{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:55:44Z","timestamp":1785804944272,"version":"3.56.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0mshalfon@buffalo.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti794","type":"journal-article","created":{"date-parts":[[2005,11,23]],"date-time":"2005-11-23T01:24:56Z","timestamp":1132709096000},"page":"381-383","source":"Crossref","is-referenced-by-count":71,"title":["<i>REDfly:<\/i> a Regulatory Element Database for <i>Drosophila<\/i>"],"prefix":"10.1093","volume":"22","author":[{"given":"Steven M.","family":"Gallo","sequence":"first","affiliation":[{"name":"Center for Computational Research 1 \u00a0 1 \u00a0 \u00a0 140 Farber Hall, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Long","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biochemistry 2 \u00a0 2 \u00a0 \u00a0 140 Farber Hall, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zihua","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Computational Research 1 \u00a0 1 \u00a0 \u00a0 140 Farber Hall, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc S.","family":"Halfon","sequence":"additional","affiliation":[{"name":"Department of Biochemistry 2 \u00a0 2 \u00a0 \u00a0 140 Farber Hall, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA"},{"name":"Center of Excellence in Bioinformatics and the Life Sciences 3 \u00a0 3 \u00a0 \u00a0 140 Farber Hall, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2005,11,22]]},"reference":[{"key":"2023012408332660400_b1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/1471-2105-6-109","article-title":"Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test","volume":"6","author":"Abnizova","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012408332660400_b2","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster","volume":"21","author":"Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408332660400_b3","doi-asserted-by":"crossref","first-page":"R61","DOI":"10.1186\/gb-2004-5-9-r61","article-title":"Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura","volume":"5","author":"Berman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012408332660400_b4","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/S0378-1119(03)00556-0","article-title":"Turnover of binding sites for transcription factors involved in early Drosophila development","volume":"310","author":"Costas","year":"2003","journal-title":"Gene"},{"key":"2023012408332660400_b5","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/bib\/2.1.68","article-title":"Phenotypic data in FlyBase","volume":"2","author":"Drysdale","year":"2001","journal-title":"Brief Bioinform."},{"issue":"Database issue","key":"2023012408332660400_b6","doi-asserted-by":"crossref","first-page":"D390","DOI":"10.1093\/nar\/gki046","article-title":"FlyBase: genes and gene models","volume":"33","author":"Drysdale","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408332660400_b7","doi-asserted-by":"crossref","first-page":"3851","DOI":"10.1073\/pnas.0400611101","article-title":"Coordinate enhancers share common organizational features in the Drosophila genome","volume":"101","author":"Erives","year":"2004","journal-title":"Proc. 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