{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T02:43:20Z","timestamp":1776048200733,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,24]],"date-time":"2017-11-24T00:00:00Z","timestamp":1511481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","award":["2014SGR687"],"award-info":[{"award-number":["2014SGR687"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein\u2013protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have developed a protocol to predict protein\u2013protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The web application PlanNET is available at https:\/\/compgen.bio.ub.edu\/PlanNET. The source code used is available at https:\/\/compgen.bio.ub.edu\/PlanNET\/downloads.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx738","type":"journal-article","created":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T20:16:26Z","timestamp":1511468186000},"page":"1016-1023","source":"Crossref","is-referenced-by-count":20,"title":["PlanNET: homology-based predicted interactome for multiple planarian transcriptomes"],"prefix":"10.1093","volume":"34","author":[{"given":"S","family":"Castillo-Lara","sequence":"first","affiliation":[{"name":"Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain"}]},{"given":"J F","family":"Abril","sequence":"additional","affiliation":[{"name":"Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2017,11,24]]},"reference":[{"key":"2023012712473038400_btx738-B1","doi-asserted-by":"crossref","first-page":"731.","DOI":"10.1186\/1471-2164-11-731","article-title":"Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea","volume":"11","author":"Abril","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012712473038400_btx738-B2","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1101\/gr.113779.110","article-title":"De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics","volume":"21","author":"Adamidi","year":"2011","journal-title":"Genome Res"},{"key":"2023012712473038400_btx738-B3","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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