Volume 5, 2004

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  Takako Takai-Igarashi, Toshihisa Takagi, Holger Michael, Edgar Wingender: Preface - Third "Ontology Workshop on Ontology and Genomes".
• 
  Vivian Lee, Evelyn Camon, Emily Dimmer, Daniel Barrell, Rolf Apweiler: GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools.
• 
  Asako Koike, Toshihisa Takagi: PRIME: automatically extracted PRotein Interactions and Molecular Information databas.
• 
  Jasmin Saric, Lars Juhl Jensen, Isabel Rojas: Large-scale extraction of gene regulation for model organisms in an ontological context.
• 
  Jacob Köhler, Christopher J. Rawlings, Paul Verrier, Rowan A. C. Mitchell, Andre Skusa, Alexander Rüegg, Stephan Philippi: Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures.
• 
  Marie-Paule Lefranc, Oliver Clément, Quentin Kaas, Elodie Duprat, Patrick Chastellan, Isabelle Coelho, Kora Combres, Chantal Ginestoux, Véronique Giudicelli, Denys Chaume, Gérard Lefranc: IMGT-Choreography for immunogenetics and immunoinformatics.
• 
  Holger Michael, Xin Chen, Ellen Fricke, Martin Haubrock, Remko Ricanek, Edgar Wingender: Deriving an ontology for human gene expression sources from the CYTOMER? database on human organs and cell types.
• 
  Kenji Satou, Kaoru Yamamoto: Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature.

• 
  Ralf Hofestädt: Preface - Dagstuhl Seminar on Integrative Bioinformatics.
• 
  Eberhard O. Voit, Simeone Marino, Raman Lall: Challenges for the identification of biological systems from in vivo time series data.
• 
  Ljudmilla Borisjuk, Mohammad-Reza Hajirezaei, Christian Klukas, Hardy Rolletschek, Falk Schreiber: Integrating data from biological experiments into metabolic networks with the DBE information system.
• 
  Thomas Dandekar, Steffen Schmidt: Metabolites, pathway flexibility.
• 
  Ming Chen, Ralf Hofestädt: An algorithm for linear metabolic pathway alignment.
• 
  Ina Koch, Markus Schüler, Monika Heiner: STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks.
• 
  David S. Wishart, Robert Yang, David Arndt, Peter Tang, Joseph A. Cruz: Dynamic cellular automata: a simple but powerful approach to cellular simulation.
• 
  Gordon Broderick, Melania Rúaini, Eugene Chan, Michael J. Ellison: A life-like virtual cell membrane using discrete automata.
• 
  Manuela Pruess, Paul Kersey, Rolf Apweiler: The Integr8 project - a resource for genomic and proteomic data.
• 
  Andrei L. Turinsky, Andrew C. Ah-Seng, Paul M. K. Gordon, Julie N. Stromer, Morgan L. Taschuk, Emily W. Xu, Christoph W. Sensen: Bioinformatics visualization and integration with open standards: the Bluejay genomic browser.
• 
  Matteo Fattore, Patrizio Arrigo: Knowledge Discovery and System Biology in molecular medicine: an application to neurodegenerative diseases.
• 
  Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Julio Collado-Vides: Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach.

• 
  Meena K. Sakharkar, Bagavathi S. Perumal, Yun Ping Lim, Lee Pern Chern, Yiting Yu, Pandjassarame Kangueane: Alternatively Spliced Human Genes by Exon Skipping - a database.
• 
  Michal Brylinski, Leszek Konieczny, Irena Roterman: SPI - Structure predictability index for protein sequences.

Volume 5, 2005

• 
  Angelica Lindlöf, Zelmina Lubovac: Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks.
• 
  Jianbin Peng, Cheng-Han Huang, Mary K. Short, Paul T. Jubinsky: Magmas gene structure and evolution.
• 
  Alexander N. Gorban, Tatyana G. Popova, Andrei Yu. Zinovyev: Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences.
• 
  Alexandre G. de Brevern: New assessment of a structural alphabet.
• 
  Matthias Wolf, Joachim Friedrich, Thomas Dandekar, Tobias Müller: CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.
• 
  Steffen Möller, Eilhard Mix, Martin Blüggel, Pablo Serrano-Fernández, Dirk Koczan, Vasilis Kotsikoris, Manfred Kunz, Michael Watson, Jens Pahnke, Harald Illges, Michael Kreutzer, Stefan Mikkat, Hans-Jürgen Thiesen, Michael O. Glocker, Uwe K. Zettl, Saleh M. Ibrahim: Collection of soluble variants of membrane proteins for transcriptomics and proteomics.
• 
  Jules J. Berman: Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching.
• 
  Anton Dormer, Gregory Beck: Evolutionary analysis of human vascular endothelial growth factor, angiopoietin, and tyrosine endothelial kinase involved in angiogenesis and immunity.
• 
  Rosario San Millán, Javier Garaizar, Joseba Bikandi: In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA.
• 
  Meena K. Sakharkar, Bagavathi S. Perumal, Kishore R. Sakharkar, Pandjassarame Kangueane: An analysis on gene architecture in human and mouse genomes.

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