for Characterization of Allergens, Allergenicity, and Allergic Crossreactivity. [Trends Immunol 2003 May;24(5):225-8]: Overview of bioinformatics tools for allergy research, including databases for management of allergen data, algorithms for the characterization of allergic crossreactivity, and tools for predicting allergenicity.


Castillo-Davis C, Hartl D. GeneMerge —Post-Genomic Analysis, Data Mining, and Hypothesis Testing. [Bioinformatics 2003 19: 891-892]: Web-based and standalone program that returns functional and genomic data for a given set of genes. Available at:


Charles Biro J. Overlapping Translation of Nucleic Acid Sequences for Bioinformatics Applications. [Med Hypotheses 2003 May;60(5):654-9]: An alternative method to TBlastX that translates nucleic acids in database and query sequences into overlapping protein-like sequences before searching with BlastP.


Engelen K, et al. MARAN: Normalizing Microarray Data. [Bioinformatics 2003 19: 893-894]: Web-based application for normalizing microarray data. Available at:


Goffard N, et al. IPPRED: Server for Protein Interactions Inference. [Bioinformatics 2003 19: 901-902]: Web-based server to infer protein-protein interactions through homology search between candidate proteins and those described as interacting. Available at:


Goh C. SPINE 2: A System for Collaborative Structural Proteomics within a Federated Database Framework. [Nucleic Acids Research 2003 31: 2833-2838]: Describes LIMS and data federation system used by the Northeast Structural Genomics Consortium for collaborative structural proteomics research projects. Available at:


Hoebeke M, Nicolas P, Bessières P. MuGeN: Simultaneous Exploration of Multiple Genomes and Computer Analysis Results. [Bioinformatics 2003 19: 859-864]: Software for navigating multiple annotated genomes. Available at:


Olman V, Xu D, Xu Y. CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. [Journal of Bioinformatics and Computational Biology Vol. 1, No. 1 (2003) 21-40]: A technique for identifying binding sites from a set of upstream regions of genes via data clustering.


Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse Engineering Gene Networks: Integrating Genetic Perturbations with Dynamical Modeling. [PNAS 2003 100: 5944-5949]: Demonstrates how the perturbation of selected genes in a microarray experiment can be used in conjunction with a reverse engineering algorithm to reveal the architecture of an underlying regulatory network.


Xu J, Li M, Xu Y, Kim D. Raptor: Optimal Protein Threading by Linear Programming. [Journal of Bioinformatics and Computational Biology Vol. 1, No. 1 (2003) 95-117]: A linear programming approach for 3D protein structure prediction via threading using the contact map graph of the protein template. Available at:


Yang P, et al. BioEditor — Simplifying Macromolecular Structure Annotation. [Bioinformatics 2003 19: 897-898]: Application for presenting structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. Available at:

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