Program

09:20-10:50 CMSB - Session 1: Opening Session (chair: Mirco Tribastone)

09:20	OPENING
09:30	Corrado Priami Digital health opportunities INVITED TALK
10:00	Jorge Lazaro, Jorge Julvez and Juergen Zanghellini Flexible Nets to Improve GEM Cell Factories by Combining Kinetic and Proteomics Data REGULAR PROCEEDINGS PAPER
10:25	Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret and Nathalie Théret A rule-based multiscale model of hepatic stellate cell plasticity: critical role of the inactivation loop in fibrosis progression HIGHLIGHT TALK
10:40	ABOUT CMSB 2024 - LOGISTIC INFO

10:50-11:20 COFFEE BREAK

11:20-13:10 CMSB - Session 2: Boolean Networks, Notations and Tools (chair: Ion Petre)

11:20	Hugo Buscemi and François Fages Graphical Conditions ensuring Equality between Differential and Mean Stochastic Dynamics (* CANDIDATE FOR BEST PAPER AWARD *) REGULAR PROCEEDINGS PAPER
11:45	Maryam Yousefian, Elisa Tonello, Anna-Simone Josefine Frank, Heike Siebert and Susanna Röblitz Uncovering dynamic structures within cyclic attractors of asynchronous Boolean networks with spectral clustering REGULAR PROCEEDINGS PAPER
12:10	Nikola Benes, Lubos Brim, Ondřej Huvar, Samuel Pastva and David Šafránek BNClassifier: Classifying Boolean Models by Dynamic Properties (* CANDIDATE FOR BEST TOOL PAPER AWARD *) SHORT OR TOOL PROCEEDINGS PAPER
12:25	Stéphanie Chevalier, Déborah Boyenval, Gustavo Magaña López, Théo Roncalli, Athénaïs Vaginay and Loïc Paulevé BoNesis: a Python-based declarative environment for the verification, reprogramming, and synthesis of most permissive Boolean networks SHORT OR TOOL PROCEEDINGS PAPER
12:40	Savandara Besse and Michael Rera Gene network-based approaches to understand aging and lifespan from D. melanogaster HIGHLIGHT TALK
12:55	Valentina Castiglioni, Michele Loreti and Simone Tini Bio-STARK SHORT OR TOOL PROCEEDINGS PAPER

13:10-14:30 LUNCH (includes CMSB Steering Committee meeting (private) from 13.45 in Room RIUNIONI OVEST)

14:30-16:00 CMSB - Session 3: Networks and Models 1 (chair: David Šafránek)

14:30	Karoline Faust Tools for microbial network analysis and community modelling INVITED TALK
15:30	Gianluca Lombardi and Alessandra Carbone MuLAN: Mutation-driven Light Attention Networks for investigating protein-protein interactions from sequences HIGHLIGHT TALK
15:45	Yunli Eric Hsieh, Kshitij Tandon, Heroen Verbruggen and Zoran Nikoloski Integration of metatranscriptomics data allow accurate prediction of microbial growth rates using community metabolic models HIGHLIGHT TALK

16:00-16:30 COFFEE BREAK

16:30-17:00 CMSB - Session 4: Applications 1 (chair: Paolo Milazzo)

16:30	Emma Crisci, Maxime Mahout and Sabine Peres Computing thermodynamically consistent Elementary Flux Modes with Answer Set Programming SHORT OR TOOL PROCEEDINGS PAPER
16:45	Safaa Al-Ali, Maria Teresa Mora, Maxime Sermesant, Beatriz Trenor and Irene Balelli Insights about ion channel blockade and electromechanical biomarkers’ interrelations using a Multi-Channel Causal Variational Autoencoder HIGHLIGHT TALK

17:00-18:10 CMSB - Session 5: Flash Poster Presentations (chair: Paolo Milazzo)

17:00	Nikola Benes, Lubos Brim, Ondřej Huvar, Samuel Pastva, David Šafránek and Eva Šmijáková AEON.py: A comprehensive Python package for Boolean network analysis FLASH POSTER PRESENTATION
17:07	Martina Cirinciani, Nicole Ziliotto, Giulio Magherini, Eleonora Da Pozzo, Claudia Martini, Andrea Caricasole and Paolo Milazzo An in-silico analysis of the functional and structural impact of mutations on proteins: a case study on ceruloplasmin FLASH POSTER PRESENTATION
17:14	Michele Fontanesi, Alessio Micheli, Paolo Milazzo and Marco Podda Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs: an overview FLASH POSTER PRESENTATION
17:21	Silvia Giulia Galfrè, Marco Fantozzi, Irene Testa, Matteo Tolloso, Andrea Alberti, Alina Sîrbu, Francesco Morandin and Corrado Priami From Gene to Cluster: COTAN v2 for Improved scRNA-seq Analysis and Clustering FLASH POSTER PRESENTATION
17:28	Justin N. Kreikemeyer, Philipp Andelfinger and Adelinde Uhrmacher Towards Learning Chemical Reaction Networks by Gradient Descent FLASH POSTER PRESENTATION
17:35	Zahra Nozari, Paul Hüttl, Jakob Simeth and Rainer Spang HARP: Harmonizer of Reference Profiles for Bulk Deconlvoution Algorithms FLASH POSTER PRESENTATION
17:42	Giang Pham and Paolo Milazzo Towards a Shapley value propagation method for Boolean networks FLASH POSTER PRESENTATION
17:49	Jakob Simeth, Paul Hüttl, Marian Schön, Zahra Nozari, Tobias Schmidt, Michael Huttner, Michael Altenbuchinger and Rainer Spang TissueResolver: Virtual Tissue Expression Analysis FLASH POSTER PRESENTATION
17:56	Hadjar Rahou and Ronan Fleming Chemical reactions are constrained combinations of conserved and reacting moieties FLASH POSTER PRESENTATION
18:03	Lukas Wolfseher, Paul Hüttl and Michael Huttner The FDLP-Project: Federated Learning in Lymphoma Pathology FLASH POSTER PRESENTATION

18:30 WELCOME COCKTAIL