{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T14:06:39Z","timestamp":1761401199436},"reference-count":22,"publisher":"World Scientific Pub Co Pte Lt","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Comp. Intel. Appl."],"published-print":{"date-parts":[[2004,12]]},"abstract":"<jats:p> Recent advances in RNA studies show that the well-ordered, structured RNAs perform a broad functions in various biological mechanisms. Included among these functions are regulations of gene expression at multiple levels by diversified ribozymes and various RNA regulatory elements. The discovered microRNAs (miRNAs) with a distinct stem-loops are a new class of RNA regulatory elements. The prediction of those well-ordered folding sequences (WFS) associated with the RNA regulatory elements in genomic sequences is very helpful for our understandings of RNA-based gene regulations. We present here a new computational method in searching for the conserved WFS in genomes. In the method, the WFS is assessed by a quantitative measure E<jats:sub> diff <\/jats:sub> that is defined as the difference of free energies between the computed optimal structure (OS) and its corresponding optimal restrained structure where all the previous base pairings in the OS are forbidden. From those WFS with high E<jats:sub> diff <\/jats:sub> scores, the conserved WFS is determined by computing the maximal similarity score (MSS) between the two compared structures. In practice, we first search for those distinct WFS with high statistical significance in genomic sequences and then seek for those conserved WFS with high MSS. The potential and implications of our discoveries in the genome of Caenorhabditis elegans are discussed. <\/jats:p>","DOI":"10.1142\/s1469026804001409","type":"journal-article","created":{"date-parts":[[2005,4,13]],"date-time":"2005-04-13T13:10:12Z","timestamp":1113397812000},"page":"417-430","source":"Crossref","is-referenced-by-count":3,"title":["FINDING CONSERVED WELL-ORDERED RNA STRUCTURES IN GENOMIC SEQUENCES"],"prefix":"10.1142","volume":"04","author":[{"given":"SHU-YUN","family":"LE","sequence":"first","affiliation":[{"name":"Laboratory of Experimental and  Computational Biology, NCI Center for Cancer Research,  National Cancer Institute, NIH, Bldg 469, Room 151, Frederick,  Maryland 21702, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr.","given":"JACOB V.","family":"MAIZEL","sequence":"additional","affiliation":[{"name":"Laboratory of Experimental and  Computational Biology, NCI Center for Cancer Research,  National Cancer Institute, NIH, Bldg 469, Room 151, Frederick,  Maryland 21702, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"KAIZHONG","family":"ZHANG","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,20]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1093\/embo-reports\/kve230"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072249"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072148"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072457"},{"key":"rf5","volume-title":"The RNA World","author":"Gestel R. 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J.","journal-title":"Nucl. Acids Res."}],"container-title":["International Journal of Computational Intelligence and Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S1469026804001409","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T20:27:18Z","timestamp":1565123238000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S1469026804001409"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,12]]},"references-count":22,"journal-issue":{"issue":"04","published-online":{"date-parts":[[2011,11,20]]},"published-print":{"date-parts":[[2004,12]]}},"alternative-id":["10.1142\/S1469026804001409"],"URL":"https:\/\/doi.org\/10.1142\/s1469026804001409","relation":{},"ISSN":["1469-0268","1757-5885"],"issn-type":[{"value":"1469-0268","type":"print"},{"value":"1757-5885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2004,12]]}}}