{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T14:29:24Z","timestamp":1759847364613},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Nuclear receptors (NRs) are a class of transcription factors playing important roles in various biological processes. An NR often impacts numerous genes and different NRs share overlapped target networks. To fulfil the need for a database incorporating binding sites of different NRs at various conditions for easy comparison and visualization to improve our understanding of NR binding mechanisms, we have developed NURBS, a database for experimental and predicted nuclear receptor binding sites of mouse (NURBS). NURBS currently contains binding sites across the whole-mouse genome of 8 NRs identified in 40 chromatin immunoprecipitation with massively parallel DNA sequencing experiments. All datasets are processed using a widely used procedure and same statistical criteria to ensure the binding sites derived from different datasets are comparable. NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model.<\/jats:p>\n               <jats:p>Availability: The GBrowse-based user interface of NURBS is freely accessible at http:\/\/shark.abl.ku.edu\/nurbs\/. NR-HMM and all results can be downloaded for free at the website.<\/jats:p>\n               <jats:p>Contact: \u00a0jwfang@ku.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts693","type":"journal-article","created":{"date-parts":[[2012,11,30]],"date-time":"2012-11-30T03:17:56Z","timestamp":1354245476000},"page":"295-297","source":"Crossref","is-referenced-by-count":7,"title":["NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse"],"prefix":"10.1093","volume":"29","author":[{"given":"Yaping","family":"Fang","sequence":"first","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui-Xin","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grace L.","family":"Guo","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Jui Yvonne","family":"Wan","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianwen","family":"Fang","sequence":"additional","affiliation":[{"name":"1 Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA, 2Department of Medical Pathology and Laboratory Medicine, University of California, Davis Health Systems, Sacramento, CA 95817, USA, 3Department of Biomedical Engineering, Tianjin University, Tianjin 300072, China and 4Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NY 08854, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,29]]},"reference":[{"key":"2023012810214383800_bts693-B1","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1186\/gb-2003-5-1-201","article-title":"Computational prediction of transcription-factor binding site locations","volume":"5","author":"Bulyk","year":"2003","journal-title":"Genome Biol."},{"key":"2023012810214383800_bts693-B2","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/bti473","article-title":"MatInspector and beyond: promoter analysis based on transcription factor binding sites","volume":"21","author":"Cartharius","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012810214383800_bts693-B3","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.mce.2010.10.021","article-title":"Evolution of the repertoire of nuclear receptor binding sites in genomes","volume":"334","author":"Cotnoir-White","year":"2011","journal-title":"Mol. 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