{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:40Z","timestamp":1772138080212,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here, we introduce rtfbsdb, a unified framework that integrates a database of more than 65 000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.<\/jats:p>\n                  <jats:p>Availability and Implementation: \u00a0rtfbsdb available at (https:\/\/github.com\/Danko-Lab\/rtfbs_db).<\/jats:p>\n                  <jats:p>Contact: \u00a0dankoc@gmail.com<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw338","type":"journal-article","created":{"date-parts":[[2016,6,10]],"date-time":"2016-06-10T23:54:37Z","timestamp":1465602877000},"page":"3024-3026","source":"Crossref","is-referenced-by-count":22,"title":["RTFBSDB: an integrated framework for transcription factor binding site analysis"],"prefix":"10.1093","volume":"32","author":[{"given":"Zhong","family":"Wang","sequence":"first","affiliation":[{"name":"1 Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}]},{"given":"Andr\u00e9 L.","family":"Martins","sequence":"additional","affiliation":[{"name":"1 Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}]},{"given":"Charles G.","family":"Danko","sequence":"additional","affiliation":[{"name":"1 Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"},{"name":"2 Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,10]]},"reference":[{"key":"2023020113475858100_btw338-B2","doi-asserted-by":"crossref","first-page":"2463","DOI":"10.1093\/bioinformatics\/btr406","article-title":"APCluster: an R package for affinity propagation clustering","volume":"27","author":"Bodenhofer","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020113475858100_btw338-B3","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1126\/science.1162228","article-title":"Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters","volume":"322","author":"Core","year":"2008","journal-title":"Science"},{"key":"2023020113475858100_btw338-B4","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/nmeth.3329","article-title":"Identification of active transcriptional regulatory elements from GRO-seq data","volume":"12","author":"Danko","year":"2015","journal-title":"Nat. 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