Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013; 14(4):288. https://doi.org/10.1038/nrg3458.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu B, Fang L, Long R, Lan X, Chou K-C. iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinformatics. 2015; 32(3):362–9. https://doi.org/10.1093/bioinformatics/btv604.
Article
PubMed
Google Scholar
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Calcar SV, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39(3):311. https://doi.org/10.1038/ng1966.
Article
CAS
PubMed
Google Scholar
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009; 457(7231):854. https://doi.org/10.1038/nature07730.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kulaeva OI, Nizovtseva EV, Polikanov YS, Ulianov SV, Studitsky VM. Distant activation of transcription: Mechanisms of enhancer action. Mol Cell Biol. 2012; 32(24):4892–7. https://doi.org/10.1128/MCB.01127-12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang G, Shi J, Zhu S, Lan Y, Xu L, Yuan H, Liao G, Liu X, Zhang Y, Xiao Y, Li X. DiseaseEnhancer: a resource of human disease-associated enhancer catalog. Nucleic Acids Res. 2017; 46(D1):78–84. https://doi.org/10.1093/nar/gkx920.
Article
Google Scholar
Corradin O, Scacheri PC. Enhancer variants: evaluating functions in common disease. Genome Med. 2014; 6(10):85. https://doi.org/10.1186/s13073-014-0085-3.
Article
PubMed
PubMed Central
Google Scholar
Herz H-M. Enhancer deregulation in cancer and other diseases. BioEssays. 2016; 38(10):1003–15. https://doi.org/10.1002/bies.201600106.
Article
PubMed
PubMed Central
Google Scholar
Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, Schweiger PJ, Pedersen AG, Rapin N, Skovgaard K, Dahlgaard K, Andersson R, Terkelsen TB, Lilje B, Troelsen JT, Petersen AM, Jensen KB, Gögenur I, Thielsen P, Seidelin JB, Nielsen OH, Bjerrum JT, Sandelin A. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun. 2018; 9(1):1661. https://doi.org/10.1038/s41467-018-03766-z.
Article
PubMed
PubMed Central
Google Scholar
Visel A, Bristow J, A.Pennacchio L. Enhancer identification through comparative genomics. Semin Cell Dev Biol. 2007; 18(1):140–52. https://doi.org/10.1016/j.semcdb.2006.12.014.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J. Accurate promoter and enhancer identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN. PloS ONE. 2017; 12(1):0169249. https://doi.org/10.1371/journal.pone.0169249.
Article
Google Scholar
Lai Y-T, Deem KD, Borràs-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, Tomoyasu DJM. Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development. 2018; 145(7):160663. https://doi.org/10.1242/dev.160663.
Article
Google Scholar
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57. https://doi.org/10.1038/nature11247.
Article
PubMed Central
Google Scholar
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012; 13(9):48. https://doi.org/10.1186/gb-2012-13-9-r48.
Article
Google Scholar
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010; 28(10):1045. https://doi.org/10.1038/nbt1010-1045.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A. High-resolution sequencing and modeling identifies distinct dynamic rna regulatory strategies. Cell. 2014; 159(7):1698–710. https://doi.org/10.1016/j.cell.2014.11.015.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, Martin DE, Tresch A, Cramer P. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol. 2011; 7(1). https://doi.org/10.1038/msb.2010.112.
Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 2011; 469(7330):368. https://doi.org/10.1038/nature09652.
Article
CAS
PubMed
Google Scholar
Fang Y, Wang Y, Zhu Q, Wang J, Li G. In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences. Sci Rep. 2016; 6:32476. https://doi.org/10.1038/srep32476.
Article
CAS
PubMed
PubMed Central
Google Scholar
Firpi HA, Ucar D, Tan K. Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics. 2010; 26(13):1579–86. https://doi.org/10.1093/bioinformatics/btq248.
Article
CAS
PubMed
PubMed Central
Google Scholar
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014; 10(6):1003677. https://doi.org/10.1371/journal.pcbi.1003677.
Article
Google Scholar
Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol. 2013; 9(3). https://doi.org/10.1371/journal.pcbi.1003677.
Bu H, Gan Y, Wang Y, Zhou S, Guan J. A new method for enhancer prediction based on deep belief network. BMC Bioinformatics. 2017; 18(12):418. https://doi.org/10.1186/s12859-017-1828-0.
Article
PubMed
PubMed Central
Google Scholar
Min X, Zeng W, Chen S, Chen N, Chen T, Jiang R. Predicting enhancers with deep convolutional neural networks. BMC Bioinformatics. 2017; 18(13):478. https://doi.org/10.1186/s12859-017-1878-3.
Article
PubMed
PubMed Central
Google Scholar
Liu B, Fang L, Long R, Lan X, Chou K-C. iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. Bioinformatics. 2015; 32(3):362–9. https://doi.org/10.1093/bioinformatics/btv604.
Article
PubMed
Google Scholar
Jiaa C, He W. EnhancerPred: a predictor for discovering enhancers based on the combination and selection of multiple features. Sci Rep. 2016; 6:38741. https://doi.org/10.1038/srep38741.
Article
Google Scholar
Liu B, Li K, Huang D-S, Chou K-C. iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. Bioinformatics. 2018; 34(22):3835–42. https://doi.org/10.1093/bioinformatics/bty458.
Article
CAS
PubMed
Google Scholar
Crooks GE, Hon G, Chandonia J-M, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004; 14(6):1188–90. https://doi.org/10.1101/gr.849004.
Article
CAS
PubMed
PubMed Central
Google Scholar
D.Schneider T, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990; 18(20):6097–100. https://doi.org/10.1093/nar/18.20.6097.
Article
Google Scholar
Chicco D. Ten quick tips for machine learning in computational biology. BioData Min. 2017; 10(1):35. https://doi.org/10.1186/s13040-017-0155-3.
Article
PubMed
PubMed Central
Google Scholar
Zhuang Z, Shen X, Pan W. A simple convolutional neural network for prediction of enhancer–promoter interactions with DNA sequence data. Bioinformatics. 2019:1–8. https://doi.org/10.1093/bioinformatics/bty1050.
Min X, Zeng W, Chen S, Chen N, Chen T, Jiang R. Predicting enhancers with deep convolutional neural networks. BMC Bioinformatics. 2017; 18(13):478. https://doi.org/10.1186/s12859-017-1878-3.
Article
PubMed
PubMed Central
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150–2. https://doi.org/10.1093/bioinformatics/bts565.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kingma DP, Ba J. Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980. 2014.