CMSB 2016

14th International Conference on Computational Methods in Systems Biology

21st - 23rd September 2016, Computer Laboratory, University of Cambridge (UK)

Accepted papers

Tool papers

  • Alejandro F. Villaverde, Kolja Becker and Julio R. Banga. PREMER: parallel reverse engineering of biological networks with information theory

  • Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Františka Romanovská and Jan Červený. A Web-based Platform for Systems Biology of Cyanobacteria

  • Andrzej Mizera, Jun Pang and Qixia Yuan. ASSA-PBN 2.0: A Software Tool for Probabilistic Boolean Networks

Regular papers

  • Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu, James Faeder, Michael Lotze and Edmund Clarke. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment

  • Chieh Lo and Radu Marculescu. Autonomous and Adaptive Control of Populations of Bacteria through Environment Regulation

  • Jasha Sommer-Simpson, John Reinitz, Leonid Fridlyand, Louis Philipson and Ovidiu Radulescu. Hybrid reductions of computational models of voltage-gated ion channels coupled to cellular biochemistry

  • Michael Backenköhler, Luca Bortolussi and Verena Wolf. Generalized Method of Moments for Stochastic Reaction Networks in Equilibrium

  • Andrzej Mizera, Jun Pang and Qixia Yuan. Fast Simulation of Probabilistic Boolean Networks

  • Loïc Paulevé. Goal-Oriented Reduction of Automata Networks

  • Carolin Loos, Anna Fiedler and Jan Hasenauer. Parameter estimation for reaction rate equation constrained mixture models

  • Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva and David Šafránek. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study

  • Jerome Feret and Quyen Kim Ly. Local traces: an over-approximation of the behaviour of the proteins in rule-based models

  • Chunyan Mu, Peter Dittrich, David Parker and Jonathan E. Rowe. Formal Quantitative Analysis of Reaction Networks Using Chemical Organisation Theory

  • Elisa Tonello, Guillaume Madelaine, Etienne Farcot, Cedric Lhoussaine and Joachim Niehren. Normalizing Chemical Reaction Networks by Confluent Structural Simplification

  • Md. Ariful Islam, Greg Byrne, Soonho Kong, Edmund Clarke, Rance Cleaveland, Radu Grosu and Scott Smolka. Bifurcation Analysis of Cardiac Alternans using δ-Decidability

  • François Fages, Thierry Martinez, David Rosenblueth and Sylvain Soliman. Influence Systems vs Reaction Systems

  • Luca Laurenti, Luca Cardelli and Marta Kwiatkowska. A Stochastic Hybrid Approximation for Chemical Kinetics Based on the Linear Noise Approximation

  • Emna Ben Abdallah, Tony Ribeiro, Morgan Magnin, Olivier Roux and Katsumi Inoue. Inference of delayed biological regulatory networks from time series data

  • Giulio Caravagna, Luca Bortolussi and Guido Sanguinetti. Matching models across abstraction levels with Gaussian Processes

  • Eugen Czeizler, Cristian Gratie, Krishna Kanhaiya and Ion Petre. Target Controllability of Linear Networks

Accepted posters

  • Priya Anand, Monika Borkowska-Panek, Karin Fink and Wolfgang Wenzel. Modelling Peptide Adsorption on Inorganic Surfaces

  • Loïc Paulevé. Pint, a static analyzer for dynamics of Automata Networks

  • Nadia S. M. Goncalves, Samuel M. D. Oliveira, Jose M. Fonseca and Andre S. Ribeiro. Temperature Dependence of Leakiness of Transcription Repression Mechanisms of Escherichia coli

  • Andrzej Mizera, Jun Pang and Qixia Yuan. GPU-accelerated Steady-State Analysis of Probabilistic Boolean Networks

  • James Smith, Kai Loell and Albert Koulman. Revealing biomarker mixtures in lipid pools from large-scale lipidomics

  • James Smith and Ahmed Ibrahim. Game theoretic consideration of transgenic bacteria in the human gut microbiota converting omega-6 to omega-3 fats

  • Benjamin Hall, Nir Piterman and Jasmin Fisher. Linear Temporal Logic for Biologists in BMA

  • Mariana Esther Sanchez, Elena Alvarez-Buylla and Marcia Hiriart. The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia

  • David Shorthouse, Angela Riedel, Jacqueline Shields and Benjamin Hall. Deregulation of Osmotic Regulation Machinery Explains and Predicts Cellular Transformation in Cancer and Disease