{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T16:41:57Z","timestamp":1761324117958},"reference-count":17,"publisher":"Institute of Electronics, Information and Communications Engineers (IEICE)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEICE Trans. Inf. &amp; Syst."],"published-print":{"date-parts":[[2017]]},"DOI":"10.1587\/transinf.2017edp7051","type":"journal-article","created":{"date-parts":[[2017,9,30]],"date-time":"2017-09-30T22:24:49Z","timestamp":1506810289000},"page":"2470-2477","source":"Crossref","is-referenced-by-count":4,"title":["Accelerating Weeder: A DNA Motif Search Tool Using the Micron Automata Processor and FPGA"],"prefix":"10.1587","volume":"E100.D","author":[{"given":"Qiong","family":"WANG","sequence":"first","affiliation":[{"name":"College of Computer, National University of Defense Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"EL-HADEDY","sequence":"additional","affiliation":[{"name":"Coordinated Science Lab, University of Illinois Urbana-Champaign"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin","family":"SKADRON","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Virginia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"WANG","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Virginia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"532","reference":[{"key":"1","unstructured":"[1] Dream challenge, http:\/\/dreamchallenges.org\/"},{"key":"2","unstructured":"[2] Micron&apos;s automata processor, https:\/\/www.micronautomata.com\/"},{"key":"3","unstructured":"[3] T.L. Bailey and C. Elkan, \u201cFitting a mixture model by expectation maximization to discover motifs in biopolymer,\u201d Proc. 2nd International Conference on Intelligent Systems for Molecular Biology, pp.28-36, 1994."},{"key":"4","doi-asserted-by":"publisher","unstructured":"[4] T.L Bailey and C. Elkan, \u201cUnsupervised learning of multiple motifs in biopolymers using expectation maximization,\u201d Machine Learning, vol.21, no.1-2, pp.51-80, 1995. 10.1007\/bf00993379","DOI":"10.1007\/BF00993379"},{"key":"5","doi-asserted-by":"publisher","unstructured":"[5] P. Dlugosch, D. Brown, P. Glendenning, M. Leventhal, and H. Noyes, \u201cAn efficient and scalable semiconductor architecture for parallel automata processing,\u201d IEEE Trans. Parallel Distrib. Syst., vol.25, no.12, pp.3088-3098, 2014. 10.1109\/tpds.2014.8","DOI":"10.1109\/TPDS.2014.8"},{"key":"6","doi-asserted-by":"publisher","unstructured":"[6] C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wootton, \u201cDetecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment,\u201d Science, vol.262, no.5131, pp.208-214, 1993. 10.1126\/science.8211139","DOI":"10.1126\/science.8211139"},{"key":"7","doi-asserted-by":"publisher","unstructured":"[7] A. Lihu and \u015e. Holban, \u201cA review of ensemble methods for <i>de novo<\/i> motif discovery in chip-seq data,\u201d Briefings in Bioinformatics, vol.16, no.6, pp.964-973, 2015. 10.1093\/bib\/bbv022","DOI":"10.1093\/bib\/bbv022"},{"key":"8","unstructured":"[8] H.B. Noyes, \u201cMicron&apos;s Automata Processor architecture: Reconfigurable and massively parallel automata processing,\u201d Proc. Fifth International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies, 2014."},{"key":"9","doi-asserted-by":"crossref","unstructured":"[9] G. Pavesi, P. Mereghetti, G. Mauri, and G. Pesole, \u201cWeeder web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes,\u201d Nucleic Acids Research, vol.32 (Web-Server-Issue), pp.199-203, 2004. 10.1093\/nar\/gkh465","DOI":"10.1093\/nar\/gkh465"},{"key":"10","doi-asserted-by":"crossref","unstructured":"[10] I. Roy and S. Aluru, \u201cFinding motifs in biological sequences using the Micron Automata Processor,\u201d Proc. 28th IEEE International Symposium on Parallel and Distributed Processing, pp.415-424. IEEE, 2014. 10.1109\/ipdps.2014.51","DOI":"10.1109\/IPDPS.2014.51"},{"key":"11","doi-asserted-by":"crossref","unstructured":"[11] M.-F. Sagot, \u201cSpelling approximate repeated or common motifs using a suffix tree,\u201d Proc. LATIN&apos;98: Theoretical Informatics, pp.374-390. Springer, 1998. 10.1007\/bfb0054337","DOI":"10.1007\/BFb0054337"},{"key":"12","doi-asserted-by":"publisher","unstructured":"[12] M. Tompa, N. Li, T.L. Bailey, G.M. Church, B. De Moor, E. Eskin, A.V. Favorov, M.C. Frith, Y. Fu, W.J. Kent, V.J. Makeev, A.A. Mironov, W.S. Noble, G. Pavesi, G. Pesole, M. R\u00e9gnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu, \u201cAssessing computational tools for the discovery of transcription factor binding sites,\u201d Nature Biotechnology, vol.23, no.1, pp.137-144, 2005. 10.1038\/nbt1053","DOI":"10.1038\/nbt1053"},{"key":"13","doi-asserted-by":"crossref","unstructured":"[13] K. Wang, Y. Qi, J.J. Fox, M.R. Stan, and K. Skadron, \u201cAssociation rule mining with the Micron Automata Processor,\u201d 2015 IEEE International Parallel and Distributed Processing Symposium, pp.689-699, 2015. 10.1109\/ipdps.2015.101","DOI":"10.1109\/IPDPS.2015.101"},{"key":"14","doi-asserted-by":"crossref","unstructured":"[14] K. Wang, E. Sadredini, and K. Skadron, \u201cSequential pattern mining with the Micron Automata Processor,\u201d Proc. ACM International Conference on Computing Frontiers, pp.135-144, 2016. 10.1145\/2903150.2903172","DOI":"10.1145\/2903150.2903172"},{"key":"15","doi-asserted-by":"crossref","unstructured":"[15] F. Zambelli, G. Pesole, and G. Pavesi, \u201cUsing weeder, pscan, and pscanchip for the discovery of enriched transcription factor binding site motifs in nucleotide sequences,\u201d Current Protocols in Bioinformatics, pp.2-11, 2014. 10.1002\/0471250953.bi0211s47","DOI":"10.1002\/0471250953.bi0211s47"},{"key":"16","doi-asserted-by":"crossref","unstructured":"[16] K. Zhou, J.J. Fox, K. Wang, D.E. Brown, and K. Skadron, \u201cBrill tagging on the Micron Automata Processor,\u201d Proc. 9th IEEE International Conference on Semantic Computing, pp.236-239, 2015. 10.1109\/icosc.2015.7050812","DOI":"10.1109\/ICOSC.2015.7050812"},{"key":"17","doi-asserted-by":"crossref","unstructured":"[17] K. Zhou, J. Wadden, J.J. Fox, K. Wang, D.E. Brown, and K. Skadron, \u201cRegular expression acceleration on the Micron Automata Processor: Brill tagging as a case study,\u201d Proc. IEEE International Conference on Big Data, pp.355-360, 2015. 10.1109\/bigdata.2015.7363776","DOI":"10.1109\/BigData.2015.7363776"}],"container-title":["IEICE Transactions on Information and Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/transinf\/E100.D\/10\/E100.D_2017EDP7051\/_pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T04:34:55Z","timestamp":1570163695000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/transinf\/E100.D\/10\/E100.D_2017EDP7051\/_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"references-count":17,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2017]]}},"URL":"https:\/\/doi.org\/10.1587\/transinf.2017edp7051","relation":{},"ISSN":["0916-8532","1745-1361"],"issn-type":[{"value":"0916-8532","type":"print"},{"value":"1745-1361","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017]]}}}