{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T11:12:35Z","timestamp":1788347555311,"version":"build-2803163510"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T00:00:00Z","timestamp":1631664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"PRIN 2017\u2014Settore ERC LS2\u2014Codice","award":["20178L3P38"],"award-info":[{"award-number":["20178L3P38"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present SWIMmeR, an open-source version of its predecessor SWIM (SWitchMiner) that is a network-based tool for mining key (switch) genes that are associated with intriguing patterns of molecular co-abundance and may play a crucial role in phenotypic transitions in various biological settings. SWIM was originally written in MATLAB\u00ae, a proprietary programming language that requires the purchase of a license to install, manipulate, operate and run the software. Over the last years, SWIM has sparked a widespread interest within the scientific community thanks to the promising results obtained through its application in a broad range of phenotype-specific scenarios, spanning from complex diseases to grapevine berry maturation. This success has created the call for it to be distributed in a freely accessible, open-source, runtime environment, such as R, aimed at a general audience of non-expert users that cannot afford the leading proprietary solution. SWIMmeR is provided as a comprehensive collection of R functions and it also includes several additional features that make it less intensive in terms of computer time and more efficient in terms of usability and further implementation and extension.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The SWIMmeR source code is freely available at https:\/\/github.com\/sportingCode\/SWIMmeR.git, along with a practical user guide, including a usage example of its application on breast cancer dataset.<\/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\/btab657","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T11:16:43Z","timestamp":1631272603000},"page":"586-588","source":"Crossref","is-referenced-by-count":15,"title":["SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9393-2047","authenticated-orcid":false,"given":"Paola","family":"Paci","sequence":"first","affiliation":[{"name":"Institute for Systems Analysis and Computer Science \u201cAntonio Ruberti\u201d, Dipartimento di Ingegneria, ICT e tecnologie per l'energia e i trasporti, National Research Council, Via dei Taurini 19 00185, Rome, Italy"},{"name":"Dipartimento di Ingegneria Informatica, Automatica e Gestionale (DIAG) \"A. Ruberti\", Sapienza Universit\u00e0 di Roma Via Ariosto, 25 00185 Roma, Italia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3354-8203","authenticated-orcid":false,"given":"Giulia","family":"Fiscon","sequence":"additional","affiliation":[{"name":"Institute for Systems Analysis and Computer Science \u201cAntonio Ruberti\u201d, Dipartimento di Ingegneria, ICT e tecnologie per l'energia e i trasporti, National Research Council, Via dei Taurini 19 00185, Rome, Italy"},{"name":"Fondazione per la Medicina Personalizzata , Via Goffredo Mameli, 3\/116122 Genova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,15]]},"reference":[{"key":"2023020108442935200_btab657-B1","doi-asserted-by":"crossref","first-page":"3915","DOI":"10.3390\/ijms22083915","article-title":"Key disease mechanisms linked to Alzheimer\u2019s disease in the entorhinal cortex","volume":"22","author":"Bottero","year":"2021","journal-title":"Int. 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