Volume 5 2004   Special Issue: Ontology Workshop Göttingen 2004    Editorial Takako Takai-Igarashi, Toshihisa Takagi, Holger Michael and Edgar Wingender Third "Ontology Workshop on Ontology and Genomes" - Preface - 0001   Communication Vivian Lee, Evelyn Camon, Emily Dimmer, Daniel Barrell and Rolf Apweiler Who tangos with GOA? - Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools 0002   Article                Asako Koike and Toshihisa Takagi PRIME: automatically extracted PRotein Interactions and Molecular Information databasE 0003   Article                   Jasmin Saric, Lars J. Jensen and Isabel Rojas Large-scale extraction of gene regulation for model organisms in an ontological context 0004   Article Jacob Koehler, Chris Rawlings, Paul Verrier, Rowan Mitchell, Andre Skusa, Alexander Ruegg and Stephan Philippi Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures 0005   Article Marie-Paule Lefranc, Oliver Clément, Quentin Kaas, Elodie Duprat, Patrick Chastellan, Isabelle Coelho, Kora Combres, Chantal Ginestoux, Véronique Giudicelli, Denys Chaume and Gérard Lefranc IMGT-Choreography for immunogenetics and immunoinformatics 0006   Communication Holger Michael, Xin Chen, Ellen Fricke, Martin Haubrock, Remko Ricanek and Edgar Wingender Deriving an ontology for human gene expression sources from the CYTOMER® database on human organs and cell types 0007   Article Kenji Satou and Kaoru Yamamoto Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature 0008      Special Issue: Dagstuhl Seminar "Integrative Bioinformatics"    Editorial Ralf Hofestädt Dagstuhl Seminar on Integrative Bioinformatics - Preface - 0009   Opinion Eberhard O. Voit, Simeone Marino and Raman Lall Challenges for the identification of biological systems from in vivo time series data 0010   Article Ljudmilla Borisjuk, Mohammad-Reza Hajirezaei, Christian Klukas, Hardy Rolletschek and Falk Schreiber Integrating data from biological experiments into metabolic networks with the DBE information system 0011   Article Thomas Dandekar and Steffen Schmidt Metabolites and pathway flexibility 0012   Article Ming Chen and Ralf Hofestädt An algorithm for linear metabolic pathway alignment 0013   Article Ina Koch, Markus Schüler and Monika Heiner STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks 0014   Article David S. Wishart, Robert Yang, David Arndt, Peter Tang and Joseph Cruz Dynamic cellular automata: a simple but powerful approach to cellular simulation 0015   Article Gordon Broderick, Melania Ru'aini, Eugene Chan and Michael J. Ellison A life-like virtual cell membrane using discrete automata 0016   Article Manuela Pruess, Paul Kersey and Rolf Apweiler The Integr8 project - a resource for genomic and proteomic data 0017   Article Andrei L. Turinsky, Andrew C. Ah-Seng, Paul M.K. Gordon, Julie N. Stromer, Morgan L. Taschuk, Emily W. Xu and Christoph W. Sensen Bioinformatics visualization and integration with open standards: the Bluejay genomic browser 0018   Article Matteo Fattore and Patrizio Arrigo Knowledge Discovery and System Biology in molecular medicine: an application to neurodegenerative diseases 0019   Article Marylens Hernández Guía, Abel González Pérez, Vladimir Espinosa Angarica, Ana T. Vasconcelos and Julio Collado-Vides Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach 0020          Further regular articles:        Communication Meena Kishore Sakharkar, Bagavathi S. Perumal, Yun Ping Lim, Lee Pern Chern, Yiting Yu and Pandjassarame Kangueane Alternatively Spliced Human Genes by Exon Skipping - a database (ASHESdb) 0021   Article Michal Brylinski, Leszek Konieczny and Irena Roterman SPI – Structure predictability index for protein sequences 0022       2005   Article Angelica Lindlöf and Zelmina Lubovac Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks 0023   Article Jianbin Peng, Cheng-Han Huang, Mary K. Short and Paul T. Jubinsky Magmas gene structure and evolution 0024   Article Alexander N. Gorban, Tatyana G. Popova and Andrei Y. Zinovyev Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences 0025   Communication Alexandre G. de Brevern New assessment of a structural alphabet 0026   Communication Matthias Wolf, Joachim Friedrich, Thomas Dandekar and Tobias Müller CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures 0027   Article 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 and Saleh M. Ibrahim Collection of soluble variants of membrane proteins for transcriptomics and proteomics 0028   Article Jules J. Berman Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching 0029   Article Anton Dormer and Gregory Beck Evolutionary analysis of human vascular endothelial growth factor, angiopoietin, and tyrosine endothelial kinase involved in angiogenesis and immunity 0030   Communication Rosario San Millán, Javier Garaizar and Joseba Bikandi In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA 0031   Article Meena Kishore Sakharkar, Bagavathi S. Perumal, Kishore R. Sakharkar and Pandjassarame Kangueane An analysis on gene architecture in human and mouse genomes 0032   Article Espen Enerly, Zeng Sheng and Kuo-Bin Li Natural antisense as potential regulator of alternative initiation, splicing and termination 0033   Article Rana Bhadra, Narayanaswamy Srinivasan and Shashi B. Pandit A new domain family in the superfamily of alkaline phosphatases 0034   Article Robin J. Johnson, Jennifer M. Williams, Barbara M. Schreiber, Charles D. Elfe, Kelley L. Lennon-Hopkins, Marek S. Skrzypek and Renee D. White Analysis of Gene Ontology features in microarray data using the Proteome BioKnowledge® Library 0035   Communication Pandurangan Arun Prasad, Krishnan Vengadesan and Namasivayam Gautham MOLS - A program to explore the potential energy surface of a peptide and locate its low energy conformations 0036   Article Clark Jeffries, Michael Jarstfer and Diana O. Perkins Folded RNA from an intron of one gene might inhibit expression of a counteracting gene 0037   Communication Tariq Riaz, Kuo-Bin Li, Francis Tang and Arun Krishnan CMDWave: Conserved Motifs Detection using Wavelets 0038   Communication Kazuharu Arakawa, Nobuaki Kono, Yohei Yamada, Hirotada Mori and Masaru Tomita KEGG-based pathway visualization tool for complex omics data 0039   Article Kumar Gaurav, Nitin Gupta and Ramanathan Sowdhamini FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs 0040   Article Zhenlin Ju, Melissa C. Wells, Al Martinez, Leona Hazlewood and Ronald B. Walter An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus 0041   Communication Francesco Piva and Giovanni Principato CORRELATION FINDER 0042   Article Francisco Prosdocimi and J. Miguel Ortega Accessing optimal primer distance from insert 0043   Article Roustem N. Miftahof The wave phenomena in smooth muscle syncytia 0044   Article Siya Ram and Rishi Shanker Computing TaqMan probes for multiplex PCR detection of E. coli O157 serotypes in water 0045   Article Quentin Kaas and Marie-Paule Lefranc T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB 0046   Communication Takako Takai-Igarashi Ontology based standardization of Petri net modeling for signaling pathways 0047   Article Juan Carlos Ulloa, Adriana Matiz, Leonardo Lareo and Maria Fernanda Gutiérrez Molecular analysis of a 348 base-pair segment of open reading frame 2 of human astrovirus. A characterization of Colombian isolates 0048   Article Igor V. Deyneko, Alexander E. Kel, Helmut Blöcker and Gerhard Kauer Signal-theoretical DNA similarity measure revealing unexpected similarities of E. coli promoters 0049   Article Sukanta Mondal, Ramachandran Vijayan, Kannambath Shichina, Rajasekaran Mohan Babu and Suryanarayanarao Ramakumar I-superfamily conotoxins: sequence and structure analysis 0050   Article ZhiGang Hu, KePing Chen, LinLing Wang and Qin Yao Identification and characterization of Bombyx mori eIF5A gene through bioinformatics approaches 0051   Article Diego Q. Cortez, Antonio Lazcano and Arturo Becerra Comparative analysis of methodologies for the detection of horizontally transferred genes: a reassessment of first-order Markov models 0052   Article Georgina A. Ankra-Badu and Samuel E. Aggrey Identification of candidate genes at quantitative trait loci on chicken chromosome Z using orthologous comparison of chicken, mouse, and human genomes 0053   Communication P. Ajay Babu, Radha Boddepalli, V. Vasantha Lakshmi and G. Nageswara Rao DoD: Database of Databases - updated molecular biology databases 0054   Communication Kishore Ramaji Sakharkar, Iti Chaturvedi, Vincent T. K. Chow, Chee Keong Kwoh, Pandjassarame Kangueane and Meena Kishore Sakharkar u-Genome: A database on Genome Design in Unicellular genomes 0055

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