-
1
-
-
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
-
2
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
3
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium., et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
-
4
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
Neph, S., et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83-90 (2012
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
-
5
-
-
84865790047
-
An Integrated Encyclopedia of DNA Elements in the Human Genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
6
-
-
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
-
7
-
-
84887852466
-
Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming
-
Apostolou, E., et al. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 12, 699-712 (2013
-
(2013)
Cell Stem Cell
, vol.12
, pp. 699-712
-
-
Apostolou, E.1
-
8
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
Sanyal, A., Lajoie, B.R., Jain, G., & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
-
9
-
-
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
-
10
-
-
79959952919
-
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA
-
Splinter, E., et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev. 25, 1371-1383 (2011
-
(2011)
Genes Dev
, vol.25
, pp. 1371-1383
-
-
Splinter, E.1
-
11
-
-
84923366733
-
Chromatin architecture reorganization during stem cell differentiation
-
Dixon, J.R., et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336 (2015
-
(2015)
Nature
, vol.518
, pp. 331-336
-
-
Dixon, J.R.1
-
12
-
-
84884134904
-
The pluripotent genome in three dimensions is shaped around pluripotency factors
-
De Wit, E., et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501, 227-231 (2013
-
(2013)
Nature
, vol.501
, pp. 227-231
-
-
De Wit, E.1
-
13
-
-
84855297335
-
A decade of 3C technologies: Insights into nuclear organization
-
De Wit, E., & De Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11-24 (2012
-
(2012)
Genes Dev
, vol.26
, pp. 11-24
-
-
De Wit, E.1
De Laat, W.2
-
14
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C
-
Simonis, M., et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354 (2006
-
(2006)
Nat. Genet
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
-
15
-
-
84867003195
-
Robust 4C-seq data analysis to screen for regulatory DNA interactions
-
Van De Werken, H.J.G., et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9, 969-972 (2012
-
(2012)
Nat. Methods
, vol.9
, pp. 969-972
-
-
Van De Werken, H.J.G.1
-
16
-
-
84875143934
-
Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions
-
Stadhouders, R., et al. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nat. Protoc. 8, 509-524 (2013
-
(2013)
Nat. Protoc
, vol.8
, pp. 509-524
-
-
Stadhouders, R.1
-
17
-
-
84870310006
-
Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
-
Splinter, E., De Wit, E., Van De Werken, H.J.G., Klous, P., & De Laat, W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods 58, 221-230 (2012
-
(2012)
Methods
, vol.58
, pp. 221-230
-
-
Splinter, E.1
De Wit, E.2
Van De Werken, H.J.G.3
Klous, P.4
De Laat, W.5
-
18
-
-
84923378921
-
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
-
Jäger, R., et al. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat. Commun. 6, 6178 (2015
-
(2015)
Nat. Commun
, vol.6
, pp. 6178
-
-
Jäger, R.1
-
19
-
-
84895832107
-
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-Throughput experiment
-
Hughes, J.R., et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-Throughput experiment. Nat. Genet. 46, 205-212 (2014
-
(2014)
Nat. Genet
, vol.46
, pp. 205-212
-
-
Hughes, J.R.1
-
20
-
-
84930092058
-
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
-
Mifsud, B., et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598-606 (2015
-
(2015)
Nat. Genet
, vol.47
, pp. 598-606
-
-
Mifsud, B.1
-
21
-
-
84904412804
-
Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements
-
Kolovos, P., et al. Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 7, 10 (2014
-
(2014)
Epigenetics Chromatin
, vol.7
, pp. 10
-
-
Kolovos, P.1
-
22
-
-
84955668492
-
Multiplexed analysis of chromosome conformation at vastly improved sensitivity
-
Davies, J.O.J., et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat. Methods 13, 74-80 (2016
-
(2016)
Nat. Methods
, vol.13
, pp. 74-80
-
-
Davies, J.O.J.1
-
23
-
-
84940034154
-
Genome-wide mapping of promoter-Anchored interactions with close to single-enhancer resolution
-
Sahlén, P., et al. Genome-wide mapping of promoter-Anchored interactions with close to single-enhancer resolution. Genome Biol. 16, 156 (2015
-
(2015)
Genome Biol
, vol.16
, pp. 156
-
-
Sahlén, P.1
-
24
-
-
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
-
25
-
-
84905593782
-
Enhancer loops appear stable during development and are associated with paused polymerase
-
Ghavi-Helm, Y., et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96-100 (2014
-
(2014)
Nature
, vol.512
, pp. 96-100
-
-
Ghavi-Helm, Y.1
-
26
-
-
80054984337
-
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
-
Yaffe, E., & Tanay, A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43, 1059-1065 (2011
-
(2011)
Nat. Genet
, vol.43
, pp. 1059-1065
-
-
Yaffe, E.1
Tanay, A.2
-
27
-
-
84901838628
-
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
-
Ay, F., Bailey, T.L., & Noble, W.S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999-1011 (2014
-
(2014)
Genome Res
, vol.24
, pp. 999-1011
-
-
Ay, F.1
Bailey, T.L.2
Noble, W.S.3
-
28
-
-
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
-
29
-
-
84870463249
-
HiCNorm: Removing biases in Hi-C data via Poisson regression
-
Hu, M., et al. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics 28, 3131-3133 (2012
-
(2012)
Bioinformatics
, vol.28
, pp. 3131-3133
-
-
Hu, M.1
-
30
-
-
84856484968
-
Counting absolute numbers of molecules using unique molecular identifiers
-
Kivioja, T., et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72-74 (2012
-
(2012)
Nat. Methods
, vol.9
, pp. 72-74
-
-
Kivioja, T.1
-
31
-
-
78651514974
-
Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
-
Bantignies, F., et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214-226 (2011
-
(2011)
Cell
, vol.144
, pp. 214-226
-
-
Bantignies, F.1
-
32
-
-
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
-
33
-
-
8644275646
-
Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: Implications for cis-element identification
-
Valverde-Garduno, V., et al. Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification. Blood 104, 3106-3116 (2004
-
(2004)
Blood
, vol.104
, pp. 3106-3116
-
-
Valverde-Garduno, V.1
-
34
-
-
84867736794
-
Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis
-
Xu, J., et al. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev. Cell 23, 796-811 (2012
-
(2012)
Dev. Cell
, vol.23
, pp. 796-811
-
-
Xu, J.1
-
35
-
-
84861070995
-
Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia
-
Porcu, M., et al. Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia. Blood 119, 4476-4479 (2012
-
(2012)
Blood
, vol.119
, pp. 4476-4479
-
-
Porcu, M.1
-
36
-
-
84862245279
-
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
-
Ye, J., et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 134
-
-
Ye, J.1
-
37
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
38
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
Sexton, T., et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472 (2012
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
-
39
-
-
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
-
40
-
-
84859169877
-
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
-
Barretina, J., et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012
-
(2012)
Nature
, vol.483
, pp. 603-607
-
-
Barretina, J.1
|