-
1
-
-
33846283384
-
Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
-
Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet. 2007;8:104-15.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 104-115
-
-
Lanctôt, C.1
Cheutin, T.2
Cremer, M.3
Cavalli, G.4
Cremer, T.5
-
2
-
-
77956651480
-
Differentiation and large scale spatial organization of the genome
-
Joffe B, Leonhardt H, Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev. 2010;20:562-9.
-
(2010)
Curr Opin Genet Dev
, vol.20
, pp. 562-569
-
-
Joffe, B.1
Leonhardt, H.2
Solovei, I.3
-
3
-
-
80052409661
-
Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment
-
Markaki Y, Gunkel M, Schermelleh L, Beichmanis S, Neumann J, Heidemann M, et al. Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment. Cold Spring Harb Symp Quant Biol. 2010;75:475-92.
-
(2010)
Cold Spring Harb Symp Quant Biol
, vol.75
, pp. 475-492
-
-
Markaki, Y.1
Gunkel, M.2
Schermelleh, L.3
Beichmanis, S.4
Neumann, J.5
Heidemann, M.6
-
4
-
-
0035316574
-
Chromosome territories, nuclear architecture and gene regulation in mammalian cells
-
Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2:292-301.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 292-301
-
-
Cremer, T.1
Cremer, C.2
-
5
-
-
25844496592
-
The role of chromatin structure in regulating the expression of clustered genes
-
Sproul D, Gilbert N, Bickmore WA. The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet. 2005;6:775-81.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 775-781
-
-
Sproul, D.1
Gilbert, N.2
Bickmore, W.A.3
-
7
-
-
33750203582
-
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
-
Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006;38:1341-7.
-
(2006)
Nat Genet
, vol.38
, pp. 1341-1347
-
-
Zhao, Z.1
Tavoosidana, G.2
Sjölinder, M.3
Göndör, A.4
Mariano, P.5
Wang, S.6
-
8
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38:1348-54.
-
(2006)
Nat Genet
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
Klous, P.2
Splinter, E.3
Moshkin, Y.4
Willemsen, R.5
Wit, E.6
-
9
-
-
33749400168
-
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
-
Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299-309.
-
(2006)
Genome Res
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
Richmond, T.A.2
Arnaout, R.A.3
Selzer, R.R.4
Lee, W.L.5
Honan, T.A.6
-
10
-
-
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
-
11
-
-
84878011578
-
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
-
Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14:390-403.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 390-403
-
-
Dekker, J.1
Marti-Renom, M.A.2
Mirny, L.A.3
-
12
-
-
77951947926
-
Ring1b compacts chromatin structure and represses gene expression independent of histone ubiquitination
-
Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, et al. Ring1b compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell. 2010;38:452-64.
-
(2010)
Mol Cell
, vol.38
, pp. 452-464
-
-
Eskeland, R.1
Leeb, M.2
Grimes, G.R.3
Kress, C.4
Boyle, S.5
Sproul, D.6
-
13
-
-
84862917808
-
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
-
Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012;30:90-8.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 90-98
-
-
Kalhor, R.1
Tjong, H.2
Jayathilaka, N.3
Alber, F.4
Chen, L.5
-
14
-
-
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
-
15
-
-
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
-
16
-
-
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
-
17
-
-
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
-
18
-
-
84866978321
-
Organization of chromosomes during spermatogenesis and in mature sperm
-
Rousseaux S, Khochbin S, editors. Berlin, Heidelberg: Springer
-
Mudrak O, Zalenskaya I, Zalensky A. Organization of chromosomes during spermatogenesis and in mature sperm. In: Rousseaux S, Khochbin S, editors. Epigenetics and human reproduction. Berlin, Heidelberg: Springer; 2011. p. 261-77.
-
(2011)
Epigenetics and human reproduction
, pp. 261-277
-
-
Mudrak, O.1
Zalenskaya, I.2
Zalensky, A.3
-
19
-
-
78650748904
-
The sperm nucleus: chromatin, RNA, and the nuclear matrix
-
Johnson GD, Lalancette C, Linnemann AK, Leduc F, Boissonneault G, Krawetz SA. The sperm nucleus: chromatin, RNA, and the nuclear matrix. Reproduction. 2011;141:21-36.
-
(2011)
Reproduction
, vol.141
, pp. 21-36
-
-
Johnson, G.D.1
Lalancette, C.2
Linnemann, A.K.3
Leduc, F.4
Boissonneault, G.5
Krawetz, S.A.6
-
20
-
-
83755163018
-
Detecting novel associations in large data sets
-
Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, et al. Detecting novel associations in large data sets. Science. 2011;334:1518-24.
-
(2011)
Science
, vol.334
, pp. 1518-1524
-
-
Reshef, D.N.1
Reshef, Y.A.2
Finucane, H.K.3
Grossman, S.R.4
McVean, G.5
Turnbaugh, P.J.6
-
21
-
-
84888018217
-
Organization of the mitotic chromosome
-
Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, et al. Organization of the mitotic chromosome. Science. 2013;342:948-53.
-
(2013)
Science
, vol.342
, pp. 948-953
-
-
Naumova, N.1
Imakaev, M.2
Fudenberg, G.3
Zhan, Y.4
Lajoie, B.R.5
Mirny, L.A.6
-
22
-
-
84873507172
-
Bayesian inference of spatial organizations of chromosomes
-
Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, et al. Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol. 2013;9, e1002893.
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Hu, M.1
Deng, K.2
Qin, Z.3
Dixon, J.4
Selvaraj, S.5
Fang, J.6
-
23
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao SSP, 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.P.1
Huntley, M.H.2
Durand, N.C.3
Stamenova, E.K.4
Bochkov, I.D.5
Robinson, J.T.6
-
24
-
-
84895522959
-
Functional and topological characteristics of mammalian regulatory domains
-
Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, et al. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014;24:390-400.
-
(2014)
Genome Res
, vol.24
, pp. 390-400
-
-
Symmons, O.1
Uslu, V.V.2
Tsujimura, T.3
Ruf, S.4
Nassari, S.5
Schwarzer, W.6
-
25
-
-
84905401266
-
Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia
-
Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, et al. Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia. Cell. 2014;158:593-606.
-
(2014)
Cell
, vol.158
, pp. 593-606
-
-
Trimarchi, T.1
Bilal, E.2
Ntziachristos, P.3
Fabbri, G.4
Dalla-Favera, R.5
Tsirigos, A.6
-
26
-
-
84908352990
-
Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling
-
Tark-Dame M, Jerabek H, Manders EMM, Heermann DW, van Driel R. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling. PLoS Comput Biol. 2014;10, e1003877.
-
(2014)
PLoS Comput Biol
, vol.10
-
-
Tark-Dame, M.1
Jerabek, H.2
Manders, E.M.M.3
Heermann, D.W.4
Driel, R.5
-
27
-
-
77953292127
-
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa
-
Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, et al. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol. 2010;17:679-87.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 679-687
-
-
Brykczynska, U.1
Hisano, M.2
Erkek, S.3
Ramos, L.4
Oakeley, E.J.5
Roloff, T.C.6
-
28
-
-
59449110630
-
Embryonic stem cell/fibroblast hybrid cells with near-tetraploid karyotype provide high yield of chimeras
-
Kruglova AA, Kizilova EA, Zhelezova AI, Gridina MM, Golubitsa AN, Serov OL. Embryonic stem cell/fibroblast hybrid cells with near-tetraploid karyotype provide high yield of chimeras. Cell Tissue Res. 2008;334:371-80.
-
(2008)
Cell Tissue Res
, vol.334
, pp. 371-380
-
-
Kruglova, A.A.1
Kizilova, E.A.2
Zhelezova, A.I.3
Gridina, M.M.4
Golubitsa, A.N.5
Serov, O.L.6
-
29
-
-
84870379849
-
Hi-C: a comprehensive technique to capture the conformation of genomes
-
Belton J-M, 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
-
30
-
-
84939205612
-
-
Hi-C data analysis tools by Leonid Mirny lab. http://mirnylab.bitbucket.org/hiclib/ .
-
-
-
-
31
-
-
84939182315
-
-
MINE tool. http://minepy.sourceforge.net/ .
-
-
-
-
32
-
-
77952744854
-
A three-dimensional model of the yeast genome
-
Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, et al. A three-dimensional model of the yeast genome. Nature. 2010;465:363-7.
-
(2010)
Nature
, vol.465
, pp. 363-367
-
-
Duan, Z.1
Andronescu, M.2
Schutz, K.3
McIlwain, S.4
Kim, Y.J.5
Lee, C.6
-
33
-
-
0041758569
-
Two rules of thumb for the approximation of the binomial distribution by the normal distribution
-
Schader M, Schmid F. Two rules of thumb for the approximation of the binomial distribution by the normal distribution. Am Stat. 1989;43:23-4.
-
(1989)
Am Stat
, vol.43
, pp. 23-24
-
-
Schader, M.1
Schmid, F.2
-
34
-
-
84868024339
-
HiTC: Exploration of high-throughput 'C' experiments
-
Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, et al. HiTC: Exploration of high-throughput 'C' experiments. Bioinformatics. 2012;28:2843-4.
-
(2012)
Bioinformatics
, vol.28
, pp. 2843-2844
-
-
Servant, N.1
Lajoie, B.R.2
Nora, E.P.3
Giorgetti, L.4
Chen, C.J.5
Heard, E.6
|