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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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