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Computational Methods in Systems Biology

19th International Conference, CMSB 2021, Bordeaux, France, September 22–24, 2021, Proceedings

  • Conference proceedings
  • © 2021

Overview

Editors:
  1. Eugenio Cinquemani

    1. Univ. Grenoble Alpes, Inria, Grenoble, France

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  2. Loïc Paulevé

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

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 12881)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: CMSB 2021.

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Table of contents (18 papers)

  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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Other volumes

  1. Computational Methods in Systems Biology

Keywords

About this book

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.

Editors and Affiliations

  • Univ. Grenoble Alpes, Inria, Grenoble, France

    Eugenio Cinquemani

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

    Loïc Paulevé

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