{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T20:24:26Z","timestamp":1780345466906,"version":"3.54.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2017,4,13]],"date-time":"2017-04-13T00:00:00Z","timestamp":1492041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1548562"],"award-info":[{"award-number":["ACI-1548562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Motif identification and analyses are important and have been long-standing computational problems in bioinformatics. Substantial efforts have been made in this field during the past several decades. However, the lack of intuitive and integrative web servers impedes the progress of making effective use of emerging algorithms and tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present an integrated web server, DMINDA 2.0, which contains: (i) five motif prediction and analyses algorithms, including a phylogenetic footprinting framework; (ii) 2125 species with complete genomes to support the above five functions, covering animals, plants and bacteria and (iii) bacterial regulon prediction and visualization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>DMINDA 2.0 is freely available at http:\/\/bmbl.sdstate.edu\/DMINDA2.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx223","type":"journal-article","created":{"date-parts":[[2017,4,12]],"date-time":"2017-04-12T19:12:20Z","timestamp":1492024340000},"page":"2586-2588","source":"Crossref","is-referenced-by-count":51,"title":["DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses"],"prefix":"10.1093","volume":"33","author":[{"given":"Jinyu","family":"Yang","sequence":"first","affiliation":[{"name":"Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Applied Mathematics, Tianjin University, Tianjin, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"McDermaid","sequence":"additional","affiliation":[{"name":"Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Ma","sequence":"additional","affiliation":[{"name":"Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA"},{"name":"Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA"},{"name":"BioSNTR, Brookings, SD, USA"},{"name":"Population Health group, Sanford Research, Sioux Falls, SD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,4,13]]},"reference":[{"key":"2023020301105156900_btx223-B1","first-page":"gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020301105156900_btx223-B2","first-page":"gkr264","article-title":"Unraveling networks of co-regulated genes on the sole basis of genome sequences","author":"Broh\u00e9e","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023020301105156900_btx223-B3","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nbt0806-959","article-title":"How does DNA sequence motif discovery work?","volume":"24","author":"D'haeseleer","year":"2006","journal-title":"Nat. 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