{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039768,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T00:00:00Z","timestamp":1593129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Lehigh University through a Faculty Innovation","award":["FIG-2019-JB"],"award-info":[{"award-number":["FIG-2019-JB"]}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["2019-105566GB-I00"],"award-info":[{"award-number":["2019-105566GB-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present TiFoSi, a computational tool to simulate the cellular dynamics of planar epithelia. TiFoSi allows to model feedbacks between cellular mechanics and gene expression (either in a deterministic or a stochastic way), the interaction between different cell populations, the custom design of the cell cycle and cleavage properties, the protein number partitioning upon cell division, and the modeling of cell communication (juxtacrine and paracrine signaling).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>http:\/\/tifosi.thesimbiosys.com.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa592","type":"journal-article","created":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T15:13:14Z","timestamp":1592406794000},"page":"4525-4526","source":"Crossref","is-referenced-by-count":9,"title":["<i>TiFoSi<\/i>\n                    : an efficient tool for mechanobiology simulations of epithelia"],"prefix":"10.1093","volume":"36","author":[{"given":"Oriol","family":"Canela-Xandri","sequence":"first","affiliation":[{"name":"MRC Human Genetics Unit at the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital , Edinburgh EH4 2XU, UK"}]},{"given":"Samira","family":"Anbari","sequence":"additional","affiliation":[{"name":"Chemical and Biomolecular Engineering Department"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1791-0011","authenticated-orcid":false,"given":"Javier","family":"Buceta","sequence":"additional","affiliation":[{"name":"Chemical and Biomolecular Engineering Department"},{"name":"Bioengineering Department, Lehigh University , Bethlehem, PA 18015, USA"},{"name":"Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cient\u00edficas (CSIC)\u2014Universitat de Val\u00e8ncia (UV) , Paterna, Valencia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,6,26]]},"reference":[{"key":"2023062213535008500_btaa592-B1","doi-asserted-by":"crossref","first-page":"2960","DOI":"10.1038\/s41467-018-05376-1","article-title":"Scutoids are a geometrical solution to three-dimensional packing of epithelia","volume":"9","author":"G\u00f3mez-G\u00e1lvez","year":"2018","journal-title":"Nat. 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Biotechnol"},{"key":"2023062213535008500_btaa592-B4","doi-asserted-by":"crossref","DOI":"10.1201\/9781135042653","volume-title":"Introduction to Cell Mechanics and Mechanobiology","author":"Jacobs","year":"2012"},{"key":"2023062213535008500_btaa592-B5","doi-asserted-by":"crossref","first-page":"e1002970","DOI":"10.1371\/journal.pcbi.1002970","article-title":"Chaste: an open source C++ library for computational physiology and biology","volume":"9","author":"Mirams","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023062213535008500_btaa592-B6","doi-asserted-by":"crossref","first-page":"R441","DOI":"10.1016\/j.cub.2012.04.038","article-title":"Developmental biology: a growing role for computer simulations","volume":"22","author":"Schwarz","year":"2012","journal-title":"Curr. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa592\/33620193\/btaa592.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/16\/4525\/50677401\/btaa592.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/16\/4525\/50677401\/btaa592.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T16:51:11Z","timestamp":1687452671000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/16\/4525\/5863247"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,6,26]]},"references-count":6,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2020,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa592","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.12.933903","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,8,15]]},"published":{"date-parts":[[2020,6,26]]}}}