{"id":1702,"date":"2019-12-21T16:29:48","date_gmt":"2019-12-21T16:29:48","guid":{"rendered":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1702"},"modified":"2019-12-21T16:38:03","modified_gmt":"2019-12-21T16:38:03","slug":"data-downloads","status":"publish","type":"page","link":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1702","title":{"rendered":"Data Downloads"},"content":{"rendered":"<ul>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/manatakisECCB2018.html\">Manatakis, Raghu, Benos (2018)<\/a> <em>Bioinformatics<\/em> (Proc ECCB 2018), <strong>34:<\/strong>i848\u2013i856\u00a0(<a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/i848\/5093235\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>Simulated network data<\/li>\n<li>Running example (for testing the code)<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/corcoranPLoSONE2009.html\">Corcoran, Pandit <em>et al.<\/em> (2009)<\/a> <em>PLoS ONE<\/em>, <strong>4:<\/strong>e5279 (<a href=\"http:\/\/dx.plos.org\/10.1371\/journal.pone.0005279\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>raw ChIP-chip data<\/li>\n<li>training datasets<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/kadriAPBC2009.html\">Kadri <em>et al.<\/em> (2009)<\/a> APBC\/<em>BMC Bioinformatics<\/em>, <strong>10<\/strong>(Suppl 1):S35 (<a href=\"http:\/\/www.biomedcentral.com\/content\/pdf\/1471-2105-10-S1-S35.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>miRNA cross-species characteristics<\/li>\n<li>HHMMiR algorithm<\/li>\n<li>Training and testing datasets<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/mahonyGenomeBiol2007.html\">Mahony <em>et al.<\/em> (2007)<\/a> <em>Genome Biol<\/em> <strong>8:<\/strong> R84 (<a href=\"http:\/\/genomebiology.com\/content\/pdf\/gb-2007-8-5-r84.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>README file (text &#8211; description fo the dataset files)<\/li>\n<li>Datasets (protein coding, microRNA, tRNA and developmental gene datasets)<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/mahonyISMB2007.html\">Mahony <em>et al.<\/em> (2007)<\/a> <em>ISMB<\/em> (Proc ISMB) <strong>23:<\/strong> i297-i304 (<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/reprint\/23\/13\/i297.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>README file (text &#8211; description fo the dataset files)<\/li>\n<li>Dataset (ZIP archive file)<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/mahonyPLoSComputBiol2007.html\">Mahony <em>et al.<\/em> (2007)<\/a> <em>PLoS Comput Biol<\/em> <strong>3:<\/strong> e61 (<a href=\"http:\/\/compbiol.plosjournals.org\/perlserv\/?request=get-pdf&amp;file=10.1371_journal.pcbi.0030061-L.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>Supplementary Table (performance of strategies for aligning DNA motifs &#8211; complete list)<\/li>\n<li>PSSM models with the corresponding family of each transcription factor<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/mahonyNeuralNetw2006.html\">Mahony <em>et al.<\/em> (2006)<\/a> <em>Neural Networks<\/em> <strong>19:<\/strong> 950-962 (<a href=\"http:\/\/www.benoslab.pitt.edu\/publications\/2006NeuralNetw_19_950.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>Supplementary Table (Comparing motif-finders in 77 yeast datasets)<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/corcoranNAR2005.html\">Corcoran <em>et al.<\/em> (2005)<\/a> <em>Nucl Acids Res<\/em> <strong>33<\/strong>(Web Server issue)<strong>:<\/strong> W442-W446 (<a href=\"http:\/\/www.benoslab.pitt.edu\/publications\/2005Corcoran_NAR.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>Supplementary Table (Footer predictions)<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/corcoranGenomeRes2005.html\">Corcoran <em>et al.<\/em> (2005)<\/a> <em>Genome Res<\/em> <strong>15:<\/strong> 840-847 (<a href=\"http:\/\/www.benoslab.pitt.edu\/publications\/2005Corcoran_GenRes.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>Supplementary Table 1 (Footer predictions)<\/li>\n<li>Supplementary Table 2 (comparison with other methods)<\/li>\n<li>Promoter regions (test set)<\/li>\n<li>DBA alignments<\/li>\n<li>PSSM models<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"http:\/\/www.benoslab.pitt.edu\/JMB.html\">Benos <em>et al.<\/em> (2002)<\/a> <em>J Mol Biol<\/em> <strong>323:<\/strong> 701-727 (<a href=\"http:\/\/www.benoslab.pitt.edu\/publications\/2002Benos_JMB.pdf\" target=\"_blank\" rel=\"noopener\">pdf<\/a>)\n<ul>\n<li>EGR selection dataset (SAMIE training set)<\/li>\n<li>SAMIE EGR model<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Manatakis, Raghu, Benos (2018) Bioinformatics (Proc ECCB 2018), 34:i848\u2013i856\u00a0(pdf) Simulated network data Running example (for testing the code) Corcoran, Pandit et al. (2009) PLoS ONE, 4:e5279 (pdf) raw ChIP-chip data training datasets Kadri et al. (2009) APBC\/BMC Bioinformatics, 10(Suppl 1):S35 (pdf) miRNA cross-species characteristics HHMMiR algorithm Training and testing datasets &#8230;<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1702\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1702","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/pages\/1702","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1702"}],"version-history":[{"count":3,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/pages\/1702\/revisions"}],"predecessor-version":[{"id":1710,"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=\/wp\/v2\/pages\/1702\/revisions\/1710"}],"wp:attachment":[{"href":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1702"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}