{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,2]],"date-time":"2025-03-02T05:43:43Z","timestamp":1740894223810,"version":"3.38.0"},"reference-count":56,"publisher":"SAGE Publications","issue":"3","license":[{"start":{"date-parts":[[2016,8,22]],"date-time":"2016-08-22T00:00:00Z","timestamp":1471824000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["The International Journal of High Performance Computing Applications"],"published-print":{"date-parts":[[2018,5]]},"abstract":"<jats:p> Gene network expansion is a task of the foremost importance in computational biology. Gene network expansion aims at finding new genes to expand a given known gene network. To this end, we developed gene@home, a BOINC-based project that finds candidate genes that expand known local gene networks using NESRA. In this paper, we present NES<jats:sup>2<\/jats:sup>RA, a novel approach that extends and improves NESRA by modeling, using a probability vector, the confidence of the presence of the genes belonging to the local gene network. NES<jats:sup>2<\/jats:sup>RA adopts intensive variable-subsetting strategies, enabled by the computational power provided by gene@home volunteers. In particular, we use the skeleton procedure of the PC-algorithm to discover candidate causal relationships within each subset of variables. Finally, we use state-of-the-art aggregators to combine the results into a single ranked candidate genes list. The resulting ranking guides the discovery of unknown relations between genes and a priori known local gene networks. Our experimental results show that NES<jats:sup>2<\/jats:sup>RA outperforms the PC-algorithm and its order-independent PC-stable version, ARACNE, and our previous approach, NESRA. In this paper we extensively discuss the computational aspects of the NES<jats:sup>2<\/jats:sup>RA approach and we also present and validate expansions performed on the model plant Arabidopsis thaliana and the model bacteria Escherichia coli. <\/jats:p>","DOI":"10.1177\/1094342016662508","type":"journal-article","created":{"date-parts":[[2016,8,23]],"date-time":"2016-08-23T01:28:55Z","timestamp":1471915735000},"page":"380-392","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":6,"title":["NES<sup>2<\/sup>RA"],"prefix":"10.1177","volume":"32","author":[{"given":"Francesco","family":"Asnicar","sequence":"first","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Luca","family":"Masera","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Emanuela","family":"Coller","sequence":"additional","affiliation":[{"name":"CRI, Fondazione Edmund Mach, Italy"}]},{"given":"Caterina","family":"Gallo","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Nadir","family":"Sella","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Thomas","family":"Tolio","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Paolo","family":"Morettin","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Luca","family":"Erculiani","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Francesca","family":"Galante","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Stanislau","family":"Semeniuta","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]},{"given":"Giulia","family":"Malacarne","sequence":"additional","affiliation":[{"name":"CRI, Fondazione Edmund Mach, Italy"}]},{"given":"Kristof","family":"Engelen","sequence":"additional","affiliation":[{"name":"CRI, Fondazione Edmund Mach, Italy"}]},{"given":"Andrea","family":"Argentini","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Ghent University and Medical Biotechnology Center VIB, Belgium"}]},{"given":"Valter","family":"Cavecchia","sequence":"additional","affiliation":[{"name":"CNR-IMEM, Trento, Italy"}]},{"given":"Claudio","family":"Moser","sequence":"additional","affiliation":[{"name":"CRI, Fondazione Edmund Mach, Italy"}]},{"given":"Enrico","family":"Blanzieri","sequence":"additional","affiliation":[{"name":"DISI, University of Trento, Italy"}]}],"member":"179","published-online":{"date-parts":[[2016,8,22]]},"reference":[{"key":"bibr1-1094342016662508","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.jbchem.a121866"},{"key":"bibr2-1094342016662508","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0029348"},{"key":"bibr3-1094342016662508","doi-asserted-by":"publisher","DOI":"10.1109\/GRID.2004.14"},{"key":"bibr4-1094342016662508","doi-asserted-by":"publisher","DOI":"10.1145\/581571.581573"},{"key":"bibr5-1094342016662508","doi-asserted-by":"publisher","DOI":"10.1109\/Trustcom.2015.640"},{"key":"bibr6-1094342016662508","unstructured":"Asnicar F, Sella N, Masera L, (2015b) TN-Grid and gene@home project: Volunteer computing for bioinformatics. 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