• regular papers: 20 minutes of talk, 5 minutes questions
  • tool papers: 15 minutes of talk, 5 minutes questions
  • presentation only: 15 minutes of talk, 5 minutes questions
  • flash presentations: 5 minutes of talk

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

Wednesday 22 September

8:30 – 9:00    Welcome

9:00 – 10:00    Invited – Ion Petre “Structural Network Controlability: theory and applications in drug repurposing”

(break)

10:30 – 12:05    Simulation and Learning

  1. Francesca Cairoli, Ginevra Carbone and Luca Bortolussi. Abstraction of Markov Population Dynamics via Generative Adversarial Nets (regular paper)
  2. Misbah Razzaq, Louisa Goumidi, Maria-Jesus Iglesias, Gaëlle Munsch, Maria Bruzelius, Manal Ibrahim-Kosta, Lynn Butler, Jacob Odeberg, Pierre-Emmanuel Morange and David Alexandre Tregouet. Explainable artificial neural network for recurrent venous thromboembolism based on plasma proteomics (regular paper)
  3. Mathilde Sautreuil, Sarah Lemler and Paul-Henry Cournède. Neural networks to predict survival from RNA-seq data in oncology (regular paper)
  4. Gaurav Saxena, Miguel Ponce de Leon, Arnau Montagud, David Vicente Dorca and Alfonso Valencia. BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems (tool paper)

12:05 – 12:25    Flash presentations (x4)

(lunch)

14:00 – 15:00    Invited – Diego di BernardoAnalysis, modelling and control of transcription factor  EB (TFEB) nuclear shuttling dynamics in mammalian cells by microfluidics.

15:00 – 15:40    Flash presentations (x8)

(break)

16:10 – 18:00 Rule-based  modeling, regulatory networks, and control

  1. Ashutosh Gupta, Ansuman Biswas, Mukund Thattai and Missula Meghana. Automated inference of production rules for glycans (regular paper)
  2. Tom Warnke and Adelinde Uhrmacher. Nonlinear pattern matching in rule-based modeling languages (regular paper)
  3. Tomislav Plesa. Integral feedback in synthetic biology: Negative-equilibrium catastrophe (presentation only)
  4. Alberto Zenere, Olof Rundquist, Mika Gustafsson and Claudio Altafini. Investigating coherence in multi-omics elementary gene regulatory network motifs (presentation only)
  5. Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas and Haris Zafeiropoulos. A new geometric algorithm for sampling the flux space of metabolic networks (presentation only)

Thursday 23 September

9:00 – 10:00    Invited – Laurence Calzone (TBA)

(break)

10:30 – 12:05    Qualitative modeling

  1. Georgios Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski and Andrea Vandin. Reducing Boolean Networks with Backward Boolean Equivalence (regular paper)
  2. Laetitia Gibart, Hélène Collavizza and Jean-Paul Comet. Greening R. Thomas’ Framework with Environment Variables: a Divide and Conquer Approach (regular paper)
  3. Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé and Anne Siegel. Learning Boolean controls in regulated metabolic networks: a case-study (regular paper)
  4. Nikola Benes, Lubos Brim, Samuel Pastva and David Šafránek. Aeon 2021: Bifurcation Decision Trees in Boolean Networks (tool paper)

12:05 – 12:25   Flash presentations (x4)

(lunch)

14:00 – 15:00    Poster Session

15:00 – 16:00    Invited – Yang-yu LiuControlling Human Microbiota

(break)

16:30 – 18:00 Population variability and microbial communities

  1. Baptiste Turpin, Eline Bijman, Hans-Michael Kaltenbach and Jörg Stelling. Population design for synthetic gene circuits (regular paper)
  2. Axel Theorell and Jörg Stelling. Microbial Community Decision Making Models in Batchand Chemostat Cultures (regular paper)
  3. David Doty and Eric Severson. ppsim: A software package for efficiently simulating and visualizing population protocols (tool paper)
  4. Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand and Anne Siegel. Metabolic complementarity applied to the screening of microbiota and the identification of key species (presentation only)

Friday 24 September

9:00 – 10:00    Invited – Giulia GiordanoA journey from biochemical reaction networks to epidemic models

(break)

10:30 – 12:25 Continuous and stochastic dynamics

  1. Candan Çelik, Pavol Bokes and Abhyudai Singh. Protein noise and distribution in a two-stage gene-expression model extended by an mRNA inactivation loop (regular paper)
  2. Mathieu Hemery, François Fages and Sylvain Soliman. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs (regular paper)
  3. Gleb Pogudin and Xingjian Zhang. Interpretable exact linear reductions via positivity (regular paper)
  4. Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Zinovyev and Ovidiu Radulescu. LNetReduce: tool for reducing linear dynamic networks with separated time scales (tool paper)
  5. Ilia Ilmer, Alexey Ovchinnikov and Gleb Pogudin. Web-based Structural Identifiability Analyzer (tool paper)