{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:37Z","timestamp":1674710437898},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Different experimental results suggest the presence of an interplay between global transcriptional regulation and chromosome spatial organization in bacteria. The identification and clear visualization of spatial clusters of contiguous genes targeted by specific DNA-binding proteins or sensitive to nucleoid perturbations can elucidate links between nucleoid structure and gene expression patterns. Similarly, statistical analysis to assess correlations between results from independent experiments can provide the integrated analysis needed in this line of research. NuST (Nucleoid Survey tools), based on the Escherichia coli genome, gives the non-expert the possibility to analyze the aggregation of genes or loci sets along the genome coordinate, at different scales of observation. It is useful to discover correlations between different sources of data (e.g. expression, binding or genomic data) and genome organization. A user can use it on datasets in the form of gene lists coming from his\/her own experiments or bioinformatic analyses, but also make use of the internal database, which collects data from many published studies.<\/jats:p>\n               <jats:p>Availability and Implementation: NuST is a web server (available at http:\/\/www.lgm.upmc.fr\/nust\/). The website is implemented in PHP, SQLite and Ajax, with all major browsers supported, while the core algorithms are optimized and implemented in C. NuST has an extensive help page and provides a direct visualization of results as well as different downloadable file formats. A template Perl code for automated access to the web server can be downloaded at http:\/\/www.lgm.upmc.fr\/nust\/downloads\/, in order to allow the users to use NuST in systematic bioinformatic analyses.<\/jats:p>\n               <jats:p>Contact: \u00a0vittore.scolari@upmc.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts201","type":"journal-article","created":{"date-parts":[[2012,4,25]],"date-time":"2012-04-25T00:58:05Z","timestamp":1335315485000},"page":"1643-1644","source":"Crossref","is-referenced-by-count":9,"title":["NuST: analysis of the interplay between nucleoid organization and gene expression"],"prefix":"10.1093","volume":"28","author":[{"given":"Vittore F.","family":"Scolari","sequence":"first","affiliation":[{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"}]},{"given":"Mina","family":"Zarei","sequence":"additional","affiliation":[{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"}]},{"given":"Matteo","family":"Osella","sequence":"additional","affiliation":[{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"}]},{"given":"Marco","family":"Cosentino Lagomarsino","sequence":"additional","affiliation":[{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"},{"name":"1 Genomic Physics Group, UMR 7238 CNRS G\u00e9nomique des Microorganismes, 2Universit\u00e9 Pierre et Marie Curie, 15 rue de L'\u00c9cole de M\u00e9decine, 75006, Paris, France, 3NCBS, Bangalore, India, 4Dip. Fisica, Universit\u00e0 di Milano, Milano, Italy and 5Dip. Fisica, Universit\u00e0 di Torino, Torino, Italy"}]}],"member":"286","published-online":{"date-parts":[[2012,4,23]]},"reference":[{"key":"2023012512324435000_B1","doi-asserted-by":"crossref","first-page":"e1002123","DOI":"10.1371\/journal.pgen.1002123","article-title":"Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria","volume":"7","author":"Dame","year":"2011","journal-title":"PLoS Genet."},{"key":"2023012512324435000_B2","doi-asserted-by":"crossref","first-page":"D98","DOI":"10.1093\/nar\/gkq1110","article-title":"RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)","volume":"39","author":"Gama-Castro","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512324435000_B3","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.jsb.2006.05.006","article-title":"The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective","volume":"156","author":"Luijsterburg","year":"2006","journal-title":"J. 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Microbiol."},{"key":"2023012512324435000_B10","doi-asserted-by":"crossref","first-page":"4330","DOI":"10.1038\/sj.emboj.7600434","article-title":"Macrodomain organization of the Escherichia coli chromosome","volume":"23","author":"Valens","year":"2004","journal-title":"EMBO J."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/12\/1643\/48874248\/bioinformatics_28_12_1643.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/12\/1643\/48874248\/bioinformatics_28_12_1643.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:20:43Z","timestamp":1674663643000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/12\/1643\/267398"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4,23]]},"references-count":10,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2012,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts201","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,6,15]]},"published":{"date-parts":[[2012,4,23]]}}}