In Silico Biology, Volume 2

Volume 2, 2001

• Björn M. Ursing, Frank H. J. van Enckevort, Jack A. M. Leunissen, Roland J. Siezen:
  EXProt - a database for EXPerimentally verified Protein functions. 1
  
• Tetsuo Nishikawa, Toshio Ota, Yuri Kawai, Shizuko Ishii, Kaoru Saito, Jun-ichi Yamamoto, Ai Wakamatsu, Masashi Ozawa, Yutaka Suzuki, Sumio Sugano, Takao Isogai:
  Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries. 2
  
• Masami Ikeda, Masafumi Arai, Demelo Madrazo Lao, Toshio Shimizu:
  Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology . 3
  

Volume 2, 2002

• Ralf Hofestädt, Nikolay A. Kolchanov, John Reinitz:
  Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface). 4
  
• Andreas Freier, Ralf Hofestädt, Matthias Lange, Uwe Scholz, Andreas Stephanik:
  BioDataServer: A SQL-based service for the online integration of life science data. 5
  
• Falk Schreiber:
  High quality visualization of biochemical pathways in BioPath. 6
  
• Isabel Rojas, Luca Bernardi, Esther Ratsch, Renate Kania, Ulrike Wittig, Jasmin Saric:
  A database system for the analysis of biochemical pathways. 7
  
• Gabriel Moreno-Hagelsieb, 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. 8
  
• Nikolay A. Kolchanov, Eugenia A. Nedosekina, Elena A. Ananko, Vitali A. Likhoshvai, Nikolay L. Podkolodny, Alexander V. Ratushny, Irina L. Stepanenko, Olga A. Podkolodnaya, Elena V. Ignatieva, Yuri G. Matushkin:
  GeneNet database: description and modeling of gene networks. 9
  
• Johannes Jaeger, Brian C. Goodwin:
  Cellular oscillators in animal segmentation. 10
  
• Konstantin Kozlov, Ekaterina Myasnikova, Andrei Pisarev, Maria Samsonova, John Reinitz:
  A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. 11
  
• Patrizio Arrigo, Giovanni Ivaldi, Pasquale Paolo Cardo:
  In silico determination of potential antisense targets for human beta-globin variants. 12
  
• Mark Cooper, Scott C. Chapman, Dean W. Podlich, Graeme L. Hammer:
  The GP problem: Quantifying gene-to-phenotype relationships. 13
  

• Edgar Wingender:
  The German Conference on Bioinformatics 2001. 14
  
• Dietmar Schomburg, Martin Vingron:
  Bioinformatics research and education in Germany. 15
  
• Jingchu Luo:
  Bioinformatics service, education and research: the EMBnet and CBI. 16
  
• Steffen Schulze-Kremer:
  Ontologies for molecular biology and bioinformatics. 17
  
• Oliver Rinner, Burkhard Morgenstern:
  AGenDA: Gene prediction by comparative sequence analysis. 18
  
• Änne Glass, Lothar Gierl:
  A system architecture for genomic data analysis. 19
  
• Ania Barbasiewicz, Lin Liu, B. Franz Lang, Gertraud Burger:
  Building a genome database using an object-oriented approach. 20
  
• Jacob Köhler, Steffen Schulze-Kremer:
  The Semantic Metadatabase (SEMEDA): Ontology Based Integration of Federated Molecular Biological Data Sources. 21
  
• Yuri L. Orlov, V. P. Filippov, V. N. Potapov, Nikolay A. Kolchanov:
  Construction of stochastic context trees for genetical texts. 22
  
• Thomas Werner:
  Finding and decrypting of promoters contributes to the elucidation of gene function. 23
  
• Eugenii E. Vityaev, Yuri L. Orlov, Oleg V. Vishnevsky, Mikhail A. Pozdnyakov, Nikolay A. Kolchanov:
  Computer system "Gene Discovery" for promoter structure analysis. 24
  
• Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang, Yu-Chang Chang:
  Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae. 25
  
• Rolf Backofen, N. S. Narayanaswamy, Firas Swidan:
  Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. 26
  
• Zhi-Ping Feng:
  An overview on predicting the subcellular location of a protein. 27
  
• Karin Wieligmann, Luis Felipe Pineda De Castro, Martin Zacharias:
  Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2. 28
  
• Daniel Hanisch, Ralf Zimmer, Thomas Lengauer:
  ProML - the Protein Markup Language for specification of protein sequences, structures and families. 29
  
• Mario Albrecht, Daniel Hanisch, Ralf Zimmer, Thomas Lengauer:
  Improving fold recognition of protein threading by experimental distance constraints. 30
  
• Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, Thomas Lengauer:
  A hypergraph-based method for unification of existing protein structure- and sequence-families. 31
  
• Kerstin Koch, Frank Zöllner, Steffen Neumann, Franz Kummert, Gerhard Sagerer:
  Comparing bound and unbound protein structures using energy calculation and rotamer statistics. 32
  
• Rainer Spang, Carrie Blanchette, Harry Zuzan, Jeffrey R. Marks, Joseph Nevins, Mike West:
  Prediction and uncertainty in the analysis of gene expression profiles. 33
  
• 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. 34
  
• Sabine Dormann, Andreas Deutsch:
  Modeling of self-organized avascular tumor growth with cellular automata. 35
  
• Thoralf Töpel, Uwe Scholz, Ulrike Mischke, Dagmar Scheible, Ralf Hofestädt, Friedrich Trefz:
  Supporting genotype-phenotype correlation with the rare metabolic diseases database Ramedis. 36
  
• Michael Forster, Andreas Pick, Marcus Raitner, Falk Schreiber, Franz-Josef Brandenburg:
  The system architecture of the BioPath system. 37
  
• Martin Frank, Andreas Bohne, Thomas Wetter, Claus-Wilhelm von der Lieth:
  Knowledge-based approach for the rapid generation of a representative ensemble of N-glycan conformations. 38
  

• Addie Nina Olsen, John Mundy, Karen Skriver:
  Peptomics, identification of novel cationic Arabidopsis peptides with conserved sequence motifs. 39
  
• Maura Cárdenas-García, Jaime Lagunez-Otero, Nikolai A. Korneev:
  The application of abstract topology to RAS-related signal transduction pathways. 40
  
• Allen Chong, Guanglan Zhang, Vladimir B. Bajic:
  Information and sequence extraction around the 5'-end and translation initiation site of human genes. 41
  
• Jochen Hurlebaus, Arne Buchholz, Wolfgang Alt, Wolfgang Wiechert, Ralf Takors:
  MMT - A pathway modeling tool for data from rapid sampling experiments. 42
  
• Demelo Madrazo Lao, Toshikatsu Okuno, Toshio Shimizu:
  Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. 43
  
• German Nudelman, Tamar Tennenbaum, Ramit Mehr, Ron Unger:
  PESI - An intelligent system for Prediction of Enzyme - Substrate Interactions based on experimental constraints. 44
  
• Ashwin Sivakumar:
  2D Gels and bioinformatics - An eye at the future. 45
  
• Amanda Clare, Ross D. King:
  How well do we understand the clusters found in microarray data? 46
  
• Susan B. Davidson, Christian J. Stoeckert Jr.:
  In memory of Vadim Aleksandrovich Ratner. 47
  
• Anna Zorzet, Mats G. Gustafsson, Ulf Hammerling:
  Prediction of food protein allergenicity: a bioinformatic learning systems approach. 48
  

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