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SysMod COSI Track Presentations

Attention Conference Presenters - please review the Speaker Information Page available here
Modeling in uncertain times
Date: Saturday, July 22
Time: 10:00 AM - 10:50 AM
Room: Panorama
  • Rainer Breitling, University of Manchester, UK
A scalable moment-closure approximation for large-scale biochemical reaction networks
Date: Saturday, July 22
Time: 10:50 AM - 11:10 AM
Room: Panorama
  • Atefeh Kazeroonian, Technische Universität München, Germany
  • Fabian Theis, Helmholtz-Zentrum München, Germany
  • Jan Hasenauer, Helmholtz-Zentrum München, Germany

Presentation Overview: Show

Motivation: Stochastic molecular processes are a leading cause of cell-to-cell variability. Their dynamics are often described by continuous-time discrete-state Markov chains and simulated using stochastic simulation algorithms. As these stochastic simulations are computationally demanding, ordinary differential equation models for the dynamics of the statistical moments have been developed. The number of state variables of these approximating models, however, grows at least quadratically with the number of biochemical species. This limits their application to small- and medium-sized processes.

Results: In this manuscript, we present a scalable moment-closure approximation (sMA) for the simulation of statistical moments of large-scale stochastic processes. The sMA exploits the structure of the biochemical reaction network to reduce the covariance matrix. We prove that sMA yields approximating models whose number of state variables depends predominantly on local properties, i.e. the average node degree of the reaction network, instead of the overall network size. The resulting complexity reduction is assessed by studying a range of medium- and large-scale biochemical reaction networks. To evaluate the approximation accuracy and the improvement in computational efficiency, we study models for JAK2/STAT5 signalling and NFkB signalling. Our method is applicable to generic biochemical reaction networks and we provide an implementation, including an SBML interface, which renders the sMA easily accessible.

Availability: The sMA is implemented in the open-source MATLAB toolbox CERENA and is available from https://github.com/CERENADevelopers/CERENA.

Efficient Simulation of Intrinsic, Extrinsic and External Noise in Biochemical Systems
Date: Saturday, July 22
Time: 11:10 AM - 11:30 AM
Room: Panorama
  • Dennis Pischel, Otto-von-Guericke University Magdeburg, Germany
  • Kai Sundmacher, Max Planck Institute for Dynamics of Complex Technical Systems, Germany
  • Robert J. Flassig, Max Planck Institute for Dynamics of Complex Technical Systems, Germany
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
Date: Saturday, July 22
Time: 11:30 AM - 11:50 AM
Room: Panorama
  • Eugenio Cinquemani, INRIA Grenoble - Rhone-Alpes, France
  • Valérie Laroute, Universite de Toulouse, France
  • Muriel Cocaign-Bousquet, INRIA, France
  • Hidde de Jong, INRIA Grenoble - Rhone-Alpes, France
  • Delphine Ropers, INRIA Grenoble - Rhone-Alpes, France
Reversed dynamics to uncover basins of attraction of asynchronous logical models
Date: Saturday, July 22
Time: 11:50 AM - 12:10 PM
Room: Panorama
  • Sébastien Fueyo, Instituto Gulbenkian de Ciência / INRIA Sophia Antipolis, France
  • Pedro T. Monteiro, INESC-ID/IST, Universidade de Lisboa, Portugal
  • Aurélien Naldi, IBENS (CNRS UMR 8197 - INSERM U1024), France
  • Julien Dorier, Vital-IT, Systems biology and medicine department, SIB Swiss Institute of Bioinformatics, Switzerland
  • Élisabeth Remy, Aix Marseille Université, CNRS, Centrale Marseille, I2M, UMR 7373, France
  • Claudine Chaouiya, Instituto Gulbenkian de Ciência, Portugal
Computational modeling of promoter occupancies in MYC-dependent gene regulation
Date: Saturday, July 22
Time: 2:00 PM - 2:50 PM
Room: Panorama
  • Jana Wolf, Max Delbrück Center for Molecular Medicine, Germany
Manatee invariants for functional analysis of signaling pathways in complex networks
Date: Saturday, July 22
Time: 2:50 PM - 3:10 PM
Room: Panorama
  • Ina Koch, Johann Wolfgang Goethe-University, Germany
Large Scale Mechanistic Modeling Enables Robust Prediction of Cancer Cell Drug Response
Date: Saturday, July 22
Time: 3:10 PM - 3:30 PM
Room: Panorama
  • Fabian Fröhlich, Helmholtz-Zentrum München, Germany
  • Alexey Shadrin , Germany
  • Thomas Kessler , Germany
  • Christoph Wierling , Germany
  • Bodo Lange , Germany
  • Fabian Theis , Germany
  • Hans Lehrach , Germany
  • Jan Hasenauer, Helmholtz-Zentrum München, Germany
Incorporating patient-specific molecular data into a logic model of prostate cancer
Date: Saturday, July 22
Time: 3:30 PM - 3:50 PM
Room: Panorama
  • Pauline Traynard, Institut Curie, France
  • Jonas Beal, Institut Curie, France
  • Emmanuel Barillot, Institut Curie, France
  • Luis Tobalina , Germany
  • Julio Saez-Rodriguez , Germany
  • Laurence Calzone, Institut Curie, France
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis
Date: Saturday, July 22
Time: 4:30 PM - 4:50 PM
Room: Panorama
  • Chiara Damiani, Dept of Informatics, Systems and Communication, University Milano-Bicocca, 20126, Milano, Italy
  • Marzia Di Filippo, Dept of Biotechnology and Biosciences, University Milano-Bicocca, 20126, Milano, Italy
  • Dario Pescini, Dept of Statistics and Quantitative Methods, University Milano-Bicocca, 20126, Milano, Italy
  • Davide Maspero, Dept of Biotechnology and Biosciences, University Milano-Bicocca, 20126, Milano, Italy
  • Riccardo Colombo, Dept of Informatics, Systems and Communication, University Milano-Bicocca, 20126, Milano, Italy
  • Giancarlo Mauri, Dept of Informatics, Systems and Communication, University Milano-Bicocca, 20126, Milano, Italy
Who's driving? Cell cycle robustness investigated by a multi-scale framework integrating cell cycle and metabolism in budding yeast
Date: Saturday, July 22
Time: 4:50 PM - 5:10 PM
Room: Panorama
  • Matteo Barberis, Universiteit van Amsterdam, Netherlands
  • Lucas van der Zee, Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
  • Thierry D.G.A. Mondeel, Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
  • Hans V. Westerhoff, Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
Explanation of drug effects using a mechanistic model automatically assembled from natural language, databases, and literature
Date: Saturday, July 22
Time: 5:10 PM - 5:30 PM
Room: Panorama
  • John A. Bachman, Harvard Medical School, United States
  • Benjamin M. Gyori , United States
  • Peter K. Sorger , United States
Tracking and Engineering the Evolution of Organismal Fitness via Multi-Organism mRNA Translation Whole Cell Simulations
Date: Saturday, July 22
Time: 5:30 PM - 5:50 PM
Room: Panorama
  • Tamir Tuller, Tel Aviv University, Israel
  • Hadas Zur, Tel Aviv University, Israel