-
1
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
[1] ENCODE, An integrated encyclopedia of DNA elements in the human genome. Nature 489 (2012), 57–74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
ENCODE1
-
2
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
[2] Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., et al. Integrative analysis of 111 reference human epigenomes. Nature 518 (2015), 317–330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
-
3
-
-
84946423189
-
-
Wiley Interdiscip Rev RNA
-
[3] Pek, J.W., Okamura, K., Regulatory RNAs Discovered in Unexpected Places, 6, 2015, Wiley Interdiscip Rev RNA, 671–686.
-
(2015)
Regulatory RNAs Discovered in Unexpected Places
, vol.6
, pp. 671-686
-
-
Pek, J.W.1
Okamura, K.2
-
4
-
-
80052815461
-
Noncoding RNAs and enhancers: complications of a long-distance relationship
-
[4] Orom, U.A., Shiekhattar, R., Noncoding RNAs and enhancers: complications of a long-distance relationship. Trends Genet. 27 (2011), 433–439.
-
(2011)
Trends Genet.
, vol.27
, pp. 433-439
-
-
Orom, U.A.1
Shiekhattar, R.2
-
5
-
-
84926205298
-
RNA-mediated epigenetic regulation of gene expression
-
[5] Holoch, D., Moazed, D., RNA-mediated epigenetic regulation of gene expression. Nat. Rev. Genet. 16 (2015), 71–84.
-
(2015)
Nat. Rev. Genet.
, vol.16
, pp. 71-84
-
-
Holoch, D.1
Moazed, D.2
-
6
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
[6] Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503 (2013), 290–294.
-
(2013)
Nature
, vol.503
, pp. 290-294
-
-
Jin, F.1
Li, Y.2
Dixon, J.R.3
Selvaraj, S.4
Ye, Z.5
Lee, A.Y.6
-
7
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
[7] Sanyal, A., Lajoie, B.R., Jain, G., Dekker, J., The long-range interaction landscape of gene promoters. Nature 489 (2012), 109–113.
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
-
8
-
-
0025101148
-
Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression
-
[8] Collis, P., Antoniou, M., Grosveld, F., Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression. EMBO J. 9 (1990), 233–240.
-
(1990)
EMBO J.
, vol.9
, pp. 233-240
-
-
Collis, P.1
Antoniou, M.2
Grosveld, F.3
-
9
-
-
0026482145
-
Transcription of the hypersensitive site HS2 enhancer in erythroid cells
-
[9] Tuan, D., Kong, S., Hu, K., Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc. Natl. Acad. Sci. U. S. A. 89 (1992), 11219–11223.
-
(1992)
Proc. Natl. Acad. Sci. U. S. A.
, vol.89
, pp. 11219-11223
-
-
Tuan, D.1
Kong, S.2
Hu, K.3
-
10
-
-
0030826364
-
Intergenic transcription and transinduction of the human beta-globin locus
-
[10] Ashe, H.L., Monks, J., Wijgerde, M., Fraser, P., Proudfoot, N.J., Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev. 11 (1997), 2494–2509.
-
(1997)
Genes Dev.
, vol.11
, pp. 2494-2509
-
-
Ashe, H.L.1
Monks, J.2
Wijgerde, M.3
Fraser, P.4
Proudfoot, N.J.5
-
11
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
[11] Kim, T.K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465 (2010), 182–187.
-
(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
-
12
-
-
84857111200
-
DNaseI sensitivity QTLs are a major determinant of human expression variation
-
[12] Degner, J.F., Pai, A.A., Pique-Regi, R., Veyrieras, J.B., Gaffney, D.J., Pickrell, J.K., et al. DNaseI sensitivity QTLs are a major determinant of human expression variation. Nature 482 (2012), 390–394.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
Pai, A.A.2
Pique-Regi, R.3
Veyrieras, J.B.4
Gaffney, D.J.5
Pickrell, J.K.6
-
13
-
-
84864073098
-
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection
-
[13] Shibata, Y., Sheffield, N.C., Fedrigo, O., Babbitt, C.C., Wortham, M., Tewari, A.K., et al. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet., 8, 2012, e1002789.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002789
-
-
Shibata, Y.1
Sheffield, N.C.2
Fedrigo, O.3
Babbitt, C.C.4
Wortham, M.5
Tewari, A.K.6
-
14
-
-
84922295278
-
Enhancer evolution across 20 mammalian species
-
[14] Villar, D., Berthelot, C., Aldridge, S., Rayner, T.F., Lukk, M., Pignatelli, M., et al. Enhancer evolution across 20 mammalian species. Cell 160 (2015), 554–566.
-
(2015)
Cell
, vol.160
, pp. 554-566
-
-
Villar, D.1
Berthelot, C.2
Aldridge, S.3
Rayner, T.F.4
Lukk, M.5
Pignatelli, M.6
-
15
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
[15] Wray, G.A., The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8 (2007), 206–216.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
16
-
-
84949091882
-
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo
-
[16] Maurano, M.T., Haugen, E., Sandstrom, R., Vierstra, J., Shafer, A., Kaul, R., et al. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nat. Genet. 47 (2015), 1393–1401.
-
(2015)
Nat. Genet.
, vol.47
, pp. 1393-1401
-
-
Maurano, M.T.1
Haugen, E.2
Sandstrom, R.3
Vierstra, J.4
Shafer, A.5
Kaul, R.6
-
17
-
-
84903640603
-
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution
-
[17] Arnold, C.D., Gerlach, D., Spies, D., Matts, J.A., Sytnikova, Y.A., Pagani, M., et al. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat. Genet. 46 (2014), 685–692.
-
(2014)
Nat. Genet.
, vol.46
, pp. 685-692
-
-
Arnold, C.D.1
Gerlach, D.2
Spies, D.3
Matts, J.A.4
Sytnikova, Y.A.5
Pagani, M.6
-
18
-
-
84879911829
-
The evolution of lineage-specific regulatory activities in the human embryonic limb
-
[18] Cotney, J., Leng, J., Yin, J., Reilly, S.K., DeMare, L.E., Emera, D., et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154 (2013), 185–196.
-
(2013)
Cell
, vol.154
, pp. 185-196
-
-
Cotney, J.1
Leng, J.2
Yin, J.3
Reilly, S.K.4
DeMare, L.E.5
Emera, D.6
-
19
-
-
46249134068
-
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
-
[19] Hare, E.E., Peterson, B.K., Iyer, V.N., Meier, R., Eisen, M.B., Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet., 4, 2008, e1000106.
-
(2008)
PLoS Genet.
, vol.4
, pp. e1000106
-
-
Hare, E.E.1
Peterson, B.K.2
Iyer, V.N.3
Meier, R.4
Eisen, M.B.5
-
20
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
[20] McLean, C.Y., Reno, P.L., Pollen, A.A., Bassan, A.I., Capellini, T.D., Guenther, C., et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471 (2011), 216–219.
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
Reno, P.L.2
Pollen, A.A.3
Bassan, A.I.4
Capellini, T.D.5
Guenther, C.6
-
21
-
-
79959825697
-
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA
-
[21] Frankel, N., Erezyilmaz, D.F., McGregor, A.P., Wang, S., Payre, F., Stern, D.L., Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474 (2011), 598–603.
-
(2011)
Nature
, vol.474
, pp. 598-603
-
-
Frankel, N.1
Erezyilmaz, D.F.2
McGregor, A.P.3
Wang, S.4
Payre, F.5
Stern, D.L.6
-
22
-
-
39749184167
-
The evolution of gene regulation underlies a morphological difference between two Drosophila sister species
-
[22] Jeong, S., Rebeiz, M., Andolfatto, P., Werner, T., True, J., Carroll, S.B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132 (2008), 783–793.
-
(2008)
Cell
, vol.132
, pp. 783-793
-
-
Jeong, S.1
Rebeiz, M.2
Andolfatto, P.3
Werner, T.4
True, J.5
Carroll, S.B.6
-
23
-
-
49549112519
-
The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila
-
[23] Williams, T.M., Selegue, J.E., Werner, T., Gompel, N., Kopp, A., Carroll, S.B., The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. Cell 134 (2008), 610–623.
-
(2008)
Cell
, vol.134
, pp. 610-623
-
-
Williams, T.M.1
Selegue, J.E.2
Werner, T.3
Gompel, N.4
Kopp, A.5
Carroll, S.B.6
-
24
-
-
84947717868
-
DNA-dependent formation of transcription factor pairs alters their binding specificity
-
[24] Jolma, A., Yin, Y., Nitta, K.R., Dave, K., Popov, A., Taipale, M., et al. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527 (2015), 384–388.
-
(2015)
Nature
, vol.527
, pp. 384-388
-
-
Jolma, A.1
Yin, Y.2
Nitta, K.R.3
Dave, K.4
Popov, A.5
Taipale, M.6
-
25
-
-
33745227338
-
Regulation of body pigmentation by the abdominal-B Hox protein and its gain and loss in Drosophila evolution
-
[25] Jeong, S., Rokas, A., Carroll, S.B., Regulation of body pigmentation by the abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell 125 (2006), 1387–1399.
-
(2006)
Cell
, vol.125
, pp. 1387-1399
-
-
Jeong, S.1
Rokas, A.2
Carroll, S.B.3
-
26
-
-
17644397256
-
Transcriptional enhancers: intelligent enhanceosomes or flexible billboards
-
[26] Arnosti, D.N., Kulkarni, M.M., Transcriptional enhancers: intelligent enhanceosomes or flexible billboards. J. Cell. Biochem. 94 (2005), 890–898.
-
(2005)
J. Cell. Biochem.
, vol.94
, pp. 890-898
-
-
Arnosti, D.N.1
Kulkarni, M.M.2
-
27
-
-
79551655285
-
Functional and mechanistic diversity of distal transcription enhancers
-
[27] Bulger, M., Groudine, M., Functional and mechanistic diversity of distal transcription enhancers. Cell 144 (2011), 327–339.
-
(2011)
Cell
, vol.144
, pp. 327-339
-
-
Bulger, M.1
Groudine, M.2
-
28
-
-
29444448047
-
On a chromosome far, far away: LCRs and gene expression
-
[28] Dean, A., On a chromosome far, far away: LCRs and gene expression. Trends Genet. 22 (2006), 38–45.
-
(2006)
Trends Genet.
, vol.22
, pp. 38-45
-
-
Dean, A.1
-
29
-
-
84943348625
-
Architectural proteins, transcription, and the three-dimensional organization of the genome
-
[29] Cubenas-Potts, C., Corces, V.G., Architectural proteins, transcription, and the three-dimensional organization of the genome. FEBS Lett. 589 (2015), 2923–2930.
-
(2015)
FEBS Lett.
, vol.589
, pp. 2923-2930
-
-
Cubenas-Potts, C.1
Corces, V.G.2
-
30
-
-
0022447855
-
Gene regulation by proteins acting nearby and at a distance
-
[30] Ptashne, M., Gene regulation by proteins acting nearby and at a distance. Nature 322 (1986), 697–701.
-
(1986)
Nature
, vol.322
, pp. 697-701
-
-
Ptashne, M.1
-
31
-
-
0032482923
-
Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA
-
[31] Kugel, J.F., Goodrich, J.A., Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA. Proc. Natl. Acad. Sci. U. S. A. 95 (1998), 9232–9237.
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 9232-9237
-
-
Kugel, J.F.1
Goodrich, J.A.2
-
32
-
-
0032540282
-
Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II
-
[32] Hoopes, B.C., LeBlanc, J.F., Hawley, D.K., Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II. J. Mol. Biol. 277 (1998), 1015–1031.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 1015-1031
-
-
Hoopes, B.C.1
LeBlanc, J.F.2
Hawley, D.K.3
-
33
-
-
84878860751
-
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
-
[33] Phillips-Cremins, J.E., Sauria, M.E., Sanyal, A., Gerasimova, T.I., Lajoie, B.R., Bell, J.S., et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153 (2013), 1281–1295.
-
(2013)
Cell
, vol.153
, pp. 1281-1295
-
-
Phillips-Cremins, J.E.1
Sauria, M.E.2
Sanyal, A.3
Gerasimova, T.I.4
Lajoie, B.R.5
Bell, J.S.6
-
34
-
-
77649261872
-
Cell type specificity of chromatin organization mediated by CTCF and cohesin
-
[34] Hou, C., Dale, R., Dean, A., Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 3651–3656.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 3651-3656
-
-
Hou, C.1
Dale, R.2
Dean, A.3
-
35
-
-
84872605250
-
The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation
-
[35] Lin, C., Garruss, A.S., Luo, Z., Guo, F., Shilatifard, A., The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell 152 (2013), 144–156.
-
(2013)
Cell
, vol.152
, pp. 144-156
-
-
Lin, C.1
Garruss, A.S.2
Luo, Z.3
Guo, F.4
Shilatifard, A.5
-
36
-
-
77957139539
-
Mediator and cohesin connect gene expression and chromatin architecture
-
[36] Kagey, M.H., Newman, J.J., Bilodeau, S., Zhan, Y., Orlando, D.A., van Berkum, N.L., et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467 (2010), 430–435.
-
(2010)
Nature
, vol.467
, pp. 430-435
-
-
Kagey, M.H.1
Newman, J.J.2
Bilodeau, S.3
Zhan, Y.4
Orlando, D.A.5
van Berkum, N.L.6
-
37
-
-
84871688165
-
Characterization of enhancer function from genome-wide analyses
-
[37] Maston, G.A., Landt, S.G., Snyder, M., Green, M.R., Characterization of enhancer function from genome-wide analyses. Annu. Rev. Genomics Hum. Genet. 13 (2012), 29–57.
-
(2012)
Annu. Rev. Genomics Hum. Genet.
, vol.13
, pp. 29-57
-
-
Maston, G.A.1
Landt, S.G.2
Snyder, M.3
Green, M.R.4
-
38
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
[38] Creyghton, M.P., Cheng, A.W., Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U. S. A. 107 (2010), 21931–21936.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, 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
-
39
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
[39] Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S.A., Flynn, R.A., Wysocka, J., A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470 (2011), 279–283.
-
(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
-
40
-
-
84870490787
-
Enhancer-associated H3K4 monomethylation by trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4
-
[40] Herz, H.M., Mohan, M., Garruss, A.S., Liang, K., Takahashi, Y.H., Mickey, K., et al. Enhancer-associated H3K4 monomethylation by trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev. 26 (2012), 2604–2620.
-
(2012)
Genes Dev.
, vol.26
, pp. 2604-2620
-
-
Herz, H.M.1
Mohan, M.2
Garruss, A.S.3
Liang, K.4
Takahashi, Y.H.5
Mickey, K.6
-
41
-
-
80051564877
-
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
-
[41] Zentner, G.E., Tesar, P.J., Scacheri, P.C., Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 21 (2011), 1273–1283.
-
(2011)
Genome Res.
, vol.21
, pp. 1273-1283
-
-
Zentner, G.E.1
Tesar, P.J.2
Scacheri, P.C.3
-
42
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
[42] Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39 (2007), 311–318.
-
(2007)
Nat. Genet.
, vol.39
, 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
-
43
-
-
84892366110
-
Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity
-
[43] Ferrari, K.J., Scelfo, A., Jammula, S., Cuomo, A., Barozzi, I., Stutzer, A., et al. Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Mol. Cell 53 (2014), 49–62.
-
(2014)
Mol. Cell
, vol.53
, pp. 49-62
-
-
Ferrari, K.J.1
Scelfo, A.2
Jammula, S.3
Cuomo, A.4
Barozzi, I.5
Stutzer, A.6
-
44
-
-
84888790012
-
Enhancer transcribed RNAs arise from hypomethylated, tet-occupied genomic regions
-
[44] Pulakanti, K., Pinello, L., Stelloh, C., Blinka, S., Allred, J., Milanovich, S., et al. Enhancer transcribed RNAs arise from hypomethylated, tet-occupied genomic regions. Epigenetics 8 (2013), 1303–1320.
-
(2013)
Epigenetics
, vol.8
, pp. 1303-1320
-
-
Pulakanti, K.1
Pinello, L.2
Stelloh, C.3
Blinka, S.4
Allred, J.5
Milanovich, S.6
-
45
-
-
79959209733
-
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
-
[45] Stroud, H., Feng, S., Morey Kinney, S., Pradhan, S., Jacobsen, S.E., 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol., 12, 2011, R54.
-
(2011)
Genome Biol.
, vol.12
, pp. R54
-
-
Stroud, H.1
Feng, S.2
Morey Kinney, S.3
Pradhan, S.4
Jacobsen, S.E.5
-
46
-
-
84895887720
-
Enhancer biology and enhanceropathies
-
[46] Smith, E., Shilatifard, A., Enhancer biology and enhanceropathies. Nat. Struct. Mol. Biol. 21 (2014), 210–219.
-
(2014)
Nat. Struct. Mol. Biol.
, vol.21
, pp. 210-219
-
-
Smith, E.1
Shilatifard, A.2
-
47
-
-
84878260646
-
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription
-
[47] Pastor, W.A., Aravind, L., Rao, A., TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14 (2013), 341–356.
-
(2013)
Nat. Rev. Mol. Cell Biol.
, vol.14
, pp. 341-356
-
-
Pastor, W.A.1
Aravind, L.2
Rao, A.3
-
48
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
[48] Stadler, M.B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Scholer, A., et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480 (2011), 490–495.
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
Murr, R.2
Burger, L.3
Ivanek, R.4
Lienert, F.5
Scholer, A.6
-
49
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
[49] Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., et al. The accessible chromatin landscape of the human genome. Nature 489 (2012), 75–82.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
-
50
-
-
84874624739
-
Dynamic DNA methylation across diverse human cell lines and tissues
-
[50] Varley, K.E., Gertz, J., Bowling, K.M., Parker, S.L., Reddy, T.E., Pauli-Behn, F., et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 23 (2013), 555–567.
-
(2013)
Genome Res.
, vol.23
, pp. 555-567
-
-
Varley, K.E.1
Gertz, J.2
Bowling, K.M.3
Parker, S.L.4
Reddy, T.E.5
Pauli-Behn, F.6
-
51
-
-
84947766170
-
Transcription factor trapping by RNA in gene regulatory elements
-
[51] Sigova, A.A., Abraham, B.J., Ji, X., Molinie, B., Hannett, N.M., Guo, Y.E., et al. Transcription factor trapping by RNA in gene regulatory elements. Science 350 (2015), 978–981.
-
(2015)
Science
, vol.350
, pp. 978-981
-
-
Sigova, A.A.1
Abraham, B.J.2
Ji, X.3
Molinie, B.4
Hannett, N.M.5
Guo, Y.E.6
-
52
-
-
33746472891
-
RNA interference machinery influences the nuclear organization of a chromatin insulator
-
[52] Lei, E.P., Corces, V.G., RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat. Genet. 38 (2006), 936–941.
-
(2006)
Nat. Genet.
, vol.38
, pp. 936-941
-
-
Lei, E.P.1
Corces, V.G.2
-
53
-
-
78349252731
-
Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
-
[53] Yao, H., Brick, K., Evrard, Y., Xiao, T., Camerini-Otero, R.D., Felsenfeld, G., Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev. 24 (2010), 2543–2555.
-
(2010)
Genes Dev.
, vol.24
, pp. 2543-2555
-
-
Yao, H.1
Brick, K.2
Evrard, Y.3
Xiao, T.4
Camerini-Otero, R.D.5
Felsenfeld, G.6
-
54
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
[54] Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A.Y., et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498 (2013), 516–520.
-
(2013)
Nature
, vol.498
, pp. 516-520
-
-
Li, W.1
Notani, D.2
Ma, Q.3
Tanasa, B.4
Nunez, E.5
Chen, A.Y.6
-
55
-
-
84873456575
-
eRNAs are required for p53-dependent enhancer activity and gene transcription
-
[55] Melo, C.A., Drost, J., Wijchers, P.J., van de Werken, H., de Wit, E., Oude Vrielink, J.A., et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49 (2013), 524–535.
-
(2013)
Mol. Cell
, vol.49
, pp. 524-535
-
-
Melo, C.A.1
Drost, J.2
Wijchers, P.J.3
van de Werken, H.4
de Wit, E.5
Oude Vrielink, J.A.6
-
56
-
-
84881171344
-
Enhancer transcripts mark active estrogen receptor binding sites
-
[56] Hah, N., Murakami, S., Nagari, A., Danko, C.G., Kraus, W.L., Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 23 (2013), 1210–1223.
-
(2013)
Genome Res.
, vol.23
, pp. 1210-1223
-
-
Hah, N.1
Murakami, S.2
Nagari, A.3
Danko, C.G.4
Kraus, W.L.5
-
57
-
-
84881526410
-
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
-
[57] Kaikkonen, M.U., Spann, N.J., Heinz, S., Romanoski, C.E., Allison, K.A., Stender, J.D., et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51 (2013), 310–325.
-
(2013)
Mol. Cell
, vol.51
, pp. 310-325
-
-
Kaikkonen, M.U.1
Spann, N.J.2
Heinz, S.3
Romanoski, C.E.4
Allison, K.A.5
Stender, J.D.6
-
58
-
-
84956624079
-
Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites
-
[58] Savic, D., Roberts, B.S., Carleton, J.B., Partridge, E.C., White, M.A., Cohen, B.A., et al. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites. Genome Res. 25 (2015), 1791–1800.
-
(2015)
Genome Res.
, vol.25
, pp. 1791-1800
-
-
Savic, D.1
Roberts, B.S.2
Carleton, J.B.3
Partridge, E.C.4
White, M.A.5
Cohen, B.A.6
-
59
-
-
84962129303
-
Unlinking an lncRNA from its associated cis element
-
[59] Paralkar, V.R., Taborda, C.C., Huang, P., Yao, Y., Kossenkov, A.V., Prasad, R., et al. Unlinking an lncRNA from its associated cis element. Mol. Cell 62 (2016), 104–110.
-
(2016)
Mol. Cell
, vol.62
, pp. 104-110
-
-
Paralkar, V.R.1
Taborda, C.C.2
Huang, P.3
Yao, Y.4
Kossenkov, A.V.5
Prasad, R.6
-
60
-
-
84860381688
-
Higher-order chromatin structure: bridging physics and biology
-
[60] Fudenberg, G., Mirny, L.A., Higher-order chromatin structure: bridging physics and biology. Curr. Opin. Genet. Dev. 22 (2012), 115–124.
-
(2012)
Curr. Opin. Genet. Dev.
, vol.22
, pp. 115-124
-
-
Fudenberg, G.1
Mirny, L.A.2
-
61
-
-
79952807125
-
Chromatin folding–from biology to polymer models and back
-
[61] Tark-Dame, M., van Driel, R., Heermann, D.W., Chromatin folding–from biology to polymer models and back. J. Cell Sci. 124 (2011), 839–845.
-
(2011)
J. Cell Sci.
, vol.124
, pp. 839-845
-
-
Tark-Dame, M.1
van Driel, R.2
Heermann, D.W.3
-
62
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
[62] Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485 (2012), 376–380.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
-
63
-
-
84869003748
-
Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains
-
[63] Hou, C., Li, L., Qin, Z.S., Corces, V.G., Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol. Cell 48 (2012), 471–484.
-
(2012)
Mol. Cell
, vol.48
, pp. 471-484
-
-
Hou, C.1
Li, L.2
Qin, Z.S.3
Corces, V.G.4
-
64
-
-
84928206081
-
Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing
-
[64] Li, L., Lyu, X., Hou, C., Takenaka, N., Nguyen, H.Q., Ong, C.T., et al. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol. Cell 58 (2015), 216–231.
-
(2015)
Mol. Cell
, vol.58
, pp. 216-231
-
-
Li, L.1
Lyu, X.2
Hou, C.3
Takenaka, N.4
Nguyen, H.Q.5
Ong, C.T.6
-
65
-
-
84878188440
-
Chromatin insulators: linking genome organization to cellular function
-
[65] Phillips-Cremins, J.E., Corces, V.G., Chromatin insulators: linking genome organization to cellular function. Mol. Cell 50 (2013), 461–474.
-
(2013)
Mol. Cell
, vol.50
, pp. 461-474
-
-
Phillips-Cremins, J.E.1
Corces, V.G.2
-
66
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
[66] Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148 (2012), 458–472.
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
Yaffe, E.2
Kenigsberg, E.3
Bantignies, F.4
Leblanc, B.5
Hoichman, M.6
-
67
-
-
85006305723
-
Insulator function and topological domain border strength scale with architectural protein occupancy
-
[67] Van Bortle, K., Nichols, M.H., Li, L., Ong, C.T., Takenaka, N., Qin, Z.S., et al. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol., 15, 2014, R82.
-
(2014)
Genome Biol.
, vol.15
, pp. R82
-
-
Van Bortle, K.1
Nichols, M.H.2
Li, L.3
Ong, C.T.4
Takenaka, N.5
Qin, Z.S.6
-
68
-
-
84890566970
-
Cohesin-mediated interactions organize chromosomal domain architecture
-
[68] Sofueva, S., Yaffe, E., Chan, W.C., Georgopoulou, D., Vietri Rudan, M., Mira-Bontenbal, H., et al. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J. 32 (2013), 3119–3129.
-
(2013)
EMBO J.
, vol.32
, pp. 3119-3129
-
-
Sofueva, S.1
Yaffe, E.2
Chan, W.C.3
Georgopoulou, D.4
Vietri Rudan, M.5
Mira-Bontenbal, H.6
-
69
-
-
84930091577
-
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions
-
[69] Lupianez, D.G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161 (2015), 1012–1025.
-
(2015)
Cell
, vol.161
, pp. 1012-1025
-
-
Lupianez, D.G.1
Kraft, K.2
Heinrich, V.3
Krawitz, P.4
Brancati, F.5
Klopocki, E.6
-
70
-
-
84959206565
-
The 3D folding of metazoan genomes correlates with the association of similar repetitive elements
-
[70] Cournac, A., Koszul, R., Mozziconacci, J., The 3D folding of metazoan genomes correlates with the association of similar repetitive elements. Nucleic Acids Res. 44 (2016), 245–255.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. 245-255
-
-
Cournac, A.1
Koszul, R.2
Mozziconacci, J.3
-
71
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
[71] Nora, E.P., Lajoie, B.R., Schulz, E.G., Giorgetti, L., Okamoto, I., Servant, N., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485 (2012), 381–385.
-
(2012)
Nature
, vol.485
, pp. 381-385
-
-
Nora, E.P.1
Lajoie, B.R.2
Schulz, E.G.3
Giorgetti, L.4
Okamoto, I.5
Servant, N.6
-
72
-
-
84918510740
-
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
-
[72] Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R.S., Paquette, D., et al. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev. 28 (2014), 2778–2791.
-
(2014)
Genes Dev.
, vol.28
, pp. 2778-2791
-
-
Williamson, I.1
Berlivet, S.2
Eskeland, R.3
Boyle, S.4
Illingworth, R.S.5
Paquette, D.6
-
73
-
-
84927711843
-
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
-
[73] Ing-Simmons, E., Seitan, V.C., Faure, A.J., Flicek, P., Carroll, T., Dekker, J., et al. Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Res. 25 (2015), 504–513.
-
(2015)
Genome Res.
, vol.25
, pp. 504-513
-
-
Ing-Simmons, E.1
Seitan, V.C.2
Faure, A.J.3
Flicek, P.4
Carroll, T.5
Dekker, J.6
-
74
-
-
84890504911
-
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
-
[74] Seitan, V.C., Faure, A.J., Zhan, Y., McCord, R.P., Lajoie, B.R., Ing-Simmons, E., et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res. 23 (2013), 2066–2077.
-
(2013)
Genome Res.
, vol.23
, pp. 2066-2077
-
-
Seitan, V.C.1
Faure, A.J.2
Zhan, Y.3
McCord, R.P.4
Lajoie, B.R.5
Ing-Simmons, E.6
-
75
-
-
84892934183
-
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
-
[75] Zuin, J., Dixon, J.R., van der Reijden, M.I., Ye, Z., Kolovos, P., Brouwer, R.W., et al. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 996–1001.
-
(2014)
Proc. Natl. Acad. Sci. U. S. A.
, vol.111
, pp. 996-1001
-
-
Zuin, J.1
Dixon, J.R.2
van der Reijden, M.I.3
Ye, Z.4
Kolovos, P.5
Brouwer, R.W.6
-
76
-
-
0037023361
-
Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development
-
[76] Kosak, S.T., Skok, J.A., Medina, K.L., Riblet, R., Le Beau, M.M., Fisher, A.G., et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296 (2002), 158–162.
-
(2002)
Science
, vol.296
, pp. 158-162
-
-
Kosak, S.T.1
Skok, J.A.2
Medina, K.L.3
Riblet, R.4
Le Beau, M.M.5
Fisher, A.G.6
-
77
-
-
2442695407
-
Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription
-
[77] Chambeyron, S., Bickmore, W.A., Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18 (2004), 1119–1130.
-
(2004)
Genes Dev.
, vol.18
, pp. 1119-1130
-
-
Chambeyron, S.1
Bickmore, W.A.2
-
78
-
-
0034065032
-
Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei
-
[78] Volpi, E.V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J. Cell Sci. 113:Pt. (9) (2000), 1565–1576.
-
(2000)
J. Cell Sci.
, vol.113
, pp. 1565-1576
-
-
Volpi, E.V.1
Chevret, E.2
Jones, T.3
Vatcheva, R.4
Williamson, J.5
Beck, S.6
-
79
-
-
79956304003
-
Relocalizing genetic loci into specific subnuclear neighborhoods
-
[79] Lee, H.Y., Johnson, K.D., Boyer, M.E., Bresnick, E.H., Relocalizing genetic loci into specific subnuclear neighborhoods. J. Biol. Chem. 286 (2011), 18834–18844.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 18834-18844
-
-
Lee, H.Y.1
Johnson, K.D.2
Boyer, M.E.3
Bresnick, E.H.4
-
80
-
-
73349090560
-
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
-
[80] Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N.F., Horton, A., Andrews, S., et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42 (2010), 53–61.
-
(2010)
Nat. Genet.
, vol.42
, pp. 53-61
-
-
Schoenfelder, S.1
Sexton, T.2
Chakalova, L.3
Cope, N.F.4
Horton, A.5
Andrews, S.6
-
81
-
-
84886777912
-
Chromosomal contact permits transcription between coregulated genes
-
[81] Fanucchi, S., Shibayama, Y., Burd, S., Weinberg, M.S., Mhlanga, M.M., Chromosomal contact permits transcription between coregulated genes. Cell 155 (2013), 606–620.
-
(2013)
Cell
, vol.155
, pp. 606-620
-
-
Fanucchi, S.1
Shibayama, Y.2
Burd, S.3
Weinberg, M.S.4
Mhlanga, M.M.5
-
82
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
[82] 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 507 (2014), 455–461.
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
-
83
-
-
84862908850
-
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
-
[83] Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148 (2012), 84–98.
-
(2012)
Cell
, vol.148
, pp. 84-98
-
-
Li, G.1
Ruan, X.2
Auerbach, R.K.3
Sandhu, K.S.4
Zheng, M.5
Wang, P.6
-
84
-
-
84861167698
-
Developmental regulation of chromatin conformation by Hox proteins in Drosophila
-
[84] Agelopoulos, M., McKay, D.J., Mann, R.S., Developmental regulation of chromatin conformation by Hox proteins in Drosophila. Cell Rep. 1 (2012), 350–359.
-
(2012)
Cell Rep.
, vol.1
, pp. 350-359
-
-
Agelopoulos, M.1
McKay, D.J.2
Mann, R.S.3
-
85
-
-
84878754528
-
A switch between topological domains underlies HoxD genes collinearity in mouse limbs
-
[85] Andrey, G., Montavon, T., Mascrez, B., Gonzalez, F., Noordermeer, D., Leleu, M., et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science, 340, 2013, 1234167.
-
(2013)
Science
, vol.340
, pp. 1234167
-
-
Andrey, G.1
Montavon, T.2
Mascrez, B.3
Gonzalez, F.4
Noordermeer, D.5
Leleu, M.6
-
86
-
-
84927641804
-
In search of the determinants of enhancer-promoter interaction specificity
-
[86] van Arensbergen, J., van Steensel, B., Bussemaker, H.J., In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol. 24 (2014), 695–702.
-
(2014)
Trends Cell Biol.
, vol.24
, pp. 695-702
-
-
van Arensbergen, J.1
van Steensel, B.2
Bussemaker, H.J.3
-
87
-
-
0035477093
-
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
-
[87] Butler, J.E., Kadonaga, J.T., Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15 (2001), 2515–2519.
-
(2001)
Genes Dev.
, vol.15
, pp. 2515-2519
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
88
-
-
54349103510
-
Caudal, a key developmental regulator, is a DPE-specific transcriptional factor
-
[88] Juven-Gershon, T., Hsu, J.Y., Kadonaga, J.T., Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev. 22 (2008), 2823–2830.
-
(2008)
Genes Dev.
, vol.22
, pp. 2823-2830
-
-
Juven-Gershon, T.1
Hsu, J.Y.2
Kadonaga, J.T.3
-
89
-
-
0032519586
-
Different core promoters possess distinct regulatory activities in the Drosophila embryo
-
[89] Ohtsuki, S., Levine, M., Cai, H.N., Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev. 12 (1998), 547–556.
-
(1998)
Genes Dev.
, vol.12
, pp. 547-556
-
-
Ohtsuki, S.1
Levine, M.2
Cai, H.N.3
-
90
-
-
38849173062
-
A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila embryo
-
[90] Akbari, O.S., Bae, E., Johnsen, H., Villaluz, A., Wong, D., Drewell, R.A., A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila embryo. Development 135 (2008), 123–131.
-
(2008)
Development
, vol.135
, pp. 123-131
-
-
Akbari, O.S.1
Bae, E.2
Johnsen, H.3
Villaluz, A.4
Wong, D.5
Drewell, R.A.6
-
91
-
-
70350023629
-
Enhancer-promoter communication at the Drosophila engrailed locus
-
[91] Kwon, D., Mucci, D., Langlais, K.K., Americo, J.L., DeVido, S.K., Cheng, Y., et al. Enhancer-promoter communication at the Drosophila engrailed locus. Development 136 (2009), 3067–3075.
-
(2009)
Development
, vol.136
, pp. 3067-3075
-
-
Kwon, D.1
Mucci, D.2
Langlais, K.K.3
Americo, J.L.4
DeVido, S.K.5
Cheng, Y.6
-
92
-
-
77956495708
-
Transcriptional enhancers in animal development and evolution
-
[92] Levine, M., Transcriptional enhancers in animal development and evolution. Curr. Biol. 20 (2010), R754–63.
-
(2010)
Curr. Biol.
, vol.20
, pp. R754-63
-
-
Levine, M.1
-
93
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
[93] Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459 (2009), 108–112.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
Harp, L.F.6
-
94
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
[94] Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., et al. The accessible chromatin landscape of the human genome. Nature 489 (2012), 75–82.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
-
95
-
-
84894589713
-
Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation
-
[95] Kieffer-Kwon, K.R., Tang, Z., Mathe, E., Qian, J., Sung, M.H., Li, G., et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155 (2013), 1507–1520.
-
(2013)
Cell
, vol.155
, pp. 1507-1520
-
-
Kieffer-Kwon, K.R.1
Tang, Z.2
Mathe, E.3
Qian, J.4
Sung, M.H.5
Li, G.6
-
96
-
-
66049117813
-
Naive and primed pluripotent states
-
[96] Nichols, J., Smith, A., Naive and primed pluripotent states. Cell Stem Cell 4 (2009), 487–492.
-
(2009)
Cell Stem Cell
, vol.4
, pp. 487-492
-
-
Nichols, J.1
Smith, A.2
-
97
-
-
34447528757
-
New cell lines from mouse epiblast share defining features with human embryonic stem cells
-
[97] Tesar, P.J., Chenoweth, J.G., Brook, F.A., Davies, T.J., Evans, E.P., Mack, D.L., et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 448 (2007), 196–199.
-
(2007)
Nature
, vol.448
, pp. 196-199
-
-
Tesar, P.J.1
Chenoweth, J.G.2
Brook, F.A.3
Davies, T.J.4
Evans, E.P.5
Mack, D.L.6
-
98
-
-
27644483064
-
Regulatory networks in embryo-derived pluripotent stem cells
-
[98] Boiani, M., Scholer, H.R., Regulatory networks in embryo-derived pluripotent stem cells. Nat. Rev. Mol. Cell Biol. 6 (2005), 872–884.
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.6
, pp. 872-884
-
-
Boiani, M.1
Scholer, H.R.2
-
99
-
-
84902177755
-
Lost in transition: dynamic enhancer organization across naive and primed stem cell states
-
[99] Van Bortle, K., Corces, V.G., Lost in transition: dynamic enhancer organization across naive and primed stem cell states. Cell Stem Cell 14 (2014), 693–694.
-
(2014)
Cell Stem Cell
, vol.14
, pp. 693-694
-
-
Van Bortle, K.1
Corces, V.G.2
-
100
-
-
84902160341
-
Epigenomic comparison reveals activation of seed enhancers during transition from naive to primed pluripotency
-
[100] Factor, D.C., Corradin, O., Zentner, G.E., Saiakhova, A., Song, L., Chenoweth, J.G., et al. Epigenomic comparison reveals activation of seed enhancers during transition from naive to primed pluripotency. Cell Stem Cell 14 (2014), 854–863.
-
(2014)
Cell Stem Cell
, vol.14
, pp. 854-863
-
-
Factor, D.C.1
Corradin, O.2
Zentner, G.E.3
Saiakhova, A.4
Song, L.5
Chenoweth, J.G.6
-
101
-
-
84902184462
-
Reorganization of enhancer patterns in transition from naive to primed pluripotency
-
[101] Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., et al. Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell 14 (2014), 838–853.
-
(2014)
Cell Stem Cell
, vol.14
, pp. 838-853
-
-
Buecker, C.1
Srinivasan, R.2
Wu, Z.3
Calo, E.4
Acampora, D.5
Faial, T.6
-
102
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
[102] Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462 (2009), 315–322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
-
103
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
[103] Ziller, M.J., Gu, H., Muller, F., Donaghey, J., Tsai, L.T., Kohlbacher, O., et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500 (2013), 477–481.
-
(2013)
Nature
, vol.500
, pp. 477-481
-
-
Ziller, M.J.1
Gu, H.2
Muller, F.3
Donaghey, J.4
Tsai, L.T.5
Kohlbacher, O.6
-
104
-
-
84885021247
-
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
-
[104] Hon, G.C., Rajagopal, N., Shen, Y., McCleary, D.F., Yue, F., Dang, M.D., et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45 (2013), 1198–1206.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1198-1206
-
-
Hon, G.C.1
Rajagopal, N.2
Shen, Y.3
McCleary, D.F.4
Yue, F.5
Dang, M.D.6
-
105
-
-
84856962477
-
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation
-
[105] Whyte, W.A., Bilodeau, S., Orlando, D.A., Hoke, H.A., Frampton, G.M., Foster, C.T., et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482 (2012), 221–225.
-
(2012)
Nature
, vol.482
, pp. 221-225
-
-
Whyte, W.A.1
Bilodeau, S.2
Orlando, D.A.3
Hoke, H.A.4
Frampton, G.M.5
Foster, C.T.6
-
106
-
-
84894598129
-
Rapid and pervasive changes in genome-wide enhancer usage during mammalian development
-
[106] Nord, A.S., Blow, M.J., Attanasio, C., Akiyama, J.A., Holt, A., Hosseini, R., et al. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155 (2013), 1521–1531.
-
(2013)
Cell
, vol.155
, pp. 1521-1531
-
-
Nord, A.S.1
Blow, M.J.2
Attanasio, C.3
Akiyama, J.A.4
Holt, A.5
Hosseini, R.6
-
107
-
-
78650141540
-
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
-
[107] Domazet-Loso, T., Tautz, D., A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468 (2010), 815–818.
-
(2010)
Nature
, vol.468
, pp. 815-818
-
-
Domazet-Loso, T.1
Tautz, D.2
-
108
-
-
78650120369
-
Gene expression divergence recapitulates the developmental hourglass model
-
[108] Kalinka, A.T., Varga, K.M., Gerrard, D.T., Preibisch, S., Corcoran, D.L., Jarrells, J., et al. Gene expression divergence recapitulates the developmental hourglass model. Nature 468 (2010), 811–814.
-
(2010)
Nature
, vol.468
, pp. 811-814
-
-
Kalinka, A.T.1
Varga, K.M.2
Gerrard, D.T.3
Preibisch, S.4
Corcoran, D.L.5
Jarrells, J.6
-
109
-
-
84882766972
-
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
-
[109] Stergachis, A.B., Neph, S., Reynolds, A., Humbert, R., Miller, B., Paige, S.L., et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 154 (2013), 888–903.
-
(2013)
Cell
, vol.154
, pp. 888-903
-
-
Stergachis, A.B.1
Neph, S.2
Reynolds, A.3
Humbert, R.4
Miller, B.5
Paige, S.L.6
-
110
-
-
84923786414
-
The selection and function of cell type-specific enhancers
-
[110] Heinz, S., Romanoski, C.E., Benner, C., Glass, C.K., The selection and function of cell type-specific enhancers. Nat. Rev. Mol. Cell Biol. 16 (2015), 144–154.
-
(2015)
Nat. Rev. Mol. Cell Biol.
, vol.16
, pp. 144-154
-
-
Heinz, S.1
Romanoski, C.E.2
Benner, C.3
Glass, C.K.4
-
111
-
-
68549136904
-
Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm
-
[111] Zaret, K.S., Watts, J., Xu, J., Wandzioch, E., Smale, S.T., Sekiya, T., Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spring Harb. Symp. Quant. Biol. 73 (2008), 119–126.
-
(2008)
Cold Spring Harb. Symp. Quant. Biol.
, vol.73
, pp. 119-126
-
-
Zaret, K.S.1
Watts, J.2
Xu, J.3
Wandzioch, E.4
Smale, S.T.5
Sekiya, T.6
-
112
-
-
84867740805
-
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
-
[112] Gautier, E.L., Shay, T., Miller, J., Greter, M., Jakubzick, C., Ivanov, S., et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat. Immunol. 13 (2012), 1118–1128.
-
(2012)
Nat. Immunol.
, vol.13
, pp. 1118-1128
-
-
Gautier, E.L.1
Shay, T.2
Miller, J.3
Greter, M.4
Jakubzick, C.5
Ivanov, S.6
-
113
-
-
84900413094
-
Tissue-specific signals control reversible program of localization and functional polarization of macrophages
-
[113] Okabe, Y., Medzhitov, R., Tissue-specific signals control reversible program of localization and functional polarization of macrophages. Cell 157 (2014), 832–844.
-
(2014)
Cell
, vol.157
, pp. 832-844
-
-
Okabe, Y.1
Medzhitov, R.2
-
114
-
-
84920724792
-
Environment drives selection and function of enhancers controlling tissue-specific macrophage identities
-
[114] Gosselin, D., Link, V.M., Romanoski, C.E., Fonseca, G.J., Eichenfield, D.Z., Spann, N.J., et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159 (2014), 1327–1340.
-
(2014)
Cell
, vol.159
, pp. 1327-1340
-
-
Gosselin, D.1
Link, V.M.2
Romanoski, C.E.3
Fonseca, G.J.4
Eichenfield, D.Z.5
Spann, N.J.6
-
115
-
-
84855720966
-
Transcriptional enhancers in development and disease
-
[115] Sakabe, N.J., Savic, D., Nobrega, M.A., Transcriptional enhancers in development and disease. Genome Biol., 13, 2012, 238.
-
(2012)
Genome Biol.
, vol.13
, pp. 238
-
-
Sakabe, N.J.1
Savic, D.2
Nobrega, M.A.3
-
116
-
-
84928017429
-
Enhancer variants: evaluating functions in common disease
-
[116] Corradin, O., Scacheri, P.C., Enhancer variants: evaluating functions in common disease. Genome Med., 6, 2014, 85.
-
(2014)
Genome Med.
, vol.6
, pp. 85
-
-
Corradin, O.1
Scacheri, P.C.2
-
117
-
-
84954240290
-
Decoding the non-coding genome: elucidating genetic risk outside the coding genome
-
[117] Barr, C.L., Misener, V.L., Decoding the non-coding genome: elucidating genetic risk outside the coding genome. Genes Brain Behav. 15 (2016), 187–204.
-
(2016)
Genes Brain Behav.
, vol.15
, pp. 187-204
-
-
Barr, C.L.1
Misener, V.L.2
-
118
-
-
70249088327
-
Genomic views of distant-acting enhancers
-
[118] Visel, A., Rubin, E.M., Pennacchio, L.A., Genomic views of distant-acting enhancers. Nature 461 (2009), 199–205.
-
(2009)
Nature
, vol.461
, pp. 199-205
-
-
Visel, A.1
Rubin, E.M.2
Pennacchio, L.A.3
-
119
-
-
84890231680
-
Beyond GWASs illuminating the dark road from association to function
-
[119] Edwards, S.L., Beesley, J., French, J.D., Dunning, A.M., Beyond GWASs illuminating the dark road from association to function. Am. J. Hum. Genet. 93 (2013), 779–797.
-
(2013)
Am. J. Hum. Genet.
, vol.93
, pp. 779-797
-
-
Edwards, S.L.1
Beesley, J.2
French, J.D.3
Dunning, A.M.4
-
120
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
[120] Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., et al. A map of human genome variation from population-scale sequencing. Nature 467 (2010), 1061–1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
Abecasis, G.R.1
Altshuler, D.2
Auton, A.3
Brooks, L.D.4
Durbin, R.M.5
Gibbs, R.A.6
-
121
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
[121] Maurano, M.T., Humbert, R., Rynes, E., Thurman, R.E., Haugen, E., Wang, H., et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337 (2012), 1190–1195.
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
Humbert, R.2
Rynes, E.3
Thurman, R.E.4
Haugen, E.5
Wang, H.6
-
122
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
[122] Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473 (2011), 43–49.
-
(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
-
123
-
-
84873086126
-
Chromatin marks identify critical cell types for fine mapping complex trait variants
-
[123] Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B.E., Liu, X.S., et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. 45 (2013), 124–130.
-
(2013)
Nat. Genet.
, vol.45
, pp. 124-130
-
-
Trynka, G.1
Sandor, C.2
Han, B.3
Xu, H.4
Stranger, B.E.5
Liu, X.S.6
-
124
-
-
84922273141
-
Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
-
[124] Gusev, A., Lee, S.H., Trynka, G., Finucane, H., Vilhjalmsson, B.J., Xu, H., et al. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am. J. Hum. Genet. 95 (2014), 535–552.
-
(2014)
Am. J. Hum. Genet.
, vol.95
, pp. 535-552
-
-
Gusev, A.1
Lee, S.H.2
Trynka, G.3
Finucane, H.4
Vilhjalmsson, B.J.5
Xu, H.6
-
125
-
-
84888015137
-
Super-enhancers in the control of cell identity and disease
-
[125] Hnisz, D., Abraham, B.J., Lee, T.I., Lau, A., Saint-Andre, V., Sigova, A.A., et al. Super-enhancers in the control of cell identity and disease. Cell 155 (2013), 934–947.
-
(2013)
Cell
, vol.155
, pp. 934-947
-
-
Hnisz, D.1
Abraham, B.J.2
Lee, T.I.3
Lau, A.4
Saint-Andre, V.5
Sigova, A.A.6
-
126
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
[126] Whyte, W.A., Orlando, D.A., Hnisz, D., Abraham, B.J., Lin, C.Y., Kagey, M.H., et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153 (2013), 307–319.
-
(2013)
Cell
, vol.153
, pp. 307-319
-
-
Whyte, W.A.1
Orlando, D.A.2
Hnisz, D.3
Abraham, B.J.4
Lin, C.Y.5
Kagey, M.H.6
-
127
-
-
84925283769
-
What are super-enhancers
-
[127] Pott, S., Lieb, J.D., What are super-enhancers. Nat. Genet. 47 (2015), 8–12.
-
(2015)
Nat. Genet.
, vol.47
, pp. 8-12
-
-
Pott, S.1
Lieb, J.D.2
-
128
-
-
84947061003
-
Super enhancers in cancers, complex disease, and developmental disorders
-
[128] Niederriter, A.R., Varshney, A., Parker, S.C., Martin, D.M., Super enhancers in cancers, complex disease, and developmental disorders. Genes (Basel) 6 (2015), 1183–1200.
-
(2015)
Genes (Basel)
, vol.6
, pp. 1183-1200
-
-
Niederriter, A.R.1
Varshney, A.2
Parker, S.C.3
Martin, D.M.4
-
129
-
-
84942945203
-
Genomic approaches for understanding the genetics of complex disease
-
[129] Lowe, W.L. Jr., Reddy, T.E., Genomic approaches for understanding the genetics of complex disease. Genome Res. 25 (2015), 1432–1441.
-
(2015)
Genome Res.
, vol.25
, pp. 1432-1441
-
-
Lowe, W.L.1
Reddy, T.E.2
-
130
-
-
84925089678
-
The role of regulatory variation in complex traits and disease
-
[130] Albert, F.W., Kruglyak, L., The role of regulatory variation in complex traits and disease. Nat. Rev. Genet. 16 (2015), 197–212.
-
(2015)
Nat. Rev. Genet.
, vol.16
, pp. 197-212
-
-
Albert, F.W.1
Kruglyak, L.2
-
131
-
-
0035865087
-
A physical map of the human genome
-
[131] McPherson, J.D., Marra, M., Hillier, L., Waterston, R.H., Chinwalla, A., Wallis, J., et al. A physical map of the human genome. Nature 409 (2001), 934–941.
-
(2001)
Nature
, vol.409
, pp. 934-941
-
-
McPherson, J.D.1
Marra, M.2
Hillier, L.3
Waterston, R.H.4
Chinwalla, A.5
Wallis, J.6
-
132
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
[132] Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001), 860–921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
-
133
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
[133] Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002), 520–562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
-
134
-
-
3042740671
-
Comparative genomics at the vertebrate extremes
-
[134] Boffelli, D., Nobrega, M.A., Rubin, E.M., Comparative genomics at the vertebrate extremes. Nat. Rev. Genet. 5 (2004), 456–465.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 456-465
-
-
Boffelli, D.1
Nobrega, M.A.2
Rubin, E.M.3
-
135
-
-
5444223488
-
Exploiting human–fish genome comparisons for deciphering gene regulation
-
13 Spec. No. 2: R261-6
-
[135] Ahituv, N., Rubin, E.M., Nobrega, M.A., Exploiting human–fish genome comparisons for deciphering gene regulation. Hum. Mol. Genet., 2004 13 Spec. No. 2: R261-6.
-
(2004)
Hum. Mol. Genet.
-
-
Ahituv, N.1
Rubin, E.M.2
Nobrega, M.A.3
-
136
-
-
0142084743
-
Scanning human gene deserts for long-range enhancers
-
[136] Nobrega, M.A., Ovcharenko, I., Afzal, V., Rubin, E.M., Scanning human gene deserts for long-range enhancers. Science, 302, 2003, 413.
-
(2003)
Science
, vol.302
, pp. 413
-
-
Nobrega, M.A.1
Ovcharenko, I.2
Afzal, V.3
Rubin, E.M.4
-
137
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
[137] Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444 (2006), 499–502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
-
138
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
[138] Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M.F., Parker, B.J., Washietl, S., et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478 (2011), 476–482.
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
-
139
-
-
0042810698
-
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
-
[139] Lettice, L.A., Heaney, S.J., Purdie, L.A., Li, L., de Beer, P., Oostra, B.A., et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12 (2003), 1725–1735.
-
(2003)
Hum. Mol. Genet.
, vol.12
, pp. 1725-1735
-
-
Lettice, L.A.1
Heaney, S.J.2
Purdie, L.A.3
Li, L.4
de Beer, P.5
Oostra, B.A.6
-
140
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
[140] Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456 (2008), 53–59.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
-
141
-
-
53649106195
-
Next-generation DNA sequencing
-
[141] Shendure, J., Ji, H., Next-generation DNA sequencing. Nat. Biotechnol. 26 (2008), 1135–1145.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
142
-
-
37749047490
-
Sequence census methods for functional genomics
-
[142] Wold, B., Myers, R.M., Sequence census methods for functional genomics. Nat. Methods 5 (2008), 19–21.
-
(2008)
Nat. Methods
, vol.5
, pp. 19-21
-
-
Wold, B.1
Myers, R.M.2
-
143
-
-
27144500218
-
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
-
[143] Meissner, A., Gnirke, A., Bell, G.W., Ramsahoye, B., Lander, E.S., Jaenisch, R., Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33 (2005), 5868–5877.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5868-5877
-
-
Meissner, A.1
Gnirke, A.2
Bell, G.W.3
Ramsahoye, B.4
Lander, E.S.5
Jaenisch, R.6
-
144
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
[144] Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5 (2008), 621–628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
145
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
[145] Johnson, D.S., Mortazavi, A., Myers, R.M., Wold, B., Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007), 1497–1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
146
-
-
30044449116
-
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
-
[146] Crawford, G.E., Holt, I.E., Whittle, J., Webb, B.D., Tai, D., Davis, S., et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16 (2006), 123–131.
-
(2006)
Genome Res.
, vol.16
, pp. 123-131
-
-
Crawford, G.E.1
Holt, I.E.2
Whittle, J.3
Webb, B.D.4
Tai, D.5
Davis, S.6
-
147
-
-
84880845871
-
Genome-scale mapping of DNase I hypersensitivity
-
(Chapter 27: Unit 21 7)
-
[147] John, S., Sabo, P.J., Canfield, T.K., Lee, K., Vong, S., Weaver, M., et al. Genome-scale mapping of DNase I hypersensitivity. Curr. Protoc. Mol. Biol., 2013 (Chapter 27: Unit 21 7).
-
(2013)
Curr. Protoc. Mol. Biol.
-
-
John, S.1
Sabo, P.J.2
Canfield, T.K.3
Lee, K.4
Vong, S.5
Weaver, M.6
-
148
-
-
0037083376
-
Capturing chromosome conformation
-
[148] Dekker, J., Rippe, K., Dekker, M., Kleckner, N., Capturing chromosome conformation. Science 295 (2002), 1306–1311.
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
149
-
-
34248524473
-
Mapping networks of physical interactions between genomic elements using 5C technology
-
[149] Dostie, J., Dekker, J., Mapping networks of physical interactions between genomic elements using 5C technology. Nat. Protoc. 2 (2007), 988–1002.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 988-1002
-
-
Dostie, J.1
Dekker, J.2
-
150
-
-
84870379849
-
Hi-C a comprehensive technique to capture the conformation of genomes
-
[150] Belton, J.M., McCord, R.P., Gibcus, J.H., Naumova, N., Zhan, Y., Dekker, J.C., Hi-C a comprehensive technique to capture the conformation of genomes. Methods 58 (2012), 268–276.
-
(2012)
Methods
, vol.58
, pp. 268-276
-
-
Belton, J.M.1
McCord, R.P.2
Gibcus, J.H.3
Naumova, N.4
Zhan, Y.5
Dekker, J.C.6
-
151
-
-
70449103609
-
An oestrogen-receptor-alpha-bound human chromatin interactome
-
[151] Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462 (2009), 58–64.
-
(2009)
Nature
, vol.462
, pp. 58-64
-
-
Fullwood, M.J.1
Liu, M.H.2
Pan, Y.F.3
Liu, J.4
Xu, H.5
Mohamed, Y.B.6
-
152
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
[152] Landt, S.G., Marinov, G.K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22 (2012), 1813–1831.
-
(2012)
Genome Res.
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
Marinov, G.K.2
Kundaje, A.3
Kheradpour, P.4
Pauli, F.5
Batzoglou, S.6
-
153
-
-
84942913353
-
CETCh-seq: CRISPR epitope tagging chIP-seq of DNA-binding proteins
-
[153] Savic, D., Partridge, E.C., Newberry, K.M., Smith, S.B., Meadows, S.K., Roberts, B.S., et al. CETCh-seq: CRISPR epitope tagging chIP-seq of DNA-binding proteins. Genome Res. 25 (2015), 1581–1589.
-
(2015)
Genome Res.
, vol.25
, pp. 1581-1589
-
-
Savic, D.1
Partridge, E.C.2
Newberry, K.M.3
Smith, S.B.4
Meadows, S.K.5
Roberts, B.S.6
-
154
-
-
84883785026
-
Mapping genome-wide transcription factor binding sites in frozen tissues
-
[154] Savic, D., Gertz, J., Jain, P., Cooper, G.M., Myers, R.M., Mapping genome-wide transcription factor binding sites in frozen tissues. Epigenet. Chromatin, 6, 2013, 30.
-
(2013)
Epigenet. Chromatin
, vol.6
, pp. 30
-
-
Savic, D.1
Gertz, J.2
Jain, P.3
Cooper, G.M.4
Myers, R.M.5
-
155
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
[155] Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J., Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10 (2013), 1213–1218.
-
(2013)
Nat. Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
156
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
[156] Core, L.J., Waterfall, J.J., Lis, J.T., Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322 (2008), 1845–1848.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
157
-
-
84930092058
-
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
-
[157] Mifsud, B., Tavares-Cadete, F., Young, A.N., Sugar, R., Schoenfelder, S., Ferreira, L., et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47 (2015), 598–606.
-
(2015)
Nat. Genet.
, vol.47
, pp. 598-606
-
-
Mifsud, B.1
Tavares-Cadete, F.2
Young, A.N.3
Sugar, R.4
Schoenfelder, S.5
Ferreira, L.6
-
158
-
-
84865121188
-
An encyclopedia of mouse DNA elements (Mouse ENCODE)
-
[158] ENCODE, Stamatoyannopoulos, J.A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol., 13, 2012, 418.
-
(2012)
Genome Biol.
, vol.13
, pp. 418
-
-
ENCODE1
Stamatoyannopoulos, J.A.2
Snyder, M.3
Hardison, R.4
Ren, B.5
Gingeras, T.6
-
159
-
-
73249130316
-
Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
-
[159] Reddy, T.E., Pauli, F., Sprouse, R.O., Neff, N.F., Newberry, K.M., Garabedian, M.J., et al. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 19 (2009), 2163–2171.
-
(2009)
Genome Res.
, vol.19
, pp. 2163-2171
-
-
Reddy, T.E.1
Pauli, F.2
Sprouse, R.O.3
Neff, N.F.4
Newberry, K.M.5
Garabedian, M.J.6
-
160
-
-
84868324642
-
Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
-
[160] Gertz, J., Reddy, T.E., Varley, K.E., Garabedian, M.J., Myers, R.M., Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. Genome Res. 22 (2012), 2153–2162.
-
(2012)
Genome Res.
, vol.22
, pp. 2153-2162
-
-
Gertz, J.1
Reddy, T.E.2
Varley, K.E.3
Garabedian, M.J.4
Myers, R.M.5
-
161
-
-
70449696134
-
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
-
[161] Cheng, Y., Wu, W., Kumar, S.A., Yu, D., Deng, W., Tripic, T., et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 19 (2009), 2172–2184.
-
(2009)
Genome Res.
, vol.19
, pp. 2172-2184
-
-
Cheng, Y.1
Wu, W.2
Kumar, S.A.3
Yu, D.4
Deng, W.5
Tripic, T.6
-
162
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
[162] Patwardhan, R.P., Hiatt, J.B., Witten, D.M., Kim, M.J., Smith, R.P., May, D., et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30 (2012), 265–270.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
Hiatt, J.B.2
Witten, D.M.3
Kim, M.J.4
Smith, R.P.5
May, D.6
-
163
-
-
84880362638
-
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
-
[163] White, M.A., Myers, C.A., Corbo, J.C., Cohen, B.A., Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc. Natl. Acad. Sci. U. S. A. 110 (2013), 11952–11957.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 11952-11957
-
-
White, M.A.1
Myers, C.A.2
Corbo, J.C.3
Cohen, B.A.4
-
164
-
-
84877147962
-
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
-
[164] 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. 23 (2013), 800–811.
-
(2013)
Genome Res.
, vol.23
, pp. 800-811
-
-
Kheradpour, P.1
Ernst, J.2
Melnikov, A.3
Rogov, P.4
Wang, L.5
Zhang, X.6
-
165
-
-
84874381107
-
Genome-wide quantitative enhancer activity maps identified by STARR-seq
-
[165] Arnold, C.D., Gerlach, D., Stelzer, C., Boryn, L.M., Rath, M., Stark, A., Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339 (2013), 1074–1077.
-
(2013)
Science
, vol.339
, pp. 1074-1077
-
-
Arnold, C.D.1
Gerlach, D.2
Stelzer, C.3
Boryn, L.M.4
Rath, M.5
Stark, A.6
-
166
-
-
84869853147
-
Complex effects of nucleotide variants in a mammalian cis-regulatory element
-
[166] Kwasnieski, J.C., Mogno, I., Myers, C.A., Corbo, J.C., Cohen, B.A., Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc. Natl. Acad. Sci. U. S. A. 109 (2012), 19498–19503.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 19498-19503
-
-
Kwasnieski, J.C.1
Mogno, I.2
Myers, C.A.3
Corbo, J.C.4
Cohen, B.A.5
-
167
-
-
84907516453
-
High-throughput functional testing of ENCODE segmentation predictions
-
[167] Kwasnieski, J.C., Fiore, C., Chaudhari, H.G., Cohen, B.A., High-throughput functional testing of ENCODE segmentation predictions. Genome Res. 24 (2014), 1595–1602.
-
(2014)
Genome Res.
, vol.24
, pp. 1595-1602
-
-
Kwasnieski, J.C.1
Fiore, C.2
Chaudhari, H.G.3
Cohen, B.A.4
-
168
-
-
84873729095
-
Multiplex genome engineering using CRISPR/Cas systems
-
[168] Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339 (2013), 819–823.
-
(2013)
Science
, vol.339
, pp. 819-823
-
-
Cong, L.1
Ran, F.A.2
Cox, D.3
Lin, S.4
Barretto, R.5
Habib, N.6
-
169
-
-
84876567971
-
RNA-programmed genome editing in human cells
-
[169] Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., Doudna, J., RNA-programmed genome editing in human cells. Elife, 2, 2013, e00471.
-
(2013)
Elife
, vol.2
, pp. e00471
-
-
Jinek, M.1
East, A.2
Cheng, A.3
Lin, S.4
Ma, E.5
Doudna, J.6
-
170
-
-
84873734105
-
RNA-guided human genome engineering via Cas9
-
[170] Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., et al. RNA-guided human genome engineering via Cas9. Science 339 (2013), 823–826.
-
(2013)
Science
, vol.339
, pp. 823-826
-
-
Mali, P.1
Yang, L.2
Esvelt, K.M.3
Aach, J.4
Guell, M.5
DiCarlo, J.E.6
-
171
-
-
34447319080
-
An improved zinc-finger nuclease architecture for highly specific genome editing
-
[171] Miller, J.C., Holmes, M.C., Wang, J., Guschin, D.Y., Lee, Y.L., Rupniewski, I., et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25 (2007), 778–785.
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 778-785
-
-
Miller, J.C.1
Holmes, M.C.2
Wang, J.3
Guschin, D.Y.4
Lee, Y.L.5
Rupniewski, I.6
-
172
-
-
79551685675
-
A TALE nuclease architecture for efficient genome editing
-
[172] Miller, J.C., Tan, S., Qiao, G., Barlow, K.A., Wang, J., Xia, D.F., et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29 (2011), 143–148.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 143-148
-
-
Miller, J.C.1
Tan, S.2
Qiao, G.3
Barlow, K.A.4
Wang, J.5
Xia, D.F.6
-
173
-
-
77952474987
-
Cellular heterogeneity: do differences make a difference
-
[173] Altschuler, S.J., Wu, L.F., Cellular heterogeneity: do differences make a difference. Cell 141 (2010), 559–563.
-
(2010)
Cell
, vol.141
, pp. 559-563
-
-
Altschuler, S.J.1
Wu, L.F.2
-
174
-
-
75549083303
-
Tumor heterogeneity: causes and consequences
-
[174] Marusyk, A., Polyak, K., Tumor heterogeneity: causes and consequences. Biochim. Biophys. Acta 1805 (2010), 105–117.
-
(2010)
Biochim. Biophys. Acta
, vol.1805
, pp. 105-117
-
-
Marusyk, A.1
Polyak, K.2
-
175
-
-
67349146589
-
mRNA-Seq whole-transcriptome analysis of a single cell
-
[175] Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6 (2009), 377–382.
-
(2009)
Nat. Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
Nordman, E.4
Lee, C.5
Xu, N.6
-
176
-
-
84866953427
-
CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification
-
[176] Hashimshony, T., Wagner, F., Sher, N., Yanai, I., CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2 (2012), 666–673.
-
(2012)
Cell Rep.
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
177
-
-
84929687805
-
The technology and biology of single-cell RNA sequencing
-
[177] Kolodziejczyk, A.A., Kim, J.K., Svensson, V., Marioni, J.C., Teichmann, S.A., The technology and biology of single-cell RNA sequencing. Mol. Cell 58 (2015), 610–620.
-
(2015)
Mol. Cell
, vol.58
, pp. 610-620
-
-
Kolodziejczyk, A.A.1
Kim, J.K.2
Svensson, V.3
Marioni, J.C.4
Teichmann, S.A.5
-
178
-
-
84905405443
-
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
-
[178] Smallwood, S.A., Lee, H.J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11 (2014), 817–820.
-
(2014)
Nat. Methods
, vol.11
, pp. 817-820
-
-
Smallwood, S.A.1
Lee, H.J.2
Angermueller, C.3
Krueger, F.4
Saadeh, H.5
Peat, J.6
-
179
-
-
84937857359
-
Single-cell chromatin accessibility reveals principles of regulatory variation
-
[179] Buenrostro, J.D., Wu, B., Litzenburger, U.M., Ruff, D., Gonzales, M.L., Snyder, M.P., et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523 (2015), 486–490.
-
(2015)
Nature
, vol.523
, pp. 486-490
-
-
Buenrostro, J.D.1
Wu, B.2
Litzenburger, U.M.3
Ruff, D.4
Gonzales, M.L.5
Snyder, M.P.6
-
180
-
-
84930006926
-
Epigenetics: multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
-
[180] Cusanovich, D.A., Daza, R., Adey, A., Pliner, H.A., Christiansen, L., Gunderson, K.L., et al. Epigenetics: multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348 (2015), 910–914.
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
Daza, R.2
Adey, A.3
Pliner, H.A.4
Christiansen, L.5
Gunderson, K.L.6
-
181
-
-
84937573360
-
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
-
[181] Kim, K.T., Lee, H.W., Lee, H.O., Kim, S.C., Seo, Y.J., Chung, W., et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol., 16, 2015, 127.
-
(2015)
Genome Biol.
, vol.16
, pp. 127
-
-
Kim, K.T.1
Lee, H.W.2
Lee, H.O.3
Kim, S.C.4
Seo, Y.J.5
Chung, W.6
-
182
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
[182] Buettner, F., Natarajan, K.N., Casale, F.P., Proserpio, V., Scialdone, A., Theis, F.J., et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33 (2015), 155–160.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 155-160
-
-
Buettner, F.1
Natarajan, K.N.2
Casale, F.P.3
Proserpio, V.4
Scialdone, A.5
Theis, F.J.6
-
183
-
-
84939548526
-
Single-cell ATAC-seq strength in numbers
-
[183] Pott, S., Lieb, J.D., Single-cell ATAC-seq strength in numbers. Genome Biol., 16, 2015, 172.
-
(2015)
Genome Biol.
, vol.16
, pp. 172
-
-
Pott, S.1
Lieb, J.D.2
-
184
-
-
84907419194
-
Immunogenetics: chromatin state dynamics during blood formation
-
[184] Lara-Astiaso, D., Weiner, A., Lorenzo-Vivas, E., Zaretsky, I., Jaitin, D.A., David, E., et al. Immunogenetics: chromatin state dynamics during blood formation. Science 345 (2014), 943–949.
-
(2014)
Science
, vol.345
, pp. 943-949
-
-
Lara-Astiaso, D.1
Weiner, A.2
Lorenzo-Vivas, E.3
Zaretsky, I.4
Jaitin, D.A.5
David, E.6
-
185
-
-
84953635706
-
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
-
[185] Brind'Amour, J., Liu, S., Hudson, M., Chen, C., Karimi, M.M., Lorincz, M.C., An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat. Commun., 6, 2015, 6033.
-
(2015)
Nat. Commun.
, vol.6
, pp. 6033
-
-
Brind'Amour, J.1
Liu, S.2
Hudson, M.3
Chen, C.4
Karimi, M.M.5
Lorincz, M.C.6
-
186
-
-
84892749369
-
Genetic screens in human cells using the CRISPR-Cas9 system
-
[186] Wang, T., Wei, J.J., Sabatini, D.M., Lander, E.S., Genetic screens in human cells using the CRISPR-Cas9 system. Science 343 (2014), 80–84.
-
(2014)
Science
, vol.343
, pp. 80-84
-
-
Wang, T.1
Wei, J.J.2
Sabatini, D.M.3
Lander, E.S.4
-
187
-
-
84892765883
-
Genome-scale CRISPR-Cas9 knockout screening in human cells
-
[187] Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelsen, T.S., et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343 (2014), 84–87.
-
(2014)
Science
, vol.343
, pp. 84-87
-
-
Shalem, O.1
Sanjana, N.E.2
Hartenian, E.3
Shi, X.4
Scott, D.A.5
Mikkelsen, T.S.6
-
188
-
-
84938744950
-
A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks
-
[188] Parnas, O., Jovanovic, M., Eisenhaure, T.M., Herbst, R.H., Dixit, A., Ye, C.J., et al. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 162 (2015), 675–686.
-
(2015)
Cell
, vol.162
, pp. 675-686
-
-
Parnas, O.1
Jovanovic, M.2
Eisenhaure, T.M.3
Herbst, R.H.4
Dixit, A.5
Ye, C.J.6
-
189
-
-
84925008880
-
Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis
-
[189] Chen, S., Sanjana, N.E., Zheng, K., Shalem, O., Lee, K., Shi, X., et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160 (2015), 1246–1260.
-
(2015)
Cell
, vol.160
, pp. 1246-1260
-
-
Chen, S.1
Sanjana, N.E.2
Zheng, K.3
Shalem, O.4
Lee, K.5
Shi, X.6
-
190
-
-
84884907424
-
CRISPR RNA-guided activation of endogenous human genes
-
[190] Maeder, M.L., Linder, S.J., Cascio, V.M., Fu, Y., Ho, Q.H., Joung, J.K., CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10 (2013), 977–979.
-
(2013)
Nat. Methods
, vol.10
, pp. 977-979
-
-
Maeder, M.L.1
Linder, S.J.2
Cascio, V.M.3
Fu, Y.4
Ho, Q.H.5
Joung, J.K.6
-
191
-
-
84884906690
-
RNA-guided gene activation by CRISPR-Cas9-based transcription factors
-
[191] Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Polstein, L.R., et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10 (2013), 973–976.
-
(2013)
Nat. Methods
, vol.10
, pp. 973-976
-
-
Perez-Pinera, P.1
Kocak, D.D.2
Vockley, C.M.3
Adler, A.F.4
Kabadi, A.M.5
Polstein, L.R.6
-
192
-
-
84929135130
-
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
-
[192] Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., Thakore, P.I., Crawford, G.E., Reddy, T.E., et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33 (2015), 510–517.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 510-517
-
-
Hilton, I.B.1
D'Ippolito, A.M.2
Vockley, C.M.3
Thakore, P.I.4
Crawford, G.E.5
Reddy, T.E.6
-
193
-
-
84949100864
-
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements
-
[193] Thakore, P.I., D'Ippolito, A.M., Song, L., Safi, A., Shivakumar, N.K., Kabadi, A.M., et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12 (2015), 1143–1149.
-
(2015)
Nat. Methods
, vol.12
, pp. 1143-1149
-
-
Thakore, P.I.1
D'Ippolito, A.M.2
Song, L.3
Safi, A.4
Shivakumar, N.K.5
Kabadi, A.M.6
-
194
-
-
84887104139
-
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
-
[194] Esvelt, K.M., Mali, P., Braff, J.L., Moosburner, M., Yaung, S.J., Church, G.M., Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10 (2013), 1116–1121.
-
(2013)
Nat. Methods
, vol.10
, pp. 1116-1121
-
-
Esvelt, K.M.1
Mali, P.2
Braff, J.L.3
Moosburner, M.4
Yaung, S.J.5
Church, G.M.6
-
195
-
-
84937908208
-
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
-
[195] Kleinstiver, B.P., Prew, M.S., Tsai, S.Q., Topkar, V.V., Nguyen, N.T., Zheng, Z., et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523 (2015), 481–485.
-
(2015)
Nature
, vol.523
, pp. 481-485
-
-
Kleinstiver, B.P.1
Prew, M.S.2
Tsai, S.Q.3
Topkar, V.V.4
Nguyen, N.T.5
Zheng, Z.6
-
196
-
-
84946221310
-
CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants
-
[196] Spisak, S., Lawrenson, K., Fu, Y., Csabai, I., Cottman, R.T., Seo, J.H., et al. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat. Med. 21 (2015), 1357–1363.
-
(2015)
Nat. Med.
, vol.21
, pp. 1357-1363
-
-
Spisak, S.1
Lawrenson, K.2
Fu, Y.3
Csabai, I.4
Cottman, R.T.5
Seo, J.H.6
-
197
-
-
70349956433
-
Finding the missing heritability of complex diseases
-
[197] Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., et al. Finding the missing heritability of complex diseases. Nature 461 (2009), 747–753.
-
(2009)
Nature
, vol.461
, pp. 747-753
-
-
Manolio, T.A.1
Collins, F.S.2
Cox, N.J.3
Goldstein, D.B.4
Hindorff, L.A.5
Hunter, D.J.6
-
198
-
-
77952557918
-
Missing heritability and strategies for finding the underlying causes of complex disease
-
[198] Eichler, E.E., Flint, J., Gibson, G., Kong, A., Leal, S.M., Moore, J.H., et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet. 11 (2010), 446–450.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 446-450
-
-
Eichler, E.E.1
Flint, J.2
Gibson, G.3
Kong, A.4
Leal, S.M.5
Moore, J.H.6
-
199
-
-
79952080610
-
Next generation DNA sequencing and the future of genomic medicine
-
[199] Anderson, M.W., Schrijver, I., Next generation DNA sequencing and the future of genomic medicine. Genes (Basel) 1 (2010), 38–69.
-
(2010)
Genes (Basel)
, vol.1
, pp. 38-69
-
-
Anderson, M.W.1
Schrijver, I.2
-
200
-
-
84876783779
-
Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics
-
[200] Gullapalli, R.R., Desai, K.V., Santana-Santos, L., Kant, J.A., Becich, M.J., Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics. J. Pathol. Inf., 3, 2012, 40.
-
(2012)
J. Pathol. Inf.
, vol.3
, pp. 40
-
-
Gullapalli, R.R.1
Desai, K.V.2
Santana-Santos, L.3
Kant, J.A.4
Becich, M.J.5
-
201
-
-
84921390202
-
Challenges and opportunities for next-generation sequencing in companion diagnostics
-
[201] Lin, E., Chien, J., Ong, F.S., Fan, J.B., Challenges and opportunities for next-generation sequencing in companion diagnostics. Expert Rev. Mol. Diagn. 15 (2015), 193–209.
-
(2015)
Expert Rev. Mol. Diagn.
, vol.15
, pp. 193-209
-
-
Lin, E.1
Chien, J.2
Ong, F.S.3
Fan, J.B.4
-
202
-
-
80051968181
-
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
-
[202] Cooper, G.M., Shendure, J., Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12 (2011), 628–640.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
203
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
[203] Kircher, M., Witten, D.M., Jain, P., O'Roak, B.J., Cooper, G.M., Shendure, J., A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46 (2014), 310–315.
-
(2014)
Nat. Genet.
, vol.46
, pp. 310-315
-
-
Kircher, M.1
Witten, D.M.2
Jain, P.3
O'Roak, B.J.4
Cooper, G.M.5
Shendure, J.6
-
204
-
-
79955884485
-
Modelling schizophrenia using human induced pluripotent stem cells
-
[204] Brennand, K.J., Simone, A., Jou, J., Gelboin-Burkhart, C., Tran, N., Sangar, S., et al. Modelling schizophrenia using human induced pluripotent stem cells. Nature 473 (2011), 221–225.
-
(2011)
Nature
, vol.473
, pp. 221-225
-
-
Brennand, K.J.1
Simone, A.2
Jou, J.3
Gelboin-Burkhart, C.4
Tran, N.5
Sangar, S.6
-
205
-
-
84856956771
-
Probing sporadic and familial Alzheimer's disease using induced pluripotent stem cells
-
[205] Israel, M.A., Yuan, S.H., Bardy, C., Reyna, S.M., Mu, Y., Herrera, C., et al. Probing sporadic and familial Alzheimer's disease using induced pluripotent stem cells. Nature 482 (2012), 216–220.
-
(2012)
Nature
, vol.482
, pp. 216-220
-
-
Israel, M.A.1
Yuan, S.H.2
Bardy, C.3
Reyna, S.M.4
Mu, Y.5
Herrera, C.6
-
206
-
-
84956945024
-
Massively parallel cis-regulatory analysis in the mammalian central nervous system
-
[206] Shen, S.Q., Myers, C.A., Hughes, A.E., Byrne, L.C., Flannery, J.G., Corbo, J.C., Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res. 26 (2016), 238–255.
-
(2016)
Genome Res.
, vol.26
, pp. 238-255
-
-
Shen, S.Q.1
Myers, C.A.2
Hughes, A.E.3
Byrne, L.C.4
Flannery, J.G.5
Corbo, J.C.6
-
207
-
-
84938876935
-
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
-
[207] Vockley, C.M., Guo, C., Majoros, W.H., Nodzenski, M., Scholtens, D.M., Hayes, M.G., et al. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. Genome Res. 25 (2015), 1206–1214.
-
(2015)
Genome Res.
, vol.25
, pp. 1206-1214
-
-
Vockley, C.M.1
Guo, C.2
Majoros, W.H.3
Nodzenski, M.4
Scholtens, D.M.5
Hayes, M.G.6
|