{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,11]],"date-time":"2026-01-11T02:02:13Z","timestamp":1768096933854,"version":"3.49.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0feenstra@few.vu.nl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp355","type":"journal-article","created":{"date-parts":[[2009,6,11]],"date-time":"2009-06-11T01:39:55Z","timestamp":1244684395000},"page":"2049-2056","source":"Crossref","is-referenced-by-count":36,"title":["Executing multicellular differentiation: quantitative predictive modelling of <i>C.elegans<\/i> vulval development"],"prefix":"10.1093","volume":"25","author":[{"given":"Nicola","family":"Bonzanni","sequence":"first","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"},{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elzbieta","family":"Krepska","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K. Anton","family":"Feenstra","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wan","family":"Fokkink","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thilo","family":"Kielmann","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henri","family":"Bal","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[{"name":"1 Centre for Integrative Bioinformatics and 2Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,6,10]]},"reference":[{"key":"2023013112093845000_B1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/348503a0","article-title":"Caenorhabditis elegans ras gene let-60 acts as a switch in the pathway of vulval induction","volume":"348","author":"Beitel","year":"1990","journal-title":"Nature"},{"key":"2023013112093845000_B2","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1126\/science.1055642","article-title":"Notch inhibition of RAS signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development","volume":"291","author":"Berset","year":"2001","journal-title":"Science"},{"key":"2023013112093845000_B3","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1101\/gad.333505","article-title":"The C. elegans homolog of the mammalian tumor suppressor Dep-1\/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions","volume":"19","author":"Berset","year":"2005","journal-title":"Genes Dev."},{"key":"2023013112093845000_B4","first-page":"86","article-title":"On priorities of parallelism","volume-title":"Logics of Programs","author":"Burkhard","year":"1980"},{"key":"2023013112093845000_B5","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1093\/bib\/bbm029","article-title":"Petri net modelling of biological networks","volume":"8","author":"Chaouiya","year":"2007","journal-title":"Brief. 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