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ORCID7th ECCB 2008: Cagliari, Italy (Supplement of Bioinformatics)
- ECCB'08 Proceedings, Seventh European Conference on Computational Biology, 22-26 September 2008, Cagliari, Italy. 2008
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, Gerbert 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 González, 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
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