List of accepted papers

 Boolean Networks

Computation of immediate neighbours of monotone Boolean functions.
José E.R. Cury, Patrı́cia Roxo, Vasco Manquinho, Claudine Chaouiya and Pedro T. Monteiro.

Three-State Gene Expression Model Parameterized for Single-Cell Multi-Omics Data.
Thibaut Peyric, Thomas Lepoutre, Anton Crombach and Thomas Guyet

On Model Reductions of Boolean Networks.
Claudine Chaouiya, Jérôme Feret and Patrı́cia T. Roxo

AEON 2025: Robust Control of Partially-Specified Boolean Networks (tool paper).
Vojtěch Veselý, Eva Šmijáková, Samuel Pastva, Nikola Beneš and David Šafránek

Looking for Signs: Reasoning About FOBNNs Using SAT.
Hans-Jörg Schurr and Athénaı̈s Vaginay

Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks.
Stefan Haar and Juri Kolčák

Continuous and Hybrid models

Efficient stochastic simulation of gene regulatory networks using hybrid models of transcriptional bursting.
Mathilde Gaillard and Ulysse Herbach

Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN.
Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber and Susanna Röblitz

Rule-based models

Reachability Analysis for Parametric Rule-Based Models.
Jerome Feret and Rebecca Ghidini

A rule-based modeling approach for studying animal collectives: a case study of juvenile honeybee thermotaxis.
Matthieu Bouguéon, Tatjana Petrov and Albin Salazar

A Formal Approach to Identify Structural Patterns in RNA.
Michele Loreti, Michela Quadrini, Matteo Scoccia and Luca Tesei

Model inference and machine learning

Kolmogorov-Arnold Network for Gene Regulatory Network Inference.
Tsz Pan Tong, Aoran Wang, George Panagopoulos and Jun Pang

Optimal input design for model selection in systems with cell-to-cell variability.
Andrea Stallvik, Hans-Michael Kaltenbach and Jörg Stelling

Decoding Gene Regulation in Alzheimer’s disease with Transfer Learning and Explainable Machine Learning.
Sergio Peignier, Amanda Lo Van, Yann Meunier, Elea Pauliat, Matis Zouari and Federica Calevro

Interaction Graphs of Phytoplankton Species Interactions using Logical Learning.
Madeleine Eyraud, Maxime Folschette, Katsumi Inoue, Sébastien Lefebvre and Cédric Lhoussaine

Evaluating PDE discovery methods for multiscale modeling of biological signals.
Andréa Ducos, Audrey Denizot, Thomas Guyet and Hugues Berry

Optimizing Feature Extraction Methods using Class Similarity Ratio for EMG-based Hand Gesture Classification.
Felicity Escarzaga, Brian Donnelly and Kyle Winfree

Population models and control

Eukaryotic ancestry in a finite world.
Juliette Luiselli and Manuel Lafond

Minimal metabolic exchanges for microbial communities in a chemostat at steady state.
Alix Moawad and Jörg Stelling

Seed inference in interacting microbial communities using combinatorial optimization.
Chabname Ghassemi Nedjad, Clémence Frioux, Loı̈c Paulevé and Sebastı́an Nelson Mendoza

A model-free control strategy for selective disruption of parkinsonian brain oscillations.
Cédric Join, Jakub Orlowski, Antoine Chaillet, Madeleine Lowery, Hugues Mounier and Michel Fliess