-
1
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond T, Davey C. The structure of DNA in the nucleosome core. Nature 2003;423:145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.1
Davey, C.2
-
2
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides T. Chromatin modifications and their function. Cell 2007;128:693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
3
-
-
80052942443
-
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification
-
Tan M, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011;146:1016-1028.
-
(2011)
Cell
, vol.146
, pp. 1016-1028
-
-
Tan, M.1
-
4
-
-
85015069067
-
Controlling the double helix
-
Felsenfeld G, Groudine M. Controlling the double helix. Nature 2003;421:448-453.
-
(2003)
Nature
, vol.421
, pp. 448-453
-
-
Felsenfeld, G.1
Groudine, M.2
-
5
-
-
84455200582
-
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
-
Ram O, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 2011;147:1628-1639.
-
(2011)
Cell
, vol.147
, pp. 1628-1639
-
-
Ram, O.1
-
6
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle A, et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 2008;132:311-322.
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.1
-
7
-
-
34250369627
-
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
-
Giresi P, Kim J, McDaniell R, Iyer V, Lieb J. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 2007;17:877-885.
-
(2007)
Genome Res
, vol.17
, pp. 877-885
-
-
Giresi, P.1
Kim, J.2
McDaniell, R.3
Iyer, V.4
Lieb, J.5
-
8
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones D, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008;132:887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.1
-
9
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007;129:823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
-
10
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
Encode Project Consortium
-
Encode Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011;9:e1001046.
-
(2011)
PLoS Biol
, vol.9
-
-
-
11
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Encode Project Consortium, et al
-
Encode Project Consortium, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
12
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Encode Project Consortium, et al.
-
Encode Project Consortium, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
13
-
-
52649097448
-
The Immunological Genome Project: networks of gene expression in immune cells
-
Heng TSP, et al. The Immunological Genome Project: networks of gene expression in immune cells. Nat Immunol 2008;9:1091-1094.
-
(2008)
Nat Immunol
, vol.9
, pp. 1091-1094
-
-
Heng, T.S.P.1
-
14
-
-
0018458970
-
The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence
-
Wu C, Bingham P, Livak K, Holmgren R, Elgin S. The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell 1979;16:797-806.
-
(1979)
Cell
, vol.16
, pp. 797-806
-
-
Wu, C.1
Bingham, P.2
Livak, K.3
Holmgren, R.4
Elgin, S.5
-
15
-
-
0018359588
-
The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity
-
Wu C, Wong Y, Elgin S. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell 1979;16:807-814.
-
(1979)
Cell
, vol.16
, pp. 807-814
-
-
Wu, C.1
Wong, Y.2
Elgin, S.3
-
16
-
-
80053539409
-
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
-
Song L, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 2011;21:1757-1767.
-
(2011)
Genome Res
, vol.21
, pp. 1757-1767
-
-
Song, L.1
-
17
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth J, et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 2009;6:283-289.
-
(2009)
Nat Methods
, vol.6
, pp. 283-289
-
-
Hesselberth, J.1
-
18
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman R, et al. The accessible chromatin landscape of the human genome. Nature 2012;489:75-82.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.1
-
19
-
-
0018199224
-
DNAase footprinting a simple method for the detection of protein-DNA binding specificity
-
Galas D, Schmitz A. DNAase footprinting a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 1978;5:3157-3170.
-
(1978)
Nucleic Acids Res
, vol.5
, pp. 3157-3170
-
-
Galas, D.1
Schmitz, A.2
-
20
-
-
79952267284
-
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
-
Boyle A, et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res 2011;21:456-464.
-
(2011)
Genome Res
, vol.21
, pp. 456-464
-
-
Boyle, A.1
-
21
-
-
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 2012;489:83-90.
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
-
22
-
-
79952266465
-
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
-
Pique-Regi R, Degner J, Pai A, Gaffney D, Gilad Y, Pritchard J. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 2011;21:447-455.
-
(2011)
Genome Res
, vol.21
, pp. 447-455
-
-
Pique-Regi, R.1
Degner, J.2
Pai, A.3
Gaffney, D.4
Gilad, Y.5
Pritchard, J.6
-
23
-
-
84893863046
-
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
-
Sherwood R, et al. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 2014;32:171-178.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 171-178
-
-
Sherwood, R.1
-
24
-
-
84894613651
-
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
-
He H, et al. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods 2014;11:73-78.
-
(2014)
Nat Methods
, vol.11
, pp. 73-78
-
-
He, H.1
-
25
-
-
0016133106
-
Internal structure of the chromatin subunit
-
Noll M. Internal structure of the chromatin subunit. Nucleic Acids Res 1974;1:1573-1578.
-
(1974)
Nucleic Acids Res
, vol.1
, pp. 1573-1578
-
-
Noll, M.1
-
26
-
-
0347914548
-
Redefinition of the cleavage sites of DNase I on the nucleosome core particle
-
Cousins DJ, Islam SA, Sanderson MR, Proykova YG, Crane-Robinson C, Staynov DZ. Redefinition of the cleavage sites of DNase I on the nucleosome core particle. J Mol Biol 2004;335:1199-1211.
-
(2004)
J Mol Biol
, vol.335
, pp. 1199-1211
-
-
Cousins, D.J.1
Islam, S.A.2
Sanderson, M.R.3
Proykova, Y.G.4
Crane-Robinson, C.5
Staynov, D.Z.6
-
27
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
Gaffney D, et al. Controls of nucleosome positioning in the human genome. PLoS Genet 2012;8:e1003036.
-
(2012)
PLoS Genet
, vol.8
-
-
Gaffney, D.1
-
28
-
-
84880051962
-
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
-
Winter D, Song L, Mukherjee S, Furey T, Crawford G. DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Res 2013;23:1118-1129.
-
(2013)
Genome Res
, vol.23
, pp. 1118-1129
-
-
Winter, D.1
Song, L.2
Mukherjee, S.3
Furey, T.4
Crawford, G.5
-
29
-
-
77955388311
-
A preoccupied position on nucleosomes
-
Pugh BF. A preoccupied position on nucleosomes. Nat Struct Mol Biol 2010;17:923.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 923
-
-
Pugh, B.F.1
-
30
-
-
34047111213
-
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
-
Albert I, et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 2007;446:572-576.
-
(2007)
Nature
, vol.446
, pp. 572-576
-
-
Albert, I.1
-
31
-
-
60349089645
-
Nucleosome positioning and gene regulation: advances through genomics
-
Jiang C, Pugh B. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2009;10:161-172.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 161-172
-
-
Jiang, C.1
Pugh, B.2
-
32
-
-
80053501181
-
Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
-
Hu G, et al. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 2011;21:1650-1658.
-
(2011)
Genome Res
, vol.21
, pp. 1650-1658
-
-
Hu, G.1
-
33
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson S, Boyd S, Smith C, Fire A, Sidow A. Determinants of nucleosome organization in primary human cells. Nature 2011;474:516-520.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.2
Boyd, S.3
Smith, C.4
Fire, A.5
Sidow, A.6
-
34
-
-
69449102464
-
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
-
Wang Z, et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 2009;138:1019-1031.
-
(2009)
Cell
, vol.138
, pp. 1019-1031
-
-
Wang, Z.1
-
35
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010;28:817-825.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
36
-
-
84857707318
-
ChromHMM: automating chromatin-state discovery and characterization
-
Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 2012;9:215-216.
-
(2012)
Nat Methods
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
37
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
Hoffman M, Buske O, Wang J, Weng Z, Bilmes J, Noble W. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 2012;9:473-476.
-
(2012)
Nat Methods
, vol.9
, pp. 473-476
-
-
Hoffman, M.1
Buske, O.2
Wang, J.3
Weng, Z.4
Bilmes, J.5
Noble, W.6
-
38
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman N, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007;39:311-318.
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.1
-
39
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He H, et al. Nucleosome dynamics define transcriptional enhancers. Nat Genet 2010;42:343-347.
-
(2010)
Nat Genet
, vol.42
, pp. 343-347
-
-
He, H.1
-
40
-
-
84888641656
-
Effect of natural genetic variation on enhancer selection and function
-
Heinz S, et al. Effect of natural genetic variation on enhancer selection and function. Nature 2013;503:487-492.
-
(2013)
Nature
, vol.503
, pp. 487-492
-
-
Heinz, S.1
-
41
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton M, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010;107:21931-21936.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.1
-
42
-
-
84875217558
-
Polycomb-group proteins in hematopoietic stem cell regulation and hematopoietic neoplasms
-
Radulović V, de Haan G, Klauke K. Polycomb-group proteins in hematopoietic stem cell regulation and hematopoietic neoplasms. Leukemia 2013;27:523-533.
-
(2013)
Leukemia
, vol.27
, pp. 523-533
-
-
Radulović, V.1
de Haan, G.2
Klauke, K.3
-
43
-
-
67349169780
-
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells
-
Araki Y, et al. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity 2009;30:912-925.
-
(2009)
Immunity
, vol.30
, pp. 912-925
-
-
Araki, Y.1
-
44
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco R, Allo M, Schor I, Kornblihtt A, Misteli T. Epigenetics in alternative pre-mRNA splicing. Cell 2011;144:16-26.
-
(2011)
Cell
, vol.144
, pp. 16-26
-
-
Luco, R.1
Allo, M.2
Schor, I.3
Kornblihtt, A.4
Misteli, T.5
-
45
-
-
84881526410
-
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
-
Kaikkonen M, et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 2013;51:310-325.
-
(2013)
Mol Cell
, vol.51
, pp. 310-325
-
-
Kaikkonen, M.1
-
46
-
-
84859157183
-
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity
-
Zhang J, Mortazavi A, Williams B, Wold B, Rothenberg E. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 2012;149:467-482.
-
(2012)
Cell
, vol.149
, pp. 467-482
-
-
Zhang, J.1
Mortazavi, A.2
Williams, B.3
Wold, B.4
Rothenberg, E.5
-
47
-
-
84856321864
-
Dissecting the regulatory architecture of gene expression QTLs
-
Gaffney D, et al. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol 2012;13:R7.
-
(2012)
Genome Biol
, vol.13
-
-
Gaffney, D.1
-
48
-
-
84857111200
-
DNase I sensitivity QTLs are a major determinant of human expression variation
-
Degner J, et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 2012;482:390-394.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.1
-
49
-
-
77950854479
-
Heritable individual-specific and allele-specific chromatin signatures in humans
-
McDaniell R, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 2010;328:235-239.
-
(2010)
Science
, vol.328
, pp. 235-239
-
-
McDaniell, R.1
-
50
-
-
84887322043
-
Identification of genetic variants that affect histone modifications in human cells
-
McVicker G, et al. Identification of genetic variants that affect histone modifications in human cells. Science 2013;342:747-749.
-
(2013)
Science
, vol.342
, pp. 747-749
-
-
McVicker, G.1
-
51
-
-
80054719497
-
Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
-
Lu R, Neff N, Quake S, Weissman I. Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotechnol 2011;29:928-933.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 928-933
-
-
Lu, R.1
Neff, N.2
Quake, S.3
Weissman, I.4
-
52
-
-
84876297531
-
Diverse and heritable lineage imprinting of early haematopoietic progenitors
-
Naik S, et al. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 2013;496:229-232.
-
(2013)
Nature
, vol.496
, pp. 229-232
-
-
Naik, S.1
-
53
-
-
58049191558
-
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
-
Cui K, et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 2009;4:80-93.
-
(2009)
Cell Stem Cell
, vol.4
, pp. 80-93
-
-
Cui, K.1
-
54
-
-
84894598129
-
Rapid and pervasive changes in genome-wide enhancer usage during mammalian development
-
Nord A, et al. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 2013;155:1521-1531.
-
(2013)
Cell
, vol.155
, pp. 1521-1531
-
-
Nord, A.1
-
55
-
-
84882766972
-
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
-
Stergachis A, et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 2013;154:888-903.
-
(2013)
Cell
, vol.154
, pp. 888-903
-
-
Stergachis, A.1
-
56
-
-
36549088118
-
Dynamic evolution of the innate immune system in Drosophila
-
Sackton T, Lazzaro B, Schlenke T, Evans J, Hultmark D, Clark A. Dynamic evolution of the innate immune system in Drosophila. Nat Genet 2007;39:1461-1468.
-
(2007)
Nat Genet
, vol.39
, pp. 1461-1468
-
-
Sackton, T.1
Lazzaro, B.2
Schlenke, T.3
Evans, J.4
Hultmark, D.5
Clark, A.6
-
57
-
-
84894589713
-
Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation
-
Kieffer-Kwon K-R, et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2013;155:1507-1520.
-
(2013)
Cell
, vol.155
, pp. 1507-1520
-
-
Kieffer-Kwon, K.-R.1
-
58
-
-
77950484789
-
Epigenetic propagation of CD4 expression is established by the Cd4 proximal enhancer in helper T cells
-
Chong M, Simpson N, Ciofani M, Chen G, Collins A, Littman D. Epigenetic propagation of CD4 expression is established by the Cd4 proximal enhancer in helper T cells. Genes Dev 2010;24:659-669.
-
(2010)
Genes Dev
, vol.24
, pp. 659-669
-
-
Chong, M.1
Simpson, N.2
Ciofani, M.3
Chen, G.4
Collins, A.5
Littman, D.6
-
59
-
-
0024294014
-
MyoD1: a nuclear phosphoprotein requiring a Myc homology region to convert fibroblasts to myoblasts
-
Tapscott S, Davis R, Thayer M, Cheng P, Weintraub H, Lassar A. MyoD1: a nuclear phosphoprotein requiring a Myc homology region to convert fibroblasts to myoblasts. Science 1988;242:405-411.
-
(1988)
Science
, vol.242
, pp. 405-411
-
-
Tapscott, S.1
Davis, R.2
Thayer, M.3
Cheng, P.4
Weintraub, H.5
Lassar, A.6
-
60
-
-
0032440334
-
GATA transcription factors as potentiators of gut endoderm differentiation
-
Bossard P, Zaret K. GATA transcription factors as potentiators of gut endoderm differentiation. Development 1998;125:4909-4917.
-
(1998)
Development
, vol.125
, pp. 4909-4917
-
-
Bossard, P.1
Zaret, K.2
-
61
-
-
0036184236
-
Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4
-
Cirillo L, Lin F, Cuesta I, Friedman D, Jarnik M, Zaret K. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell 2002;9:279-289.
-
(2002)
Mol Cell
, vol.9
, pp. 279-289
-
-
Cirillo, L.1
Lin, F.2
Cuesta, I.3
Friedman, D.4
Jarnik, M.5
Zaret, K.6
-
62
-
-
40849085514
-
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
-
Lupien M, et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 2008;132:958-970.
-
(2008)
Cell
, vol.132
, pp. 958-970
-
-
Lupien, M.1
-
63
-
-
0033388099
-
An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA
-
Cirillo L, Zaret K. An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. Mol Cell 1999;4:961-969.
-
(1999)
Mol Cell
, vol.4
, pp. 961-969
-
-
Cirillo, L.1
Zaret, K.2
-
64
-
-
84866303839
-
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
-
Garber M, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 2012;47:810-822.
-
(2012)
Mol Cell
, vol.47
, pp. 810-822
-
-
Garber, M.1
-
65
-
-
84867581744
-
A validated regulatory network for Th17 cell specification
-
Ciofani M, et al. A validated regulatory network for Th17 cell specification. Cell 2012;151:289-303.
-
(2012)
Cell
, vol.151
, pp. 289-303
-
-
Ciofani, M.1
-
66
-
-
77953763449
-
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate
-
Lin Y, et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol 2010;11:635-643.
-
(2010)
Nat Immunol
, vol.11
, pp. 635-643
-
-
Lin, Y.1
-
67
-
-
71449125977
-
Forcing cells to change lineages
-
Graf T, Enver T. Forcing cells to change lineages. Nature 2009;462:587-594.
-
(2009)
Nature
, vol.462
, pp. 587-594
-
-
Graf, T.1
Enver, T.2
-
68
-
-
84893969121
-
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells
-
Di Stefano B, et al. C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells. Nature 2014;506:235-239.
-
(2014)
Nature
, vol.506
, pp. 235-239
-
-
Di Stefano, B.1
-
69
-
-
0034624828
-
A clonogenic common myeloid progenitor that gives rise to all myeloid lineages
-
Akashi K, Traver D, Miyamoto T, Weissman I. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 2000;404:193-197.
-
(2000)
Nature
, vol.404
, pp. 193-197
-
-
Akashi, K.1
Traver, D.2
Miyamoto, T.3
Weissman, I.4
-
70
-
-
80053516108
-
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
-
Wu W, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res 2011;21:1659-1671.
-
(2011)
Genome Res
, vol.21
, pp. 1659-1671
-
-
Wu, W.1
-
71
-
-
34250214880
-
Myeloid lineage commitment from the hematopoietic stem cell
-
Iwasaki H, Akashi K. Myeloid lineage commitment from the hematopoietic stem cell. Immunity 2007;26:726-740.
-
(2007)
Immunity
, vol.26
, pp. 726-740
-
-
Iwasaki, H.1
Akashi, K.2
-
72
-
-
33747196725
-
Multilineage transcriptional priming and determination of alternate hematopoietic cell fates
-
Laslo P, et al. Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell 2006;126:755-766.
-
(2006)
Cell
, vol.126
, pp. 755-766
-
-
Laslo, P.1
-
73
-
-
13244277736
-
Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors
-
Nutt S, Metcalf D, D'Amico A, Polli M, Wu L. Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors. J Exp Med 2005;201:221-231.
-
(2005)
J Exp Med
, vol.201
, pp. 221-231
-
-
Nutt, S.1
Metcalf, D.2
D'Amico, A.3
Polli, M.4
Wu, L.5
-
74
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz S, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010;38:576-589.
-
(2010)
Mol Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
75
-
-
77949977555
-
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages
-
Ghisletti S, et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 2010;32:317-328.
-
(2010)
Immunity
, vol.32
, pp. 317-328
-
-
Ghisletti, S.1
-
76
-
-
0033533891
-
Commitment to the B-lymphoid lineage depends on the transcription factor Pax5
-
Nutt S, Heavey B, Rolink A, Busslinger M. Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 1999;401:556-562.
-
(1999)
Nature
, vol.401
, pp. 556-562
-
-
Nutt, S.1
Heavey, B.2
Rolink, A.3
Busslinger, M.4
-
77
-
-
34848853915
-
Conversion of mature B cells into T cells by dedifferentiation to uncommitted progenitors
-
Cobaleda C, Jochum W, Busslinger M. Conversion of mature B cells into T cells by dedifferentiation to uncommitted progenitors. Nature 2007;449:473-477.
-
(2007)
Nature
, vol.449
, pp. 473-477
-
-
Cobaleda, C.1
Jochum, W.2
Busslinger, M.3
-
78
-
-
70349446453
-
The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development
-
Gascoyne D, et al. The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development. Nat Immunol 2009;10:1118-1124.
-
(2009)
Nat Immunol
, vol.10
, pp. 1118-1124
-
-
Gascoyne, D.1
-
79
-
-
84866975037
-
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification
-
Samstein R, et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 2012;151:153-166.
-
(2012)
Cell
, vol.151
, pp. 153-166
-
-
Samstein, R.1
-
80
-
-
84891439321
-
Deciphering cis-regulatory control in inflammatory cells
-
Ghisletti S, Natoli G. Deciphering cis-regulatory control in inflammatory cells. Philos Trans Royal Soc Lond B 2013;368:20120370.
-
(2013)
Philos Trans Royal Soc Lond B
, vol.368
, pp. 20120370
-
-
Ghisletti, S.1
Natoli, G.2
-
81
-
-
77957672080
-
Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage
-
Liber D, et al. Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage. Cell Stem Cell 2010;7:114-126.
-
(2010)
Cell Stem Cell
, vol.7
, pp. 114-126
-
-
Liber, D.1
-
82
-
-
84872522528
-
Latent enhancers activated by stimulation in differentiated cells
-
Ostuni R, et al. Latent enhancers activated by stimulation in differentiated cells. Cell 2013;152:157-171.
-
(2013)
Cell
, vol.152
, pp. 157-171
-
-
Ostuni, R.1
-
83
-
-
34250823515
-
Gene-specific control of inflammation by TLR-induced chromatin modifications
-
Foster S, Hargreaves D, Medzhitov R. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 2007;447:972-978.
-
(2007)
Nature
, vol.447
, pp. 972-978
-
-
Foster, S.1
Hargreaves, D.2
Medzhitov, R.3
-
84
-
-
70350754328
-
Jmjd3 contributes to the control of gene expression in LPS-activated macrophages
-
De Santa F, et al. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO J 2009;28:3341-3352.
-
(2009)
EMBO J
, vol.28
, pp. 3341-3352
-
-
De Santa, F.1
-
85
-
-
84855286273
-
Mechanisms establishing TLR4-responsive activation states of inflammatory response genes
-
Escoubet-Lozach L, et al. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet 2011;7:e1002401.
-
(2011)
PLoS Genet
, vol.7
-
-
Escoubet-Lozach, L.1
-
86
-
-
84880815366
-
Short-term memory of danger signals and environmental stimuli in immune cells
-
Monticelli S, Natoli G. Short-term memory of danger signals and environmental stimuli in immune cells. Nat Immunol 2013;14:777-784.
-
(2013)
Nat Immunol
, vol.14
, pp. 777-784
-
-
Monticelli, S.1
Natoli, G.2
-
87
-
-
70349443224
-
Transcriptional control of the inflammatory response
-
Medzhitov R, Horng T. Transcriptional control of the inflammatory response. Nat Rev Immunol 2009;9:692-703.
-
(2009)
Nat Rev Immunol
, vol.9
, pp. 692-703
-
-
Medzhitov, R.1
Horng, T.2
-
88
-
-
84870485829
-
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
-
Fenouil R, et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res 2012;22:2399-2408.
-
(2012)
Genome Res
, vol.22
, pp. 2399-2408
-
-
Fenouil, R.1
-
89
-
-
31944432339
-
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
-
Saxonov S, Berg P, Brutlag D. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006;103:1412-1417.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 1412-1417
-
-
Saxonov, S.1
Berg, P.2
Brutlag, D.3
-
90
-
-
67649669255
-
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
-
Ramirez-Carrozzi V, et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 2009;138:114-128.
-
(2009)
Cell
, vol.138
, pp. 114-128
-
-
Ramirez-Carrozzi, V.1
-
91
-
-
77954928774
-
Maintaining cell identity through global control of genomic organization
-
Natoli G. Maintaining cell identity through global control of genomic organization. Immunity 2010;33:12-24.
-
(2010)
Immunity
, vol.33
, pp. 12-24
-
-
Natoli, G.1
-
92
-
-
79851485916
-
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
-
Rach E, et al. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet 2011;7:e1001274.
-
(2011)
PLoS Genet
, vol.7
-
-
Rach, E.1
-
93
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006;38:626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
-
94
-
-
84886694563
-
Regulatory T cells in nonlymphoid tissues
-
Burzyn D, Benoist C, Mathis D. Regulatory T cells in nonlymphoid tissues. Nat Immunol 2013;14:1007-1013.
-
(2013)
Nat Immunol
, vol.14
, pp. 1007-1013
-
-
Burzyn, D.1
Benoist, C.2
Mathis, D.3
-
96
-
-
84867740805
-
Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
-
Gautier E, et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol 2012;13:1118-1128.
-
(2012)
Nat Immunol
, vol.13
, pp. 1118-1128
-
-
Gautier, E.1
-
97
-
-
31044433663
-
Macrophages: obligate partners for tumor cell migration, invasion, and metastasis
-
Condeelis J, Pollard J. Macrophages: obligate partners for tumor cell migration, invasion, and metastasis. Cell 2006;124:263-266.
-
(2006)
Cell
, vol.124
, pp. 263-266
-
-
Condeelis, J.1
Pollard, J.2
-
98
-
-
70350728931
-
Tumor-associated macrophages (TAM) as major players of the cancer-related inflammation
-
Solinas G, Germano G, Mantovani A, Allavena P. Tumor-associated macrophages (TAM) as major players of the cancer-related inflammation. J Leukoc Biol 2009;86:1065-1073.
-
(2009)
J Leukoc Biol
, vol.86
, pp. 1065-1073
-
-
Solinas, G.1
Germano, G.2
Mantovani, A.3
Allavena, P.4
-
100
-
-
84875207585
-
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states
-
Blecher-Gonen R, Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, Lara-Astiaso D, Amit I. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protocols 2013;8:539-554.
-
(2013)
Nat Protocols
, vol.8
, pp. 539-554
-
-
Blecher-Gonen, R.1
Barnett-Itzhaki, Z.2
Jaitin, D.3
Amann-Zalcenstein, D.4
Lara-Astiaso, D.5
Amit, I.6
-
101
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro J, Giresi P, Zaba L, Chang H, Greenleaf W. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 2013;10:1213-1218.
-
(2013)
Nat Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.1
Giresi, P.2
Zaba, L.3
Chang, H.4
Greenleaf, W.5
-
103
-
-
33749400168
-
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
-
Dostie J, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 2006;16:1299-1309.
-
(2006)
Genome Res
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
-
104
-
-
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 2009;326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
-
105
-
-
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 2011;43:1059-1065.
-
(2011)
Nat Genet
, vol.43
, pp. 1059-1065
-
-
Yaffe, E.1
Tanay, A.2
-
106
-
-
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 2013;502:59-64.
-
(2013)
Nature
, vol.502
, pp. 59-64
-
-
Nagano, T.1
-
107
-
-
84877123760
-
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
-
Sheffield N, et al. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res 2013;23:777-788.
-
(2013)
Genome Res
, vol.23
, pp. 777-788
-
-
Sheffield, N.1
-
108
-
-
84885990989
-
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers
-
Taher L, Smith R, Kim M, Ahituv N, Ovcharenko I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol 2013;14:R117.
-
(2013)
Genome Biol
, vol.14
-
-
Taher, L.1
Smith, R.2
Kim, M.3
Ahituv, N.4
Ovcharenko, I.5
-
109
-
-
84865840434
-
Predicting cell-type-specific gene expression from regions of open chromatin
-
Natarajan A, Yardimci G, Sheffield N, Crawford G, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res 2012;22:1711-1722.
-
(2012)
Genome Res
, vol.22
, pp. 1711-1722
-
-
Natarajan, A.1
Yardimci, G.2
Sheffield, N.3
Crawford, G.4
Ohler, U.5
-
110
-
-
84880310432
-
Uniform, optimal signal processing of mapped deep-sequencing data
-
Kumar V, et al. Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol 2013;31:615-622.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 615-622
-
-
Kumar, V.1
-
111
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang Z, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008;40:897-903.
-
(2008)
Nat Genet
, vol.40
, pp. 897-903
-
-
Wang, Z.1
|