-
1
-
-
0037041395
-
An extensive network of coupling among gene expression machines.
-
10.1038/416499a, 11932736
-
Maniatis T, Reed R. An extensive network of coupling among gene expression machines. Nature 2002, 416:499-506. 10.1038/416499a, 11932736.
-
(2002)
Nature
, vol.416
, pp. 499-506
-
-
Maniatis, T.1
Reed, R.2
-
2
-
-
37249034083
-
Coupling and coordination in gene expression processes: a systems biology view.
-
10.1038/nrg2223, 18071322
-
Komili S, Silver PA. Coupling and coordination in gene expression processes: a systems biology view. Nat Rev Genet 2008, 9:38-48. 10.1038/nrg2223, 18071322.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 38-48
-
-
Komili, S.1
Silver, P.A.2
-
3
-
-
0036532201
-
Deciphering gene expression regulatory networks.
-
10.1016/S0959-437X(02)00277-0, 11893484
-
Wyrick JJ, Young RA. Deciphering gene expression regulatory networks. Curr Opin Genet Dev 2002, 12:130-136. 10.1016/S0959-437X(02)00277-0, 11893484.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 130-136
-
-
Wyrick, J.J.1
Young, R.A.2
-
4
-
-
67749113808
-
Transcriptional regulatory circuits: predicting numbers from alphabets.
-
2745280, 19628860
-
Kim HD, Shay T, O'Shea EK, Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science 2009, 325:429-432. 2745280, 19628860.
-
(2009)
Science
, vol.325
, pp. 429-432
-
-
Kim, H.D.1
Shay, T.2
O'Shea, E.K.3
Regev, A.4
-
5
-
-
67249117049
-
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
-
10.1073/pnas.0903103106, 2687147, 19474294
-
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 9362-9367
-
-
Hindorff, L.A.1
Sethupathy, P.2
Junkins, H.A.3
Ramos, E.M.4
Mehta, J.P.5
Collins, F.S.6
Manolio, T.A.7
-
6
-
-
77951439152
-
Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
-
10.1371/journal.pgen.1000888, 2848547, 20369019
-
Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010, 6:e1000888. 10.1371/journal.pgen.1000888, 2848547, 20369019.
-
(2010)
PLoS Genet
, vol.6
-
-
Nicolae, D.L.1
Gamazon, E.2
Zhang, W.3
Duan, S.4
Dolan, M.E.5
Cox, N.J.6
-
7
-
-
77952367694
-
Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
-
10.1371/journal.pgen.1000895, 2848550, 20369022
-
Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 2010, 6:e1000895. 10.1371/journal.pgen.1000895, 2848550, 20369022.
-
(2010)
PLoS Genet
, vol.6
-
-
Nica, A.C.1
Montgomery, S.B.2
Dimas, A.S.3
Stranger, B.E.4
Beazley, C.5
Barroso, I.6
Dermitzakis, E.T.7
-
8
-
-
14544280757
-
Transcriptional regulation and the role of diverse coactivators in animal cells.
-
10.1016/j.febslet.2004.12.007, 15680973
-
Roeder RG. Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS Lett 2005, 579:909-915. 10.1016/j.febslet.2004.12.007, 15680973.
-
(2005)
FEBS Lett
, vol.579
, pp. 909-915
-
-
Roeder, R.G.1
-
9
-
-
0024282827
-
The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.
-
10.1016/S0092-8674(88)91087-2, 3136931
-
Rougvie AE, Lis JT. The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 1988, 54:795-804. 10.1016/S0092-8674(88)91087-2, 3136931.
-
(1988)
Cell
, vol.54
, pp. 795-804
-
-
Rougvie, A.E.1
Lis, J.T.2
-
10
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
-
10.1126/science.1162228, 2833333, 19056941
-
Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322:1845-1848. 10.1126/science.1162228, 2833333, 19056941.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
11
-
-
74549132843
-
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.
-
10.1126/science.1181421, 20007866
-
Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 2010, 327:335-338. 10.1126/science.1181421, 20007866.
-
(2010)
Science
, vol.327
, pp. 335-338
-
-
Nechaev, S.1
Fargo, D.C.2
dos Santos, G.3
Liu, L.4
Gao, Y.5
Adelman, K.6
-
12
-
-
78751659330
-
Nascent transcript sequencing visualizes transcription at nucleotide resolution.
-
10.1038/nature09652, 21248844
-
Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011, 469:368-373. 10.1038/nature09652, 21248844.
-
(2011)
Nature
, vol.469
, pp. 368-373
-
-
Churchman, L.S.1
Weissman, J.S.2
-
13
-
-
57849140661
-
Divergent transcription from active promoters.
-
10.1126/science.1162253, 2692996, 19056940
-
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. Divergent transcription from active promoters. Science 2008, 322:1849-1851. 10.1126/science.1162253, 2692996, 19056940.
-
(2008)
Science
, vol.322
, pp. 1849-1851
-
-
Seila, A.C.1
Calabrese, J.M.2
Levine, S.S.3
Yeo, G.W.4
Rahl, P.B.5
Flynn, R.A.6
Young, R.A.7
Sharp, P.A.8
-
14
-
-
57849123049
-
RNA exosome depletion reveals transcription upstream of active human promoters.
-
10.1126/science.1164096, 19056938
-
Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008, 322:1851-1854. 10.1126/science.1164096, 19056938.
-
(2008)
Science
, vol.322
, pp. 1851-1854
-
-
Preker, P.1
Nielsen, J.2
Kammler, S.3
Lykke-Andersen, S.4
Christensen, M.S.5
Mapendano, C.K.6
Schierup, M.H.7
Jensen, T.H.8
-
15
-
-
78649276218
-
The meaning of pausing.
-
10.1016/j.molcel.2010.11.025, 21095581
-
Espinosa JM. The meaning of pausing. Mol Cell 2010, 40:507-508. 10.1016/j.molcel.2010.11.025, 21095581.
-
(2010)
Mol Cell
, vol.40
, pp. 507-508
-
-
Espinosa, J.M.1
-
16
-
-
79953164741
-
Promoter proximal pausing and the control of gene expression.
-
10.1016/j.gde.2011.01.010, 21324670
-
Li J, Gilmour DS. Promoter proximal pausing and the control of gene expression. Curr Opin Genet Dev 2011, 21:231-235. 10.1016/j.gde.2011.01.010, 21324670.
-
(2011)
Curr Opin Genet Dev
, vol.21
, pp. 231-235
-
-
Li, J.1
Gilmour, D.S.2
-
17
-
-
79955795581
-
Paused RNA polymerase II as a developmental checkpoint.
-
10.1016/j.cell.2011.04.021, 21565610
-
Levine M. Paused RNA polymerase II as a developmental checkpoint. Cell 2011, 145:502-511. 10.1016/j.cell.2011.04.021, 21565610.
-
(2011)
Cell
, vol.145
, pp. 502-511
-
-
Levine, M.1
-
18
-
-
78149477660
-
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.
-
10.1016/j.cell.2010.10.004, 2991113, 21074046
-
Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 2010, 143:540-551. 10.1016/j.cell.2010.10.004, 2991113, 21074046.
-
(2010)
Cell
, vol.143
, pp. 540-551
-
-
Gilchrist, D.A.1
Dos Santos, G.2
Fargo, D.C.3
Xie, B.4
Gao, Y.5
Li, L.6
Adelman, K.7
-
19
-
-
78649289872
-
Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
-
10.1016/j.molcel.2010.11.004, 21095587
-
Carrillo Oesterreich F, Preibisch S, Neugebauer KM. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 2010, 40:571-581. 10.1016/j.molcel.2010.11.004, 21095587.
-
(2010)
Mol Cell
, vol.40
, pp. 571-581
-
-
Carrillo Oesterreich, F.1
Preibisch, S.2
Neugebauer, K.M.3
-
20
-
-
78649303325
-
Splicing-dependent RNA polymerase pausing in yeast.
-
10.1016/j.molcel.2010.11.005, 3000496, 21095588
-
Alexander RD, Innocente SA, Barrass JD, Beggs JD. Splicing-dependent RNA polymerase pausing in yeast. Mol Cell 2010, 40:582-593. 10.1016/j.molcel.2010.11.005, 3000496, 21095588.
-
(2010)
Mol Cell
, vol.40
, pp. 582-593
-
-
Alexander, R.D.1
Innocente, S.A.2
Barrass, J.D.3
Beggs, J.D.4
-
21
-
-
77956276383
-
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.
-
pdb prot5384
-
Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc 2010, 2010. pdb prot5384.
-
(2010)
Cold Spring Harb Protoc
, vol.2010
-
-
Song, L.1
Crawford, G.E.2
-
22
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state.
-
10.1073/pnas.1016071107, 3003124, 21106759
-
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010, 107:21931-21936. 10.1073/pnas.1016071107, 3003124, 21106759.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
Cheng, A.W.2
Welstead, G.G.3
Kooistra, T.4
Carey, B.W.5
Steine, E.J.6
Hanna, J.7
Lodato, M.A.8
Frampton, G.M.9
Sharp, P.A.10
Boyer, L.A.11
Young, R.A.12
Jaenisch, R.13
-
23
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans.
-
10.1038/nature09692, 21160473
-
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011, 470:279-283. 10.1038/nature09692, 21160473.
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Swigut, T.3
Brugmann, S.A.4
Flynn, R.A.5
Wysocka, J.6
-
24
-
-
67549119096
-
CTCF: master weaver of the genome.
-
10.1016/j.cell.2009.06.001, 3040116, 19563753
-
Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009, 137:1194-1211. 10.1016/j.cell.2009.06.001, 3040116, 19563753.
-
(2009)
Cell
, vol.137
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
25
-
-
74949102277
-
Does CTCF mediate between nuclear organization and gene expression?.
-
10.1002/bies.200900118, 20020479
-
Ohlsson R, Lobanenkov V, Klenova E. Does CTCF mediate between nuclear organization and gene expression?. Bioessays 2010, 32:37-50. 10.1002/bies.200900118, 20020479.
-
(2010)
Bioessays
, vol.32
, pp. 37-50
-
-
Ohlsson, R.1
Lobanenkov, V.2
Klenova, E.3
-
26
-
-
23844519339
-
A high-resolution map of active promoters in the human genome.
-
10.1038/nature03877, 1895599, 15988478
-
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature 2005, 436:876-880. 10.1038/nature03877, 1895599, 15988478.
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
Barrera, L.O.2
Zheng, M.3
Qu, C.4
Singer, M.A.5
Richmond, T.A.6
Wu, Y.7
Green, R.D.8
Ren, B.9
-
27
-
-
36549013619
-
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
-
10.1038/ng.2007.26, 2824921, 17994019
-
Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 2007, 39:1512-1516. 10.1038/ng.2007.26, 2824921, 17994019.
-
(2007)
Nat Genet
, vol.39
, pp. 1512-1516
-
-
Zeitlinger, J.1
Stark, A.2
Kellis, M.3
Hong, J.W.4
Nechaev, S.5
Adelman, K.6
Levine, M.7
Young, R.A.8
-
28
-
-
36549061004
-
RNA polymerase is poised for activation across the genome.
-
10.1038/ng.2007.21, 2365887, 17994021
-
Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K. RNA polymerase is poised for activation across the genome. Nat Genet 2007, 39:1507-1511. 10.1038/ng.2007.21, 2365887, 17994021.
-
(2007)
Nat Genet
, vol.39
, pp. 1507-1511
-
-
Muse, G.W.1
Gilchrist, D.A.2
Nechaev, S.3
Shah, R.4
Parker, J.S.5
Grissom, S.F.6
Zeitlinger, J.7
Adelman, K.8
-
29
-
-
79952901680
-
Enhancer function: new insights into the regulation of tissue-specific gene expression.
-
3175006, 21358745
-
Ong CT, Corces VG. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet 2011, 12:283-293. 3175006, 21358745.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 283-293
-
-
Ong, C.T.1
Corces, V.G.2
-
30
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types.
-
10.1038/nature09906, 3088773, 21441907
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49. 10.1038/nature09906, 3088773, 21441907.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
Ku, M.11
Durham, T.12
Kellis, M.13
Bernstein, B.E.14
-
31
-
-
79954562232
-
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.
-
10.1101/gad.2005511, 3070936, 21460038
-
Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev 2011, 25:742-754. 10.1101/gad.2005511, 3070936, 21460038.
-
(2011)
Genes Dev
, vol.25
, pp. 742-754
-
-
Min, I.M.1
Waterfall, J.J.2
Core, L.J.3
Munroe, R.J.4
Schimenti, J.5
Lis, J.T.6
-
32
-
-
64149122182
-
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.
-
10.1101/gr.086983.108, 2665778, 19251738
-
Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res 2009, 19:590-601. 10.1101/gr.086983.108, 2665778, 19251738.
-
(2009)
Genome Res
, vol.19
, pp. 590-601
-
-
Schnetz, M.P.1
Bartels, C.F.2
Shastri, K.3
Balasubramanian, D.4
Zentner, G.E.5
Balaji, R.6
Zhang, X.7
Song, L.8
Wang, Z.9
Laframboise, T.10
Crawford, G.E.11
Scacheri, P.C.12
-
33
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
-
10.1016/j.cell.2008.04.043, 18555785
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
Loh, Y.H.11
Yeo, H.C.12
Yeo, Z.X.13
Narang, V.14
Govindarajan, K.R.15
Leong, B.16
Shahab, A.17
Ruan, Y.18
Bourque, G.19
Sung, W.K.20
Clarke, N.D.21
Wei, C.L.22
Ng, H.H.23
more..
-
34
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
-
10.1038/nature06008, 2921165, 17603471
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560. 10.1038/nature06008, 2921165, 17603471.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
35
-
-
80051564877
-
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions.
-
10.1101/gr.122382.111, 3149494, 21632746
-
Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 2011, 21:1273-1283. 10.1101/gr.122382.111, 3149494, 21632746.
-
(2011)
Genome Res
, vol.21
, pp. 1273-1283
-
-
Zentner, G.E.1
Tesar, P.J.2
Scacheri, P.C.3
-
36
-
-
33947201809
-
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
-
10.1016/j.cell.2006.12.048, 2572726, 17382889
-
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128:1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
-
(2007)
Cell
, vol.128
, pp. 1231-1245
-
-
Kim, T.H.1
Abdullaev, Z.K.2
Smith, A.D.3
Ching, K.A.4
Loukinov, D.I.5
Green, R.D.6
Zhang, M.Q.7
Lobanenkov, V.V.8
Ren, B.9
-
37
-
-
33847200412
-
CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide.
-
10.1128/MCB.01993-06, 1820452, 17210645
-
Chernukhin I, Shamsuddin S, Kang SY, Bergström R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, Morrison I, Vigneron M, Wu SY, Chiang CM, Loukinov D, Lobanenkov V, Ohlsson R, Klenova E. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 2007, 27:1631-1648. 10.1128/MCB.01993-06, 1820452, 17210645.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 1631-1648
-
-
Chernukhin, I.1
Shamsuddin, S.2
Kang, S.Y.3
Bergström, R.4
Kwon, Y.W.5
Yu, W.6
Whitehead, J.7
Mukhopadhyay, R.8
Docquier, F.9
Farrar, D.10
Morrison, I.11
Vigneron, M.12
Wu, S.Y.13
Chiang, C.M.14
Loukinov, D.15
Lobanenkov, V.16
Ohlsson, R.17
Klenova, E.18
-
38
-
-
70849129503
-
A wave of nascent transcription on activated human genes.
-
10.1073/pnas.0902573106, 2761237, 19826084
-
Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, Kitakami J, Oshida N, Papantonis A, Izumi A, Kobayashi M, Meguro H, Kanki Y, Mimura I, Yamamoto K, Mataki C, Hamakubo T, Shirahige K, Aburatani H, Kimura H, Kodama T, Cook PR, Ihara S. A wave of nascent transcription on activated human genes. Proc Natl Acad Sci USA 2009, 106:18357-18361. 10.1073/pnas.0902573106, 2761237, 19826084.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 18357-18361
-
-
Wada, Y.1
Ohta, Y.2
Xu, M.3
Tsutsumi, S.4
Minami, T.5
Inoue, K.6
Komura, D.7
Kitakami, J.8
Oshida, N.9
Papantonis, A.10
Izumi, A.11
Kobayashi, M.12
Meguro, H.13
Kanki, Y.14
Mimura, I.15
Yamamoto, K.16
Mataki, C.17
Hamakubo, T.18
Shirahige, K.19
Aburatani, H.20
Kimura, H.21
Kodama, T.22
Cook, P.R.23
Ihara, S.24
more..
-
39
-
-
79551632681
-
Detection and removal of biases in the analysis of next-generation sequencing reads.
-
10.1371/journal.pone.0016685, 3031631, 21304912
-
Schwartz S, Oren R, Ast G. Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One 2011, 6:e16685. 10.1371/journal.pone.0016685, 3031631, 21304912.
-
(2011)
PLoS One
, vol.6
-
-
Schwartz, S.1
Oren, R.2
Ast, G.3
-
40
-
-
79959198166
-
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA.
-
10.1038/nature10006, 3117022, 21572438
-
Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, Glass CK, Rosenfeld MG, Fu XD. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 2011, 474:390-394. 10.1038/nature10006, 3117022, 21572438.
-
(2011)
Nature
, vol.474
, pp. 390-394
-
-
Wang, D.1
Garcia-Bassets, I.2
Benner, C.3
Li, W.4
Su, X.5
Zhou, Y.6
Qiu, J.7
Liu, W.8
Kaikkonen, M.U.9
Ohgi, K.A.10
Glass, C.K.11
Rosenfeld, M.G.12
Fu, X.D.13
-
41
-
-
79952261920
-
Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors.
-
Palmer AC, Egan JB, Shearwin KE. Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors. Transcr 2011, 2:9-14.
-
(2011)
Transcr
, vol.2
, pp. 9-14
-
-
Palmer, A.C.1
Egan, J.B.2
Shearwin, K.E.3
-
42
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers.
-
10.1371/journal.pbio.1000384, 2867938, 20485488
-
De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010, 8:e1000384. 10.1371/journal.pbio.1000384, 2867938, 20485488.
-
(2010)
PLoS Biol
, vol.8
-
-
De Santa, F.1
Barozzi, I.2
Mietton, F.3
Ghisletti, S.4
Polletti, S.5
Tusi, B.K.6
Muller, H.7
Ragoussis, J.8
Wei, C.L.9
Natoli, G.10
-
43
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers.
-
10.1038/nature09033, 3020079, 20393465
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010, 465:182-187. 10.1038/nature09033, 3020079, 20393465.
-
(2010)
Nature
, vol.465
, 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
Harmin, D.A.7
Laptewicz, M.8
Barbara-Haley, K.9
Kuersten, S.10
Markenscoff-Papadimitriou, E.11
Kuhl, D.12
Bito, H.13
Worley, P.F.14
Kreiman, G.15
Greenberg, M.E.16
-
44
-
-
84874116949
-
UCSC Table Browser.
-
UCSC Table Browser. , http://genome.ucsc.edu/cgi-bin/hgTables
-
-
-
-
45
-
-
84858072018
-
Human Epigenome Atlas.
-
Human Epigenome Atlas. , http://www.genboree.org/EdaccData/Release-3/
-
-
-
-
46
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS).
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
47
-
-
78049446282
-
Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.
-
10.1016/j.cmet.2010.09.012, 3026436, 21035756, NISC Comparative Sequencing Program
-
Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, , Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS. NISC Comparative Sequencing Program Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab 2010, 12:443-455. 10.1016/j.cmet.2010.09.012, 3026436, 21035756, NISC Comparative Sequencing Program.
-
(2010)
Cell Metab
, vol.12
, pp. 443-455
-
-
Stitzel, M.L.1
Sethupathy, P.2
Pearson, D.S.3
Chines, P.S.4
Song, L.5
Erdos, M.R.6
Welch, R.7
Parker, S.C.8
Boyle, A.P.9
Scott, L.J.10
Margulies, E.H.11
Boehnke, M.12
Furey, T.S.13
Crawford, G.E.14
Collins, F.S.15
-
48
-
-
84858080305
-
IMR90 CTCF ChIP-chip Data.
-
IMR90 CTCF ChIP-chip Data. , http://licr-renlab.ucsd.edu/download.html
-
-
-
|