Program

All times are in the CEST time zone (UTC+2).

Wednesday 13 September 2023

08.30-09.15 Registration

09.15-09.30 Opening

09.30-10.30 Invited Talk. Philippe Jacques, Optimizing NonRibosomal Peptide Synthesis by Biocomputing Approaches. (Session chair: Joachim Niehren)

10.30-11.00 Coffee Break

11.00-12.30 Session 1: Reaction Networks and Mechanistic Modeling (Session chair: Paolo Ballarini)

• Joachim Niehren, Cedric Lhoussaine and Athénaïs Vaginay. Core SBML and its Formal Semantics.
• Mathieu Hemery and François Fages. On Estimating Derivatives of Input Signals in Biochemistry.
• Rocco De Nicola, Luca Di Stefano, Omar Inverso and Serenella Valiani. Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants.

12.30-14.00 Lunch Break

14.00-15.30 Session 2: Boolean Networks A (Session chair: Loic Paulevé)

• Nikola Beneš, Luboš Brim, Samuel Pastva, David Šafránek and Eva Šmijáková. Phenotype Control of Partially Specified Boolean Networks.
• Honglu Sun, Maxime Folschette and Morgan Magnin. Condition for periodic attractor in 4-dimensional repressilators.
• Élisabeth Remy and Paul Ruet. Average sensitivity of nested canalizing multivalued functions.

15.30-16.00 Coffee Break

16.00-16.45 Tools (Session chair: Andrzej Mizera)

• Lorenzo Contento, Paul Stapor, Daniel Weindl and Jan Hasenauer. A more expressive spline representation for SBML models improves code generation performance in AMICI.
• Takehide Soh, Morgan Magnin, Daniel Le Berre, Mutsunori Banbara and Naoyuki Tamura. SAF: SAT-based Attractor Finder in Asynchronous Automata Networks.
• Ulysse Herbach. Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting.

16.45-17.30 Posters 1 (Session chair: Andrzej Mizera)

• (flash presentation) Atte Aalto, Francois Lamoline, Isabel Haasler, Johan Karlsson and Jorge Goncalves. Gene expression modelling from single-cell data using optimal transport.
• (flash presentation) Apurva Badkas, Sebastien De Landtsheer and Thomas Sauter. Assessment of topological network measures for drug-response prediction.
• (flash presentation) Odile Burckard. Benchmark for quantitative characterization of circadian clock models.
• (flash presentation) Vincent Deman, Philippe Castera, Marine Ciantar, Anne-Sophie Beignon and Laurent Naudin. Algebraic calibration of Boolean networks.
• (flash presentation) Jeff Didier, Sébastien De Landtsheer, Maria Pacheco, Ali Kishk, Jochen G. Schneider, Ilja Demuth, Elisabeth Steinhagen-Thiessen, Thomas Siedler, Dominik Spira and Thomas Sauter. Sex-specific Classification of Frailty Outperforms Mixed Models and Reveals Underlying Differences In The Respective Frailty Development – Data from the Berlin Aging Study II (BASE-II).
• (flash presentation) Jesús Fuentes, Maria Moscardo and Jorge Gonçalves. A Geometry-Driven Approach to Morphogenesis.
• (flash presentation) Xin He and Jorge Goncalves. A Pipeline for Analyzing Large-Scale Time-course Bulk mRNA Data.
• (flash presentation) Ahmed Hemedan, Reinhard Schneider and Marek Ostaszewski. Cohort-specific Boolean models highlight different regulatory modules during Parkinson’s disease progression and therapeutics.
• (flash presentation) Juri Kolčák, Daniel Merkle and Stefanie Widder. Using Boolean networks to model microbial interactions and microbiome stability.

18.00-20.00 Conference Reception Dinner

Thursday 14 September 2023

09.00-10.00 Invited Talk. Mirco Tribastone. Lumping and Expanding Reaction Networks. (Session chair: François Fages)

10.00-10.30 Session 3: Lumping (Session chair: François Fages)

• Alexander Leguizamon-Robayo, Antonio Jiménez-Pastor, Mirco Tribastone, Max Tschaikowski and Andrea Vandin. Approximate Constrained Lumping of Polynomial Differential Equations.

10.30-11.00 Coffee Break

11.00-11.30 Posters 2 (Session chair: Samuel Pastva)

• (flash presentation) Gustavo Magaña López and Loïc Paulevé. BoNesis: a declarative framework for the synthesis of Boolean networks from rich dynamical properties.
• (flash presentation) Stefano Magni and Jorge Goncalves. Towards Inference of Gene Regulatory Networks from Single-Cell RNA-Sequencing Data by the Chemical Master Equation to elucidate the onset of Parkinson’s Disease.
• (flash presentation) Andreas Ruscheinski, Philipp Henning, Marian Zuska and Adelinde M. Uhrmacher. Towards using Bayesian Networks for Identifying Pathogenic Genetic Variants.
• (flash presentation) Irene Testa, Giuseppe Prencipe, Corrado Priami and Alina Sîrbu. Comparison of predictive models on integrated omics data.
• (flash presentation) Valérie Voorsluijs, Francesco Avanzini, Gianmaria Falasco, Massimiliano Esposito and Alexander Skupin. Nonequilibrium calcium dynamics optimizes the energetic efficiency of mitochondrial metabolism.

11.30-12.30 Session 4: Boolean Networks B (Session chair: David Šafránek)

• Elisa Tonello and Loïc Paulevé. Attractor identification in asynchronous Boolean dynamics with network reduction.
• Sara Riva, Jean-Marie Lagniez, Gustavo Magaña López and Loïc Paulevé. Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks.

12.30-14.00 Lunch Break

14.00-15.00 Invited Talk. Verena Wolf. Integrating Machine Learning and Mechanistic Modeling: Unlocking the Potential of Hybrid Approaches in the Life Sciences. (Session chair: Jun Pang)

15.00-15.30 Coffee Break

15.30-17.00 Session 5: Stochastic Modeling and Learning (Session chair: Abhyudai Singh)

• Iryna Zabaikina, Pavol Bokes and Abhyudai Singh. Joint distribution of protein concentration and cell volume coupled by feedback in dilution.
• Pelin Gundogdu, Miriam Payá-Milans, María Inmaculada Álamo Álvarez, Isabel Nepomuceno, Joaquin Dopazo and Carlos Loucera. Cell-level pathway scoring comparison with a biologically constrained variational autoencoder.
• Paolo Ballarini, Mahmoud Bentriou and Paul-Henry Cournède. A Formal Approach For Tuning Stochastic Oscillators.

17.30-19.30 Guided City Tour

• Highlights: Discover all the main places of interest, as well as the unusual and secret places that the former fortress-city has to offer. Explore, among other things, the exterior of the prestigious Grand Ducal Palace, the Corniche, commonly known as “the most beautiful balcony in Europe”, and the Bock rock, the birthplace of Luxembourg City.
• Meeting point: Luxembourg City Tourist Office (LCTO), 30 place Guillaume II, L-1648 Luxembourg (Google Map) at 17.30
• Language: English

19.30-22.00 Conference Dinner and Award Session (at Restaurant Porta Nova, 14 Av. de la Faiencerie, 1510 Limpertsberg Luxembourg, Google Map)

Friday 15 September 2023

09.00-10.00 Invited Talk. Jorge Goncalves. Causal dynamical network inference: from theory to applications in biology. (Session chair: Thomas Sauter)

10.00-10.30: Session 6: Network Inference (Session chair: Thomas Sauter)

• Tony Ribeiro, Maxime Folschette, Morgan Magnin and Katsumi Inoue. Learning any memory-less discrete semantics for dynamical systems represented by logic programs.

10.30-11.00 Coffee Break

11.00-12.30: Session 7: DNA Computing and Cellular Automata (Session chair: Jean-Marie Jacquet)

• Lancelot Wathieu, Gus Smith, Luis Ceze and Chris Thachuk. Fridge Compiler: Optimal Circuits From Molecular Inventories.
• Lilly Maria Treml. 3D Hybrid Cellular Automata Approach: A Concept Study.
• Pierre Vallois. Modeling short-range interactions between fibrocytes and CD8+ T cells in COPD bronchial 3 inflammatory response. (Cancelled)

12:30-12:40 Closing Session

12:40-14:00 Lunch Break