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For: Burzynski GM, Reed X, Taher L, Stine ZE, Matsui T, Ovcharenko I, McCallion AS. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. Genome Res 2012;22:2278-89. [PMID: 22759862 PMCID: PMC3483557 DOI: 10.1101/gr.139717.112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Wang Y, Jaime-Lara RB, Roy A, Sun Y, Liu X, Joseph PV. SeqEnhDL: sequence-based classification of cell type-specific enhancers using deep learning models. BMC Res Notes 2021;14:104. [PMID: 33741075 PMCID: PMC7980595 DOI: 10.1186/s13104-021-05518-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/09/2021] [Indexed: 11/12/2022]  Open
2
Tobias IC, Abatti LE, Moorthy SD, Mullany S, Taylor T, Khader N, Filice MA, Mitchell JA. Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale. Genome 2020;64:426-448. [PMID: 32961076 DOI: 10.1139/gen-2020-0104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
3
Colbran LL, Chen L, Capra JA. Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Genetics 2019;211:1205-1217. [PMID: 30696717 PMCID: PMC6456323 DOI: 10.1534/genetics.118.301895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023]  Open
4
Chen L, Fish AE, Capra JA. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol 2018;14:e1006484. [PMID: 30286077 PMCID: PMC6191148 DOI: 10.1371/journal.pcbi.1006484] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 10/16/2018] [Accepted: 09/02/2018] [Indexed: 12/30/2022]  Open
5
Bu H, Gan Y, Wang Y, Zhou S, Guan J. A new method for enhancer prediction based on deep belief network. BMC Bioinformatics 2017;18:418. [PMID: 29072144 PMCID: PMC5657043 DOI: 10.1186/s12859-017-1828-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
6
Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput Biol 2017;13:e1005720. [PMID: 28827824 PMCID: PMC5578682 DOI: 10.1371/journal.pcbi.1005720] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/31/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022]  Open
7
Colbran LL, Chen L, Capra JA. Short DNA sequence patterns accurately identify broadly active human enhancers. BMC Genomics 2017;18:536. [PMID: 28716036 PMCID: PMC5512948 DOI: 10.1186/s12864-017-3934-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/09/2017] [Indexed: 12/25/2022]  Open
8
Grice J, Noyvert B, Doglio L, Elgar G. A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PLoS One 2015;10:e0130413. [PMID: 26131856 PMCID: PMC4489388 DOI: 10.1371/journal.pone.0130413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/19/2015] [Indexed: 12/17/2022]  Open
9
Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC. An integrative computational approach for prioritization of genomic variants. PLoS One 2014;9:e114903. [PMID: 25506935 PMCID: PMC4266634 DOI: 10.1371/journal.pone.0114903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/15/2014] [Indexed: 12/27/2022]  Open
10
Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol 2014;10:e1003677. [PMID: 24967590 PMCID: PMC4072507 DOI: 10.1371/journal.pcbi.1003677] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 05/06/2014] [Indexed: 01/02/2023]  Open
11
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res 2014;24:1147-56. [PMID: 24714811 PMCID: PMC4079970 DOI: 10.1101/gr.169243.113] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 2014;15:272-86. [PMID: 24614317 DOI: 10.1038/nrg3682] [Citation(s) in RCA: 960] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
13
Schulte D, Frank D. TALE transcription factors during early development of the vertebrate brain and eye. Dev Dyn 2013;243:99-116. [DOI: 10.1002/dvdy.24030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/25/2022]  Open
14
Taher L, Smith RP, Kim MJ, Ahituv N, Ovcharenko I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol 2013;14:R117. [PMID: 24156763 PMCID: PMC3983659 DOI: 10.1186/gb-2013-14-10-r117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/24/2013] [Indexed: 01/22/2023]  Open
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