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ORCID23rd CMSB 2025: Lyon, France
- François Fages, Sabine Pérès:
Computational Methods in Systems Biology - 23rd International Conference, CMSB 2025, Lyon, France, September 10-12, 2025, Proceedings. Lecture Notes in Computer Science 15959, Springer 2026, ISBN 978-3-032-01435-1
Boolean Networks
- José E. R. Cury, Patrícia Tenera Roxo
, Vasco Manquinho, Claudine Chaouiya, Pedro T. Monteiro:
Computation of Immediate Neighbours of Monotone Boolean Functions. 3-22 - Thibaut Peyric, Thomas Lepoutre, Anton Crombach, Thomas Guyet:
Three-State Gene Expression Model Parameterized for Single-Cell Multi-omics Data. 23-41 - Claudine Chaouiya, Jérôme Feret, Patrícia Tenera Roxo:
On Model Reductions of Boolean Networks. 42-60 - Vojtech Veselý, Eva Smijáková, Samuel Pastva, Nikola Benes, David Safránek:
AEON 2025: Robust Control of Partially-Specified Boolean Networks. 61-68 - Hans-Jörg Schurr, Athénaïs Vaginay:
Looking for Signs: Reasoning About FOBNNs Using SAT. 69-88 - Stefan Haar, Juraj Kolcák:
Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks. 89-105
Continuous and Hybrid Models
- Mathilde Gaillard, Ulysse Herbach:
Efficient Stochastic Simulation of Gene Regulatory Networks Using Hybrid Models of Transcriptional Bursting. 109-125 - Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber, Susanna Röblitz:
Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN. 126-149
Rule-Based Models
- Jérôme Feret, Rebecca Ghidini:
Reachability Analysis for Parametric Rule-Based Models. 153-173 - Matthieu Bouguéon, Tatjana Petrov, Albin Salazar:
A Rule-Based Modeling Approach for Studying Animal Collectives: A Case Study of Juvenile Honeybee Thermotaxis. 174-194 - Michele Loreti, Michela Quadrini, Matteo Scoccia, Luca Tesei:
A Formal Approach to Identify Structural Patterns in RNA. 195-217
Model Inference and Machine Learning
- Tsz Pan Tong, Aoran Wang, George Panagopoulos, Jun Pang:
Kolmogorov-Arnold Network for Gene Regulatory Network Inference. 221-239 - Andrea Stallvik, Hans-Michael Kaltenbach, Jörg Stelling:
Optimal Input Design for Model Selection in Systems with Cell-to-Cell Variability. 240-257 - Sergio Peignier, Amanda Lo Van, Yann Meunier, Elea Pauliat, Matis Zouari, Federica Calevro:
Decoding Gene Regulation in Alzheimer's Disease with Transfer Learning and Explainable Machine Learning. 258-275 - Madeleine Eyraud, Maxime Folschette, Katsumi Inoue, Sébastien Lefebvre, Cédric Lhoussaine:
Interaction Graphs of Phytoplankton Species Interactions Using Logical Learning. 276-296 - Andréa Ducos, Audrey Denizot, Thomas Guyet, Hugues Berry:
Evaluating PDE Discovery Methods for Multiscale Modeling of Biological Signals. 297-312 - Felicity Escarzaga, Brian Donnelly, Kyle Winfree:
Optimizing Feature Extraction Methods Using Class Similarity Ratio for EMG-Based Hand Gesture Classification. 313-333
Population Models and Control
- Juliette Luiselli, Manuel Lafond:
Eukaryotic Ancestry in a Finite World. 337-355 - Alix Moawad, Jörg Stelling:
Minimal Metabolic Exchanges for Microbial Communities in a Chemostat at Steady State. 356-369 - Chabname Ghassemi Nedjad, Sebastián Nelson Mendoza, Clémence Frioux, Loïc Paulevé:
Seed Inference in Interacting Microbial Communities Using Combinatorial Optimization. 370-387 - Cédric Join, Jakub Orlowski, Antoine Chaillet, Madeleine Lowery, Hugues Mounier, Michel Fliess:
A Model-Free Control Strategy for Selective Disruption of Parkinsonian Brain Oscillations. 388-401
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