{"id":"https://openalex.org/W2273569416","doi":"https://doi.org/10.1093/bioinformatics/btv527","title":"Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model","display_name":"Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model","publication_year":2015,"publication_date":"2015-09-05","ids":{"openalex":"https://openalex.org/W2273569416","doi":"https://doi.org/10.1093/bioinformatics/btv527","mag":"2273569416","pmid":"https://pubmed.ncbi.nlm.nih.gov/26342230"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv527","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv527","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/219/49016459/bioinformatics_32_2_219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/219/49016459/bioinformatics_32_2_219.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052124720","display_name":"Miquel Mar\u00edn-Riera","orcid":"https://orcid.org/0000-0002-0746-6503"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miquel Marin-Riera","raw_affiliation_strings":["1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026062668","display_name":"Miguel Brun\u2010Usan","orcid":"https://orcid.org/0000-0002-8846-7494"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miguel Brun-Usan","raw_affiliation_strings":["1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033127609","display_name":"Roland Zimm","orcid":"https://orcid.org/0000-0002-0388-7052"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Roland Zimm","raw_affiliation_strings":["2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037131782","display_name":"Tommi V\u00e4likangas","orcid":"https://orcid.org/0000-0002-6046-1920"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tommi V\u00e4likangas","raw_affiliation_strings":["2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025275078","display_name":"Isaac Salazar\u2010Ciudad","orcid":"https://orcid.org/0000-0003-1607-0962"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES","FI"],"is_corresponding":true,"raw_author_name":"Isaac Salazar-Ciudad","raw_affiliation_strings":["1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and","2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetics, Universitat Aut\u00f2noma de Barcelona, Edifici C. 08193, Spain and","institution_ids":["https://openalex.org/I123044942"]},{"raw_affiliation_string":"2 Center of Excellence in Experimental and Computational Biology, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5025275078"],"corresponding_institution_ids":["https://openalex.org/I123044942","https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6127,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.89425845,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"32","issue":"2","first_page":"219","last_page":"225"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11190","display_name":"3D Printing in Biomedical Research","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10336","display_name":"Cancer Cells and Metastasis","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mesenchyme","display_name":"Mesenchyme","score":0.6757388710975647},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6356852650642395},{"id":"https://openalex.org/keywords/extracellular-matrix","display_name":"Extracellular matrix","score":0.5601678490638733},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.5443439483642578},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.44256097078323364},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4308532178401947},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3401974141597748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30492931604385376},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.1777670681476593},{"id":"https://openalex.org/keywords/embryo","display_name":"Embryo","score":0.13405171036720276},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11983096599578857}],"concepts":[{"id":"https://openalex.org/C2776340970","wikidata":"https://www.wikidata.org/wiki/Q32838","display_name":"Mesenchyme","level":3,"score":0.6757388710975647},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6356852650642395},{"id":"https://openalex.org/C189165786","wikidata":"https://www.wikidata.org/wiki/Q193825","display_name":"Extracellular matrix","level":2,"score":0.5601678490638733},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.5443439483642578},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.44256097078323364},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4308532178401947},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3401974141597748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30492931604385376},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.1777670681476593},{"id":"https://openalex.org/C196843134","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryo","level":2,"score":0.13405171036720276},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11983096599578857}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004848","descriptor_name":"Epithelium","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008648","descriptor_name":"Mesoderm","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009024","descriptor_name":"Morphogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009024","descriptor_name":"Morphogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009024","descriptor_name":"Morphogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D047108","descriptor_name":"Embryonic Development","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv527","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv527","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/219/49016459/bioinformatics_32_2_219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26342230","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26342230","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/2/219","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/2/219","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv527","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv527","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/219/49016459/bioinformatics_32_2_219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310174","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2273569416.pdf","grobid_xml":"https://content.openalex.org/works/W2273569416.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W57885350","https://openalex.org/W1522339824","https://openalex.org/W1576871725","https://openalex.org/W1649878614","https://openalex.org/W1967487044","https://openalex.org/W1969365435","https://openalex.org/W1974673184","https://openalex.org/W1989184968","https://openalex.org/W1989737139","https://openalex.org/W1990289037","https://openalex.org/W1996198135","https://openalex.org/W2002785668","https://openalex.org/W2024857915","https://openalex.org/W2036227059","https://openalex.org/W2036338631","https://openalex.org/W2050728487","https://openalex.org/W2076180442","https://openalex.org/W2096021672","https://openalex.org/W2096832005","https://openalex.org/W2100345558","https://openalex.org/W2105135903","https://openalex.org/W2112966482","https://openalex.org/W2122969640","https://openalex.org/W2129960309","https://openalex.org/W2134347395","https://openalex.org/W2137700068","https://openalex.org/W2154289334","https://openalex.org/W2154831559","https://openalex.org/W2155154349","https://openalex.org/W2161149725","https://openalex.org/W2171939937","https://openalex.org/W2483741417","https://openalex.org/W4205644073","https://openalex.org/W4211213832","https://openalex.org/W6721925311"],"related_works":["https://openalex.org/W1988297300","https://openalex.org/W90965816","https://openalex.org/W4245200655","https://openalex.org/W2013706434","https://openalex.org/W1984951277","https://openalex.org/W2001821340","https://openalex.org/W2083218509","https://openalex.org/W2086256517","https://openalex.org/W2415904712","https://openalex.org/W1982140659"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
