-
1
-
-
84858440747
-
Metazoan promoters: Emerging characteristics and insights into transcriptional regulation
-
PMID: 22392219
-
Lenhard B, Sandelin A, Carninci P. Metazoan promoters: Emerging characteristics and insights into transcriptional regulation. Nat Rev Genet. 2012; 13(4):233-245. doi:10.1038/nrg3163 PMID: 22392219.
-
(2012)
Nat Rev Genet
, vol.13
, Issue.4
, pp. 233-245
-
-
Lenhard, B.1
Sandelin, A.2
Carninci, P.3
-
2
-
-
0019811465
-
Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences
-
PMID: 6277502
-
Banerji J, Rusconi S, Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell. 1981; 27(2 Pt 1):299-308. PMID: 6277502.
-
(1981)
Cell
, vol.27
, Issue.2
, pp. 299-308
-
-
Banerji, J.1
Rusconi, S.2
Schaffner, W.3
-
3
-
-
84907516453
-
High-Throughput functional testing of ENCODE segmentation predictions
-
PMID: 25035418
-
Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-Throughput functional testing of ENCODE segmentation predictions. Genome Res. 2014; 24(10):1595-1602. doi:10.1101/gr.173518.114 PMID: 25035418.
-
(2014)
Genome Res
, vol.24
, Issue.10
, pp. 1595-1602
-
-
Kwasnieski, J.C.1
Fiore, C.2
Chaudhari, H.G.3
Cohen, B.A.4
-
4
-
-
84877147962
-
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
-
PMID: 23512712
-
Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 2013; 23(5):800-811. doi:10.1101/gr.144899.112 PMID: 23512712.
-
(2013)
Genome Res
, vol.23
, Issue.5
, pp. 800-811
-
-
Kheradpour, P.1
Ernst, J.2
Melnikov, A.3
Rogov, P.4
Wang, L.5
Zhang, X.6
-
5
-
-
84874381107
-
Genome-wide quantitative enhancer activity maps identified by STARR-seq
-
PMID: 23328393
-
Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013; 339(6123):1074-1077. doi:10.1126/science.1232542 PMID: 23328393.
-
(2013)
Science
, vol.339
, Issue.6123
, pp. 1074-1077
-
-
Arnold, C.D.1
Gerlach, D.2
Stelzer, C.3
Boryn, L.M.4
Rath, M.5
Stark, A.6
-
6
-
-
84899450857
-
Transcriptional enhancers: From properties to genome-wide predictions
-
PMID: 24614317
-
Shlyueva D, Stampfel G, Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 2014; 15(4):272-286. doi:10.1038/nrg3682 PMID: 24614317.
-
(2014)
Nat Rev Genet
, vol.15
, Issue.4
, pp. 272-286
-
-
Shlyueva, D.1
Stampfel, G.2
Stark, A.3
-
7
-
-
84925684704
-
Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model
-
PMID: 25450156
-
Andersson R. Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model. BioEssays. 2015; 37(3):314-323. doi:10.1002/bies.201400162 PMID: 25450156.
-
(2015)
BioEssays
, vol.37
, Issue.3
, pp. 314-323
-
-
Andersson, R.1
-
8
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
PMID: 20657582
-
Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010; 28(8):817-825. doi:10.1038/nbt.1662 PMID: 20657582.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.8
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
9
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
PMID: 22426492
-
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012; 9(5):473-476. doi:10.1038/nmeth.1937 PMID: 22426492.
-
(2012)
Nat Methods
, vol.9
, Issue.5
, pp. 473-476
-
-
Hoffman, M.M.1
Buske, O.J.2
Wang, J.3
Weng, Z.4
Bilmes, J.A.5
Noble, W.S.6
-
10
-
-
85038129705
-
Progress and challenges in bioinformatics approaches for enhancer identification
-
Epub ahead of print. PMID: 26634919
-
Kleftogiannis D, Kalnis P, Bajic VB. Progress and challenges in bioinformatics approaches for enhancer identification. Brief Bioinformatics. 2015;[Epub ahead of print]. doi:10.1093/bib/bbv101 PMID: 26634919.
-
(2015)
Brief Bioinformatics
-
-
Kleftogiannis, D.1
Kalnis, P.2
Bajic, V.B.3
-
11
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
PMID: 22955616
-
Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74. doi:10.1038/nature11247 PMID: 22955616.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 57-74
-
-
Dunham, I.1
Kundaje, A.2
Aldred, S.F.3
Collins, P.J.4
Davis, C.A.5
Doyle, F.6
-
12
-
-
84865754452
-
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
-
PMID: 22950945
-
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012; 13(9):R48. doi:10.1186/gb-2012-13-9-r48 PMID: 22950945.
-
(2012)
Genome Biol
, vol.13
, Issue.9
, pp. R48
-
-
Yip, K.Y.1
Cheng, C.2
Bhardwaj, N.3
Brown, J.B.4
Leng, J.5
Kundaje, A.6
-
13
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
PMID: 25693563
-
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317-330. doi:10.1038/nature14248 PMID: 25693563.
-
(2015)
Nature
, vol.518
, Issue.7539
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
-
15
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
PMID: 24670763
-
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014; 507(7493):455-461. doi:10.1038/nature12787 PMID: 24670763.
-
(2014)
Nature
, vol.507
, Issue.7493
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
-
16
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
PMID: 24670764
-
Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, et al. A promoter-level mammalian expression atlas. Nature. 2014; 507(7493):462-470. doi:10.1038/nature13182 PMID: 24670764.
-
(2014)
Nature
, vol.507
, Issue.7493
, pp. 462-470
-
-
Forrest, A.R.1
Kawaji, H.2
Rehli, M.3
Baillie, J.K.4
De Hoon, M.J.5
Haberle, V.6
-
17
-
-
84943143082
-
DEEP: A general computational framework for predicting enhancers
-
PMID: 25378307
-
Kleftogiannis D, Kalnis P, Bajic VB. DEEP: A general computational framework for predicting enhancers. Nucleic Acids Res. 2015; 43(1):e6. doi:10.1093/nar/gku1058 PMID: 25378307.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.1
, pp. e6
-
-
Kleftogiannis, D.1
Kalnis, P.2
Bajic, V.B.3
-
18
-
-
83055181959
-
Discriminative prediction of mammalian enhancers from DNA sequence
-
PMID: 21875935
-
Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21(12):2167-2180. doi:10.1101/gr.121905.111 PMID: 21875935.
-
(2011)
Genome Res
, vol.21
, Issue.12
, pp. 2167-2180
-
-
Lee, D.1
Karchin, R.2
Beer, M.A.3
-
19
-
-
84876007572
-
RFECS: A random-forest based algorithm for enhancer identification from chromatin state
-
PMID: 23526891
-
Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, et al. RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol. 2013; 9(3): E1002968. doi:10.1371/journal.pcbi.1002968 PMID: 23526891.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.3
, pp. e1002968
-
-
Rajagopal, N.1
Xie, W.2
Li, Y.3
Wagner, U.4
Wang, W.5
Stamatoyannopoulos, J.6
-
20
-
-
84877254043
-
Comparative annotation of functional regions in the human genome using epigenomic data
-
PMID: 23482391
-
Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, et al. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res. 2013; 41(8):4423-4432. doi:10.1093/nar/gkt143 PMID: 23482391.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.8
, pp. 4423-4432
-
-
Won, K.J.1
Zhang, X.2
Wang, T.3
Ding, B.4
Raha, D.5
Snyder, M.6
-
21
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
PMID: 21441907
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473(7345):43-49. doi:10.1038/nature09906PMID: 21441907.
-
(2011)
Nature
, vol.473
, Issue.7345
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
-
22
-
-
84875448918
-
Integrative annotation of chromatin elements from ENCODE data
-
PMID: 23221638
-
Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013; 41(2):827-841. doi:10.1093/nar/gks1284 PMID: 23221638.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.2
, pp. 827-841
-
-
Hoffman, M.M.1
Ernst, J.2
Wilder, S.P.3
Kundaje, A.4
Harris, R.S.5
Libbrecht, M.6
-
23
-
-
84939123947
-
The ensembl regulatory build
-
PMID: 25887522
-
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The ensembl regulatory build. Genome Biol. 2015; 16:56. doi:10.1186/s13059-015-0621-5 PMID: 25887522.
-
(2015)
Genome Biol
, vol.16
, pp. 56
-
-
Zerbino, D.R.1
Wilder, S.P.2
Johnson, N.3
Juettemann, T.4
Flicek, P.R.5
-
24
-
-
79953060951
-
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
-
PMID: 21179089
-
Kharchenko PV, Alekseyenko Aa, Schwartz YB, Minoda A, Riddle NC, Ernst J, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011; 471(7339):480-485. doi:10.1038/nature09725 PMID: 21179089.
-
(2011)
Nature
, vol.471
, Issue.7339
, pp. 480-485
-
-
Kharchenko, P.V.1
Alekseyenko, A.2
Schwartz, Y.B.3
Minoda, A.4
Riddle, N.C.5
Ernst, J.6
-
25
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner LR. A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE. 1989; 77(2):257-286. doi:10.1109/5.18626.
-
(1989)
Proc IEEE
, vol.77
, Issue.2
, pp. 257-286
-
-
Rabiner, L.R.1
-
26
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
PMID: 22373907
-
Ernst J, Kellis M. ChromHMM: Automating chromatin-state discovery and characterization. Nat Methods. 2012; 9(3):215-216. doi:10.1038/nmeth.1906 PMID: 22373907.
-
(2012)
Nat Methods
, vol.9
, Issue.3
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
27
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
PMID: 17277777
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39 (3):311-318. doi:10.1038/ng1966 PMID: 17277777.
-
(2007)
Nat Genet
, vol.39
, Issue.3
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
-
28
-
-
84937776714
-
Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome
-
PMID: 26206277
-
Mammana A, Chung HR. Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biol. 2015; 16:151. doi:10.1186/s13059-015-0708-zPMID: 26206277.
-
(2015)
Genome Biol
, vol.16
, pp. 151
-
-
Mammana, A.1
Chung, H.R.2
-
29
-
-
84921675383
-
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle
-
PMID: 25527639
-
Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. Mol Syst Biol. 2014; 10:768. doi:10.15252/msb.20145654 PMID: 25527639.
-
(2014)
Mol Syst Biol
, vol.10
, pp. 768
-
-
Zacher, B.1
Lidschreiber, M.2
Cramer, P.3
Gagneur, J.4
Tresch, A.5
-
30
-
-
0015981751
-
On fitting the poisson lognormal distribution to species-Abundance data
-
Bulmer MG. On Fitting the Poisson Lognormal Distribution to Species-Abundance Data. Biometrics. 2011; 30(1):101-110. doi:10.2307/2529621.
-
(2011)
Biometrics
, vol.30
, Issue.1
, pp. 101-110
-
-
Bulmer, M.G.1
-
32
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka R, Gentleman R. R: A Language for Data Analysis and Graphics. J Comp Graph Stat. 1996; 5 (3):299-314. doi:10.2307/1390807.
-
(1996)
J Comp Graph Stat
, vol.5
, Issue.3
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
33
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-Throughput RNA sequencing data analysis
-
PMID: 22988256
-
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, et al. A comprehensive evaluation of normalization methods for Illumina high-Throughput RNA sequencing data analysis. Brief Bioinformatics. 2013; 14(6):671-683. doi:10.1093/bib/bbs046 PMID: 22988256.
-
(2013)
Brief Bioinformatics
, vol.14
, Issue.6
, pp. 671-683
-
-
Dillies, M.A.1
Rau, A.2
Aubert, J.3
Hennequet-Antier, C.4
Jeanmougin, M.5
Servant, N.6
-
34
-
-
84864803359
-
Normalization of ChIP-seq data with control
-
PMID: 22883957
-
Liang K, Sunduz K. Normalization of ChIP-seq data with control. BMC Bioinformatics. 2012; 13 (6290):199. doi:10.1186/1471-2105-13-199 PMID: 22883957.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.6290
, pp. 199
-
-
Liang, K.1
Sunduz, K.2
-
35
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
PMID: 22388286
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357- 359. doi:10.1038/nmeth.1923 PMID: 22388286.
-
(2012)
Nat Methods
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
36
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
PMID: 19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-2079. doi:10.1093/bioinformatics/btp352 PMID: 19505943.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
37
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
PMID: 15461798
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. doi:10.1186/gb-2004-5-10-r80 PMID: 15461798.
-
(2004)
Genome Biol
, vol.5
, Issue.10
, pp. R80
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
-
38
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
PMID: 17571346
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007; 447(7146):799-816. doi:10.1038/nature05874 PMID: 17571346.
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
-
39
-
-
67649837030
-
Rtracklayer: An R package for interfacing with genome browsers
-
PMID: 19468054
-
Lawrence M, Gentleman R, Carey V. rtracklayer: An R package for interfacing with genome browsers. Bioinformatics. 2009; 25:1841-1842. doi:10.1093/bioinformatics/btp328 PMID: 19468054.
-
(2009)
Bioinformatics
, vol.25
, pp. 1841-1842
-
-
Lawrence, M.1
Gentleman, R.2
Carey, V.3
-
40
-
-
84883368195
-
Software for computing and annotating genomic ranges
-
PMID: 23950696
-
Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):e1003118. doi:10.1371/journal.pcbi.1003118 PMID: 23950696.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.8
, pp. e1003118
-
-
Lawrence, M.1
Huber, W.2
Pages, H.3
Aboyoun, P.4
Carlson, M.5
Gentleman, R.6
-
41
-
-
84975072539
-
TT-seq maps the human transient transcriptome
-
PMID: 27257258
-
Schwalb B, Michel M, Zacher B, Fruhauf K, Demel C, Tresch A, et al. TT-seq maps the human transient transcriptome. Science. 2016; 352(6290):1225-1228. doi:10.1126/science.aad9841 PMID: 27257258.
-
(2016)
Science
, vol.352
, Issue.6290
, pp. 1225-1228
-
-
Schwalb, B.1
Michel, M.2
Zacher, B.3
Fruhauf, K.4
Demel, C.5
Tresch, A.6
-
42
-
-
84880064679
-
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
-
PMID: 23595227
-
Ernst J, Kellis M. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Res. 2013; 23(7):1142-1154. doi:10.1101/gr.144840.112 PMID: 23595227.
-
(2013)
Genome Res
, vol.23
, Issue.7
, pp. 1142-1154
-
-
Ernst, J.1
Kellis, M.2
-
43
-
-
84891790401
-
The NHGRI GWAS Catalog, a curated resource of SNP-Trait associations
-
Database issue: PMID: 24316577
-
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-Trait associations. Nucleic Acids Res. 2014; 42(Database issue):D1001- D1006. doi:10.1093/nar/gkt1229 PMID: 24316577.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D1001-D1006
-
-
Welter, D.1
MacArthur, J.2
Morales, J.3
Burdett, T.4
Hall, P.5
Junkins, H.6
-
44
-
-
0035733108
-
The control of the false discovery rate in multiple testing under dependency
-
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics. 2001; 29(4):1165-1188.
-
(2001)
The Annals of Statistics
, vol.29
, Issue.4
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
45
-
-
84923786414
-
The selection and function of cell type-specific enhancers
-
PMID: 25650801
-
Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015; 16(3):144-154. doi:10.1038/nrm3949 PMID: 25650801.
-
(2015)
Nat Rev Mol Cell Biol
, vol.16
, Issue.3
, pp. 144-154
-
-
Heinz, S.1
Romanoski, C.E.2
Benner, C.3
Glass, C.K.4
-
46
-
-
84927559450
-
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
-
PMID: 25383968
-
Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014; 46 (12):1311-1320. doi:10.1038/ng.3142 PMID: 25383968.
-
(2014)
Nat Genet
, vol.46
, Issue.12
, pp. 1311-1320
-
-
Core, L.J.1
Martins, A.L.2
Danko, C.G.3
Waters, C.T.4
Siepel, A.5
Lis, J.T.6
-
47
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
PMID: 20393465
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010; 465(7295):182-187. doi:10.1038/nature09033 PMID: 20393465.
-
(2010)
Nature
, vol.465
, Issue.7295
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
-
48
-
-
84860503075
-
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature
-
PMID: 22499593
-
Kvon EZ, Stampfel G, Yanez-Cuna JO, Dickson BJ, Stark A. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 2012; 26(9):908-913. doi:10.1101/gad.188052.112 PMID: 22499593.
-
(2012)
Genes Dev
, vol.26
, Issue.9
, pp. 908-913
-
-
Kvon, E.Z.1
Stampfel, G.2
Yanez-Cuna, J.O.3
Dickson, B.J.4
Stark, A.5
-
49
-
-
84933511619
-
Functional annotation of HOT regions in the human genome: Implications for human disease and cancer
-
PMID: 26113264
-
Li H, Chen H, Liu F, Ren C, Wang S, Bo X, et al. Functional annotation of HOT regions in the human genome: implications for human disease and cancer. Sci Rep. 2015; 5:11633. doi:10.1038/srep11633 PMID: 26113264.
-
(2015)
Sci Rep
, vol.5
, pp. 11633
-
-
Li, H.1
Chen, H.2
Liu, F.3
Ren, C.4
Wang, S.5
Bo, X.6
-
50
-
-
84926632357
-
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
-
PMID: 25690853
-
Ernst J, Kellis M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat Biotechnol. 2015; 33(4):364-376. doi:10.1038/nbt.3157 PMID: 25690853.
-
(2015)
Nat Biotechnol
, vol.33
, Issue.4
, pp. 364-376
-
-
Ernst, J.1
Kellis, M.2
-
51
-
-
84908894973
-
Genome-wide analysis of noncoding regulatory mutations in cancer
-
PMID: 25261935
-
Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014; 46(11):1160-1165. doi:10.1038/ng.3101 PMID: 25261935.
-
(2014)
Nat Genet
, vol.46
, Issue.11
, pp. 1160-1165
-
-
Weinhold, N.1
Jacobsen, A.2
Schultz, N.3
Sander, C.4
Lee, W.5
-
52
-
-
84976873328
-
HaploReg v4: Systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
-
PMID: 26657631
-
Ward LD, Kellis M. HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res. 2016; 44(D1):D877-D881. doi:10.1093/nar/gkv1340PMID: 26657631.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D877-D881
-
-
Ward, L.D.1
Kellis, M.2
-
53
-
-
84873086126
-
Chromatin marks identify critical cell types for fine mapping complex trait variants
-
PMID: 23263488
-
Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet. 2013; 45(2):124-130. doi:10.1038/ng.2504 PMID: 23263488.
-
(2013)
Nat Genet
, vol.45
, Issue.2
, pp. 124-130
-
-
Trynka, G.1
Sandor, C.2
Han, B.3
Xu, H.4
Stranger, B.E.5
Liu, X.S.6
-
54
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
PMID: 21993624
-
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011; 478(7370):476-482. doi:10.1038/nature10530 PMID: 21993624.
-
(2011)
Nature
, vol.478
, Issue.7370
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
-
55
-
-
74549125753
-
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
-
PMID: 20011106
-
Ramskold D, Wang ET, Burge CB, Sandberg R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol. 2009; 5(12):e1000598. doi:10.1371/journal.pcbi.1000598 PMID: 20011106.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.12
, pp. e1000598
-
-
Ramskold, D.1
Wang, E.T.2
Burge, C.B.3
Sandberg, R.4
-
56
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
PMID: 22955619
-
Gerstein MB, Kundaje A, Hariharan M, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012; 489(7414):91-100. doi:10.1038/nature11245 PMID: 22955619.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Weissman, S.M.4
Snyder, M.5
-
57
-
-
84865852567
-
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
-
PMID: 22955990
-
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012; 22(9):1798-1812. doi:10.1101/gr.139105.112 PMID: 22955990.
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1798-1812
-
-
Wang, J.1
Zhuang, J.2
Iyer, S.3
Lin, X.4
Whitfield, T.W.5
Greven, M.C.6
-
58
-
-
84924912759
-
Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence
-
PMID: 25564442
-
Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerenyi MA, et al. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J. 2015; 34 (6):759-777. doi:10.15252/embj.201490542 PMID: 25564442.
-
(2015)
EMBO J.
, vol.34
, Issue.6
, pp. 759-777
-
-
Org, T.1
Duan, D.2
Ferrari, R.3
Montel-Hagen, A.4
Van Handel, B.5
Kerenyi, M.A.6
-
59
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
PMID: 19212405
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009; 457(7231):854-858. doi:10.1038/nature07730 PMID: 19212405.
-
(2009)
Nature
, vol.457
, Issue.7231
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
-
60
-
-
84655164920
-
Large-scale discovery of enhancers from human heart tissue
-
PMID: 22138689
-
May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2012; 44(1):89-93. doi:10.1038/ng.1006 PMID: 22138689.
-
(2012)
Nat Genet
, vol.44
, Issue.1
, pp. 89-93
-
-
May, D.1
Blow, M.J.2
Kaplan, T.3
McCulley, D.J.4
Jensen, B.C.5
Akiyama, J.A.6
-
61
-
-
80051564877
-
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
-
PMID: 21632746
-
Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 2011; 21(8):1273-1283. doi:10.1101/gr.122382.111 PMID: 21632746.
-
(2011)
Genome Res
, vol.21
, Issue.8
, pp. 1273-1283
-
-
Zentner, G.E.1
Tesar, P.J.2
Scacheri, P.C.3
-
62
-
-
84919952154
-
High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies
-
PMID: 25497548
-
Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, et al. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell. 2014; 159 (7):1698-1710. doi:10.1016/j.cell.2014.11.015 PMID: 25497548.
-
(2014)
Cell
, vol.159
, Issue.7
, pp. 1698-1710
-
-
Rabani, M.1
Raychowdhury, R.2
Jovanovic, M.3
Rooney, M.4
Stumpo, D.J.5
Pauli, A.6
-
63
-
-
78650930357
-
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
-
PMID: 21206491
-
Miller C, Schwalb B, Maier K, Schulz D, Dumcke S, Zacher B, et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol. 2011; 7:458. doi:10.1038/msb.2010.112 PMID: 21206491.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 458
-
-
Miller, C.1
Schwalb, B.2
Maier, K.3
Schulz, D.4
Dumcke, S.5
Zacher, B.6
-
64
-
-
78751659330
-
Nascent transcript sequencing visualizes transcription at nucleotide resolution
-
PMID: 21248844
-
Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 2011; 469(7330):368-373. doi:10.1038/nature09652 PMID: 21248844.
-
(2011)
Nature
, vol.469
, Issue.7330
, pp. 368-373
-
-
Churchman, L.S.1
Weissman, J.S.2
-
65
-
-
84957602988
-
High-Throughput mapping of regulatory DNA
-
PMID: 26807528
-
Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, et al. High-Throughput mapping of regulatory DNA. Nat Biotechnol. 2016; 34(2):167-174. doi:10.1038/nbt.3468 PMID: 26807528.
-
(2016)
Nat Biotechnol
, vol.34
, Issue.2
, pp. 167-174
-
-
Rajagopal, N.1
Srinivasan, S.2
Kooshesh, K.3
Guo, Y.4
Edwards, M.D.5
Banerjee, B.6
|