-
1
-
-
84884294269
-
The spatial organization of the human genome
-
Bickmore WA. The spatial organization of the human genome. Annu Rev Genomics Hum Genet. 2013;14:67-84.
-
(2013)
Annu Rev Genomics Hum Genet.
, vol.14
, pp. 67-84
-
-
Bickmore, W.A.1
-
2
-
-
84903785480
-
A mechanistic link between gene regulation and genome architecture in mammalian development
-
Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev. 2014;27:92-101.
-
(2014)
Curr Opin Genet Dev.
, vol.27
, pp. 92-101
-
-
Bonora, G.1
Plath, K.2
Denholtz, M.3
-
3
-
-
84886853624
-
Topology of mammalian developmental enhancers and their regulatory landscapes
-
de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature. 2013;502:499-506.
-
(2013)
Nature.
, vol.502
, pp. 499-506
-
-
Laat, W.1
Duboule, D.2
-
4
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61-70.
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
5
-
-
84861576201
-
The landscape of cancer genes and mutational processes in breast cancer
-
Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486:400-4.
-
(2012)
Nature.
, vol.486
, pp. 400-404
-
-
Stephens, P.J.1
Tarpey, P.S.2
Davies, H.3
Loo, P.4
Greenman, C.5
Wedge, D.C.6
-
6
-
-
84885735554
-
Mutational landscape and significance across 12 major cancer types
-
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333-9.
-
(2013)
Nature.
, vol.502
, pp. 333-339
-
-
Kandoth, C.1
McLellan, M.D.2
Vandin, F.3
Ye, K.4
Niu, B.5
Lu, C.6
-
9
-
-
77951726845
-
Cancer nucleus: morphology and beyond
-
Dey P. Cancer nucleus: morphology and beyond. Diagn Cytopathol. 2010;38:382-90.
-
(2010)
Diagn Cytopathol.
, vol.38
, pp. 382-390
-
-
Dey, P.1
-
10
-
-
84876838711
-
The hierarchy of the 3D genome
-
Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013;49:773-82.
-
(2013)
Mol Cell.
, vol.49
, pp. 773-782
-
-
Gibcus, J.H.1
Dekker, J.2
-
11
-
-
33646526019
-
Chromosome territories--a functional nuclear landscape
-
Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol. 2006;18:307-16.
-
(2006)
Curr Opin Cell Biol.
, vol.18
, pp. 307-316
-
-
Cremer, T.1
Cremer, M.2
Dietzel, S.3
Muller, S.4
Solovei, I.5
Fakan, S.6
-
12
-
-
0034750744
-
Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells
-
Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, et al. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 2001;9:541-67.
-
(2001)
Chromosome Res.
, vol.9
, pp. 541-567
-
-
Cremer, M.1
Hase, J.2
Volm, T.3
Brero, A.4
Kreth, G.5
Walter, J.6
-
13
-
-
21844444077
-
Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes
-
Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 2005;3:e157.
-
(2005)
PLoS Biol.
, vol.3
, pp. e157
-
-
Bolzer, A.1
Kreth, G.2
Solovei, I.3
Koehler, D.4
Saracoglu, K.5
Fauth, C.6
-
15
-
-
0036233630
-
Alteration of large-scale chromatin structure by estrogen receptor
-
Nye AC, Rajendran RR, Stenoien DL, Mancini MA, Katzenellenbogen BS, Belmont AS. Alteration of large-scale chromatin structure by estrogen receptor. Mol Cell Biol. 2002;22:3437-49.
-
(2002)
Mol Cell Biol.
, vol.22
, pp. 3437-3449
-
-
Nye, A.C.1
Rajendran, R.R.2
Stenoien, D.L.3
Mancini, M.A.4
Katzenellenbogen, B.S.5
Belmont, A.S.6
-
16
-
-
74049123435
-
Disease-specific gene repositioning in breast cancer
-
Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol. 2009;187:801-12.
-
(2009)
J Cell Biol.
, vol.187
, pp. 801-812
-
-
Meaburn, K.J.1
Gudla, P.R.2
Khan, S.3
Lockett, S.J.4
Misteli, T.5
-
17
-
-
38349080953
-
Locus-specific and activity-independent gene repositioning during early tumorigenesis
-
Meaburn KJ, Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol. 2008;180:39-50.
-
(2008)
J Cell Biol.
, vol.180
, pp. 39-50
-
-
Meaburn, K.J.1
Misteli, T.2
-
18
-
-
0038054340
-
Spatial proximity of translocation-prone gene loci in human lymphomas
-
Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet. 2003;34:287-91.
-
(2003)
Nat Genet.
, vol.34
, pp. 287-291
-
-
Roix, J.J.1
McQueen, P.G.2
Munson, P.J.3
Parada, L.A.4
Misteli, T.5
-
19
-
-
84866870443
-
Close proximity to Igh is a contributing factor to AID-mediated translocations
-
Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, et al. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell. 2012;47:873-85.
-
(2012)
Mol Cell.
, vol.47
, pp. 873-885
-
-
Rocha, P.P.1
Micsinai, M.2
Kim, J.R.3
Hewitt, S.L.4
Souza, P.P.5
Trimarchi, T.6
-
20
-
-
84862778059
-
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations
-
Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012;148:908-21.
-
(2012)
Cell.
, vol.148
, pp. 908-921
-
-
Zhang, Y.1
McCord, R.P.2
Ho, Y.J.3
Lajoie, B.R.4
Hildebrand, D.G.5
Simon, A.C.6
-
21
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289-93.
-
(2009)
Science.
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
-
22
-
-
84873349707
-
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome
-
McCord RP, Nazario-Toole A, Zhang H, Chines PS, Zhan Y, Erdos MR, et al. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013;23:260-9.
-
(2013)
Genome Res.
, vol.23
, pp. 260-269
-
-
McCord, R.P.1
Nazario-Toole, A.2
Zhang, H.3
Chines, P.S.4
Zhan, Y.5
Erdos, M.R.6
-
23
-
-
84890504911
-
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
-
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res. 2013;23:2066-77.
-
(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
-
24
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-80.
-
(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
-
25
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381-5.
-
(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
-
26
-
-
84881613036
-
Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?
-
Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays. 2013;35:818-28.
-
(2013)
Bioessays.
, vol.35
, pp. 818-828
-
-
Nora, E.P.1
Dekker, J.2
Heard, E.3
-
27
-
-
84900297485
-
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription
-
Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell. 2014;157:950-63.
-
(2014)
Cell.
, vol.157
, pp. 950-963
-
-
Giorgetti, L.1
Galupa, R.2
Nora, E.P.3
Piolot, T.4
Lam, F.5
Dekker, J.6
-
28
-
-
84907512608
-
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
-
Le Dily F, Bau D, Pohl A, Vicent GP, Serra F, Soronellas D, et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev. 2014;28:2151-62.
-
(2014)
Genes Dev.
, vol.28
, pp. 2151-2162
-
-
Dily, F.1
Bau, D.2
Pohl, A.3
Vicent, G.P.4
Serra, F.5
Soronellas, D.6
-
29
-
-
70449103609
-
An oestrogen-receptor-alpha-bound human chromatin interactome
-
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462:58-64.
-
(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
-
30
-
-
84862908850
-
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
-
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84-98.
-
(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
-
31
-
-
84881171344
-
Enhancer transcripts mark active estrogen receptor binding sites
-
Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013;23:1210-23.
-
(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
-
32
-
-
84881510124
-
Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer
-
Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, et al. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell. 2013;24:197-212.
-
(2013)
Cancer Cell.
, vol.24
, pp. 197-212
-
-
Hsu, P.Y.1
Hsu, H.K.2
Lan, X.3
Juan, L.4
Yan, P.S.5
Labanowska, J.6
-
33
-
-
84915756658
-
Estrogen induces global reorganization of chromatin structure in human breast cancer cells
-
Mourad R, Hsu PY, Juan L, Shen C, Koneru P, Lin H, et al. Estrogen induces global reorganization of chromatin structure in human breast cancer cells. PLoS One. 2014;9:e113354.
-
(2014)
PLoS One.
, vol.9
, pp. e113354
-
-
Mourad, R.1
Hsu, P.Y.2
Juan, L.3
Shen, C.4
Koneru, P.5
Lin, H.6
-
34
-
-
84873027803
-
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
-
Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, et al. Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics. 2013;14:70.
-
(2013)
BMC Genomics.
, vol.14
, pp. 70
-
-
Wang, J.1
Lan, X.2
Hsu, P.Y.3
Hsu, H.K.4
Huang, K.5
Parvin, J.6
-
35
-
-
84884915535
-
Estrogen represses gene expression through reconfiguring chromatin structures
-
Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, et al. Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Res. 2013;41:8061-71.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 8061-8071
-
-
Osmanbeyoglu, H.U.1
Lu, K.N.2
Oesterreich, S.3
Day, R.S.4
Benos, P.V.5
Coronnello, C.6
-
36
-
-
44849142755
-
Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer
-
Barnett DH, Sheng S, Charn TH, Waheed A, Sly WS, Lin CY, et al. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. Cancer Res. 2008;68:3505-15.
-
(2008)
Cancer Res.
, vol.68
, pp. 3505-3515
-
-
Barnett, D.H.1
Sheng, S.2
Charn, T.H.3
Waheed, A.4
Sly, W.S.5
Lin, C.Y.6
-
37
-
-
46849122491
-
E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements
-
Bretschneider N, Kangaspeska S, Seifert M, Reid G, Gannon F, Denger S. E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements. Mol Oncol. 2008;2:182-90.
-
(2008)
Mol Oncol.
, vol.2
, pp. 182-190
-
-
Bretschneider, N.1
Kangaspeska, S.2
Seifert, M.3
Reid, G.4
Gannon, F.5
Denger, S.6
-
38
-
-
65549121213
-
Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1alpha,25-dihydroxyvitamin D3
-
Saramaki A, Diermeier S, Kellner R, Laitinen H, Vaisanen S, Carlberg C. Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1alpha,25-dihydroxyvitamin D3. J Biol Chem. 2009;284:8073-82.
-
(2009)
J Biol Chem.
, vol.284
, pp. 8073-8082
-
-
Saramaki, A.1
Diermeier, S.2
Kellner, R.3
Laitinen, H.4
Vaisanen, S.5
Carlberg, C.6
-
39
-
-
77954910711
-
The number of vitamin D receptor binding sites defines the different vitamin D responsiveness of the CYP24 gene in malignant and normal mammary cells
-
Matilainen JM, Malinen M, Turunen MM, Carlberg C, Vaisanen S. The number of vitamin D receptor binding sites defines the different vitamin D responsiveness of the CYP24 gene in malignant and normal mammary cells. J Biol Chem. 2010;285:24174-83.
-
(2010)
J Biol Chem.
, vol.285
, pp. 24174-24183
-
-
Matilainen, J.M.1
Malinen, M.2
Turunen, M.M.3
Carlberg, C.4
Vaisanen, S.5
-
40
-
-
77749323471
-
Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells
-
Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol. 2010;30:1411-20.
-
(2010)
Mol Cell Biol.
, vol.30
, pp. 1411-1420
-
-
Wright, J.B.1
Brown, S.J.2
Cole, M.D.3
-
41
-
-
84883315768
-
Genomic interaction profiles in breast cancer reveal altered chromatin architecture
-
Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, et al. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One. 2013;8:e73974.
-
(2013)
PLoS One.
, vol.8
, pp. e73974
-
-
Zeitz, M.J.1
Ay, F.2
Heidmann, J.D.3
Lerner, P.L.4
Noble, W.S.5
Steelman, B.N.6
-
42
-
-
84923823453
-
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
-
Dryden NH, Broome LR, Dudbridge F, Johnson N, Orr N, Schoenfelder S, et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res. 2014;24:1854-68.
-
(2014)
Genome Res.
, vol.24
, pp. 1854-1868
-
-
Dryden, N.H.1
Broome, L.R.2
Dudbridge, F.3
Johnson, N.4
Orr, N.5
Schoenfelder, S.6
-
43
-
-
84895832107
-
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
-
Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet. 2014;46:205-12.
-
(2014)
Nat Genet.
, vol.46
, pp. 205-212
-
-
Hughes, J.R.1
Roberts, N.2
McGowan, S.3
Hay, D.4
Giannoulatou, E.5
Lynch, M.6
-
44
-
-
84899652185
-
Classifying leukemia types with chromatin conformation data
-
Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, et al. Classifying leukemia types with chromatin conformation data. Genome Biol. 2014;15:R60.
-
(2014)
Genome Biol.
, vol.15
, pp. R60
-
-
Rousseau, M.1
Ferraiuolo, M.A.2
Crutchley, J.L.3
Wang, X.Q.4
Miura, H.5
Blanchette, M.6
-
45
-
-
78349288865
-
Higher-order genome organization in human disease
-
Misteli T. Higher-order genome organization in human disease. Cold Spring Harb Perspect Biol. 2010;2:a000794.
-
(2010)
Cold Spring Harb Perspect Biol.
, vol.2
, pp. a000794
-
-
Misteli, T.1
-
46
-
-
84870379849
-
Hi-C: a comprehensive technique to capture the conformation of genomes
-
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods. 2012;58:268-76.
-
(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.6
-
47
-
-
84927779326
-
The Hitchhiker's guide to Hi-C analysis: Practical guidelines
-
Lajoie BR, Dekker J, Kaplan N. The Hitchhiker's guide to Hi-C analysis: Practical guidelines. Methods. 2015;72:65-75.
-
(2015)
Methods.
, vol.72
, pp. 65-75
-
-
Lajoie, B.R.1
Dekker, J.2
Kaplan, N.3
-
48
-
-
84866997011
-
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
-
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9:999-1003.
-
(2012)
Nat Methods.
, vol.9
, pp. 999-1003
-
-
Imakaev, M.1
Fudenberg, G.2
McCord, R.P.3
Naumova, N.4
Goloborodko, A.5
Lajoie, B.R.6
-
49
-
-
0033732413
-
Molecular cytogenetic analysis of breast cancer cell lines
-
Davidson JM, Gorringe KL, Chin SF, Orsetti B, Besret C, Courtay-Cahen C, et al. Molecular cytogenetic analysis of breast cancer cell lines. Br J Cancer. 2000;83:1309-17.
-
(2000)
Br J Cancer.
, vol.83
, pp. 1309-1317
-
-
Davidson, J.M.1
Gorringe, K.L.2
Chin, S.F.3
Orsetti, B.4
Besret, C.5
Courtay-Cahen, C.6
-
50
-
-
67651007228
-
Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines
-
Marella NV, Malyavantham KS, Wang J, Matsui S, Liang P, Berezney R. Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines. Cancer Res. 2009;69:5946-53.
-
(2009)
Cancer Res.
, vol.69
, pp. 5946-5953
-
-
Marella, N.V.1
Malyavantham, K.S.2
Wang, J.3
Matsui, S.4
Liang, P.5
Berezney, R.6
-
51
-
-
67650252530
-
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery
-
Kao J, Salari K, Bocanegra M, Choi YL, Girard L, Gandhi J, et al. Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One. 2009;4:e6146.
-
(2009)
PLoS One.
, vol.4
, pp. e6146
-
-
Kao, J.1
Salari, K.2
Bocanegra, M.3
Choi, Y.L.4
Girard, L.5
Gandhi, J.6
-
52
-
-
84923366733
-
Chromatin architecture reorganization during stem cell differentiation
-
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518:331-6.
-
(2015)
Nature.
, vol.518
, pp. 331-336
-
-
Dixon, J.R.1
Jung, I.2
Selvaraj, S.3
Shen, Y.4
Antosiewicz-Bourget, J.E.5
Lee, A.Y.6
-
53
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665-80.
-
(2014)
Cell.
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.1
Huntley, M.H.2
Durand, N.C.3
Stamenova, E.K.4
Bochkov, I.D.5
Robinson, J.T.6
-
54
-
-
85006305723
-
Insulator function and topological domain border strength scale with architectural protein occupancy
-
Van Bortle K, Nichols MH, Li L, Ong CT, Takenaka N, Qin ZS, et al. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol. 2014;15:R82.
-
(2014)
Genome Biol.
, vol.15
, pp. R82
-
-
Bortle, K.1
Nichols, M.H.2
Li, L.3
Ong, C.T.4
Takenaka, N.5
Qin, Z.S.6
-
55
-
-
84911478490
-
Topologically associating domains are stable units of replication-timing regulation
-
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014;515:402-5.
-
(2014)
Nature.
, vol.515
, pp. 402-405
-
-
Pope, B.D.1
Ryba, T.2
Dileep, V.3
Yue, F.4
Wu, W.5
Denas, O.6
-
56
-
-
84891780257
-
Higher-order chromatin domains link eQTLs with the expression of far-away genes
-
Duggal G, Wang H, Kingsford C. Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Res. 2014;42:87-96.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 87-96
-
-
Duggal, G.1
Wang, H.2
Kingsford, C.3
-
57
-
-
84873288058
-
Integrative eQTL-based analyses reveal the biology of breast cancer risk loci
-
Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, et al. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell. 2013;152:633-41.
-
(2013)
Cell.
, vol.152
, pp. 633-641
-
-
Li, Q.1
Seo, J.H.2
Stranger, B.3
McKenna, A.4
Pe'er, I.5
Laframboise, T.6
-
58
-
-
84875398193
-
A model of the large-scale organization of chromatin
-
Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, et al. A model of the large-scale organization of chromatin. Biochem Soc Trans. 2013;41:508-12.
-
(2013)
Biochem Soc Trans.
, vol.41
, pp. 508-512
-
-
Barbieri, M.1
Chotalia, M.2
Fraser, J.3
Lavitas, L.M.4
Dostie, J.5
Pombo, A.6
-
59
-
-
0036795327
-
Conservation of relative chromosome positioning in normal and cancer cells
-
Parada LA, McQueen PG, Munson PJ, Misteli T. Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol. 2002;12:1692-7.
-
(2002)
Curr Biol.
, vol.12
, pp. 1692-1697
-
-
Parada, L.A.1
McQueen, P.G.2
Munson, P.J.3
Misteli, T.4
-
60
-
-
35648941611
-
Moving chromatin within the interphase nucleus-controlled transitions?
-
Chuang CH, Belmont AS. Moving chromatin within the interphase nucleus-controlled transitions? Semin Cell Dev Biol. 2007;18:698-706.
-
(2007)
Semin Cell Dev Biol.
, vol.18
, pp. 698-706
-
-
Chuang, C.H.1
Belmont, A.S.2
-
61
-
-
84918539650
-
Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells
-
Therizols P, Illingworth RS, Courilleau C, Boyle S, Wood AJ, Bickmore WA. Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells. Science. 2014;346:1238-42.
-
(2014)
Science.
, vol.346
, pp. 1238-1242
-
-
Therizols, P.1
Illingworth, R.S.2
Courilleau, C.3
Boyle, S.4
Wood, A.J.5
Bickmore, W.A.6
-
62
-
-
70349158606
-
Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination
-
Draskovic I, Arnoult N, Steiner V, Bacchetti S, Lomonte P, Londono-Vallejo A. Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination. Proc Natl Acad Sci U S A. 2009;106:15726-31.
-
(2009)
Proc Natl Acad Sci U S A.
, vol.106
, pp. 15726-15731
-
-
Draskovic, I.1
Arnoult, N.2
Steiner, V.3
Bacchetti, S.4
Lomonte, P.5
Londono-Vallejo, A.6
-
63
-
-
80053229934
-
Prevalence of the alternative lengthening of telomeres telomere maintenance mechanism in human cancer subtypes
-
Heaphy CM, Subhawong AP, Hong SM, Goggins MG, Montgomery EA, Gabrielson E, et al. Prevalence of the alternative lengthening of telomeres telomere maintenance mechanism in human cancer subtypes. Am J Pathol. 2011;179:1608-15.
-
(2011)
Am J Pathol.
, vol.179
, pp. 1608-1615
-
-
Heaphy, C.M.1
Subhawong, A.P.2
Hong, S.M.3
Goggins, M.G.4
Montgomery, E.A.5
Gabrielson, E.6
-
64
-
-
0037603113
-
Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures
-
Debnath J, Muthuswamy SK, Brugge JS. Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods. 2003;30:256-68.
-
(2003)
Methods.
, vol.30
, pp. 256-268
-
-
Debnath, J.1
Muthuswamy, S.K.2
Brugge, J.S.3
-
65
-
-
84965186660
-
Lighter: fast and memory-efficient sequencing error correction without counting
-
Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 2014;15:509.
-
(2014)
Genome Biol.
, vol.15
, pp. 509
-
-
Song, L.1
Florea, L.2
Langmead, B.3
-
66
-
-
79961123152
-
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
-
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
67
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
68
-
-
70449477656
-
Next generation software for functional trend analysis
-
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics. 2009;25:3043-3044.
-
(2009)
Bioinformatics
, vol.25
, pp. 3043-3044
-
-
Berriz, G.F.1
Beaver, J.E.2
Cenik, C.3
Tasan, M.4
Roth, F.P.5
-
69
-
-
84899493057
-
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
-
Shen L, Shao N, Liu X, Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284.
-
(2014)
BMC Genomics.
, vol.15
, pp. 284
-
-
Shen, L.1
Shao, N.2
Liu, X.3
Nestler, E.4
-
70
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489:109-13.
-
(2012)
Nature.
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
-
71
-
-
84949227547
-
BEDTools: The Swiss-army tool for genome feature analysis
-
11 12
-
Quinlan AR. BEDTools: The Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11 12 11-34.
-
(2014)
Curr Protoc Bioinformatics
, vol.47
, pp. 11-34
-
-
Quinlan, A.R.1
|