{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T16:28:01Z","timestamp":1747844881412},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: One of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities between the promoters of similarly expressed genes. This new tool, cisExpress, is especially designed for use with large datasets, such as those generated by publicly accessible whole genome and transcriptome projects. cisExpress uses a task farming algorithm to exploit all available computational cores within a shared memory node. We demonstrate the robust nature and validity of the proposed method. It is applicable for use with a wide range of genomic databases for any species of interest.<\/jats:p>\n               <jats:p>Availability: \u00a0cisExpress is available at www.cisexpress.org.<\/jats:p>\n               <jats:p>Contact: \u00a0tatiana.tatarinova@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt366","type":"journal-article","created":{"date-parts":[[2013,6,23]],"date-time":"2013-06-23T00:20:14Z","timestamp":1371946814000},"page":"2203-2205","source":"Crossref","is-referenced-by-count":18,"title":["<i>cisExpress<\/i>: motif detection in DNA sequences"],"prefix":"10.1093","volume":"29","author":[{"given":"Martin","family":"Triska","sequence":"first","affiliation":[{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Grocutt","sequence":"additional","affiliation":[{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Southern","sequence":"additional","affiliation":[{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denis J.","family":"Murphy","sequence":"additional","affiliation":[{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatiana","family":"Tatarinova","sequence":"additional","affiliation":[{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"},{"name":"1 Genomics and Computational Biology Research Group, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd CF37 1DL, UK, 2Technical Computing Research Division, Fujitsu Laboratories of Europe, Hayes, Middlesex, UB4 8FE, UK and 3Laboratory of Applied Pharmacokinetics and Bioinformatics, Keck School of Medicine and Children's Hospital Los Angeles, University of 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