-
1
-
-
0036144048
-
DNA methylation patterns and epigenetic memory
-
Bird,A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev., 16, 6-21.
-
(2002)
Genes Dev.
, vol.16
, pp. 6-21
-
-
Bird, A.1
-
2
-
-
0016439429
-
DNA modification mechanisms and gene activity during development
-
Holliday,R. and Pugh,J.E. (1975) DNA modification mechanisms and gene activity during development. Science, 187, 226-232.
-
(1975)
Science
, vol.187
, pp. 226-232
-
-
Holliday, R.1
Pugh, J.E.2
-
3
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
Ziller,M.J., Gu,H., Muller,F., Donaghey,J., Tsai,L.T., Kohlbacher,O., De Jager,P.L., Rosen,E.D., Bennett,D.A., Bernstein,B.E. et al. (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature, 500, 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
De Jager, P.L.7
Rosen, E.D.8
Bennett, D.A.9
Bernstein, B.E.10
-
4
-
-
77249137168
-
Principles and challenges of genome-wide DNA methylation analysis
-
Laird,P.W. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 191-203
-
-
Laird, P.W.1
-
5
-
-
0022540321
-
CpG-rich islands and the function of DNA methylation
-
Bird,A.P. (1986) CpG-rich islands and the function of DNA methylation. Nature, 321, 209-213.
-
(1986)
Nature
, vol.321
, pp. 209-213
-
-
Bird, A.P.1
-
6
-
-
59149084538
-
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
-
Irizarry,R.A., Ladd-Acosta,C., Wen,B., Wu,Z., Montano,C., Onyango,P., Cui,H., Gabo,K., Rongione,M., Webster,M. et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
-
(2009)
Nat. Genet.
, vol.41
, pp. 178-186
-
-
Irizarry, R.A.1
Ladd-Acosta, C.2
Wen, B.3
Wu, Z.4
Montano, C.5
Onyango, P.6
Cui, H.7
Gabo, K.8
Rongione, M.9
Webster, M.10
-
7
-
-
50649108994
-
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
-
Rakyan,V.K., Down,T.A., Thorne,N.P., Flicek,P., Kulesha,E., Graf,S., Tomazou,E.M., Backdahl,L., Johnson,N., Herberth,M. et al. (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res., 18, 1518-1529.
-
(2008)
Genome Res.
, vol.18
, pp. 1518-1529
-
-
Rakyan, V.K.1
Down, T.A.2
Thorne, N.P.3
Flicek, P.4
Kulesha, E.5
Graf, S.6
Tomazou, E.M.7
Backdahl, L.8
Johnson, N.9
Herberth, M.10
-
8
-
-
84899630492
-
DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
-
Lokk,K., Modhukur,V., Rajashekar,B., Martens,K., Magi,R., Kolde,R., Kolt Ina,M., Nilsson,T.K., Vilo,J., Salumets,A. et al. (2014) DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biol., 15, R54.
-
(2014)
Genome Biol.
, vol.15
, pp. R54
-
-
Lokk, K.1
Modhukur, V.2
Rajashekar, B.3
Martens, K.4
Magi, R.5
Kolde, R.6
Kolt Ina, M.7
Nilsson, T.K.8
Vilo, J.9
Salumets, A.10
-
9
-
-
84898758414
-
Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
-
Court,F., Tayama,C., Romanelli,V., Martin-Trujillo,A., Iglesias-Platas,I., Okamura,K., Sugahara,N., Simon,C., Moore,H., Harness,J.V. et al. (2014) Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res., 24, 554-569.
-
(2014)
Genome Res.
, vol.24
, pp. 554-569
-
-
Court, F.1
Tayama, C.2
Romanelli, V.3
Martin-Trujillo, A.4
Iglesias-Platas, I.5
Okamura, K.6
Sugahara, N.7
Simon, C.8
Moore, H.9
Harness, J.V.10
-
10
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister,R., Pelizzola,M., Dowen,R.H., Hawkins,R.D., Hon,G., Tonti-Filippini,J., Nery,J.R., Lee,L., Ye,Z., Ngo,Q.M. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 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
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
-
11
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie,W., Schultz,M.D., Lister,R., Hou,Z., Rajagopal,N., Ray,P., Whitaker,J.W., Tian,S., Hawkins,R.D., Leung,D. et al. (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell, 153, 1134-1148.
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
Schultz, M.D.2
Lister, R.3
Hou, Z.4
Rajagopal, N.5
Ray, P.6
Whitaker, J.W.7
Tian, S.8
Hawkins, R.D.9
Leung, D.10
-
12
-
-
84891372425
-
Large conserved domains of low DNA methylation maintained by Dnmt3a
-
Jeong,M., Sun,D., Luo,M., Huang,Y., Challen,G.A., Rodriguez,B., Zhang,X., Chavez,L., Wang,H., Hannah,R. et al. (2014) Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat. Genet., 46, 17-23.
-
(2014)
Nat. Genet.
, vol.46
, pp. 17-23
-
-
Jeong, M.1
Sun, D.2
Luo, M.3
Huang, Y.4
Challen, G.A.5
Rodriguez, B.6
Zhang, X.7
Chavez, L.8
Wang, H.9
Hannah, R.10
-
13
-
-
14744267496
-
Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression
-
Song,F., Smith,J.F., Kimura,M.T., Morrow,A.D., Matsuyama,T., Nagase,H. and Held,W.A. (2005) Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc. Natl. Acad. Sci. U.S.A., 102, 3336-3341.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 3336-3341
-
-
Song, F.1
Smith, J.F.2
Kimura, M.T.3
Morrow, A.D.4
Matsuyama, T.5
Nagase, H.6
Held, W.A.7
-
14
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
Bock,C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 705-719
-
-
Bock, C.1
-
15
-
-
84883668746
-
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
-
Zhang,B., Zhou,Y., Lin,N., Lowdon,R.F., Hong,C., Nagarajan,R.P., Cheng,J.B., Li,D., Stevens,M., Lee,H.J. et al. (2013) Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res., 23, 1522-1540.
-
(2013)
Genome Res.
, vol.23
, pp. 1522-1540
-
-
Zhang, B.1
Zhou, Y.2
Lin, N.3
Lowdon, R.F.4
Hong, C.5
Nagarajan, R.P.6
Cheng, J.B.7
Li, D.8
Stevens, M.9
Lee, H.J.10
-
16
-
-
84884692057
-
DNA methylation presents distinct binding sites for human transcription factors
-
Hu,S., Wan,J., Su,Y., Song,Q., Zeng,Y., Nguyen,H.N., Shin,J., Cox,E., Rho,H.S., Woodard,C. et al. (2013) DNA methylation presents distinct binding sites for human transcription factors. eLife, 2, e00726.
-
(2013)
eLife
, vol.2
-
-
Hu, S.1
Wan, J.2
Su, Y.3
Song, Q.4
Zeng, Y.5
Nguyen, H.N.6
Shin, J.7
Cox, E.8
Rho, H.S.9
Woodard, C.10
-
17
-
-
84899068616
-
Effects of cytosine methylation on transcription factor binding sites
-
Medvedeva,Y.A., Khamis,A.M., Kulakovskiy,I.V., Ba-Alawi,W., Bhuyan,M.S., Kawaji,H., Lassmann,T., Harbers,M., Forrest,A.R., Bajic,V.B. et al. (2014) Effects of cytosine methylation on transcription factor binding sites. BMC Genomics, 15, 119.
-
(2014)
BMC Genomics
, vol.15
, pp. 119
-
-
Medvedeva, Y.A.1
Khamis, A.M.2
Kulakovskiy, I.V.3
Ba-Alawi, W.4
Bhuyan, M.S.5
Kawaji, H.6
Lassmann, T.7
Harbers, M.8
Forrest, A.R.9
Bajic, V.B.10
-
18
-
-
84865836579
-
Widespread plasticity in CTCF occupancy linked to DNA methylation
-
Wang,H., Maurano,M.T., Qu,H., Varley,K.E., Gertz,J., Pauli,F., Lee,K., Canfield,T., Weaver,M., Sandstrom,R. et al. (2012) Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res., 22, 1680-1688.
-
(2012)
Genome Res.
, vol.22
, pp. 1680-1688
-
-
Wang, H.1
Maurano, M.T.2
Qu, H.3
Varley, K.E.4
Gertz, J.5
Pauli, F.6
Lee, K.7
Canfield, T.8
Weaver, M.9
Sandstrom, R.10
-
19
-
-
79952901680
-
Enhancer function: New insights into the regulation of tissue-specific gene expression
-
Ong,C.T. and Corces,V.G. (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat. Rev. Genet., 12, 283-293.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 283-293
-
-
Ong, C.T.1
Corces, V.G.2
-
20
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson,R., Gebhard,C., Miguel-Escalada,I., Hoof,I., Bornholdt,J., Boyd,M., Chen,Y., Zhao,X., Schmidl,C., Suzuki,T. et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507, 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
Chen, Y.7
Zhao, X.8
Schmidl, C.9
Suzuki, T.10
-
21
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
Whyte,W.A., Orlando,D.A., Hnisz,D., Abraham,B.J., Lin,C.Y., Kagey,M.H., Rahl,P.B., Lee,T.I. and Young,R.A. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 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
Rahl, P.B.7
Lee, T.I.8
Young, R.A.9
-
22
-
-
84888015137
-
Super-enhancers in the control of cell identity and disease
-
Hnisz,D., Abraham,B.J., Lee,T.I., Lau,A., Saint-Andre,V., Sigova,A.A., Hoke,H.A. and Young,R.A. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155, 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
Hoke, H.A.7
Young, R.A.8
-
23
-
-
79961022522
-
DNA methylation status predicts cell type-specific enhancer activity
-
Wiench,M., John,S., Baek,S., Johnson,T.A., Sung,M.H., Escobar,T., Simmons,C.A., Pearce,K.H., Biddie,S.C., Sabo,P.J. et al. (2011) DNA methylation status predicts cell type-specific enhancer activity. EMBO J., 30, 3028-3039.
-
(2011)
EMBO J.
, vol.30
, pp. 3028-3039
-
-
Wiench, M.1
John, S.2
Baek, S.3
Johnson, T.A.4
Sung, M.H.5
Escobar, T.6
Simmons, C.A.7
Pearce, K.H.8
Biddie, S.C.9
Sabo, P.J.10
-
24
-
-
84884994148
-
Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development
-
Ko,Y.A., Mohtat,D., Suzuki,M., Park,A.S., Izquierdo,M.C., Han,S.Y., Kang,H.M., Si,H., Hostetter,T., Pullman,J.M. et al. (2013) Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development. Genome Biol., 14, R108.
-
(2013)
Genome Biol.
, vol.14
, pp. R108
-
-
Ko, Y.A.1
Mohtat, D.2
Suzuki, M.3
Park, A.S.4
Izquierdo, M.C.5
Han, S.Y.6
Kang, H.M.7
Si, H.8
Hostetter, T.9
Pullman, J.M.10
-
25
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister,R., O'Malley,R.C., Tonti-Filippini,J., Gregory,B.D., Berry,C.C., Millar,A.H. and Ecker,J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
26
-
-
84884829249
-
Mapping human epigenomes
-
Rivera,C.M. and Ren,B. (2013) Mapping human epigenomes. Cell, 155, 39-55.
-
(2013)
Cell
, vol.155
, pp. 39-55
-
-
Rivera, C.M.1
Ren, B.2
-
27
-
-
79952264847
-
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
-
Lister,R., Pelizzola,M., Kida,Y.S., Hawkins,R.D., Nery,J.R., Hon,G., Antosiewicz-Bourget,J., O'Malley,R., Castanon,R., Klugman,S. et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 471, 68-73.
-
(2011)
Nature
, vol.471
, pp. 68-73
-
-
Lister, R.1
Pelizzola, M.2
Kida, Y.S.3
Hawkins, R.D.4
Nery, J.R.5
Hon, G.6
Antosiewicz-Bourget, J.7
O'Malley, R.8
Castanon, R.9
Klugman, S.10
-
28
-
-
84885021247
-
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
-
Hon,G.C., Rajagopal,N., Shen,Y., McCleary,D.F., Yue,F., Dang,M.D. and Ren,B. (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat .Genet., 45, 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
Ren, B.7
-
29
-
-
84871799766
-
CpG-MPs: Identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data
-
Su,J., Yan,H., Wei,Y., Liu,H., Wang,F., Lv,J., Wu,Q. and Zhang,Y. (2013) CpG-MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res., 41,e4.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e4
-
-
Su, J.1
Yan, H.2
Wei, Y.3
Liu, H.4
Wang, F.5
Lv, J.6
Wu, Q.7
Zhang, Y.8
-
30
-
-
84923366467
-
Transcription factor binding dynamics during human ES cell differentiation
-
Tsankov,A.M., Gu,H., Akopian,V., Ziller,M.J., Donaghey,J., Amit,I., Gnirke,A. and Meissner,A. (2015) Transcription factor binding dynamics during human ES cell differentiation. Nature, 518, 344-349.
-
(2015)
Nature
, vol.518
, pp. 344-349
-
-
Tsankov, A.M.1
Gu, H.2
Akopian, V.3
Ziller, M.J.4
Donaghey, J.5
Amit, I.6
Gnirke, A.7
Meissner, A.8
-
31
-
-
79956006215
-
QDMR: A quantitative method for identification of differentially methylated regions by entropy
-
Zhang,Y., Liu,H., Lv,J., Xiao,X., Zhu,J., Liu,X., Su,J., Li,X., Wu,Q., Wang,F. et al. (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res., 39, e58.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. e58
-
-
Zhang, Y.1
Liu, H.2
Lv, J.3
Xiao, X.4
Zhu, J.5
Liu, X.6
Su, J.7
Li, X.8
Wu, Q.9
Wang, F.10
-
32
-
-
58749087364
-
Errors in the bisulfite conversion of DNA: Modulating inappropriate- and failed-conversion frequencies
-
Genereux,D.P., Johnson,W.C., Burden,A.F., Stoger,R. and Laird,C.D. (2008) Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. Nucleic Acids Res., 36, e150.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e150
-
-
Genereux, D.P.1
Johnson, W.C.2
Burden, A.F.3
Stoger, R.4
Laird, C.D.5
-
33
-
-
0347755531
-
The UCSC Table Browser data retrieval tool
-
Karolchik,D., Hinrichs,A.S., Furey,T.S., Roskin,K.M., Sugnet,C.W., Haussler,D. and Kent,W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493-D496.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. D493-D496
-
-
Karolchik, D.1
Hinrichs, A.S.2
Furey, T.S.3
Roskin, K.M.4
Sugnet, C.W.5
Haussler, D.6
Kent, W.J.7
-
34
-
-
84883764464
-
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes
-
Liu,H., Chen,Y., Lv,J., Zhu,R., Su,J., Liu,X., Zhang,Y. and Wu,Q. (2013) Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. Sci. Rep., 3, 2576.
-
(2013)
Sci. Rep.
, vol.3
, pp. 2576
-
-
Liu, H.1
Chen, Y.2
Lv, J.3
Zhu, R.4
Su, J.5
Liu, X.6
Zhang, Y.7
Wu, Q.8
-
35
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan,A.R. and Hall,I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
36
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Kundaje,A., Meuleman,W., Ernst,J., Bilenky,M., Yen,A., Heravi-Moussavi,A., Kheradpour,P., Zhang,Z., Wang,J., Ziller,M.J. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 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
Kheradpour, P.7
Zhang, Z.8
Wang, J.9
Ziller, M.J.10
-
37
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
38
-
-
84899493057
-
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
-
Shen,L., Shao,N., Liu,X. and Nestler,E. (2014) ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics, 15, 284.
-
(2014)
BMC Genomics
, vol.15
, pp. 284
-
-
Shen, L.1
Shao, N.2
Liu, X.3
Nestler, E.4
-
39
-
-
33646361583
-
GenePattern 2.0
-
Reich,M., Liefeld,T., Gould,J., Lerner,J., Tamayo,P. and Mesirov,J.P. (2006) GenePattern 2.0. Nat. Genet., 38, 500-501.
-
(2006)
Nat. Genet.
, vol.38
, pp. 500-501
-
-
Reich, M.1
Liefeld, T.2
Gould, J.3
Lerner, J.4
Tamayo, P.5
Mesirov, J.P.6
-
40
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz,S., Benner,C., Spann,N., Bertolino,E., Lin,Y.C., Laslo,P., Cheng,J.X., Murre,C., Singh,H. and Glass,C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
41
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
42
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili,M.N., Trapnell,C., Goff,L., Koziol,M., Tazon-Vega,B., Regev,A. and Rinn,J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
-
(2011)
Genes Dev.
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
43
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
Vaquerizas,J.M., Kummerfeld,S.K., Teichmann,S.A. and Luscombe,N.M. (2009) A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet., 10, 252-263.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
44
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U.S.A., 95, 14863-14868.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
45
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da,W., Sherman,B.T. and Lempicki,R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
46
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean,C.Y., Bristor,D., Hiller,M., Clarke,S.L., Schaar,B.T., Lowe,C.B., Wenger,A.M. and Bejerano,G. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495-501.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
-
47
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber,M., Guttman,M., Clamp,M., Zody,M.C., Friedman,N. and Xie,X. (2009) Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics, 25, i54-i62.
-
(2009)
Bioinformatics
, vol.25
, pp. i54-i62
-
-
Garber, M.1
Guttman, M.2
Clamp, M.3
Zody, M.C.4
Friedman, N.5
Xie, X.6
-
48
-
-
84902167799
-
MetaImprint: An information repository of mammalian imprinted genes
-
Wei,Y., Su,J., Liu,H., Lv,J., Wang,F., Yan,H., Wen,Y., Liu,H., Wu,Q. and Zhang,Y. (2014) MetaImprint: an information repository of mammalian imprinted genes. Development, 141, 2516-2523.
-
(2014)
Development
, vol.141
, pp. 2516-2523
-
-
Wei, Y.1
Su, J.2
Liu, H.3
Lv, J.4
Wang, F.5
Yan, H.6
Wen, Y.7
Liu, H.8
Wu, Q.9
Zhang, Y.10
-
49
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton,M.P., Cheng,A.W., Welstead,G.G., Kooistra,T., Carey,B.W., Steine,E.J., Hanna,J., Lodato,M.A., Frampton,G.M., Sharp,P.A. et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U.S.A., 107, 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
Hanna, J.7
Lodato, M.A.8
Frampton, G.M.9
Sharp, P.A.10
-
50
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst,J., Kheradpour,P., Mikkelsen,T.S., Shoresh,N., Ward,L.D., Epstein,C.B., Zhang,X., Wang,L., Issner,R., Coyne,M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 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
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
51
-
-
40849139208
-
Epigenetics in cancer
-
Esteller,M. (2008) Epigenetics in cancer. N. Engl. J. Med., 358, 1148-1159.
-
(2008)
N. Engl. J. Med.
, vol.358
, pp. 1148-1159
-
-
Esteller, M.1
-
52
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C., Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 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
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
53
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach,A., McDaniel,I.E., Silva,P. and Zilberman,D. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
McDaniel, I.E.2
Silva, P.3
Zilberman, D.4
-
54
-
-
22844457491
-
DNA methylation and human disease
-
Robertson,K.D. (2005) DNA methylation and human disease. Nat. Rev. Genet., 6, 597-610.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 597-610
-
-
Robertson, K.D.1
-
55
-
-
77954661906
-
DNA hypomethylation in cancer cells
-
Ehrlich,M. (2009) DNA hypomethylation in cancer cells. Epigenomics, 1, 239-259.
-
(2009)
Epigenomics
, vol.1
, pp. 239-259
-
-
Ehrlich, M.1
-
56
-
-
52949138674
-
On the nature of human housekeeping genes
-
Zhu,J., He,F., Hu,S. and Yu,J. (2008) On the nature of human housekeeping genes. Trends Genet., 24, 481-484.
-
(2008)
Trends Genet.
, vol.24
, pp. 481-484
-
-
Zhu, J.1
He, F.2
Hu, S.3
Yu, J.4
-
57
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden,M. and Frommer,M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
-
(1987)
J. Mol. Biol.
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
58
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton,A.M. and Bird,A. (2011) CpG islands and the regulation of transcription. Genes Dev., 25, 1010-1022.
-
(2011)
Genes Dev.
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
59
-
-
77951116072
-
CpG islands influence chromatin structure via the CpG-binding protein Cfp1
-
Thomson,J.P., Skene,P.J., Selfridge,J., Clouaire,T., Guy,J., Webb,S., Kerr,A.R., Deaton,A., Andrews,R., James,K.D. et al. (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature, 464, 1082-1086.
-
(2010)
Nature
, vol.464
, pp. 1082-1086
-
-
Thomson, J.P.1
Skene, P.J.2
Selfridge, J.3
Clouaire, T.4
Guy, J.5
Webb, S.6
Kerr, A.R.7
Deaton, A.8
Andrews, R.9
James, K.D.10
-
60
-
-
78651552406
-
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
-
Bell,J.T., Pai,A.A., Pickrell,J.K., Gaffney,D.J., Pique-Regi,R., Degner,J.F., Gilad,Y. and Pritchard,J.K. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol., 12, R10.
-
(2011)
Genome Biol.
, vol.12
, pp. R10
-
-
Bell, J.T.1
Pai, A.A.2
Pickrell, J.K.3
Gaffney, D.J.4
Pique-Regi, R.5
Degner, J.F.6
Gilad, Y.7
Pritchard, J.K.8
-
61
-
-
0035901508
-
Glucocorticoid-induced DNA demethylation and gene memory during development
-
Thomassin,H., Flavin,M., Espinas,M.L. and Grange,T. (2001) Glucocorticoid-induced DNA demethylation and gene memory during development. EMBO J., 20, 1974-1983.
-
(2001)
EMBO J.
, vol.20
, pp. 1974-1983
-
-
Thomassin, H.1
Flavin, M.2
Espinas, M.L.3
Grange, T.4
-
62
-
-
84943543379
-
Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin
-
Yang,X., Shao,X., Gao,L. and Zhang,S. (2015) Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. Hum. Mol. Genet., 24, 4374-4384.
-
(2015)
Hum. Mol. Genet.
, vol.24
, pp. 4374-4384
-
-
Yang, X.1
Shao, X.2
Gao, L.3
Zhang, S.4
-
63
-
-
84930221683
-
Modeling the relationship of epigenetic modifications to transcription factor binding
-
Liu,L., Jin,G. and Zhou,X. (2015) Modeling the relationship of epigenetic modifications to transcription factor binding. Nucleic Acids Res., 43, 3873-3885.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 3873-3885
-
-
Liu, L.1
Jin, G.2
Zhou, X.3
-
64
-
-
84929836984
-
Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage
-
Carrio,E., Diez-Villanueva,A., Lois,S., Mallona,I., Cases,I., Forn,M., Peinado,M.A. and Suelves,M. (2015) Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. Stem Cells, 33, 2025-2036.
-
(2015)
Stem Cells
, vol.33
, pp. 2025-2036
-
-
Carrio, E.1
Diez-Villanueva, A.2
Lois, S.3
Mallona, I.4
Cases, I.5
Forn, M.6
Peinado, M.A.7
Suelves, M.8
-
65
-
-
84905705842
-
Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma
-
Affer,M., Chesi,M., Chen,W.D., Keats,J.J., Demchenko,Y.N., Tamizhmani,K., Garbitt,V.M., Riggs,D.L., Brents,L.A., Roschke,A.V. et al. (2014) Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma. Leukemia, 28, 1725-1735.
-
(2014)
Leukemia
, vol.28
, pp. 1725-1735
-
-
Affer, M.1
Chesi, M.2
Chen, W.D.3
Keats, J.J.4
Demchenko, Y.N.5
Tamizhmani, K.6
Garbitt, V.M.7
Riggs, D.L.8
Brents, L.A.9
Roschke, A.V.10
-
66
-
-
84876222028
-
Selective inhibition of tumor oncogenes by disruption of super-enhancers
-
Loven,J., Hoke,H.A., Lin,C.Y., Lau,A., Orlando,D.A., Vakoc,C.R., Bradner,J.E., Lee,T.I. and Young,R.A. (2013) Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell, 153, 320-334.
-
(2013)
Cell
, vol.153
, pp. 320-334
-
-
Loven, J.1
Hoke, H.A.2
Lin, C.Y.3
Lau, A.4
Orlando, D.A.5
Vakoc, C.R.6
Bradner, J.E.7
Lee, T.I.8
Young, R.A.9
-
67
-
-
84983775821
-
Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
-
Wu,H., Xu,T., Feng,H., Chen,L., Li,B., Yao,B., Qin,Z., Jin,P. and Conneely,K.N. (2015) Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res., doi:10.1093/nar/gkv1715.
-
(2015)
Nucleic Acids Res.
-
-
Wu, H.1
Xu, T.2
Feng, H.3
Chen, L.4
Li, B.5
Yao, B.6
Qin, Z.7
Jin, P.8
Conneely, K.N.9
-
68
-
-
84938495948
-
Human body epigenome maps reveal noncanonical DNA methylation variation
-
Schultz,M.D., He,Y., Whitaker,J.W., Hariharan,M., Mukamel,E.A., Leung,D., Rajagopal,N., Nery,J.R., Urich,M.A., Chen,H. et al. (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature, 523, 212-216.
-
(2015)
Nature
, vol.523
, pp. 212-216
-
-
Schultz, M.D.1
He, Y.2
Whitaker, J.W.3
Hariharan, M.4
Mukamel, E.A.5
Leung, D.6
Rajagopal, N.7
Nery, J.R.8
Urich, M.A.9
Chen, H.10
-
69
-
-
84937203002
-
Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
-
Cacchiarelli,D., Trapnell,C., Ziller,M.J., Soumillon,M., Cesana,M., Karnik,R., Donaghey,J., Smith,Z.D., Ratanasirintrawoot,S., Zhang,X. et al. (2015) Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell, 162, 412-424.
-
(2015)
Cell
, vol.162
, pp. 412-424
-
-
Cacchiarelli, D.1
Trapnell, C.2
Ziller, M.J.3
Soumillon, M.4
Cesana, M.5
Karnik, R.6
Donaghey, J.7
Smith, Z.D.8
Ratanasirintrawoot, S.9
Zhang, X.10
-
70
-
-
84924601067
-
Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
-
Farlik,M., Sheffield,N.C., Nuzzo,A., Datlinger,P., Schonegger,A., Klughammer,J. and Bock,C. (2015) Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep., 10, 1386-1397.
-
(2015)
Cell Rep.
, vol.10
, pp. 1386-1397
-
-
Farlik, M.1
Sheffield, N.C.2
Nuzzo, A.3
Datlinger, P.4
Schonegger, A.5
Klughammer, J.6
Bock, C.7
-
71
-
-
84862161024
-
DiseaseMeth: A human disease methylation database
-
Lv,J., Liu,H., Su,J., Wu,X., Li,B., Xiao,X., Wang,F., Wu,Q. and Zhang,Y. (2012) DiseaseMeth: a human disease methylation database. Nucleic Acids Res., 40, D1030-D1035.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D1030-D1035
-
-
Lv, J.1
Liu, H.2
Su, J.3
Wu, X.4
Li, B.5
Xiao, X.6
Wang, F.7
Wu, Q.8
Zhang, Y.9
|