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Volume 5
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 -
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
Article                Asako Koike and Toshihisa Takagi
PRIME: automatically extracted PRotein Interactions and Molecular Information databasE
Article                   Jasmin Saric, Lars J. Jensen and Isabel Rojas
Large-scale extraction of gene regulation for model organisms in an ontological context
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
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
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
Article Kenji Satou and Kaoru Yamamoto
Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature

Special Issue: Dagstuhl Seminar "Integrative Bioinformatics"
Editorial Ralf Hofestädt
Dagstuhl Seminar on Integrative Bioinformatics
- Preface -
Opinion Eberhard O. Voit, Simeone Marino and Raman Lall
Challenges for the identification of biological systems from in vivo time series data
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
Article Thomas Dandekar and Steffen Schmidt
Metabolites and pathway flexibility
Article Ming Chen and Ralf Hofestädt
An algorithm for linear metabolic pathway alignment
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
Article David S. Wishart, Robert Yang, David Arndt, Peter Tang and Joseph Cruz
Dynamic cellular automata: a simple but powerful approach to cellular simulation
Article Gordon Broderick, Melania Ru'aini, Eugene Chan and Michael J. Ellison
A life-like virtual cell membrane using discrete automata
Article Manuela Pruess, Paul Kersey and Rolf Apweiler
The Integr8 project - a resource for genomic and proteomic data
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
Article Matteo Fattore and Patrizio Arrigo
Knowledge Discovery and System Biology in molecular medicine: an application to neurodegenerative diseases
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

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)
Article Michal Brylinski, Leszek Konieczny and Irena Roterman
SPI – Structure predictability index for protein sequences

Article Angelica Lindlöf and Zelmina Lubovac
Simulations of simple artificial genetic networks reveal features in the use of Relevance Networks
Article Jianbin Peng, Cheng-Han Huang, Mary K. Short and Paul T. Jubinsky
Magmas gene structure and evolution
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
Communication Alexandre G. de Brevern
New assessment of a structural alphabet
Communication Matthias Wolf, Joachim Friedrich, Thomas Dandekar and Tobias Müller
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures
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
Article Jules J. Berman
Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching
Article Anton Dormer and Gregory Beck
Evolutionary analysis of human vascular endothelial growth factor, angiopoietin, and tyrosine endothelial kinase involved in angiogenesis and immunity
Communication Rosario San Millán, Javier Garaizar and Joseba Bikandi
In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA
Article Meena Kishore Sakharkar, Bagavathi S. Perumal, Kishore R. Sakharkar and Pandjassarame Kangueane
An analysis on gene architecture in human and mouse genomes
Article Espen Enerly, Zeng Sheng and Kuo-Bin Li
Natural antisense as potential regulator of alternative initiation, splicing and termination
Article Rana Bhadra, Narayanaswamy Srinivasan and Shashi B. Pandit
A new domain family in the superfamily of alkaline phosphatases
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
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
Article Clark Jeffries, Michael Jarstfer and Diana O. Perkins
Folded RNA from an intron of one gene might inhibit expression of a counteracting gene
Communication Tariq Riaz, Kuo-Bin Li, Francis Tang and Arun Krishnan
CMDWave: Conserved Motifs Detection using Wavelets
Communication Kazuharu Arakawa, Nobuaki Kono, Yohei Yamada, Hirotada Mori and Masaru Tomita
KEGG-based pathway visualization tool for complex omics data
Article Kumar Gaurav, Nitin Gupta and Ramanathan Sowdhamini
FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs
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
Communication Francesco Piva and Giovanni Principato
Article Francisco Prosdocimi and J. Miguel Ortega
Accessing optimal primer distance from insert
Article Roustem N. Miftahof
The wave phenomena in smooth muscle syncytia
Article Siya Ram and Rishi Shanker
Computing TaqMan probes for multiplex PCR detection of E. coli O157 serotypes in water
Article Quentin Kaas and Marie-Paule Lefranc
T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB
Communication Takako Takai-Igarashi
Ontology based standardization of Petri net modeling for signaling pathways
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
Article Igor V. Deyneko, Alexander E. Kel, Helmut Blöcker and Gerhard Kauer
Signal-theoretical DNA similarity measure revealing unexpected similarities of E. coli promoters
Article Sukanta Mondal, Ramachandran Vijayan, Kannambath Shichina, Rajasekaran Mohan Babu and Suryanarayanarao Ramakumar
I-superfamily conotoxins: sequence and structure analysis
Article ZhiGang Hu, KePing Chen, LinLing Wang and Qin Yao
Identification and characterization of Bombyx mori eIF5A gene through bioinformatics approaches
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
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
Communication P. Ajay Babu, Radha Boddepalli, V. Vasantha Lakshmi and G. Nageswara Rao
DoD: Database of Databases - updated molecular biology databases
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

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