CMSB2013 Accepted Papers

Ferdinanda Camporesi, Jerome Feret and Jonathan Hayman. Context-sensitive flow analyses: a hierarchy of model reductions
Frits Dannenberg, Ernst Moritz Hahn and Marta Kwiatkowska. Computing Cumulative Rewards using Fast Adaptive Uniformisation
Anastasis Georgoulas, Jane Hillston and Guido Sanguinetti. ABC-Fun: A Probabilistic Programming Language for Biology
Lucian Bentea, Peter Olveczky and Eduard Bentea. Using Probabilistic Strategies to Formalize and Compare $\alpha$-Synuclein Aggregation and Propagation under Different Biological Conditions
Courtney Chancellor, Francisco Chinesta and Olivier Roux. Linking Discrete and Stochastic Models: the Chemical Master Equation as a bridge between Process Hitting and PGD
Attila Gábor, Katalin M. Hangos, Gábor Szederkényi and Julio R. Banga. On the Verification and Correction of Large-scale Kinetic Models in System Biology
Katherine Chiang, François Fages, Jie-Hong Jiang and Sylvain Soliman. On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models
Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu, P. S. Thiagarajan and Edmund M. Clarke. Statistical model checking based calibration and analysis of bio-pathway models
Ovidiu Parvu, David Gilbert, Monika Heiner, Fei Liu and Nigel Saunders. Modelling and Analysis of Phase Variation in Bacterial Colony Growth
Srivathsan Adivarahan, Denis Menshykau, Odysse Michos and Dagmar Iber. Dynamic Image-Based Modelling of Kidney Branching Morphogenesis
Ferdinando Fioretto and Enrico Pontelli. Constraint Programming in Community-based Gene Regulatory Network Inference
Ezio Bartocci, Luca Bortolussi and Laura Nenzi. A temporal logic approach to modular design of synthetic biological circuits
Michael Klann, Loic Pauleve, Petrov Tatjana and Heinz Koeppl. Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models
Tobias Helms, Martin Luboschik, Heidrun Schumann and Adelinde Uhrmacher. An Approximate Execution of Rule-based Multi-level Models
Yaron Goldstein and Alexander Bockmayr. A lattice-theoretic framework for metabolic pathway analysis

CMSB2013 Accepted Posters

Nataly Maimari, Calin-Rares Turliuc, Krysia Broda, Antonis Kakas, Rob Krams and Alessandra Russo. ARNI: Abductive inference of complex regulatory network structures.
Marianna Taffi, Nicola Paoletti, Pietro Liò, Luca Tesei, Emanuela Merelli and Mauro Marini. A Computational Framework for POPs Bioaccumulation in Marine Ecosystems
Emmanuelle Gallet, Matthieu Manceny, Pascale Le Gall and Paolo Ballarini. A Symbolic Approach Based on Model Checking and Constraint Solving Techniques for Reverse Engineering of Thomas Networks Parameters
Md. Ariful Islam, Abhishek Murthy, Ezio Bartocci, Antoine Girard, Scott A. Smolka and Radu Grosu. Compositionality Results for Cardiac Cell Dynamics
Florian Martin, Alain Sewer, Marja Talika, Yang Xiang, Julia Hoeng and Manuel Peitsch. Quantification of biological network perturbations: Impact assessment and diagnostic using causal biological networks
Bo Zhou, Beat Christen, Eduardo Abeliuk, Harley McAdams and Lucy Shapiro. Deciphering the Transcriptional Landscape of Caulobacter crescentus
Eszter Lakatos, Domokos Meszena and Gabor Szederkenyi. Identifiablity analysis and improved parameter estimation of a human blood glucose control system model
Jesús Miró-Bueno. RNA interference in cancer and cell cycle networks: a case study of E2F proteins
Andrzej Mizera, Jun Pang, Thomas Sauter and Panuwat Trairatphisan. A Balancing Act: Parameter Estimation for Biological Models with Steady-state Measurements
Anke Ryll, Joachim Bucher, Jens Niklas and Steffen Klamt. A Fusion Approach Linking Signaling Logic and Metabolic Mass-Flow Kinetics in Hepatocytes
Adam Streck, Juraj Kolčák, Heike Siebert and David Šafránek. Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks
Ivan Kondofersky, Christiane Fuchs and Fabian J. Theis. Identifying latent dynamic components in biological systems
Marc Bruckskotten, Mario Looso and Thomas Braun. Next-Newtomics: The next generation repository for bioinformatical interpreted omics datasets from the newt Notophthalmus viridescens
Mario Herzog, Stefan Günther and Mario Looso. miRNA expression analysis during heart regeneration of N. viridescens
Bedrat Amina, Guédin Aurore, Amrane Samir, Renaud De La Faverie Amandine and Mergny Jean-Louis. Algorithm to predict G-quadruplex folding sequences through score computing
Melik Oksuz, Hasan Sadikoglu and Tunahan Cakir. Optimization based Inference of Metabolic Networks from Metabolome Data
Saliha Durmus Tekir, Tunahan Cakir, Emre Ardic, Ilknur Karadeniz, Arzucan Ozgur, F. Erdogan Sevilgen and Kutlu Ulgen. PHISTO: A NEW WEB PLATFORM FOR PATHOGEN-HUMAN INTERACTIONS
Stephan Neese and Mario Looso. Frameshift correction in de novo assembled transcriptome data using peptide data, Blast sequence alignments and hidden markov models
Carsten Künne. From Prokaryote Genome Sequencing to Pan-genomic Modeling
Jorge Julvez. A simulation approach to detect oscillating behaviour in stochastic population models
Bernhard Kramer and Carsten Conradi. On Bistability causing structures in Escherichia coli's metabolism
Leonie Amstein, Nadine Schöne, Simone Fulda and Ina Koch. Mathematical modelling of the function of ubiquitylation in TNFR1-mediated NF-κB signalling
Raquel L Costa, Jean-Marc Schwartz, David L Robertson and Fábio Porto. SIV Gene Network Module in Graph Database

IST Research Posters

Tiago Paixão and Ulrich Bauer. Using Reebs graphs to inestigate fitness landscapes
Georg Rieckh and Gasper Tkacik. Noise and information capacity in promoter models with multiple states