{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T11:44:20Z","timestamp":1770723860931,"version":"3.49.0"},"reference-count":103,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11]]},"DOI":"10.1093\/bib\/bbv101","type":"journal-article","created":{"date-parts":[[2017,2,3]],"date-time":"2017-02-03T12:58:22Z","timestamp":1486126702000},"page":"967-979","source":"Crossref","is-referenced-by-count":85,"title":["Progress and challenges in bioinformatics approaches for enhancer identification"],"prefix":"10.1093","volume":"17","author":[{"given":"Dimitrios","family":"Kleftogiannis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panos","family":"Kalnis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir B.","family":"Bajic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,12,3]]},"reference":[{"key":"key\n\t\t\t\t20170214143217_bbv101-B1","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","year":"2001","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B2","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","year":"2001","journal-title":"Science"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B3","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1146\/annurev.genom.7.080505.115623","article-title":"Transcriptional regulatory elements in the human genome","volume":"7","year":"2006","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B4","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.gde.2009.09.006","article-title":"Finding distal regulatory elements in the human genome","volume":"19","year":"2009","journal-title":"Curr Opin Genet Dev"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B5","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/0092-8674(81)90413-X","article-title":"Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences","volume":"27","year":"1981","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B6","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature08451","article-title":"Genomic views of distant-acting enhancers","volume":"461","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B7","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.ydbio.2009.11.035","article-title":"Enhancers: the abundance and function of regulatory sequences beyond promoters","volume":"339","year":"2010","journal-title":"Dev Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B8","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1038\/nature09033","article-title":"Widespread transcription at neuronal activity-regulated enhancers","volume":"465","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B9","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1242\/dev.124.10.1851","article-title":"The hardwiring of development: organization and function of genomic regulatory systems","volume":"124","year":"1997","journal-title":"Development"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B10","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/nature09298","article-title":"Integrating common and rare genetic variation in diverse human populations","volume":"467","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B11","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.cell.2012.06.013","article-title":"Cancer epigenetics: from mechanism to therapy","volume":"150","year":"2012","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B12","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.molcel.2014.02.033","article-title":"Enhancer malfunction in cancer","volume":"53","year":"2014","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B13","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nsmb.2784","article-title":"Enhancer biology and enhanceropathies","volume":"21","year":"2014","journal-title":"Nat Struct Mol Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B14","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/nrm3949","article-title":"The selection and function of cell type-specific enhancers","volume":"16","year":"2015","journal-title":"Nat Rev Mol Cell Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B15","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1016\/S1097-2765(02)00786-4","article-title":"Dynamics of enhancer-promoter communication during differentiation-induced gene activation","volume":"10","year":"2002","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B16","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.molcel.2014.06.015","article-title":"Enhancer function: mechanistic and genome-wide insights come together","volume":"55","year":"2014","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B17","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nrg3682","article-title":"Transcriptional enhancers: from properties to genome-wide predictions","volume":"15","year":"2014","journal-title":"Nat Rev Genet"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B18","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1016\/j.molcel.2013.01.038","article-title":"Modification of enhancer chromatin: what, how, and why?","volume":"49","year":"2013","journal-title":"Mol Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B19","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/gb-2013-14-5-205","article-title":"Machine learning and genome annotation: a match meant to be?","volume":"14","year":"2013","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B20","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.semcdb.2006.12.014","article-title":"Enhancer identification through comparative genomics","volume":"18","year":"2007","journal-title":"Semin Cell Dev Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B21","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/ng1966","article-title":"Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome","volume":"39","year":"2007","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B22","doi-asserted-by":"crossref","first-page":"e1000201","DOI":"10.1371\/journal.pcbi.1000201","article-title":"ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome","volume":"4","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B23","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/1741-7007-9-80","article-title":"Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements","volume":"9","year":"2011","journal-title":"BMC Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B24","doi-asserted-by":"crossref","first-page":"4063","DOI":"10.1093\/nar\/gkr016","article-title":"Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering","volume":"39","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B25","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1101\/gr.112656.110","article-title":"High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells","volume":"21","year":"2011","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B26","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1101\/gr.112623.110","article-title":"Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data","volume":"21","year":"2011","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B27","doi-asserted-by":"crossref","first-page":"e201","DOI":"10.1093\/nar\/gkt850","article-title":"Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data","volume":"41","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B28","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1038\/nature07730","article-title":"ChIP-seq accurately predicts tissue-specific activity of enhancers","volume":"457","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B29","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2010-11-1-r7","article-title":"Genome-wide prediction of transcription factor binding sites using an integrated model","volume":"11","year":"2010","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B30","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","year":"2012","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B31","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","year":"2012","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B32","doi-asserted-by":"crossref","first-page":"4423","DOI":"10.1093\/nar\/gkt143","article-title":"Comparative annotation of functional regions in the human genome using epigenomic data","volume":"41","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B33","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1093\/bioinformatics\/btq248","article-title":"Discover regulatory DNA elements using chromatin signatures and artificial neural network","volume":"26","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B34","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1093\/nar\/gks149","article-title":"Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines","volume":"40","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B35","doi-asserted-by":"crossref","first-page":"e1003677","DOI":"10.1371\/journal.pcbi.1003677","article-title":"Integrating diverse datasets improves developmental enhancer prediction","volume":"10","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B36","doi-asserted-by":"crossref","first-page":"e6","DOI":"10.1093\/nar\/gku1058","article-title":"DEEP: a general computational framework for predicting enhancers","volume":"43","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B37","doi-asserted-by":"crossref","first-page":"e1002968","DOI":"10.1371\/journal.pcbi.1002968","article-title":"RFECS: a random-forest based algorithm for enhancer identification from chromatin state","volume":"9","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B38","doi-asserted-by":"crossref","first-page":"e0130622","DOI":"10.1371\/journal.pone.0130622","article-title":"DELTA: a distal enhancer locating tool based on AdaBoost algorithm and shape features of chromatin modifications","volume":"10","year":"2015","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B39","doi-asserted-by":"crossref","first-page":"W544","DOI":"10.1093\/nar\/gkt519","article-title":"kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets","volume":"41","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B40","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature12787","article-title":"An atlas of active enhancers across human cell types and tissues","volume":"507","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B41","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1038\/nmeth.3329","article-title":"Identification of active transcriptional regulatory elements from GRO-seq data","volume":"12","year":"2015","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B42","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1101\/gr.144899.112","article-title":"Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay","volume":"23","year":"2013","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B43","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1101\/gr.173518.114","article-title":"High-throughput functional testing of ENCODE segmentation predictions","volume":"24","year":"2014","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B44","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1232542","article-title":"Genome-wide quantitative enhancer activity maps identified by STARR-seq","volume":"339","year":"2013","journal-title":"Science"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B45","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1101\/gr.157891.113","article-title":"Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants","volume":"23","year":"2013","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B46","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nmeth.2885","article-title":"FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells","volume":"11","year":"2014","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B47","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/nmeth.2558","article-title":"Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos","volume":"10","year":"2013","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B48","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nbt.2137","article-title":"Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay","volume":"30","year":"2012","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B49","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nbt.2136","article-title":"Massively parallel functional dissection of mammalian enhancers in vivo","volume":"30","year":"2012","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B50","doi-asserted-by":"crossref","first-page":"bav085","DOI":"10.1093\/database\/bav085","article-title":"DENdb: database of integrated human enhancers","volume":"2015","year":"2015","journal-title":"Database (Oxford)"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B51","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1101\/gr.121905.111","article-title":"Discriminative prediction of mammalian enhancers from DNA sequence","volume":"21","year":"2011","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B52","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1101\/gr.169243.113","article-title":"Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features","volume":"24","year":"2014","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B53","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1101\/gr.098657.109","article-title":"Genome-wide discovery of human heart enhancers","volume":"20","year":"2010","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B54","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1186\/1471-2105-9-547","article-title":"Prediction of regulatory elements in mammalian genomes using chromatin signatures","volume":"9","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B55","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature07829","article-title":"Histone modifications at human enhancers reflect global cell-type-specific gene expression","volume":"459","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B56","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nature09692","article-title":"A unique chromatin signature uncovers early developmental enhancers in humans","volume":"470","year":"2011","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B57","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1016\/j.cell.2011.09.057","article-title":"Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells","volume":"147","year":"2011","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B58","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1101\/gr.144840.112","article-title":"Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types","volume":"23","year":"2013","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B59","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.cell.2005.10.042","article-title":"Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity","volume":"124","year":"2006","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B60","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.cell.2012.12.009","article-title":"DNA-binding specificities of human transcription factors","volume":"152","year":"2013","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B61","doi-asserted-by":"crossref","first-page":"R48","DOI":"10.1186\/gb-2012-13-9-r48","article-title":"Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors","volume":"13","year":"2012","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B62","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/489045a","article-title":"Presenting ENCODE","volume":"489","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B63","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1016\/j.cell.2009.06.049","article-title":"Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes","volume":"138","year":"2009","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B64","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nature10985","article-title":"Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function","volume":"484","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B65","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature11232","article-title":"The accessible chromatin landscape of the human genome","volume":"489","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B66","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.164079.113","article-title":"Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits","volume":"24","year":"2014","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B67","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1093\/bib\/5.4.328","article-title":"Biological applications of support vector machines","volume":"5","year":"2004","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B68","first-page":"315","article-title":"An introduction to artificial neural networks in bioinformatics\u2013application to complex microarray and mass spectrometry datasets in cancer studies","volume":"10","year":"2009","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B69","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/bib\/bbs006","article-title":"Class-imbalanced classifiers for high-dimensional data","volume":"14","year":"2013","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B70","article-title":"A roadmap to multifactor dimensionality reduction methods","year":"2015","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B71","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/bib\/bbu046","article-title":"A selective review of robust variable selection with applications in bioinformatics","volume":"16","year":"2015","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B72","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1093\/bib\/bbk007","article-title":"Machine learning in bioinformatics","volume":"7","year":"2006","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B73","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1093\/nar\/gks1284","article-title":"Integrative annotation of chromatin elements from ENCODE data","volume":"41","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B74","doi-asserted-by":"crossref","first-page":"i292","DOI":"10.1093\/bioinformatics\/btg1040","article-title":"A probabilistic method to detect regulatory modules","volume":"19","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B75","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s13059-015-0708-z","article-title":"Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome","volume":"16","year":"2015","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B76","doi-asserted-by":"crossref","first-page":"D122","DOI":"10.1093\/nar\/gkl879","article-title":"PReMod: a database of genome-wide mammalian cis-regulatory module predictions","volume":"35","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B77","doi-asserted-by":"crossref","first-page":"D88","DOI":"10.1093\/nar\/gkl822","article-title":"VISTA Enhancer Browser\u2013a database of tissue-specific human enhancers","volume":"35","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B78","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH roadmap epigenomics mapping consortium","volume":"28","year":"2010","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B79","doi-asserted-by":"crossref","first-page":"e6901","DOI":"10.1371\/journal.pone.0006901","article-title":"Identifying cis-regulatory sequences by word profile similarity","volume":"4","year":"2009","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B80","doi-asserted-by":"crossref","first-page":"e1003711","DOI":"10.1371\/journal.pcbi.1003711","article-title":"Enhanced regulatory sequence prediction using gapped k-mer features","volume":"10","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B81","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/nbt.2205","article-title":"Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters","volume":"30","year":"2012","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B82","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1126\/science.1231382","article-title":"A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb","volume":"339","year":"2013","journal-title":"Science"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B83","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.cell.2010.01.044","article-title":"An atlas of combinatorial transcriptional regulation in mouse and man","volume":"140","year":"2010","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B84","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.1259418","article-title":"Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells","volume":"347","year":"2015","journal-title":"Science"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B85","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1038\/ng.3142","article-title":"Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers","volume":"46","year":"2014","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B86","doi-asserted-by":"crossref","first-page":"E2191","DOI":"10.1073\/pnas.1320308111","article-title":"Global view of enhancer-promoter interactome in human cells","volume":"111","year":"2014","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B87","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","year":"2011","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B88","article-title":"Chromosome conformation capture carbon copy technology","year":"2007","journal-title":"Curr Protoc Mol Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B89","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-alpha-bound human chromatin interactome","volume":"462","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B90","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1038\/ng.3152","article-title":"A shared architecture for promoters and enhancers","volume":"46","year":"2014","journal-title":"Nat Genet"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B91","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.gde.2009.10.006","article-title":"Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information","volume":"19","year":"2009","journal-title":"Curr Opin Genet Dev"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B92","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","year":"2008","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B93","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1093\/bioinformatics\/btp340","article-title":"A clustering approach for identification of enriched domains from histone modification ChIP-Seq data","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B94","doi-asserted-by":"crossref","first-page":"e96303","DOI":"10.1371\/journal.pone.0096303","article-title":"A comparison of peak callers used for DNase-Seq data","volume":"9","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B95","doi-asserted-by":"crossref","first-page":"e11471","DOI":"10.1371\/journal.pone.0011471","article-title":"Evaluation of algorithm performance in ChIP-seq peak detection","volume":"5","year":"2010","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B96","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/nbt.3157","article-title":"Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues","volume":"33","year":"2015","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B97","doi-asserted-by":"crossref","first-page":"18602","DOI":"10.1073\/pnas.1316064110","article-title":"Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins","volume":"110","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B98","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1093\/bib\/1.3.214","article-title":"Comparing the success of different prediction software in sequence analysis: a review","volume":"1","year":"2000","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B99","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1093\/bib\/bbu034","article-title":"Predictive modelling of gene expression from transcriptional regulatory elements","volume":"16","year":"2015","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B100","doi-asserted-by":"crossref","first-page":"14946","DOI":"10.1073\/pnas.0802636105","article-title":"Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock","volume":"105","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B101","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.cell.2013.03.036","article-title":"Selective inhibition of tumor oncogenes by disruption of super-enhancers","volume":"153","year":"2013","journal-title":"Cell"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B102","doi-asserted-by":"crossref","first-page":"D195","DOI":"10.1093\/nar\/gks1089","article-title":"HOCOMOCO: a comprehensive collection of human transcription factor binding sites models","volume":"41","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170214143217_bbv101-B103","doi-asserted-by":"crossref","first-page":"2560","DOI":"10.1093\/bioinformatics\/btv158","article-title":"4DGenome: a comprehensive database of chromatin interactions","volume":"31","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/17\/6\/967\/8280356\/bbv101.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,23]],"date-time":"2022-07-23T11:27:26Z","timestamp":1658575646000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/2606433\/Progress"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,3]]},"references-count":103,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2015,12,3]]},"published-print":{"date-parts":[[2016,11]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbv101","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12,3]]}}}