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 language | English |
|---|---|
| Pages (from-to) | 2049-56 |
| Number of pages | 8 |
| Journal | Bioinformatics |
| Volume | 25 |
| Issue number | 16 |
| DOIs | |
| Publication status | Published - 15 Aug 2009 |
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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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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 Journal › Article › Academic › peer-review
TY - JOUR
T1 - Executing multicellular differentiation
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.
PY - 2009/8/15
Y1 - 2009/8/15
N2 - 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.
AB - 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.
KW - Animals
KW - Body Patterning
KW - Caenorhabditis elegans
KW - Cell Differentiation
KW - Computational Biology
KW - Computer Simulation
KW - Female
KW - MicroRNAs
KW - Organogenesis
KW - Vulva
KW - Journal Article
KW - Research Support, Non-U.S. Gov't
U2 - 10.1093/bioinformatics/btp355
DO - 10.1093/bioinformatics/btp355
M3 - Article
VL - 25
SP - 2049
EP - 2056
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 16
ER -