Volume 2 2001   Article Björn M. Ursing, Frank H.J. van Enckevort, Jack A.M. Leunissen and Roland J. Siezen EXProt - a database for EXPerimentally verified Protein functions 0001   Article Tetsuo Nishikawa, Toshio Ota, Yuri Kawai, Shizuko Ishii, Kaoru Saito, Jun-ichi Yamamoto, Ai Wakamatsu, Masashi Ozawa, Yutaka Suzuki, Sumio Sugano and Takao Isogai Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries 0002   Article               Masami Ikeda, Masafumi Arai, Demelo M. Lao and Toshio Shimizu Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology 0003      2002 Special Issue: Dagstuhl Seminar "Functional Genomics"    Editorial Ralf Hofestädt, Nikolay Kolchanov and John Reinitz Information and simulation systems for the analysis of gene regulation and metabolic pathways - Preface - 0004   Article Andreas Freier, Ralf Hofestädt, Matthias Lange, Uwe Scholz and Andreas Stephanik BioDataServer: A SQL-based service for the online integration of life science data 0005   Article Falk Schreiber High quality visualization of biochemical pathways in BioPath 0006   Article Isabel Rojas, Luca Bernardi, Esther Ratsch, Renate Kania, Ulrike Wittig and Jasmin Saric A database system for the analysis of biochemical pathways 0007   Article Gabriel Moreno-Hagelsieb and Julio Collado-Vides Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context 0008   Article Nikolay A. Kolchanov, Eugenia A. Nedosekina, Elena A. Ananko, Vitaly A. Likhoshvai, Nikolay L. Podkolodny, Alexander V. Ratushny, Irina L. Stepanenko, Olga A. Podkolodnaya, Elena V. Ignatieva and Yury G. Matushkin GeneNet database: description and modeling of gene networks 0009   Article Johannes Jaeger and Brian C. Goodwin Cellular oscillators in animal segmentation 0010   Article Konstantin Kozlov, Ekaterina Myasnikova, Andrei Pisarev, Maria Samsonova and John Reinitz A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ 0011   Article Patrizio Arrigo, Giovanni Ivaldi and Pasquale Paolo Cardo In silico determination of potential antisense targets for human beta-globin variants 0012   Article               Mark Cooper, Scott C. Chapman, Dean W. Podlich and Graeme L. Hammer The GP problem: Quantifying gene-to-phenotype relationships 0013      Special Issue:    G C B ' 0 1"    Editorial Edgar Wingender The German Conference on Bioinformatics 2001 0014   Report Dietmar Schomburg and Martin Vingron Bioinformatics research and education in Germany 0015   Report Jingchu Luo Bioinformatics service, education and research: the EMBnet and CBI 0016   Review Steffen Schulze-Kremer Ontologies for molecular biology and bioinformatics 0017   Article Oliver Rinner and Burkhard Morgenstern AGenDA: Gene prediction by comparative sequence analysis 0018   Communication Änne Glass and Lothar Gierl A system architecture for genomic data analysis 0019   Article A. Barbasiewicz, L. Liu, B.F. Lang and G. Burger Building a genome database using an object-oriented approach 0020   Article Jacob Köhler and Steffen Schulze-Kremer The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources 0021   Article Yuri L. Orlov, V. P. Filippov, V. N. Potapov and Nikolay A. Kolchanov Construction of stochastic context trees for genetical texts 0022   Review Thomas Werner Finding and decrypting of promoters contributes to the elucidation of gene function 0023   Communication Eugenii E. Vityaev, Yury L. Orlov, Oleg V. Vishnevsky, Mikhail A. Pozdnyakov and Nikolay A. Kolchanov Computer system "Gene Discovery" for promoter structure analysis 0024   Article Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang and Yu-Chang Chang Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae 0025   Article Rolf Backofen, N. S. Narayanaswamy and Firas Swidan Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation 0026   Article Zhi-Ping Feng An overview on predicting the subcellular location of a protein 0027   Communication Karin Wieligmann, Luis Felipe Pineda De Castro and Martin Zacharias Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2 0028   Article Daniel Hanisch, Ralf Zimmer and Thomas Lengauer ProML - the Protein Markup Language for specification of protein sequences, structures and families 0029   Article Mario Albrecht, Daniel Hanisch, Ralf Zimmer and Thomas Lengauer Improving fold recognition of protein threading by experimental distance constraints 0030   Article Jan Freudenberg, Ralf Zimmer, Daniel Hanisch and Thomas Lengauer A hypergraph-based method for unification of existing protein structure- and sequence-families 0031   Article Kerstin Koch, Frank Zöllner, Steffen Neumann, Franz Kummert and Gerhard Sagerer Comparing bound and unbound protein structures using energy calculation and rotamer statistics 0032   Article Rainer Spang, Carrie Blanchette, Harry Zuzan, Jeffrey R. Marks, Joseph Nevins and Mike West Prediction and uncertainty in the analysis of gene expression profiles 0033   Article Martin Dugas, Claudia Schoch, Susanne Schnittger, Alexander Kohlmann, Wolfgang Kern, Torsten Haferlach, Karl Überla Integration of clinical and genetic information - from patient data to gene expression analysis 0034   Article Sabine Dormann and Andreas Deutsch Modeling of self-organized avascular tumor growth with cellular automata 0035   Article Thoralf Töpel, Uwe Scholz, Ulrike Mischke, Dagmar Scheible, Ralf Hofestädt and Friedrich Trefz Supporting genotype-phenotype correlation with the rare metabolic diseases database Ramedis 0036   Article Michael Forster, Andreas Pick, Marcus Raitner, Falk Schreiber and Franz J. Brandenburg The system architecture of the BioPath system 0037   Article Martin Frank, Andreas Bohne, Thomas Wetter and Claus-W. v. d. Lieth Knowledge-based approach for the rapid generation of a representative ensemble of N-glycan conformations 0038 Further regular articles:        Article Addie Nina Olsen, John Mundy and Karen Skriver Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs 0039   Article Maura Cárdenas-García, Jaime Lagunez Otero and Nikolai A. Korneev The application of abstract topology to RAS-related signal transduction pathways 0040   Communication Allen Chong, Guanglan Zhang and Vladimir B. Bajic Information and sequence extraction around the 5'-end and translation initiation site of human genes                0041   Article Jochen Hurlebaus, Arne Buchholz, Wolfgang Alt, Wolfgang Wiechert and Ralf Takors MMT - A pathway modeling tool for data from rapid sampling experiments 0042   Article Demelo Madrazo Lao, Toshikatsu Okuno and Toshio Shimizu Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction 0043   Article German Nudelman, Tamar Tennenbaum, Ramit Mehr and Ron Unger PESI - An intelligent system for Prediction of Enzyme - Substrate Interactions based on experimental constraints 0044   Review Ashwin Sivakumar 2D Gels and bioinformatics - An eye at the future 0045   Article Amanda Clare and Ross D. King How well do we understand the clusters found in microarray data? 0046   Editorial   In memory of Vadim Aleksandrovich Ratner 0047   Article Anna Zorzet, Mats Gustafsson and Ulf Hammerling Prediction of food protein allergenicity: a bioinformatic learning systems approach 0048          ------------------ This completes volume 2 ------------------

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