{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T18:02:06Z","timestamp":1759773726322},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Mechanotransduction\u2014the ability to output a biochemical signal from a mechanical input\u2014is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms.<\/jats:p><jats:p>Results: We here present a molecular map of mechanotransduction, built in CellDesigner to warrant that maximum information is embedded in a compact network format. To validate the map\u2019s necessity we tested its redundancy in comparison with existing pathways, and to estimate its sufficiency, we quantified its ability to reproduce biological events with dynamic simulations, using Signaling Petri Networks.<\/jats:p><jats:p>Availability and implementation: SMBL language map is available in the Supplementary Data: core_map.xml, basic_map.xml.<\/jats:p><jats:p>Contact: christine.nardini.rsrc@gmail.com<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu776","type":"journal-article","created":{"date-parts":[[2014,11,27]],"date-time":"2014-11-27T01:24:52Z","timestamp":1417051492000},"page":"1053-1059","source":"Crossref","is-referenced-by-count":7,"title":["Mechanotransduction map: simulation model, molecular pathway, gene set"],"prefix":"10.1093","volume":"31","author":[{"given":"Jennifer E.","family":"Dent","sequence":"first","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"},{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Devescovi","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han","family":"Li","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Di Lena","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youtao","family":"Lu","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanhua","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Nardini","sequence":"additional","affiliation":[{"name":"1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People\u2019s Republic of China, 2Quintiles, Global Biostatistics, Reading, Berkshire, UK and 3Department of Computer Science and Engineering - 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