In Silico Biology, Volume 5

Volume 5, 2004

• 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.