-
1
-
-
84862778066
-
Intragenic enhancers act as alternative promoters
-
Kowalczyk, M.S. et al. Intragenic enhancers act as alternative promoters. Mol. Cell 45, 447-458 (2012
-
(2012)
Mol. Cell
, vol.45
, pp. 447-458
-
-
Kowalczyk, M.S.1
-
2
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
-
3
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
-
4
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
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
-
-
-
5
-
-
84870317191
-
3C-based technologies to study the shape of the genome
-
De Laat, W. & Dekker, J. 3C-based technologies to study the shape of the genome. Methods 58, 189-191 (2012
-
(2012)
Methods
, vol.58
, pp. 189-191
-
-
De Laat, W.1
Dekker, J.2
-
6
-
-
84872446709
-
Methods for identifying higher-order chromatin structure
-
Sajan, S.A. & Hawkins, R.D. Methods for identifying higher-order chromatin structure. Annu. Rev. Genomics Hum. Genet. 13, 59-82 (2012
-
(2012)
Annu. Rev. Genomics Hum. Genet
, vol.13
, pp. 59-82
-
-
Sajan, S.A.1
Hawkins, R.D.2
-
7
-
-
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
-
8
-
-
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
-
9
-
-
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
-
10
-
-
84867003195
-
Robust 4C-seq data analysis to screen for regulatory DNA interactions
-
van De Werken, H.J. 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.1
-
11
-
-
84865777825
-
Linking disease associations with regulatory information in the human genome
-
Schaub, M.A., Boyle, A.P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012
-
(2012)
Genome Res
, vol.22
, pp. 1748-1759
-
-
Schaub, M.A.1
Boyle, A.P.2
Kundaje, A.3
Batzoglou, S.4
Snyder, M.5
-
12
-
-
77953565946
-
Whole exome capture in solution with 3 Gbp of data
-
Bainbridge, M.N. et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol. 11, R62 (2010
-
(2010)
Genome Biol
, vol.11
-
-
Bainbridge, M.N.1
-
13
-
-
39449139894
-
High-resolution circular chromosome conformation capture assay
-
Göndör, A., Rougier, C. & Ohlsson, R. High-resolution circular chromosome conformation capture assay. Nat. Protoc. 3, 303-313 (2008
-
(2008)
Nat. Protoc
, vol.3
, pp. 303-313
-
-
Göndör, A.1
Rougier, C.2
Ohlsson, R.3
-
14
-
-
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
-
15
-
-
22244458301
-
Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences
-
Hughes, J.R. et al. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc. Natl. Acad. Sci. USA 102, 9830-9835 (2005
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 9830-9835
-
-
Hughes, J.R.1
-
16
-
-
39049120185
-
Tissue-specific histone modification and transcription factor binding in a globin gene expression
-
De Gobbi, M. et al. Tissue-specific histone modification and transcription factor binding in a globin gene expression. Blood 110, 4503-4510 (2007
-
(2007)
Blood
, vol.110
, pp. 4503-4510
-
-
De Gobbi, M.1
-
17
-
-
29444452159
-
Defining a genomic radius for long-range enhancer action: Duplicated conserved non-coding elements hold the key
-
Vavouri, T., McEwen, G.K., Woolfe, A., Gilks, W.R. & Elgar, G. Defining a genomic radius for long-range enhancer action: Duplicated conserved non-coding elements hold the key. Trends Genet. 22, 5-10 (2006
-
(2006)
Trends Genet
, vol.22
, pp. 5-10
-
-
Vavouri, T.1
McEwen, G.K.2
Woolfe, A.3
Gilks, W.R.4
Elgar, G.5
-
18
-
-
33846011896
-
Manipulating the mouse genome to engineer precise functional syntenic replacements with human sequence
-
Wallace, H.A. et al. Manipulating the mouse genome to engineer precise functional syntenic replacements with human sequence. Cell 128, 197-209 (2007
-
(2007)
Cell
, vol.128
, pp. 197-209
-
-
Wallace, H.A.1
-
19
-
-
76049106672
-
Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition
-
Lower, K.M. et al. Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition. Proc. Natl. Acad. Sci. USA 106, 21771-21776 (2009
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 21771-21776
-
-
Lower, K.M.1
-
20
-
-
76049125820
-
Chromosome looping at the human a-globin locus is mediated via the major upstream regulatory element (HS-40
-
Vernimmen, D. et al. Chromosome looping at the human a-globin locus is mediated via the major upstream regulatory element (HS-40). Blood 114, 4253-4260 (2009
-
(2009)
Blood
, vol.114
, pp. 4253-4260
-
-
Vernimmen, D.1
-
21
-
-
78650994865
-
The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules
-
Ba?, D. et al. The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules. Nat. Struct. Mol. Biol. 18, 107-114 (2011
-
(2011)
Nat. Struct. Mol. Biol
, vol.18
, pp. 107-114
-
-
Baù, D.1
-
22
-
-
84877124067
-
High-resolution analysis of cis-Acting regulatory networks at the a-globin locus
-
Hughes, J.R. et al. High-resolution analysis of cis-Acting regulatory networks at the a-globin locus. Phil. Trans. R. Soc. Lond. B 368, 20120361 (2013
-
(2013)
Phil. Trans. R. Soc. Lond. B
, vol.368
, pp. 20120361
-
-
Hughes, J.R.1
-
23
-
-
34247272882
-
Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression
-
Vernimmen, D., De Gobbi, M., Sloane-Stanley, J.A., Wood, W.G. & Higgs, D.R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J. 26, 2041-2051 (2007
-
(2007)
EMBO J.
, vol.26
, pp. 2041-2051
-
-
Vernimmen, D.1
De Gobbi, M.2
Sloane-Stanley, J.A.3
Wood, W.G.4
Higgs, D.R.5
-
24
-
-
84874705284
-
Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression
-
Ferreira, R. et al. Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression. Mol. Cell. Biol. 33, 1254-1266 (2013
-
(2013)
Mol. Cell. Biol
, vol.33
, pp. 1254-1266
-
-
Ferreira, R.1
-
25
-
-
35148870447
-
The SCL +40 enhancer targets the midbrain together with primitive and definitive hematopoiesis and is regulated by SCL and GATA proteins
-
Ogilvy, S. et al. The SCL +40 enhancer targets the midbrain together with primitive and definitive hematopoiesis and is regulated by SCL and GATA proteins. Mol. Cell. Biol. 27, 7206-7219 (2007
-
(2007)
Mol. Cell. Biol
, vol.27
, pp. 7206-7219
-
-
Ogilvy, S.1
-
26
-
-
2942526253
-
The scl +18/19 stem cell enhancer is not required for hematopoiesis: Identification of a 5' bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1
-
Göttgens, B. et al. The scl +18/19 stem cell enhancer is not required for hematopoiesis: Identification of a 5' bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1. Mol. Cell. Biol. 24, 1870-1883 (2004
-
(2004)
Mol. Cell. Biol
, vol.24
, pp. 1870-1883
-
-
Göttgens, B.1
-
27
-
-
79953080042
-
HIF1a synergizes with glucocorticoids to promote BFU-E progenitor self-renewal
-
Flygare, J., Rayon Estrada, V., Shin, C., Gupta, S. & Lodish, H.F. HIF1a synergizes with glucocorticoids to promote BFU-E progenitor self-renewal. Blood 117, 3435-3444 (2011
-
(2011)
Blood
, vol.117
, pp. 3435-3444
-
-
Flygare, J.1
Rayon Estrada, V.2
Shin, C.3
Gupta, S.4
Lodish, H.F.5
-
28
-
-
33644748145
-
Mitoferrin is essential for erythroid iron assimilation
-
Shaw, G.C. et al. Mitoferrin is essential for erythroid iron assimilation. Nature 440, 96-100 (2006
-
(2006)
Nature
, vol.440
, pp. 96-100
-
-
Shaw, G.C.1
-
29
-
-
79953790695
-
Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis
-
Amigo, J.D. et al. Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis. Mol. Cell. Biol. 31, 1344-1356 (2011
-
(2011)
Mol. Cell. Biol
, vol.31
, pp. 1344-1356
-
-
Amigo, J.D.1
-
30
-
-
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
-
31
-
-
84879662840
-
Causes and consequences of chromatin variation between inbred mice
-
Hosseini, M. et al. Causes and consequences of chromatin variation between inbred mice. PLoS Genet. 9, e1003570 (2013
-
(2013)
PLoS Genet
, vol.9
-
-
Hosseini, M.1
-
32
-
-
3042559681
-
Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase
-
Kang, J.H. et al. Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase. Eur. J. Biochem. 271, 2452-2461 (2004
-
(2004)
Eur. J. Biochem
, vol.271
, pp. 2452-2461
-
-
Kang, J.H.1
-
33
-
-
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
-
34
-
-
57649136554
-
Progress and challenges in genome-wide association studies in humans
-
Donnelly, P. Progress and challenges in genome-wide association studies in humans. Nature 456, 728-731 (2008
-
(2008)
Nature
, vol.456
, pp. 728-731
-
-
Donnelly, P.1
-
35
-
-
84872040426
-
Chapter 11: Genome-wide association studies
-
Bush, W.S. & Moore, J.H. Chapter 11: Genome-wide association studies. PLoS Comput. Biol. 8, e1002822 (2012
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Bush, W.S.1
Moore, J.H.2
-
36
-
-
84875156063
-
Enhancers: Five essential questions
-
Pennacchio, L.A., Bickmore, W., Dean, A., Nobrega, M.A. & Bejerano, G. Enhancers: Five essential questions. Nat. Rev. Genet. 14, 288-295 (2013
-
(2013)
Nat. Rev. Genet
, vol.14
, pp. 288-295
-
-
Pennacchio, L.A.1
Bickmore, W.2
Dean, A.3
Nobrega, M.A.4
Bejerano, G.5
-
37
-
-
84855508402
-
Enhancers and silencers: An integrated and simple model for their function
-
Kolovos, P., Knoch, T.A., Grosveld, F.G., Cook, P.R. & Papantonis, A. Enhancers and silencers: An integrated and simple model for their function. Epigenetics Chromatin 5, 1 (2012
-
(2012)
Epigenetics Chromatin
, vol.5
, Issue.1
-
-
Kolovos, P.1
Knoch, T.A.2
Grosveld, F.G.3
Cook, P.R.4
Papantonis, A.5
-
38
-
-
0015827914
-
Effect of phenylhydrazine-induced hemolytic anemia on nuclear RNA polymerase activity of the mouse spleen
-
Spivak, J.L., Toretti, D. & Dickerman, H.W. Effect of phenylhydrazine-induced hemolytic anemia on nuclear RNA polymerase activity of the mouse spleen. Blood 42, 257-266 (1973
-
(1973)
Blood
, vol.42
, pp. 257-266
-
-
Spivak, J.L.1
Toretti, D.2
Dickerman, H.W.3
-
39
-
-
0025666925
-
Establishment of germ-line-competent embryonic stem (ES) cells using differentiation inhibiting activity
-
Nichols, J., Evans, E.P. & Smith, A.G. Establishment of germ-line-competent embryonic stem (ES) cells using differentiation inhibiting activity. Development 110, 1341-1348 (1990
-
(1990)
Development
, vol.110
, pp. 1341-1348
-
-
Nichols, J.1
Evans, E.P.2
Smith, A.G.3
-
40
-
-
34548565667
-
Quantitative analysis of chromosome conformation capture assays (3C-qPCR
-
Hagège, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722-1733 (2007
-
(2007)
Nat. Protoc
, vol.2
, pp. 1722-1733
-
-
Hagège, H.1
-
41
-
-
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
-
42
-
-
77955131763
-
Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells
-
Kassouf, M.T. et al. Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells. Genome Res. 20, 1064-1083 (2010
-
(2010)
Genome Res
, vol.20
, pp. 1064-1083
-
-
Kassouf, M.T.1
-
43
-
-
77955155544
-
A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells
-
Tallack, M.R. et al. A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells. Genome Res. 20, 1052-1063 (2010
-
(2010)
Genome Res
, vol.20
, pp. 1052-1063
-
-
Tallack, M.R.1
-
44
-
-
84877296422
-
GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis
-
Papadopoulos, G.L. et al. GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. Nucleic Acids Res. 41, 4938-4948 (2013
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 4938-4948
-
-
Papadopoulos, G.L.1
-
45
-
-
77952328090
-
USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the β-globin gene locus
-
Zhou, Z. et al. USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the β-globin gene locus. J. Biol. Chem. 285, 15894-15905 (2010
-
(2010)
J. Biol. Chem
, vol.285
, pp. 15894-15905
-
-
Zhou, Z.1
-
46
-
-
84867116639
-
The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome
-
Horakova, A.H., Moseley, S.C., McLaughlin, C.R., Tremblay, D.C. & Chadwick, B.P. The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. Hum. Mol. Genet. 21, 4367-4377 (2012
-
(2012)
Hum. Mol. Genet
, vol.21
, pp. 4367-4377
-
-
Horakova, A.H.1
Moseley, S.C.2
McLaughlin, C.R.3
Tremblay, D.C.4
Chadwick, B.P.5
-
47
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
48
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
49
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent, W.J. BLAT-The BLAST-like alignment tool. Genome Res. 12, 656-664 (2002)
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
51
-
-
84891145366
-
MIG: Multi-Image genome viewer
-
McGowan, S.J., Hughes, J.R., Han, Z.P. & Taylor, S. MIG: Multi-Image Genome Viewer. Bioinformatics 29, 2477-2478 (2013
-
(2013)
Bioinformatics
, vol.29
, pp. 2477-2478
-
-
McGowan, S.J.1
Hughes, J.R.2
Han, Z.P.3
Taylor, S.4
-
52
-
-
84875628769
-
Using GBrowse 2.0 to visualize and share next-generation sequence data
-
Stein, L.D. Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief. Bioinform. 14, 162-171 (2013.
-
(2013)
Brief. Bioinform
, vol.14
, pp. 162-171
-
-
Stein, L.D.1
|