4. ECCB / 6. JBI 2005: Madrid, Spain (Supplement of Bioinformatics)

• Roderic Guigó, Federico Morán, Alfonso Valencia, Josep F. Abril:
  ECCB/JBI 2005. 2
  
• ECCB/JBI 2005 Organization. 5
  
• Cigdem Demir, S. Humayun Gultekin, Bülent Yener:
  Augmented cell-graphs for automated cancer diagnosis. 12
  
• David de Juan, Mario Mellado, José Miguel Rodríguez-Frade, Patricia Hernanz-Falcón, Antonio Serrano, Antonio del Sol, Alfonso Valencia, Carlos Martínez-A, Ana María Rojas:
  A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. 18
  
• Gisele L. Pappa, Anthony J. Baines, Alex Alves Freitas:
  Predicting post-synaptic activity in proteins with data mining. 25
  
• Sònia Casillas, Natalia Petit, Antonio Barbadilla:
  DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. 30
  
• Myungeun Lim, Myunggeun Chung, Myungnam Bae, Sunhee Park:
  Design of a description language for generating wrapper to collect biological data. 32
  
• Ulf Leser:
  A query language for biological networks. 39
  
• Andreas Prlic, Thomas A. Down, Tim J. P. Hubbard:
  Adding Some SPICE to DAS. 41
  
• Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Hans-Werner Mewes:
  SIMAP - The similarity matrix of proteins. 46
  
• Oranit Dror, Ruth Nussinov, Haim J. Wolfson:
  ARTS: alignment of RNA tertiary structures. 53
  
• Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio:
  Predicting protein stability changes from sequences using support vector machines. 58
  
• Koji Tsuda, Hyunjung Shin, Bernhard Schölkopf:
  Fast protein classification with multiple networks. 65
  
• Joseph D. Szustakowski, Simon Kasif, Zhiping Weng:
  Less is more: towards an optimal universal description of protein folds. 71
  
• Alejandro Giorgetti, Domenico Raimondo, Adriana Erica Miele, Anna Tramontano:
  Evaluating the usefulness of protein structure models for molecular replacement. 76
  
• Kristin Missal, Dominic Rose, Peter F. Stadler:
  Non-coding RNAs in Ciona intestinalis. 78
  
• Eugene W. Myers:
  The fragment assembly string graph. 85
  
• Henry C. M. Leung, Francis Y. L. Chin:
  Finding exact optimal motifs in matrix representation by partitioning. 92
  
• Sungroh Yoon, Giovanni De Micheli:
  Prediction of regulatory modules comprising microRNAs and target genes. 100
  
• Tho Hoan Pham, José Carlos Clemente, Kenji Satou, Tu Bao Ho:
  Computational discovery of transcriptional regulatory rules. 107
  
• Sach Mukherjee, Stephen J. Roberts, Mark J. van der Laan:
  Data-adaptive test statistics for microarray data. 114
  
• Florian Sohler, Ralf Zimmer:
  Identifying active transcription factors and kinases from expression data using pathway queries. 122
  
• Elisabeth Georgii, Lothar Richter, Ulrich Rückert, Stefan Kramer:
  Analyzing microarray data using quantitative association rules. 129
  
• C. Vogl, Fatima Sanchez-Cabo, Gernot Stocker, S. Hubbard, Olaf Wolkenhauer, Zlatko Trajanoski:
  A fully Bayesian model to cluster gene-expression profiles. 136
  
• Walter R. Gilks, Brian D. M. Tom, Alvis Brazma:
  Fusing microarray experiments with multivariate regression. 143
  
• Toni Gabaldón, Martijn A. Huynen:
  Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. 150
  
• Itay Mayrose, Nir Friedman, Tal Pupko:
  A Gamma mixture model better accounts for among site rate heterogeneity. 158
  
• Daniel H. Huson, Tobias H. Klöpper:
  Computing recombination networks from binary sequences. 165
  
• Dirk Husmeier:
  Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. 172
  
• Mathieu Lajoie, Nadia El-Mabrouk:
  Recovering haplotype structure through recombination and gene conversion. 179
  
• Tomàs Marquès-Bonet, Oscar Lao, Robert Goertsches, Manuel Comabella, Xavier Montalban, Arcadi Navarro:
  Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans. 181
  
• Yiping Zhan, David Kulp:
  Model-P: a basecalling method for resequencing microarrays of diploid samples. 189
  
• E. Simão, Elisabeth Remy, Denis Thieffry, Claudine Chaouiya:
  Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli. 196
  
• Dmitriy Leyfer, Zhiping Weng:
  Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. 203
  
• Jean-Marc Schwartz, Minoru Kanehisa:
  A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. 205
  
• Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano:
  Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. 212
  
• Nam Tran, Chitta Baral, Vinay J. Nagaraj, Lokesh Joshi:
  Knowledge-based framework for hypothesis formation in biochemical networks. 219
  
• Mario Albrecht, Carola Huthmacher, Silvio C. E. Tosatto, Thomas Lengauer:
  Decomposing protein networks into domain-domain interactions. 221
  
• Csaba Pál, Balázs Papp, Martin J. Lercher:
  Horizontal gene transfer depends on gene content of the host. 223
  
• José M. Peña, Johan Björkegren, Jesper Tegnér:
  Growing Bayesian network models of gene networks from seed genes. 229
  
• Olga Vitek, Chris Bailey-Kellogg, Bruce Craig, Paul Kuliniewicz, Jan Vitek:
  Reconsidering complete search algorithms for protein backbone NMR assignment. 236
  
• Kengo Sato, Yasubumi Sakakibara:
  RNA secondary structural alignment with conditional random fields. 242
  
• Sjors H. W. Scheres, Mikel Valle, José María Carazo:
  Fast maximum-likelihood refinement of electron microscopy images. 244
  
• Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka:
  A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. 251
  
• Robert Hoffmann, Alfonso Valencia:
  Implementing the iHOP concept for navigation of biomedical literature. 258
  
• Robert Küffner, Katrin Fundel, Ralf Zimmer:
  Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. 267
  
• Martin Szugat, Daniel Güttler, Katrin Fundel, Florian Sohler, Ralf Zimmer:
  Web servicing the biological office. 269