Full Papers

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  Christine Sinoquet, Raphaël Mourad, Philippe Leray: Forests of Latent Tree Models for the Detection of Genetic Associations. 5-14
• 
  Manish P. Kurhekar, Umesh A. Deshpande: A Deterministic Model of Bone Marrow with Homeostatic Properties and with Steady Production of Differentiated Cells. 15-23
• 
  Edite Figueiras, Rita Campos, Ricardo Oliveira, Luis F. Requicha Ferreira, Frits F. M. de Mul, Anne Humeau-Heurtier: Laser Doppler Flowmeters Prototypes Validation using Monte Carlo Simulations. 24-33
• 
  Anna A. Nilulova, Alexander V. Favorov, Vsevolod Makeev, Andrey A. Mironov: A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure. 34-41
• 
  Heorhiy Byelas, Martijn Dijkstra, Morris A. Swertz: Introducing Data Provenance and Error Handling for NGS Workflows within the MOLGENIS Computational Framework. 42-50
• 
  Pawel Blazej, Pawel Mackiewicz, Stanislaw Cebrat: Simulation of Bacterial Genome Evolution under Replicational Mutational Pressures. 51-57
• 
  Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré: Genome Halving by Block Interchange. 58-65
• 
  Markus E. Nebel, Anika Scheid: A n2 RNA Secondary Structure Prediction Algorithm. 66-75
• 
  Santiago Alonso-Quesada, Manuel de la Sen, Asier Ibeas: A Vaccination Control Law based on Feedback Linearization Techniques for SEIR Epidemic Models. 76-85
• 
  Fernando Izquierdo-Carrasco, Julien Gagneur, Alexandros Stamatakis: Trading Running Time for Memory in Phylogenetic Likelihood Computations. 86-95
• 
  Alexander Tsouknidas, Nikolaos Michailidis, Kleovoulos Anagnostidis, Antonios Lontos: Dual-energy X-ray Absorptiometry as an Indicator for Fragility Fracture Risks of the Femoral Neck. 96-101
• 
  Lubomir D. Antonov, Christian Andreetta, Thomas Hamelryck: An Efficient Parallel GPU Evaluation of Small Angle X-ray Scattering Profiles. 102-108

Short Papers

• 
  António dos Anjos, Bjarne Kjær Ersbøll, Faroq Al-Tam, Hamid Reza Shahbazkia: Matching Two-dimensional Gel Electrophoresis' Spots. 111-117
• 
  Oliver Bezuidt, Kingdom Mncube, Oleg N. Reva: Application of Genome Linguistic Approaches for Identification of Genomic Island in Bacterial Genomes and Tracking down their Origins - Genome Linguistics to Visualize Horizontal Gene Exchange. 118-123
• 
  Matej Lexa, Lucie Navrátilová, Karel Nejedlý, Marie Brázdová: Prediction of Significant Cruciform Structures from Sequence in Topologically Constrained DNA - A Probabilistic Modelling Approach. 124-130
• 
  Jyh-Jong Tsay, Shih-Chieh Su: A Memetic Algorithm for Protein Structure Prediction based on the 2D Triangular Lattice Model. 131-136
• 
  Eduardo Campos dos Santos, Bráulio Roberto Gonçalves Marinho Couto, Marcos Augusto dos Santos, Julio Cesar Dias Lopes: Predicting New Human Drug Targets by using Feature Selection Techniques. 137-142
• 
  Fábio Madeira, Ludwig Krippahl: Pycoevol - A Python Workflow to Study Protein-protein Coevolution. 143-149
• 
  Ramouna Fouladi, Emad Fatemizadeh, S. Shahriar Arab: Inference of Gene Regulatory Networks by Extended Kalman Filtering using Gene Expression Time Series Data. 150-155
• 
  Maysson Al-Haj Ibrahim, Sabah Jassim, Michael Anthony Cawthorne, Kenneth Langlands: Integrating Pathway Enrichment and Gene Network Analysis Provides Accurate Disease Classification. 156-163
• 
  Kartick Chandra Mondal, Nicolas Pasquier, Anirban Mukhopadhyay, Célia da Costa Pereira, Ujjwal Maulik, Andrea Tettamanzi: Prediction of Protein Interactions on HIV-1-Human PPI Data using a Novel Closure-based Integrated Approach. 164-173
• 
  Cody Ashby, Kun Wang, Carole L. Cramer, Xiuzhen Huang: Study of Protein Structure Alignment Problem in Parameterized Computation. 174-181
• 
  Charalampos S. Kouzinopoulos, Panagiotis D. Michailidis, Konstantinos G. Margaritis: Performance Study of Parallel Hybrid Multiple Pattern Matching Algorithms for Biological Sequences. 182-187
• 
  Trent Higgs, Bela Stantic, Tamjidul Hoque, Abdul Sattar: Benefits of Genetic Algorithm Feature-based Resampling for Protein Structure Prediction. 188-194
• 
  Philipp Rescheneder, Arndt von Haeseler, Fritz J. Sedlazeck: MASon: Million Alignments in Seconds - A Platform Independent Pairwise Sequence Alignment Library for next Generation Sequencing Data. 195-201
• 
  Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu: Efficient Path Kernels for Reaction Function Prediction. 202-207
• 
  Vojtech Bystrý, Matej Lexa: cswHMM: A Novel Context Switching Hidden Markov Model for Biological Sequence Analysis. 208-213
• 
  S. Garcia López, Jorge Alberto Jaramillo-Garzón, J. C. Higuita-Vásquez, C. G. Castellanos-Domínguez: Wrapper and Filter Metrics for PSO-based Class Balance Applied to Protein Subcellular Localization. 214-219
• 
  Cigdem Sevim Bayrak, Burak Erman: Statistical Mechanics of Proteins in the Random Coil State. 220-225
• 
  André Atanasio M. Almeida, Zanoni Dias: Improvements to a Multiple Protein Sequence Alignment Tool. 226-233
• 
  Ruben Acuña, Zoé Lacroix, Fayez Hadji, Jacques Chomilier, Nikolaos Papandreou: Prediction of Chimeric Protein Fold. 234-239
• 
  Ana Stanescu, Doina Caragea: Semi-supervised Learning of Alternatively Spliced Exons using Expectation Maximization Type Approaches. 240-245
• 
  Malgorzata Wanczyk, Pawel Blazej, Pawel Mackiewicz, Stanislaw Cebrat: How to Deal with Small Open Reading Frames?. 246-250
• 
  Italo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Francesco Rocco, Giancarlo Albo, André M. Deelder, Yuri E. M. van der Burgt, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri: Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. 251-256
• 
  Alexander E. Nezhinsky, Esther Stoop, Astrid van der Sar, Fons J. Verbeek: Numerical Analysis of Image based High Throughput Zebrafish Infection Screens - Matching Meaning with Data. 257-262
• 
  Jennifer Hallinan, S. Park, Anil Wipat: Bridging the Gap between Design and Reality - A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits. 263-268

Posters

• 
  Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti, Roberto Marangoni: A Taste of Yeast Mobilomics. 271-274
• 
  Sergio Torres-Sánchez, Manuel García Sánchez, Germán Arroyo, Nuria Medina-Medina, Rosana Montes-Soldado, Francisco Soler-Martínez, María M. Abad-Grau: 3D Visualization of Haplotype Risk Maps. 275-280
• 
  Marco Franke, Klaus-Dieter Thoben, Rainer Söller: Approach to Enable an Automatic Pre-processing of qRT-PCR - Analysis. 281-285
• 
  András Hartmann, Susana Vinga, João M. Lemos: Identification of Hiv-1 Dynamics - Estimating the Noise Model, Constant and Time-varying Parameters of Long-term Clinical Data. 286-289
• 
  Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda Petzold: Abstractions for Scaling eScience Applications to Distributed Computing Environments - A StratUm Integration Case Study in Molecular Systems Biology. 290-294
• 
  Sandra M. Venske, Richard A. Gonçalves, Myriam Regattieri Delgado: Differential Evolution to Multi-objective Protein Structure Prediction. 295-298
• 
  Bich Hai Ho, Ngoc Tu Le, Tu Bao Ho: Bayesian Network Analysis of Relationships between Nucleosome Dynamics and Transcriptional Regulatory Factors. 299-302
• 
  Paolo Piro, Wafa Bel Haj Ali, Lydie Crescence, Oumelkheir Ferhat, Jacques Darcourt, Thierry Pourcher, Michel Barlaud: Universal k-NN (UNN) Classification of Cell Images using Histograms of DoG Coefficients. 303-307
• 
  Diogo Pratas, Armando J. Pinho, Sara P. Garcia: Computation of the Normalized Compression Distance of DNA Sequences using a Mixture of Finite-context Models. 308-311
• 
  Preetam Ghosh, Bhaswati Datta, Vijayaraghavan Rangachari: Computational Predictions for the Nucleation Mass and Lag times Involved in Aβ42 Peptide Aggregation. 312-316
• 
  Rafael S. Costa, Daniel Machado, A. R. Neves, Susana Vinga: Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation. 317-321
• 
  Elena D. Stavrovskaya, Andrey A. Mironov, Dmitry A. Rodionov, Inna Dubchak, Pavel S. Novichkov: Automated Regulon Content Prediction and Estimation of PWM Quality. 322-325
• 
  Thanapat Kangkachit, Kitsana Waiyamai: Fuzzy Concept Lattice-based Approach for Reactive Motifs Discovery. 326-330
• 
  Francesco Abate, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra, Alberto Ferrarini, Massimo Delledonne, Enrico Macii: A Novel Analysis Flow for Fused Transcripts Discovery from Paired-end RNA-Seq Data. 331-334
• 
  Massimo Natale, Alfonso Caiazzo, Enrico M. Bucci, Elisa Ficarra: A Novel Gaussian Fitting Approach for 2D Gel Electrophoresis Saturated Protein Spots. 335-338
• 
  Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, Mario Orsi, Enrico Macii: Characterization of Coarse Grain Molecular Dynamic Simulation Performance on Graphic Processing Unit Architectures. 339-342
• 
  Kirill Lassounski, Sahudy Montenegro González, Annabell Del Real Tamariz, Gabriel Lima de Oliveira: PubMed Dataset: A Java Library for Automatic Construction of Evaluation Datasets. 343-346
• 
  Jan Schier, Bohumil Kovár, Eduard Kocárek: Automated Detection of Interphase and Metaphase Nuclei in the FISH Images. 347-350
• 
  Gopi Chand Nutakki, Leyla Zhuhadar, Robert Wyatt: Appearance based Disease Recognition of Human Brains. 351-355
• 
  Byung-Cheol Kim, Sunghoon Kim: Landscaping the Framework of Bio Research Project - Generation of the 3D Atlas for Drug Target Discovery. 356-359
• 
  María M. Abad-Grau, Nuria Medina-Medina, Andrés R. Masegosa, Serafín Moral: Haplotype-based Classifiers to Predict Individual Susceptibility to Complex Diseases - An Example for Multiple Sclerosis. 360-366

Special Session on Training in Bioinformatics

Full Papers

• 
  Ronen Tal-Botzer, Rachel S. Levy-Drummer, Gidi Rechavi, Ron Unger: Building Today the Future Cadre of Informatics-oriented Physicians - Lessons from a New Biomedical Informatics Curriculum for Medical Doctors. 371-377
• 
  Gerald Lirk, Peter Kulczycki, Stefan Winkler, Jörg Zumbach: A Web-based Introduction to Bioinformatics - Epistemological Beliefs in Bioinformatics. 378-385
• 
  Frédérique Lisacek, Patrick Koks, Pascale Berthault, Grégoire Rossier, Guy Bottu, Jacques van Helden, Jean Sylvestre, Jean-Pierre Kraehenbuhl, Jack A. M. Leunissen: eBiomics - A Website Promoting Good Practices and Specific Methods for using Bioinformatics Resources. 386-391

Short Papers

• 
  Kristian Rother: Exit Polls - Instant Feedback from Teaching Events and Conference Talks. 395-398

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