Computational Methods in Systems Biology

1. Front Matter

   Pages i-xii

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2. Reducing Boolean Networks with Backward Boolean Equivalence

   • Georgios Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski, Andrea Vandin

   Pages 1-18

3. Abstraction of Markov Population Dynamics via Generative Adversarial Nets

   • Francesca Cairoli, Ginevra Carbone, Luca Bortolussi

   Pages 19-35

4. Greening R. Thomas’ Framework with Environment Variables: A Divide and Conquer Approach

   • Laetitia Gibart, Hélène Collavizza, Jean-Paul Comet

   Pages 36-56

5. Automated Inference of Production Rules for Glycans

   • Ansuman Biswas, Ashutosh Gupta, Meghana Missula, Mukund Thattai

   Pages 57-73

6. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs

   • Mathieu Hemery, François Fages, Sylvain Soliman

   Pages 74-90

7. Interpretable Exact Linear Reductions via Positivity

   • Gleb Pogudin, Xingjian Zhang

   Pages 91-107

8. Explainable Artificial Neural Network for Recurrent Venous Thromboembolism Based on Plasma Proteomics

   • Misbah Razzaq, Louisa Goumidi, Maria-Jesus Iglesias, Gaëlle Munsch, Maria Bruzelius, Manal Ibrahim-Kosta et al.

   Pages 108-121

9. Neural Networks to Predict Survival from RNA-seq Data in Oncology

   • Mathilde Sautreuil, Sarah Lemler, Paul-Henry Cournède

   Pages 122-140

10. Microbial Community Decision Making Models in Batch and Chemostat Cultures

    • Axel Theorell, Jörg Stelling

    Pages 141-158Open Access

11. Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study

    • Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, Anne Siegel

    Pages 159-180

12. Population Design for Synthetic Gene Circuits

    • Baptiste Turpin, Eline Y. Bijman, Hans-Michael Kaltenbach, Jörg Stelling

    Pages 181-197Open Access

13. Nonlinear Pattern Matching in Rule-Based Modeling Languages

    • Tom Warnke, Adelinde M. Uhrmacher

    Pages 198-214

14. Protein Noise and Distribution in a Two-Stage Gene-Expression Model Extended by an mRNA Inactivation Loop

    • Candan Çelik, Pavol Bokes, Abhyudai Singh

    Pages 215-229

15. Aeon 2021: Bifurcation Decision Trees in Boolean Networks

    • Nikola Beneš, Luboš Brim, Samuel Pastva, David Šafránek

    Pages 230-237

16. LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales

    • Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Zinovyev, Ovidiu Radulescu

    Pages 238-244

17. Ppsim: A Software Package for Efficiently Simulating and Visualizing Population Protocols

    • David Doty, Eric Severson

    Pages 245-253

18. Web-Based Structural Identifiability Analyzer

    • Ilia Ilmer, Alexey Ovchinnikov, Gleb Pogudin

    Pages 254-265

19. BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems

    • Gaurav Saxena, Miguel Ponce-de-Leon, Arnau Montagud, David Vicente Dorca, Alfonso Valencia

    Pages 266-279Open Access

20. Back Matter

    Pages 281-281

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This book constitutes the refereed proceedings of the 19th International Conference on Computational Methods in Systems Biology, CMSB 2021, held in Bordeaux, France, September 22–24, 2021.*The 13 full papers and 5 tool papers were carefully reviewed and selected from 32 submissions. The topics of interest include biological process modelling; biological system model verification, validation, analysis, and simulation; high-performance computational systems biology; model inference from experimental data; multi-scale modeling and analysis methods; computational approaches for synthetic biology; machine learning and data-driven approaches; microbial ecology modelling and analysis; methods and protocols for populations and their variability; models, applications, and case studies in systems and synthetic biology. The chapters "Microbial Community Decision Making Models in Batch", "Population design for synthetic gene circuits", "BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems" are published open access under a CC BY license (Creative Commons Attribution 4.0 International License). 


* The conference was held in a hybrid mode due to the COVID-19 pandemic.

• adaptive control systems
• artificial intelligence
• automation
• computer networks
• computer programming
• computer systems
• differential equations
• distributed computer systems
• embedded systems
• formal logic
• fuzzy control
• fuzzy sets
• linear matrix inequalities
• matrix algebra
• network architecture
• network protocols
• numerical methods
• probability
• signal processing
• software engineering

• Univ. Grenoble Alpes, Inria, Grenoble, France

  Eugenio Cinquemani

• Univ. Bordeaux, Bordeaux INP, CNRS, LaBRI, UMR5800, Talence, France

  Loïc Paulevé

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