{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:14:45Z","timestamp":1778634885286,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The transformation of the embryo during development requires complex gene networks, cell signaling and gene-regulated cell behaviors (division, adhesion, polarization, apoptosis, contraction, extracellular matrix secretion, signal secretion and reception, etc.). There are several models of development implementing these phenomena, but none considers at the same time the very different bio-mechanical properties of epithelia, mesenchyme, extracellular matrix and their interactions.<\/jats:p>\n               <jats:p>Results: Here, we present a new computational model and accompanying open-source software, EmbryoMaker, that allows the user to simulate custom developmental processes by designing custom gene networks capable of regulating cell signaling and all animal basic cell behaviors. We also include an editor to implement different initial conditions, mutations and experimental manipulations. We show the applicability of the model by simulating several complex examples of animal development.<\/jats:p>\n               <jats:p>Availability and implementation: The source code can be downloaded from: http:\/\/www.biocenter.helsinki.fi\/salazar\/software.html.<\/jats:p>\n               <jats:p>Contact: \u00a0isalazar@mappi.helsinki.fi<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv527","type":"journal-article","created":{"date-parts":[[2015,9,6]],"date-time":"2015-09-06T00:18:10Z","timestamp":1441498690000},"page":"219-225","source":"Crossref","is-referenced-by-count":60,"title":["Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model"],"prefix":"10.1093","volume":"32","author":[{"given":"Miquel","family":"Marin-Riera","sequence":"first","affiliation":[{"name":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel","family":"Brun-Usan","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roland","family":"Zimm","sequence":"additional","affiliation":[{"name":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tommi","family":"V\u00e4likangas","sequence":"additional","affiliation":[{"name":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isaac","family":"Salazar-Ciudad","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and"},{"name":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,9,5]]},"reference":[{"key":"2023020110254776200_btv527-B1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.semcdb.2014.01.007","article-title":"Early inductive events in ectodermal appendage morphogenesis","volume":"25\u201326","author":"Biggs","year":"2014","journal-title":"Semin. 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