-
1
-
-
84960334782
-
The 3D genome as moderator of chromosomal communication
-
Dekker, J., & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110-1121 (2016
-
(2016)
Cell
, vol.164
, pp. 1110-1121
-
-
Dekker, J.1
Mirny, L.2
-
2
-
-
84940399163
-
A long-distance chromatin affair
-
Denker, A., & de Laat, W A long-distance chromatin affair. Cell 162, 942-943 (2015
-
(2015)
Cell
, vol.162
, pp. 942-943
-
-
Denker, A.1
De Laat, W.2
-
3
-
-
84991585399
-
Organization and function of the 3D genome
-
Bonev, B., & Cavalli, G. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661-678 (2016
-
(2016)
Nat. Rev. Genet
, vol.17
, pp. 661-678
-
-
Bonev, B.1
Cavalli, G.2
-
4
-
-
84984804790
-
Genome-wide mapping and analysis of chromosome architecture
-
Schmitt, A. D., Hu, M., & Ren, B. Genome-wide mapping and analysis of chromosome architecture. Nat. Rev. Mol. Cell Biol. 17, 743-755 (2016
-
(2016)
Nat. Rev. Mol. Cell Biol
, vol.17
, pp. 743-755
-
-
Schmitt, A.D.1
Hu, M.2
Ren, B.3
-
5
-
-
0037083376
-
Capturing chromosome conformation
-
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002
-
(2002)
Science
, vol.295
, pp. 1306-1311
-
-
Dekker, J.1
Rippe, K.2
Dekker, M.3
Kleckner, N.4
-
6
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden, E., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
-
7
-
-
84885617426
-
Single-cell Hi-C reveals cell-To-cell variability in chromosome structure
-
Nagano, T., et al. Single-cell Hi-C reveals cell-To-cell variability in chromosome structure. Nature 502, 59-64 (2013
-
(2013)
Nature
, vol.502
, pp. 59-64
-
-
Nagano, T.1
-
8
-
-
84943198135
-
Modeling chromosomes: Beyond pretty pictures
-
Imakaev, M. V., Fudenberg, G., & Mirny, L. A. Modeling chromosomes: beyond pretty pictures. FEBS Lett. 589 20 Pt A, 3031-3036 (2015
-
(2015)
FEBS Lett
, vol.589
, Issue.20
, pp. 3031-3036
-
-
Imakaev, M.V.1
Fudenberg, G.2
Mirny, L.A.3
-
9
-
-
84940473396
-
An overview of genome organization and how we got there: From FISH to Hi-C
-
Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. An overview of genome organization and how we got there: from FISH to Hi-C. Microbiol. Mol. Biol. Rev. 79, 347-372 (2015
-
(2015)
Microbiol. Mol. Biol. Rev
, vol.79
, pp. 347-372
-
-
Fraser, J.1
Williamson, I.2
Bickmore, W.A.3
Dostie, J.4
-
10
-
-
0028965156
-
A random -walk/giant-loop model for interphase chromosomes
-
Sachs, R. K., van den Engh, G., Trask, B., Yokota, H., & Hearst, J. E A random-walk/giant-loop model for interphase chromosomes. Proc. Natl. Acad. Sci. USA 92, 2710-2714 (1995
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 2710-2714
-
-
Sachs, R.K.1
Van Den Engh, G.2
Trask, B.3
Yokota, H.4
Hearst, J.E.5
-
11
-
-
33745593972
-
Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence
-
Shopland, L. S., et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biol. 174, 27-38 (2006
-
(2006)
J. Cell Biol
, vol.174
, pp. 27-38
-
-
Shopland, L.S.1
-
12
-
-
33646729244
-
Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
-
Branco, M. R., & Pombo, A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol. 4, e138 (2006
-
(2006)
PLoS Biol
, vol.4
, pp. e138
-
-
Branco, M.R.1
Pombo, A.2
-
13
-
-
0037007044
-
Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates
-
Tanabe, H., et al. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc. Natl. Acad. Sci. USA 99, 4424-4429 (2002
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4424-4429
-
-
Tanabe, H.1
-
14
-
-
21844444077
-
Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes
-
Bolzer, A., et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005
-
(2005)
PLoS Biol
, vol.3
, pp. e157
-
-
Bolzer, A.1
-
15
-
-
84939489844
-
Identification of gene positioning factors using high-Throughput imaging mapping
-
Shachar, S., Voss, T. C., Pegoraro, G., Sciascia, N., & Misteli, T. Identification of gene positioning factors using high-Throughput imaging mapping. Cell 162, 911-923 (2015
-
(2015)
Cell
, vol.162
, pp. 911-923
-
-
Shachar, S.1
Voss, T.C.2
Pegoraro, G.3
Sciascia, N.4
Misteli, T.5
-
16
-
-
84863653627
-
Identification of genes that promote or antagonize somatic homolog pairing using a high-Throughput FISH-based screen
-
Joyce, E. F., Williams, B. R., Xie, T., & Wu, C.-T. Identification of genes that promote or antagonize somatic homolog pairing using a high-Throughput FISH-based screen. PLoS Genet. 8, e1002667 (2012
-
(2012)
PLoS Genet
, vol.8
, pp. e1002667
-
-
Joyce, E.F.1
Williams, B.R.2
Xie, T.3
Wu, C.-T.4
-
17
-
-
84955290042
-
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
-
Boettiger, A. N., et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418-422 (2016
-
(2016)
Nature
, vol.529
, pp. 418-422
-
-
Boettiger, A.N.1
-
18
-
-
84929180062
-
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
-
Beliveau, B. J., et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun. 6, 7147 (2015
-
(2015)
Nat. Commun
, vol.6
, pp. 7147
-
-
Beliveau, B.J.1
-
19
-
-
84946811459
-
Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states
-
Fabre, P. J., et al. Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states. Proc. Natl. Acad. Sci. USA 112, 13964-13969 (2015
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 13964-13969
-
-
Fabre, P.J.1
-
20
-
-
84992202526
-
Closing the loop: 3c versus DNA fish
-
Giorgetti, L., & Heard, E. Closing the loop: 3C versus DNA FISH. Genome Biol. 17, 215 (2016
-
(2016)
Genome Biol
, vol.17
, pp. 215
-
-
Giorgetti, L.1
Heard, E.2
-
21
-
-
79955569948
-
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
-
Hakim, O., et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21, 697-706 (2011
-
(2011)
Genome Res
, vol.21
, pp. 697-706
-
-
Hakim, O.1
-
22
-
-
84900297485
-
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription
-
Giorgetti, L., et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157, 950-963 (2014
-
(2014)
Cell
, vol.157
, pp. 950-963
-
-
Giorgetti, L.1
-
23
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao, S. S. P., et al A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.P.1
-
24
-
-
84861100147
-
Spatial partitioning of the regulatory landscape of the X-inactivation centre
-
Nora, E. P., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381-385 (2012
-
(2012)
Nature
, vol.485
, pp. 381-385
-
-
Nora, E.P.1
-
25
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon, J. R., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
-
26
-
-
84980417141
-
Spatial organization of chromatin domains and compartments in single chromosomes
-
Wang, S., et al. Spatial organization of chromatin domains and compartments in single chromosomes. Science 353, 598-602 (2016
-
(2016)
Science
, vol.353
, pp. 598-602
-
-
Wang, S.1
-
27
-
-
84918510740
-
Spatial genome organization: Contrasting views from chromosome conformation capture and fluorescence in situ hybridization
-
Williamson, I., et al. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev. 28, 2778-2791 (2014
-
(2014)
Genes Dev
, vol.28
, pp. 2778-2791
-
-
Williamson, I.1
-
28
-
-
85007356745
-
Coupling 1D modifications and 3D nuclear organization: Data, models and function
-
Jost, D., Vaillant, C., & Meister, P. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr. Opin. Cell Biol. 44, 20-27 (2017
-
(2017)
Curr. Opin. Cell Biol
, vol.44
, pp. 20-27
-
-
Jost, D.1
Vaillant, C.2
Meister, P.3
-
29
-
-
84908333387
-
Chromatin loops as allosteric modulators of enhancer-promoter interactions
-
Doyle, B., Fudenberg, G., Imakaev, M., & Mirny, L. A. Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput. Biol. 10, e1003867 (2014
-
(2014)
PLoS Comput. Biol
, vol.10
, pp. e1003867
-
-
Doyle, B.1
Fudenberg, G.2
Imakaev, M.3
Mirny, L.A.4
-
30
-
-
84872152631
-
OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation
-
Eastman, P., et al. OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation. J. Chem. Theory Comput. 9, 461-469 (2013
-
(2013)
J. Chem. Theory Comput
, vol.9
, pp. 461-469
-
-
Eastman, P.1
-
32
-
-
84943361248
-
The role of loops on the order of eukaryotes and prokaryotes
-
Hofmann, A., & Heermann, D. W. The role of loops on the order of eukaryotes and prokaryotes. FEBS Lett. 589 20 Pt A, 2958-2965 (2015
-
(2015)
FEBS Lett
, vol.589
, Issue.20 PT A
, pp. 2958-2965
-
-
Hofmann, A.1
Heermann, D.W.2
-
33
-
-
84875463382
-
Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
-
Gavrilov, A. A., et al. Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub. Nucleic Acids Res. 41, 3563-3575 (2013
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 3563-3575
-
-
Gavrilov, A.A.1
-
34
-
-
84887942741
-
Large-scale chromatin organization: The good, the surprising, and the still perplexing
-
Belmont, A. S. Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr. Opin. Cell Biol. 26, 69-78 (2014
-
(2014)
Curr. Opin. Cell Biol
, vol.26
, pp. 69-78
-
-
Belmont, A.S.1
-
35
-
-
84940023613
-
Comparison of Hi-C results using in-solution versus in-nucleus ligation
-
Nagano, T., et al. Comparison of Hi-C results using in-solution versus in-nucleus ligation. Genome Biol. 16, 175 (2015
-
(2015)
Genome Biol
, vol.16
, pp. 175
-
-
Nagano, T.1
-
36
-
-
84927779326
-
The hitchhiker?s guide to hi-c analysis: Practical guidelines
-
Lajoie, B. R., Dekker, J., & Kaplan, N. The Hitchhiker?s guide to Hi-C analysis: practical guidelines. Methods 72, 65-75 (2015
-
(2015)
Methods
, vol.72
, pp. 65-75
-
-
Lajoie, B.R.1
Dekker, J.2
Kaplan, N.3
-
37
-
-
84990923288
-
Micro-C XL: Assaying chromosome conformation from the nucleosome to the entire genome
-
Hsieh, T. S., Fudenberg, G., Goloborodko, A., & Rando, O. J. Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome. Nat. Methods 13, 1009-1011 (2016
-
(2016)
Nat. Methods
, vol.13
, pp. 1009-1011
-
-
Hsieh, T.S.1
Fudenberg, G.2
Goloborodko, A.3
Rando, O.J.4
-
38
-
-
84971324235
-
Formation of chromosomal domains by loop extrusion
-
Fudenberg, G., et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 15, 2038-2049 (2016
-
(2016)
Cell Rep
, vol.15
, pp. 2038-2049
-
-
Fudenberg, G.1
-
39
-
-
84939240549
-
A CTCF code for 3D genome architecture
-
Nichols, M. H., & Corces, V. G A CTCF code for 3D genome architecture. Cell 162, 703-705 (2015
-
(2015)
Cell
, vol.162
, pp. 703-705
-
-
Nichols, M.H.1
Corces, V.G.2
-
40
-
-
84948403758
-
Chromatin extrusion explains key features of loop and domain formation in wild-Type and engineered genomes
-
Sanborn, A. L., et al. Chromatin extrusion explains key features of loop and domain formation in wild-Type and engineered genomes. Proc. Natl. Acad. Sci. USA 112, E6456-E6465 (2015
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. E6456-E6465
-
-
Sanborn, A.L.1
-
41
-
-
85019959732
-
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
-
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife http://dx.doi.org/10.7554/eLife.25776 (2017
-
(2017)
ELife
-
-
Hansen, A.S.1
Pustova, I.2
Cattoglio, C.3
Tjian, R.4
Darzacq, X.5
-
42
-
-
85019568830
-
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
-
Nora, E. P., et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930-944 (2017
-
(2017)
Cell
, vol.169
, pp. 930-944
-
-
Nora, E.P.1
-
43
-
-
85013069660
-
Cohesin biology meets the loop extrusion model
-
Barrington, C., Finn, R., & Hadjur, S. Cohesin biology meets the loop extrusion model. Chromosom. Res. 25, 51-60 (2017
-
(2017)
Chromosom. Res
, vol.25
, pp. 51-60
-
-
Barrington, C.1
Finn, R.2
Hadjur, S.3
-
46
-
-
84969756512
-
Chromosome compaction by active loop extrusion
-
Goloborodko, A., Marko, J. F., & Mirny, L. A. Chromosome compaction by active loop extrusion. Biophys. J. 110, 2162-2168 (2016
-
(2016)
Biophys. J
, vol.110
, pp. 2162-2168
-
-
Goloborodko, A.1
Marko, J.F.2
Mirny, L.A.3
-
47
-
-
84919951683
-
Effects of topological constraints on globular polymers
-
Imakaev, M. V., Tchourine, K. M., Nechaev, S. K., & Mirny, L. A. Effects of topological constraints on globular polymers. Soft Matter 11, 665-671 (2015
-
(2015)
Soft Matter
, vol.11
, pp. 665-671
-
-
Imakaev, M.V.1
Tchourine, K.M.2
Nechaev, S.K.3
Mirny, L.A.4
-
48
-
-
84893398836
-
From a melt of rings to chromosome territories: The role of topological constraints in genome folding
-
Halverson, J. D., Smrek, J., Kremer, K., & Grosberg, A. Y. From a melt of rings to chromosome territories: the role of topological constraints in genome folding. Rep. Prog. Phys. 77, 022601 (2014
-
(2014)
Rep. Prog. Phys
, vol.77
, pp. 022601
-
-
Halverson, J.D.1
Smrek, J.2
Kremer, K.3
Grosberg, A.Y.4
-
49
-
-
84866997011
-
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
-
Imakaev, M., et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003 (2012
-
(2012)
Nat. Methods
, vol.9
, pp. 999-1003
-
-
Imakaev, M.1
|