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20th International Conference on Computational Methods in Systems Biology (CMSB 2022)

September 14-16, 2022, Bucharest, Romania


The talks will be streamed through Zoom. The link will be sent to the registered participants a few days before the conference.

All accepted papers are available free on Springer Nature for the duration of the conference at

Wednesday September 14, 2022

8.15-8.50 Registration

8.50-9.00 Opening session (session chair Andrei Paun)

9.00-10.00 Invited talk. Gabriela Chiosis, Targeting and controlling protein-protein interaction networks in disease. (session chair Ion Petre)

10.00-10.30 Coffee break and poster session

10.30-12.40 Session 1: Chemical Reaction Networks (session chair Ion Petre)

Mathieu Hemery and François Fages. Algebraic Biochemistry: a Framework for On-line Analog Computation in Cells.

Martin Helfrich, Milan Ceska, Jan Kretinsky and Štefan Martiček. Abstraction-Based Segmental Simulation of Chemical Reaction Networks.

Joachim Niehren, Athénaïs Vaginay and Cristian Versari. Abstract Simulation of Reaction Networks via Boolean Networks.

Aurélien Desoeuvres, Peter Szmolyan and Ovidiu Radulescu. Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations.

(flash presentation) Albin Salazar and Jerome Feret. A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation.

(flash presentation) Vaidhiswaran Ramesh and Krishnan J. Leveraging symmetry and symmetry breaking in multisite modification networks.

(flash presentation) Kaan Öcal, Guido Sanguinetti and Ramon Grima. Variational Model Reduction with the Chemical Master Equation.

12.40-14.00 Lunch break

14.00-15.00 Invited talk. Erik Sonnhammer, How to infer accurate gene regulatory networks from gene expression. (session chair David Šafránek)

15.00-15.30 Coffee break and poster session

15.30-17.40 Session 2: Boolean Networks (session chair David Šafránek)

Clémence Réda and Andrée Delahaye-Duriez. Prioritisation of candidate genes through Boolean networks.

Samuel Pastva. Variable Stabilisation in Boolean Monotonic Model Pools.

Théo Roncalli and Loïc Paulevé. Variable-Depth Simulation of Most Permissive Boolean Networks.

Van-Giang Trinh, Belaid Benhamou, Kunihiko Hiraishi and Sylvain Soliman. Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding.

(flash presentation) Gustavo Magaña López, Laurence Calzone, Andrei Zinovyev and Loïc Paulevé. scBoolSeq: scRNA-Seq data binarization and synthetic generation from Boolean dynamics.

(flash presentation) Kyungduk Moon, Kangbok Lee and Loïc Paulevé. Computational Complexity of Trap Spaces in Boolean Networks.

(flash presentation) Deniz Seçilmiş, Thomas Hillerton and Erik Sonnhammer. GRNbenchmark: A web server for online benchmarking of gene regulatory network inference methods.

Thursday September 15

9.00-10.00 Invited talk. Loïc Paulevé, Boolean networks as a link between knowledge, data, and quantitative models. (session chair François Fages)

10.00-10.30 Coffee break and poster session

10.30-12.30 Session 3: Networks and Machine Learning (session chair François Fages)

Svitlana Braichenko, Ramon Grima and Guido Sanguinetti. Bayesian learning of effective chemical master equations in crowded intracellular conditions.

Ville Laitinen and Leo Lahti. Probabilistic Multivariate Early Warning Signals.

(highlight talk) Till Köster, Tom Warnke and Adelinde Uhrmacher. Generating Fast Specialized Simulators for Stochastic Reaction Networks via PartialEvaluation.

(highlight talk) Kyungduk Moon and Kangbok Lee. Bilevel Integer Programming Approach for Solving Control Problems on Boolean Networks.

(flash presentation) Augustinas Sukys, Kaan Öcal and Ramon Grima. Approximating Solutions of the Chemical Master Equation using Neural Networks.

(flash presentation) Joel Sjöberg, Adrian Lita, Orieta Celiku, David Păcioianu, Nicoleta Siminea, Andrei Paun, Mark R. Gilbert, Houtan Noushmehr, Mioara Larion and Ion Petre. Tumor detection in glioma samples using Raman spectroscopy and unsupervised machine learning.

12.30-14.30 Lunch break and steering committee meeting

14.30-16.35 Session 4: Software (session chair Loïc Paulevé)

Fabricio Cravo, Matthias Függer, Thomas Nowak and Gayathri Prakash. MobsPy: A Meta-Species Language for Chemical Reaction Networks.

Hanna Josephine Wiederanders, Anne-Lena Moor and Christoph Zechner. Automated Generation of Conditional Moment Equations for Stochastic Reaction Networks.

Georgios Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski and Andrea Vandin. An Extension of ERODE to Reduce Boolean Networks by Backward Boolean Equivalence.

Matej Troják, David Šafránek, Branislav Brozmann and Lubos Brim. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-based Systems.

(flash presentation) Emma Persson and Erik L L Sonnhammer. InParanoid-DIAMOND: Faster orthology analysis with the InParanoid algorithm.

(flash presentation) Davide Buzzao, Miguel Castresana-Aguirre, Dimitri Guala and Erik L.L. Sonnhammer. TOPAS, a network-based iterative approach to detect disease modules in a top-down fashion.

(flash presentation) Reinis Muiznieks and Egils Stalidzans. The implementation of Total Optimisation Potential (TOP) approach in the metabolic engineering by COPASI wrapper SpaceScanner.

16.45-19.00 Walking tour of the old town (weather permitting).

19.00-22.00 Conference dinner: the old, traditional “Brewers’ Inn” restaurant. Website here. Location here.

Friday September 16

9.00-9.10 Award Ceremony

9.10-10.10 Invited talk. Alessandra Carbone, Sequence space and deep learning to better understand proteins. (session chair Andrei Paun)

10.10-10.40 Coffee break and poster session

10.40-12.10 Session 5: Continuous and Hybrid Models (session chair Andrei Paun)

Greugny Eléa, Stamatas Georgios and François Fages. Stability versus Metastability in a Model of Skin Microbiome.

Antonio Jiménez-Pastor, Joshua Jacob and Gleb Pogudin. Exact linear reduction for rational dynamical systems.

Honglu Sun, Maxime Folschette and Morgan Magnin. Limit cycle analysis of a class of hybrid gene regulatory networks.

(flash presentation) Ethan Hunter and Jessica Enright. An Exact Dynamical Approach to Compartmental Graph Models of Disease.

(flash presentation) Andreas Ruscheinski, Anna Lena Reimler, Roland Ewald and Adelinde M. Uhrmacher. Towards Analyzing the Reclassification Dynamics of ClinVar Variants.

12.10-12.25 Closing session

Important dates

  • Abstract submission: May 8, 2022
  • Paper submission: May 15, 2022
  • Notification: June 10, 2022
  • Camera ready: June 17, 2022
  • Poster/highlight talk: July 14, 2022
  • Conference: September 14-16, 2022

Proceedings published in

Sponsored by

  • The Faculty of Mathematics and Computer Science, University of Bucharest.
  • The Faculty of Biology, University of Bucharest.
  • ICUB, University of Bucharest.
  • The National Institute for R&D in Biological Sciences (INCDSB), Romania
  • Springer Nature