7. ECCB 2008: Cagliari, Italy (Supplement of Bioinformatics)

Editorials

• Anna Tramontano:
  Editorial. 1
  
• ECCB 2008 Organization. 3-5
  

Databases

• Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz:
  Annotation of metagenome short reads using proxygenes. 7-13
  
• Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, Chi-Ying F. Huang:
  PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. 14-20
  
• A. M. Willemsen, G. A. Jansen, J. C. Komen, S. van Hooff, H. R. Waterham, P. M. T. Brites, Ronald J. A. Wanders, Antoine H. C. van Kampen:
  Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. 21-27
  

Pathways/Interactions/Proteomics

• Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama:
  Functional coherence in domain interaction networks. 28-34
  
• Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht:
  An integrative approach for predicting interactions of protein regions. 35-41
  
• Lukas Käll, John D. Storey, William Stafford Noble:
  Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. 42-48
  
• Sebastian Böcker, Florian Rasche:
  Towards de novo identification of metabolites by analyzing tandem mass spectra. 49-55
  
• Gabi Kastenmüller, Johann Gasteiger, Hans-Werner Mewes:
  An environmental perspective on large-scale genome clustering based on metabolic capabilities. 56-62
  

Transcriptomics

• Elena Tsiporkova, Veselka Boeva:
  Fusing time series expression data through hybrid aggregation and hierarchical merge. 63-69
  
• Pei Gao, Antti Honkela, Magnus Rattray, Neil D. Lawrence:
  Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. 70-75
  
• Fantine Mordelet, Jean-Philippe Vert:
  SIRENE: supervised inference of regulatory networks. 76-82
  
• Hubert Rehrauer, Susan Schönmann, Leo Eberl, Ralph Schlapbach:
  PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. 83-89
  
• Israel Steinfeld, Roy Navon, Diego Ardigò, Ivana Zavaroni, Zohar Yakhini:
  Clinically driven semi-supervised class discovery in gene expression data. 90-97
  

Structural Bioinformatics

• Gergely Csaba, Fabian Birzele, Ralf Zimmer:
  Protein structure alignment considering phenotypic plasticity. 98-104
  
• Rafael Najmanovich, Natalja Kurbatova, Janet M. Thornton:
  Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. 105-111
  
• Emidio Capriotti, Marc A. Martí-Renom:
  RNA structure alignment by a unit-vector approach. 112-118
  

Text Mining

• Shi Yu, Steven Van Vooren, Léon-Charles Tranchevent, Bart De Moor, Yves Moreau:
  Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. 119-125
  
• Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez:
  Inter-species normalization of gene mentions with GNAT. 126-132
  
• Crystal L. Kahn, Benjamin J. Raphael:
  Analysis of segmental duplications via duplication distance. 133-138
  

Algorithms and Phylogeny

• Erez Ben-Yaacov, Yonina C. Eldar:
  A fast and flexible method for the segmentation of aCGH data. 139-145
  
• Andrew Wei Xu, Benoît Alain, David Sankoff:
  Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases. 146-152
  
• Vikas Bansal, Vineet Bafna:
  HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. 153-159
  
• Paulo G. S. da Fonseca, Katia S. Guimarães, Marie-France Sagot:
  Efficient representation and P-value computation for high-order Markov motifs. 160-166
  
• Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka:
  Mining significant tree patterns in carbohydrate sugar chains. 167-173
  

Genomes and Protein Analysis

• Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Rätsch:
  Optimal spliced alignments of short sequence reads. 174-180
  
• Marie-Laure Martin-Magniette, Tristan Mary-Huard, Caroline Bérard, Stéphane Robin:
  ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. 181-186
  
• Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert:
  Segment-based multiple sequence alignment. 187-192
  
• Yaniv Loewenstein, Michal Linial:
  Connect the dots: exposing hidden protein family connections from the entire sequence tree. 193-199
  
• Nir Yosef, Roded Sharan, William Stafford Noble:
  Improved network-based identification of protein orthologs. 200-206
  
• Yana Bromberg, Burkhard Rost:
  Comprehensive in silico mutagenesis highlights functionally important residues in proteins. 207-212
  

Systems Biology

• Julio Saez-Rodriguez, Stefan Gayer, Martin Ginkel, Ernst Dieter Gilles:
  Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. 213-219
  
• Elisabeth Remy, Paul Ruet:
  From minimal signed circuits to the dynamics of Boolean regulatory networks. 220-226
  
• Pedro T. Monteiro, Delphine Ropers, Radu Mateescu, Ana T. Freitas, Hidde de Jong:
  Temporal logic patterns for querying dynamic models of cellular interaction networks. 227-233
  
• Aitor Gonzalez, Claudine Chaouiya, Denis Thieffry:
  Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. 234-240
  

Bioinformatics for Diseases

• Predrag Radivojac, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, Sean D. Mooney:
  Gain and loss of phosphorylation sites in human cancer. 241-247
  
• Louis-Philippe Kronek, Anupama Reddy:
  Logical analysis of survival data: prognostic survival models by detecting high-degree interactions in right-censored data. 248-253