{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T06:23:56Z","timestamp":1778739836939,"version":"3.51.4"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859\u20131867, 2007; Nucleic Acids Res., 36, 6269\u20136283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/lief.if.ufrgs.br\/pub\/biosoftwares\/viacomplex<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0mauro@ufrgs.br or rita@if.ufrgs.br<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp246","type":"journal-article","created":{"date-parts":[[2009,4,16]],"date-time":"2009-04-16T01:28:58Z","timestamp":1239845338000},"page":"1468-1469","source":"Crossref","is-referenced-by-count":36,"title":["ViaComplex: software for landscape analysis of gene expression networks in genomic context"],"prefix":"10.1093","volume":"25","author":[{"given":"Mauro A. A.","family":"Castro","sequence":"first","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 L. Rybarczyk","family":"Filho","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo J. S.","family":"Dalmolin","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marialva","family":"Sinigaglia","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 C. F.","family":"Moreira","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 C. M.","family":"Mombach","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita M. C.","family":"de Almeida","sequence":"additional","affiliation":[{"name":"1 Unidade de Bioinform\u00e1tica, Departamento de Bioqu\u00edmica, 2Instituto de F\u00edsica, 3N\u00facleo de Bioinform\u00e1tica, Departamento de Gen\u00e9tica, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003 and 4Departamento de F\u00edsica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,4,15]]},"reference":[{"key":"2023013111503782900_B1","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1093\/nar\/gkm061","article-title":"Impaired expression of NER gene network in sporadic solid tumors","volume":"35","author":"Castro","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023013111503782900_B2","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1093\/nar\/gkn636","article-title":"Evolutionary origins of human apoptosis and genome-stability gene networks","volume":"36","author":"Castro","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023013111503782900_B3","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/35077232","article-title":"Genome maintenance mechanisms for preventing cancer","volume":"411","author":"Hoeijmakers","year":"2001","journal-title":"Nature"},{"key":"2023013111503782900_B4","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrm1443","article-title":"Apoptosis and genomic instability","volume":"5","author":"Zhivotovsky","year":"2004","journal-title":"Nat. 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