{"id":"https://openalex.org/W2157999920","doi":"https://doi.org/10.1093/bib/bbm024","title":"Combining experiments with multi-cell agent-based modeling to study biological tissue patterning","display_name":"Combining experiments with multi-cell agent-based modeling to study biological tissue patterning","publication_year":2007,"publication_date":"2007-03-29","ids":{"openalex":"https://openalex.org/W2157999920","doi":"https://doi.org/10.1093/bib/bbm024","mag":"2157999920","pmid":"https://pubmed.ncbi.nlm.nih.gov/17584763"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbm024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm024","pdf_url":"https://academic.oup.com/bib/article-pdf/8/4/245/590520/bbm024.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/8/4/245/590520/bbm024.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052174681","display_name":"Bryan C. Thorne","orcid":null},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"B. C. Thorne","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, PO Box 800759, Charlottesville, VA 22908, USA. bthorne@virginia.edu"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, PO Box 800759, Charlottesville, VA 22908, USA. bthorne@virginia.edu","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103579164","display_name":"Alexander M. Bailey","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. M. Bailey","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5017480661","display_name":"Shayn M. Peirce","orcid":"https://orcid.org/0000-0001-5857-5606"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. M. Peirce","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052174681"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":8.1797,"has_fulltext":false,"cited_by_count":145,"citation_normalized_percentile":{"value":0.97871598,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"8","issue":"4","first_page":"245","last_page":"257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.991100013256073,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular 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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9509999752044678,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular 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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7207856774330139},{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.5769856572151184},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5511332750320435},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5410128831863403},{"id":"https://openalex.org/keywords/agent-based-model","display_name":"Agent-based model","score":0.48209670186042786},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40332815051078796},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.3920660614967346},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3569720983505249},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.13534539937973022}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7207856774330139},{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.5769856572151184},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5511332750320435},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5410128831863403},{"id":"https://openalex.org/C2780873155","wikidata":"https://www.wikidata.org/wiki/Q392811","display_name":"Agent-based model","level":2,"score":0.48209670186042786},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40332815051078796},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3920660614967346},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3569720983505249},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.13534539937973022},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D023822","descriptor_name":"Tissue Engineering","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D044968","descriptor_name":"Regenerative Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044968","descriptor_name":"Regenerative Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044968","descriptor_name":"Regenerative Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbm024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm024","pdf_url":"https://academic.oup.com/bib/article-pdf/8/4/245/590520/bbm024.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17584763","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17584763","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbm024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm024","pdf_url":"https://academic.oup.com/bib/article-pdf/8/4/245/590520/bbm024.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157999920.pdf","grobid_xml":"https://content.openalex.org/works/W2157999920.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W111524940","https://openalex.org/W164528865","https://openalex.org/W1483113211","https://openalex.org/W1539819149","https://openalex.org/W1601557407","https://openalex.org/W1967522361","https://openalex.org/W1968763381","https://openalex.org/W1974034376","https://openalex.org/W1977523316","https://openalex.org/W1981477992","https://openalex.org/W1982233439","https://openalex.org/W1986008808","https://openalex.org/W1996449803","https://openalex.org/W2002098652","https://openalex.org/W2008191529","https://openalex.org/W2016932039","https://openalex.org/W2024771744","https://openalex.org/W2027022480","https://openalex.org/W2034269086","https://openalex.org/W2036338634","https://openalex.org/W2046314718","https://openalex.org/W2062630837","https://openalex.org/W2063811624","https://openalex.org/W2067462917","https://openalex.org/W2075052929","https://openalex.org/W2086705790","https://openalex.org/W2087271480","https://openalex.org/W2088519259","https://openalex.org/W2092375071","https://openalex.org/W2097591929","https://openalex.org/W2110059498","https://openalex.org/W2120889810","https://openalex.org/W2122138696","https://openalex.org/W2130929414","https://openalex.org/W2137783233","https://openalex.org/W2141890333","https://openalex.org/W2143494711","https://openalex.org/W2144926082","https://openalex.org/W2150752805","https://openalex.org/W2154718031","https://openalex.org/W2154755377","https://openalex.org/W2156171664","https://openalex.org/W2165620349","https://openalex.org/W2169137217","https://openalex.org/W2171151276","https://openalex.org/W2325808791","https://openalex.org/W2991981398"],"related_works":["https://openalex.org/W2381566602","https://openalex.org/W4246418678","https://openalex.org/W2003806119","https://openalex.org/W4246426965","https://openalex.org/W4229820691","https://openalex.org/W2355215981","https://openalex.org/W3106945349","https://openalex.org/W4244911058","https://openalex.org/W2371931285","https://openalex.org/W4247658307"],"abstract_inverted_index":{"Agent-based":[0],"modeling":[1,6],"(ABM),":[2],"also":[3],"termed":[4],"'Individual-based":[5],"(IBM)',":[7],"is":[8,74],"a":[9,117],"computational":[10],"approach":[11],"that":[12,127],"simulates":[13],"the":[14,41,55,93,106],"interactions":[15],"of":[16,43,71,95,119,122],"autonomous":[17],"entities":[18],"(agents,":[19],"or":[20],"individual":[21,45],"cells)":[22],"with":[23,98,131,143,148],"each":[24,44],"other":[25],"and":[26,57,101,109,134],"their":[27],"local":[28],"environment":[29],"to":[30,75,79,86,112],"predict":[31],"higher":[32],"level":[33],"emergent":[34],"patterns.":[35],"A":[36],"literature-derived":[37],"rule":[38],"set":[39],"governs":[40],"actions":[42],"agent.":[46],"While":[47],"this":[48,72,136,149],"technique":[49],"has":[50,61,83,128],"been":[51,64,84],"widely":[52],"used":[53,85],"in":[54,66],"ecological":[56],"social":[58],"sciences,":[59],"it":[60,82],"only":[62],"recently":[63],"applied":[65],"biomedical":[67,113],"research.":[68,114],"The":[69],"purpose":[70],"review":[73],"provide":[76],"an":[77],"introduction":[78],"ABM":[80,107,132],"as":[81],"study":[87],"complex":[88],"multi-cell":[89],"biological":[90],"phenomena,":[91],"underscore":[92],"importance":[94],"coupling":[96],"models":[97],"experimental":[99,130],"work,":[100],"outline":[102],"future":[103],"challenges":[104],"for":[105,145],"field":[108],"its":[110],"application":[111],"We":[115,141],"highlight":[116],"number":[118],"published":[120],"examples":[121],"ABM,":[123],"focusing":[124],"on":[125],"work":[126],"combined":[129],"analyses":[133],"how":[135],"pairing":[137],"produces":[138],"new":[139],"understanding.":[140],"conclude":[142],"suggestions":[144],"moving":[146],"forward":[147],"parallel":[150],"approach.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":12}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}