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Cuellar-Partida","year":"2012","journal-title":"Bioinformatics"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1007\/s00500-012-0820-x","article-title":"Computational localization of transcription factor binding sites using extreme learning machines","volume":"16","author":"D Wang","year":"2012","journal-title":"Soft Comput"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature09906","article-title":"Mapping and analysis of chromatin state dynamics in nine human cell types","volume":"473","author":"J Ernst","year":"2011","journal-title":"Nature"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/nmeth.1937","article-title":"Unsupervised pattern discovery in human chromatin structure through genomic segmentation","volume":"9","author":"MM Hoffman","year":"2012","journal-title":"Nature 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Renthal","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1002\/ajmg.a.20053","article-title":"Further delineation of the phenotype associated with heterozygous mutations in ZFHX1B","volume":"119A","author":"M Wilson","year":"2003","journal-title":"American journal of medical genetics Part A"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"5429","DOI":"10.1093\/hmg\/dds389","article-title":"A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes","volume":"21","author":"MM El-Kasti","year":"2012","journal-title":"Human molecular genetics"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"e168","DOI":"10.1371\/journal.pgen.0020168","article-title":"Forces shaping the fastest evolving regions in the human genome","volume":"2","author":"KS 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America"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"E Birney","year":"2007","journal-title":"Nature"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/978-1-60327-241-4_13","article-title":"A user's guide to support vector machines","volume":"609","author":"A Ben-Hur","year":"2010","journal-title":"Methods in molecular biology"},{"key":"ref98","first-page":"1799","article-title":"The SHOGUN Machine Learning Toolbox","volume":"99","author":"S Sonnenburg","year":"2010","journal-title":"J Mach Learn Res"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1023\/A:1009752403260","article-title":"On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach","volume":"1","author":"S Salzberg","year":"1997","journal-title":"Data Mining and Knowledge Discovery"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1162\/089976698300017197","article-title":"Approximate statistical tests for comparing supervised classification learning algorithms","volume":"10","author":"TG Dietterich","year":"1998","journal-title":"Neural Comput"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes","volume":"101","author":"AI Su","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"CY McLean","year":"2010","journal-title":"Nature biotechnology"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"CE Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1016\/j.ydbio.2009.10.019","article-title":"A systematic approach to identify functional motifs within vertebrate developmental enhancers","volume":"337","author":"Q Li","year":"2010","journal-title":"Developmental biology"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"e1003221","DOI":"10.1371\/journal.pgen.1003221","article-title":"Function and regulation of AUTS2, a gene 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