Table of Contents

• New Challenges in Gene Expression Data Analysis and the Extended GEPASJavier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo. 1-5
• Consensus Clustering and Functional Interpretation of Gene Expression DataPaul Kellam, Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel J. Martin, Christine A. Orengo, Xiaohui Liu. 6
• Bridging the Gap between Gene Expression and Physiological Phenotype: Is there still Room for Kinetic Models?Albert Sorribas, Ester Vilaprinyó. 7-11
• Optimized Desolvation for Rigid-Body Docking: Fast Prediction of Protein Interaction SitesJuan Fernández-Recio. 12-15
• Triplex-Forming Sequences in Regulatory RegionsJosep Ramon Goñi, Modesto Orozco. 16-19
• What Works (and What Doesn t) in Estimating the Change in Free Energy due to Point Mutations in the Protein InteriorMarta Bueno, Carlos J. Camacho, Javier Sancho. 20-22
• Semi-Empirical NMR-Based Protein Homology Modelling driven by Chemical Shift Back CalculationsDaniel Monleón, Vicent Esteve, Lucía Yim, Marta Martínez-Vicente, María-Eugenia Armengod, Bernardo Celda. 23-24
• Proposal of a Minimal Genome for Bacterial LifeRosario Gil, Francisco J. Silva, Juli Peretó, Andrés Moya. 25-29
• M-GCAT: Multiple Genome Comparison and Alignment ToolTodd J. Treangen, Xavier Messeguer. 30-33
• On the Biological Relevance of Modules in Protein Interaction NetworksJuan F. Poyatos, Laurence D. Hurst. 34-36
• Analysis of Evolutionary Patterns from Huge DNA Sequence DataAlbert J. Vilella, Angel Blanco-Garcia, Stephan Hutter, Julio Rozas. 37-39
• Exploring the Phylogenetic Landscape of {P}roteobacteria using Phylogenomic ApproachesIñaki Comas, Andrés Moya, Fernando González-Candelas. 40-42
• Microeconomic Principles Explain an Optimal Genome Size in BacteriaJuan Garcia Ranea, Alastair Grant, Janet M. Thornton, Christine A. Orengo. 43
• The Novel Virus Genotyping Tool (STAR) and its Use in Subtyping Human Immunodeficiency Virus Type-1 and Hepatitis B VirusesRichard Myers, Catherine V. Gale, Caroline Clark, Julie Bennett, Richard S. Tedder, Ian G. Williams, Paul Kellam. 44
• Properties of Genes involved in Human Genetic DiseaseNúria López-Bigas, Christos A. Ouzounis. 45-46
• Variable Selection from Random Forests: Application to Gene Expression DataRamón Díaz-Uriarte. 47-52
• UVCLUSTER: Searching For Regularities in Complex GraphsVicente Arnau, Sergio Mars, Ignacio Marín. 53-55
• Artificial Chemistries and Metabolic PathwaysLiliana Félix, Francesc Rosselló, Gabriel Valiente. 56-59
• Simulation of the Notch Genetic Network during Early Development of the Vertebrate Inner EarAdrián López García de Lomana, Gina Abelló, Berta Alsina, Jordi Villà-Freixa. 60-62
• Automatic Annotation of Alternative of Alternative Splicing in Eukaryotic GenomesEduardo Eyras. 63-67
• On the Analysis of the Intersection of the Interactome and the MetabolomeJoan Planas-Iglesias, Daniel Aguilar, Baldomero Oliva. 68-69
• Bioinformatic Analyses of the Dio Family of ProteinsAna María Rojas, Luis Sánchez-Pulido, Agnes Fütterer, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia. 70-71
• Detection of Functional Motifs in Biosequences: A Grammatical Inference ApproachDamián López, Antonio Cano, Manuel Vazquez de Parga, Belén Calles, José M. Sempere, Tomás Pérez, José Ruiz, Pedro García. 72-75
• The Long and Short Flavodoxins: Evolutionary Origin and Role of the Differentiating Loop in Apoflavodoxin StructureMarta Bueno, Jesus Tejero, Javier Sancho. 76-79
• Integration and Comparison of Interactome DatabasesCarlos Prieto, Alberto de Luis, Javier De Las Rivas. 80-83
• AMarge: Automated Extensive Quality Assessment of Affymetrix ChipsJuan José Lozano, Susana G. Kalko. 84-86
• Kernel-Based Fisher Discriminant Analysis for Microarray DataFerran Reverter, Esteban Vegas. 87-91
• Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp ProteomesLeonardo Arbiza, Joaquín Dopazo, Hernán Dopazo. 92-99
• MutRes and LsdbRes: A Bioinformatics Platform for Mutation DatabasesPablo Marín-García, Heikki Lehväslaiho. 100
• Codon Based Amino Acid Encoding for the Neural Network Prediction of Protein Secondary StructureJosé Santos. 101-106
• The Gene Identification Problem from a Hypotheses Test PerspectiveMireia Vilardell, Alex Sánchez. 107-112
• A Web-Based Utility for High-Throughput SNP Data AnalysisCarlos Morcillo-Suarez, Josep Alegre, Marc Esteve, Jaume Bertranpetit, Francesc Calafell, Arcadi Navarro. 113
• Comparative Study of MAPK 9 Alternative Splicing from Human and MouseDavid Talavera, Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz. 114-117
• A Tool for Heuristic Detection of Association Clusters in Whole-Genome ScansTomàs Marquès-Bonet, Oscar Lao, Robert Goertsches, Manuel Comabella, Xavier Montalban, Arcadi Navarro. 118
• A Bioinformatic Approach to the Comparative Study of Human and Mouse ProteomesSergio Lois, Xavier de la Cruz. 119-121
• Investigating the 3D Conformation of N-Terminally Constrained OligopeptidesItizar Frades, Richard J. Edwards, Denis C. Shields. 122-123
• A Study of the Impact of Sequence Variability in Protein CavitiesDavid Piedra, Miquel Calvo, Xavier de la Cruz. 124-127
• Annotation of Non-Human Pathological Mutations utilising Human-Parameterised Neural NetworksCarles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz. 128-131
• Highly Specific and Accurate Selection of siRNAs for High-Throughput Functional AssaysJavier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo. 132-136
• Storage, Representation and Analysis of Nucleotide PolymorphismSònia Casillas, Natalia Petit, Raquel Egea, Antonio Barbadilla. 137-141
• On Supertrees of Phylogenetic TreesMercè Llabrés, Francesc Rosselló, Gabriel Valiente. 142-145
• Investigating the Assignment of Probes to Transcripts in Affymetrix MicroarraysAlberto de Luis, Javier De Las Rivas. 146-147
• New Relations in the Edge Ideal Metrics Family for BiopolymersRicardo Alberich, Jairo Rocha. 148-153
• The Use of Weighted Least Squares Test Statistic in Branch and Topology TestingBorys Wróbel, Rafael Sanjuán, Andrés Moya, Fernando González-Candelas. 154-156
• Finding SNPs with Putative Phenotypic Effect at Transcriptional LevelLucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Joaquín Dopazo. 157-160
• An Approach to the Modular Structure of CancerÁlvaro Mateos, Joaquín Dopazo. 161-165
• XML Databases, are Ready for Bioinformatics?José María Fernández, Alfonso Valencia. 166-170
• Prediction of Transcription Factor Binding Sites with PROMO v.3: Improving the Specificity of Weight Matrices and the Searching ProcessDomènec Farré, David García, M. Mar Albà, Xavier Messeguer. 171-172
• Can we Find Molecular Signatures from Gene Expression Data?Ramón Díaz-Uriarte, David Casado. 173-178
• Virtual Screening of Small Molecules Binding to an Engineered Protein Cavity in Flavodoxin using Freely Available Docking SoftwareJorge Estrada, Marta Bueno, Adrián Velázquez, Nunilo Cremades, Javier Sancho. 179-181
• Ordering BAC Clones from Fingerprint Data obtained through Four Enzymes Digestion and Fluorescent LabelingGiulio Marcon, Nicola Cannata, Mercè Llabrés, Marta Simeoni, Giorgio Valle. 182-190
• Repetitive Extragenic Palindromic Sequences in Pseudomonas syringae pv./ tomato DC3000 GenomeRaquel Tobes, Eduardo Pareja. 191-193
• A Web Based Suite of Tools for Microarray Quality Control and Data AnalysisJuanjo Lozano, David Otero, Belén Miñana, Eva González, Lauro Sumoy. 194-195
• Bioinformatic Analysis of Functional Characteristics of Enzymatic Active Centres using both Sequence and Structure Information: An Application to the Carnitine/Choline Acyltransferases Protein FamilyEduardo López-Viñas, Antonio G. Cordente, Montserrat Morillas, Fausto G. Hegardt, Paulino Gómez-Puertas. 196-203
• Fold Recognition using Residual Dipolar CouplingsJesús Villajos, Angel R. Ortiz. 204
• Comparison of Active Centers of Proteins: The Kinesin Family as a Test CaseAntoni Valencia, Martín Pérez, Adam Hospital, Joan Carles Fernández, Elena Manresa, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco. 205
• Hydration Free Energy in MacromoleculesAntonio Morreale, Xavier de la Cruz, Tim Meyer, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco. 206-207
• Assessment of Genetic Association using Haplotypes Inferred with UncertaintyXavier Solé, Raquel Iniesta, Elisabet Guinó, Joan Valls, Víctor Moreno. 208-210
• Blast2GO: A Universal Annotation and Visualization Tool for Functional Genomics ResearchAna Conesa, Stefan Götz, Juan Miguel García-Gómez, Montserrat Robles, Manuel Talón. 211
• maSigPro: a Method to Identify Significantly Differential Expression Profiles in Time-Course Microarray ExperimentsAna Conesa, María José Nueda, Alberto Ferrer, Manuel Talón. 212