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Computational Methods in Systems Biology

20th International Conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022, Proceedings

  • Conference proceedings
  • © 2022

Overview

Editors:
  1. Ion Petre

    1. University of Turku, Turku, Finland

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  2. Andrei Păun

    1. University of Bucharest, Bucharest, Romania

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 13447)

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

Included in the following conference series:

Conference proceedings info: CMSB 2022.

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Table of contents (17 papers)

  1. Front Matter

    Pages i-xxii
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  2. Chemical Reaction Networks

    1. Front Matter

      Pages 1-1
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    2. Algebraic Biochemistry: A Framework for Analog Online Computation in Cells

      • Mathieu Hemery, François Fages
      Pages 3-20

    3. Abstract Simulation of Reaction Networks via Boolean Networks

      • Joachim Niehren, Athénaïs Vaginay, Cristian Versari
      Pages 21-40

    4. Abstraction-Based Segmental Simulation of Chemical Reaction Networks

      • Martin Helfrich, Milan Češka, Jan Křetínský, Štefan Martiček
      Pages 41-60

    5. Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations

      • Aurélien Desoeuvres, Peter Szmolyan, Ovidiu Radulescu
      Pages 61-85

  3. Boolean Networks

    1. Front Matter

      Pages 87-87
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    2. Prioritization of Candidate Genes Through Boolean Networks

      • Clémence Réda, Andrée Delahaye-Duriez
      Pages 89-121

    3. Variable Stabilisation in Boolean Monotonic Model Pools

      • Samuel Pastva
      Pages 122-137

    4. Variable-Depth Simulation of Most Permissive Boolean Networks

      • Théo Roncalli, Loïc Paulevé
      Pages 138-157

    5. Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding

      • Van-Giang Trinh, Belaid Benhamou, Kunihiko Hiraishi, Sylvain Soliman
      Pages 158-176

  4. Continuous and Hybrid Models

    1. Front Matter

      Pages 177-177
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    2. Stability Versus Meta-stability in a Skin Microbiome Model

      • Eléa Thibault Greugny, Georgios N. Stamatas, François Fages
      Pages 179-197

    3. Exact Linear Reduction for Rational Dynamical Systems

      • Antonio Jiménez-Pastor, Joshua Paul Jacob, Gleb Pogudin
      Pages 198-216

    4. Limit Cycle Analysis of a Class of Hybrid Gene Regulatory Networks

      • Honglu Sun, Maxime Folschette, Morgan Magnin
      Pages 217-236

  5. Machine Learning

    1. Front Matter

      Pages 237-237
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    2. Bayesian Learning of Effective Chemical Master Equations in Crowded Intracellular Conditions

      • Svitlana Braichenko, Ramon Grima, Guido Sanguinetti
      Pages 239-258

    3. Probabilistic Multivariate Early Warning Signals

      • Ville Laitinen, Leo Lahti
      Pages 259-274

  6. Software

    1. Front Matter

      Pages 275-275
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    2. MobsPy: A Meta-species Language for Chemical Reaction Networks

      • Fabricio Cravo, Matthias Függer, Thomas Nowak, Gayathri Prakash
      Pages 277-285
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  1. Computational Methods in Systems Biology

Keywords

About this book

This book constitutes the refereed proceedings of the 20th International Conference on Computational Methods in Systems Biology, CMSB 2022, held in Bucharest, Romania, in September 2022.

The 13 full papers and 4 tool papers were carefully reviewed and selected from 43 submissions. CMSB focuses on modeling, simulation, analysis, design and control of biological systems. The papers are arranged thematically as follows: Chemical reaction networks; Boolean networks; continuous and hybrid models; machine learning; software.

Editors and Affiliations

  • University of Turku, Turku, Finland

    Ion Petre

  • University of Bucharest, Bucharest, Romania

    Andrei Păun

Bibliographic Information

  • Book Title: Computational Methods in Systems Biology

  • Book Subtitle: 20th International Conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022, Proceedings

  • Editors: Ion Petre, Andrei Păun

  • Series Title: Lecture Notes in Computer Science

  • DOI: https://doi.org/10.1007/978-3-031-15034-0

  • Publisher: Springer Cham

  • eBook Packages: Computer Science, Computer Science (R0)

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022

  • Softcover ISBN: 978-3-031-15033-3Published: 20 August 2022

  • eBook ISBN: 978-3-031-15034-0Published: 18 August 2022

  • Series ISSN: 0302-9743

  • Series E-ISSN: 1611-3349

  • Edition Number: 1

  • Number of Pages: XXII, 311

  • Number of Illustrations: 15 b/w illustrations, 72 illustrations in colour

  • Topics: Bioinformatics, Computer System Implementation, Artificial Intelligence, Biological Techniques

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