Day 1 – 15th May 2014

09:30 - 10:00           José Fonseca
                                Welcome address
10:00 - 10:30           Olli Yli-Harja
                                Big data, machine learning, and cancer
10.30 - 11.30           Session A – Chair: André Ribeiro
                                Jake Lin and Patrick May
                                Systemic Integration and Exploration of Genomic Variants
                                Kristin Blacklock and Gennady Verkhivker
                                Integrative Studies of Allosteric Regulation in Signal Transduction Networks: a
                                Synergistic Perspective From Computational Systems Biology and Proteomics
                                Approaches
                                Gianluca Selvaggio, Pedro Coelho and Armindo Salvador
                                Design Space Analysis Supports Role of Peroxiredoxin/Thioredoxin/Thioredoxin-
                                Reductase System in Integrating Redox Signaling And Anticipatory Blocking
                                Vincenzo Belcastro
                                Identification of Signalling Mediators
11:30 - 12:00          Discussion & Coffee break
12:00 - 12:30          Antti Ylipää
                               Identifying previously unannotated cancer specific transcripts using RNA-sequencing
12:30 – 13:00         Meenakshisundaram Kandhavelu
                               Advances in understanding noisy signal transmission in neuronal cancer cells - GPR17
                               as a case study
13:00 – 14:30         Lunch
14:30 – 15:00         Sara Madeira
                               The NEUROCLINOMICS project: Understanding NEUROdegenerative Diseases
                               through CLINical and OMICS Data Integration
15:00 – 16:00         Session B – Chair: Reija Autio
                               Christoph Zimmer and Sven Sahle
                               Parameter inference for stochastic models: A comparison of multiple shooting for
                               stochastic systems to conventional least squares
                               Eszter Lakatos, Paul Kirk and Michael P. H. Stumpf
                               Multivariate moment closure techniques for stochastic kinetic models
                               Charalampos Kyriakopoulos and Verena Wolf
                               Optimal Observation Time Points in Stochastic Chemical Kinetics
                               Alexander Andreychenko, Linar Mikeev and Verena Wolf
                               Distribution reconstruction for stochastic chemical kinetics from conditional
                               moment data
16:00 – 16:30         Discussion & Coffee break
16:30 – 17:00         Isabel Gordo
                              Adaptation of bacterial populations approaching a fitness peak
19:30 - 23:00        Conference Dinner
 

Day 2 – 16th May 2014

 10:00 - 10:30       Reija Autio
                             Recycling high-throughput data: combining existing data can lead to new knowledge
10:30 - 11:30        Session C – Chair: Meenakshisundaram Kandhavelu
                             Domokos Meszéna, Eszter Lakatos and Gabor Szederkenyi
                             Sensitivity analysis and parameter estimation of a human blood glucose regulatory
                             system model
                             Anton Salykin, Dominique Chu, Petr Fojtik, Miriama Kruta, Katka Schrammova, Petr Skladal, Petr Dvorak
                             and Vladimir Rotrekl
                             Computational Model of Fgf2 Signalling Network In Human Embryonic Stem Cells
                              Revealed Oxygen Triggered Metabolic Switch
                             João Santinha, Antti Häkkinen, Abhishekh Gupta, Teppo Annila, Jason Lloyd-Price, Andre S. Ribeiro and
                             José Fonseca
                             Image Alignment and Lineage Construction Tool to Study Segregation and
                             Partitioning in Division of Unwanted Protein Aggregates in Escherichia Coli
                             Leonardo Martins, Andre S. Ribeiro and Jose Fonseca
                             Generator of Synthetic Time-Lapsed, Phase-Contrast Microscopy Images of
                             Growing E. Coli Cell Populations
11.30 - 12-00        Discussion & Coffee break

12:00 - 12:30        Samuli Niiranen
                              Convergence in clinical diagnostics
12:30 – 13:00        Andre Ribeiro
                              Effects of stress on the in vivo dynamics of non-stress-responsive
                              genes in Escherichia coli
13:00 – 14:30        Lunch

14:30 – 15:00        Ilda Sanches
                              Unraveling the host-specificity within streptococci
15:00 – 16:30        Session D - Chair: Antti Ylipää
                                Tomasz Ignac, Alexander Skupin, Nikita Sakhanenko and David Galas
                                 Detecting Genetic Interactions in Case-Control Data: Information Theory Based
                                 Methods
                              Alessandro Bolli and Armindo Salvador
                              Microorganism's Growth-Robustness Trade-Off Explained by Simple General
                              Principles
                              Nadia Goncalves, Ramakanth Neeli Venkata, Antti Martikainen, Joao Santinha, Jose Fonseca and
                              Andre Ribeiro
                              In Vivo Retention of Protein Aggregates in Escherichia Coli
                              Samuel M.D. Oliveira, Jerome G. Chandraseelan, Antti Häkkinen, Olli Yli-Harja and Andre S. Ribeiro
                              Analysis of The Robustness of a Single Copy Repressilator
                              Jerome G. Chandraseelan, Jason Lloyd-Price, Olli Yli-Harja and Andre S. Ribeiro
                              Estimating the Duration of Open Complex Formation From in Vivo Measurements
                              Florbela Pereira, Diogo A. R. S. Latino and Susana P. Gaudêncio
                              In Silico Screening of Lead-Like Molecules en Route to Antitumor and Antibiotic
                              Drugs from Marine and Microbial Natural Products Using Empirical and Semi-
                              Empirical Quantum-Chemical Descriptors
16:30 – 17:00        Olli Yli-Harja
                              Closing speech