Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

MOTIVATION: Understanding the processes involved in multi-cellular pattern formation is a central problem of developmental biology, hopefully leading to many new insights, e.g. in the treatment of various diseases. Defining suitable computational techniques for development modelling, able to perform in silico simulation experiments, is an open and challenging problem.

RESULTS: Previously, we proposed a coarse-grained, quantitative approach based on the basic Petri net formalism, to mimic the behaviour of the biological processes during multicellular differentiation. Here, we apply our modelling approach to the well-studied process of Caenorhabditis elegans vulval development. We show that our model correctly reproduces a large set of in vivo experiments with statistical accuracy. It also generates gene expression time series in accordance with recent biological evidence. Finally, we modelled the role of microRNA mir-61 during vulval development and predict its contribution in stabilizing cell pattern formation.

Original languageEnglish
Pages (from-to)2049-56
Number of pages8
JournalBioinformatics
Volume25
Issue number16
DOIs
Publication statusPublished - 15 Aug 2009

Fingerprint

Predictive Modeling
Biological Phenomena
Developmental Biology
Caenorhabditis elegans
MicroRNAs
Computer Simulation
Pattern Formation
Gene Expression
Petri nets
Gene expression
Cell Formation
Time series
MicroRNA
Computational Techniques
Experiments
Modeling
Petri Nets
Large Set
Simulation Experiment
Predict

Keywords

  • Animals
  • Body Patterning
  • Caenorhabditis elegans
  • Cell Differentiation
  • Computational Biology
  • Computer Simulation
  • Female
  • MicroRNAs
  • Organogenesis
  • Vulva
  • Journal Article
  • Research Support, Non-U.S. Gov't

Cite this

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title = "Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development",
abstract = "MOTIVATION: Understanding the processes involved in multi-cellular pattern formation is a central problem of developmental biology, hopefully leading to many new insights, e.g. in the treatment of various diseases. Defining suitable computational techniques for development modelling, able to perform in silico simulation experiments, is an open and challenging problem.RESULTS: Previously, we proposed a coarse-grained, quantitative approach based on the basic Petri net formalism, to mimic the behaviour of the biological processes during multicellular differentiation. Here, we apply our modelling approach to the well-studied process of Caenorhabditis elegans vulval development. We show that our model correctly reproduces a large set of in vivo experiments with statistical accuracy. It also generates gene expression time series in accordance with recent biological evidence. Finally, we modelled the role of microRNA mir-61 during vulval development and predict its contribution in stabilizing cell pattern formation.",
keywords = "Animals, Body Patterning, Caenorhabditis elegans, Cell Differentiation, Computational Biology, Computer Simulation, Female, MicroRNAs, Organogenesis, Vulva, Journal Article, Research Support, Non-U.S. Gov't",
author = "N. Bonzanni and E. Krepska and K.A. Feenstra and W.J. Fokkink and T. Kielmann and H.E. Bal and J. Heringa",
year = "2009",
month = "8",
day = "15",
doi = "10.1093/bioinformatics/btp355",
language = "English",
volume = "25",
pages = "2049--56",
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issn = "1367-4803",
publisher = "Oxford University Press",
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Executing multicellular differentiation : quantitative predictive modelling of C.elegans vulval development. / Bonzanni, N.; Krepska, E.; Feenstra, K.A.; Fokkink, W.J.; Kielmann, T.; Bal, H.E.; Heringa, J.

In: Bioinformatics, Vol. 25, No. 16, 15.08.2009, p. 2049-56.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

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T2 - quantitative predictive modelling of C.elegans vulval development

AU - Bonzanni, N.

AU - Krepska, E.

AU - Feenstra, K.A.

AU - Fokkink, W.J.

AU - Kielmann, T.

AU - Bal, H.E.

AU - Heringa, J.

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KW - Body Patterning

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