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18th CMSB 2020: Konstanz, Germany

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Alessandro Abate, Tatjana Petrov, Verena Wolf:
Computational Methods in Systems Biology - 18th International Conference, CMSB 2020, Konstanz, Germany, September 23-25, 2020, Proceedings. Lecture Notes in Computer Science 12314, Springer 2020, ISBN 978-3-030-60326-7

Modelling and Analysis

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Vincent Danos, Tobias Heindel, Ricardo Honorato-Zimmer, Sandro Stucki:
Rate Equations for Graphs. 3-26
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Candan Çelik, Pavol Bokes, Abhyudai Singh:
Stationary Distributions and Metastable Behaviour for Self-regulating Proteins with General Lifetime Distributions. 27-43
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Pavol Bokes, Julia Klein, Tatjana Petrov:
Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression. 44-60
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Elisabeth Degrand, François Fages, Sylvain Soliman:
Graphical Conditions for Rate Independence in Chemical Reaction Networks. 61-78
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Aurélien Desoeuvres, Gilles Trombettoni, Ovidiu Radulescu:
Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity. 79-101
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Alexandru Oarga, Bridget Bannerman, Jorge Júlvez:
Growth Dependent Computation of Chokepoints in Metabolic Networks. 102-119
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Mathieu Hemery, François Fages, Sylvain Soliman:
On the Complexity of Quadratization for Polynomial Differential Equations. 120-140
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Sophie Le Bars, Jérémie Bourdon, Carito Guziolowski:
Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model. 141-156

Boolean Networks

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Laura Cifuentes Fontanals, Elisa Tonello, Heike Siebert:
Control Strategy Identification via Trap Spaces in Boolean Networks. 159-175
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Ousmane Diop, Madalena Chaves, Laurent Tournier:
Qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness. 176-192
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  - conf/cmsb/ChevalierNCZP20
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Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé:
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. 193-209
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Robert Schwieger, Matías R. Bender, Heike Siebert, Christian Haase:
Classifier Construction in Boolean Networks Using Algebraic Methods. 210-233
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Cui Su, Jun Pang:
Sequential Temporary and Permanent Control of Boolean Networks. 234-251

Inference and Identification

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Gareth W. Molyneux, Alessandro Abate:
ABC(SMC)²: Simultaneous Inference and Model Checking of Chemical Reaction Networks. 255-279
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Eva Smijáková, Samuel Pastva, David Safránek, Lubos Brim:
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. 280-297
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Marielle Péré, Madalena Chaves, Jérémie Roux:
Core Models of Receptor Reactions to Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis. 298-320
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Stefan Haar, Loïc Paulevé, Stefan Schwoon:
Drawing the Line: Basin Boundaries in Safe Petri Nets. 321-336

Tools

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Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks. 339-348
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Jorge Júlvez, Stephen G. Oliver:
fnyzer: A Python Package for the Analysis of Flexible Nets. 349-355
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Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim:
eBCSgen: A Software Tool for Biochemical Space Language. 356-361
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Déborah Boyenval, Gilles Bernot, Hélène Collavizza, Jean-Paul Comet:
What is a Cell Cycle Checkpoint? The TotemBioNet Answer. 362-372
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Luca Cardelli:
Kaemika App: Integrating Protocols and Chemical Simulation - Integrating Protocols and Chemical Simulation. 373-379

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