-
1
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
-
(2005)
PLoS Biol
, vol.3
-
-
Woolfe, A.1
Goodson, M.2
Goode, D.K.3
Snell, P.4
McEwen, G.K.5
-
2
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, I.3
Stephen, S.4
Kent, W.J.5
-
3
-
-
22144473057
-
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
-
Sandelin A, Bailey P, Bruce S, Engstrom PG, Klos JM, et al. (2004) Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99.
-
(2004)
BMC Genomics
, vol.5
, pp. 99
-
-
Sandelin, A.1
Bailey, P.2
Bruce, S.3
Engstrom, P.G.4
Klos, J.M.5
-
4
-
-
0142084743
-
Scanning human gene deserts for long-range enhancers
-
Nobrega MA, Ovcharenko I, Afzal V, Rubin EM, (2003) Scanning human gene deserts for long-range enhancers. Science 302: 413.
-
(2003)
Science
, vol.302
, pp. 413
-
-
Nobrega, M.A.1
Ovcharenko, I.2
Afzal, V.3
Rubin, E.M.4
-
5
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
-
6
-
-
23744502709
-
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
-
de la Calle-Mustienes E, Feijoo CG, Manzanares M, Tena JJ, Rodríguez-Seguel E, et al. (2005) A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res 15: 1061-1072.
-
(2005)
Genome Res
, vol.15
, pp. 1061-1072
-
-
de la Calle-Mustienes, E.1
Feijoo, C.G.2
Manzanares, M.3
Tena, J.J.4
Rodríguez-Seguel, E.5
-
7
-
-
72649101692
-
A systematic approach to identify functional motifs within vertebrate developmental enhancers
-
Li Q, Ritter D, Yang N, Dong Z, Li H, et al. (2010) A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol 337: 484-495.
-
(2010)
Dev Biol
, vol.337
, pp. 484-495
-
-
Li, Q.1
Ritter, D.2
Yang, N.3
Dong, Z.4
Li, H.5
-
8
-
-
33645519275
-
Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis
-
McEwen GK, Woolfe A, Goode D, Vavouri T, Callaway H, et al. (2006) Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res 16: 451-465.
-
(2006)
Genome Res
, vol.16
, pp. 451-465
-
-
McEwen, G.K.1
Woolfe, A.2
Goode, D.3
Vavouri, T.4
Callaway, H.5
-
9
-
-
70349336077
-
Conserved noncoding elements and the evolution of animal body plans
-
Vavouri T, Lehner B, (2009) Conserved noncoding elements and the evolution of animal body plans. Bioessays 31: 727-735.
-
(2009)
Bioessays
, vol.31
, pp. 727-735
-
-
Vavouri, T.1
Lehner, B.2
-
10
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature.
-
(2011)
Nature
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
-
11
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. (2011) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
-
(2011)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
Kheradpour, P.4
Negre, N.5
-
12
-
-
79953060951
-
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
-
Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480-485.
-
(2011)
Nature
, vol.471
, pp. 480-485
-
-
Kharchenko, P.V.1
Alekseyenko, A.A.2
Schwartz, Y.B.3
Minoda, A.4
Riddle, N.C.5
-
13
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
-
14
-
-
79953046943
-
A cis-regulatory map of the Drosophila genome
-
Negre N, Brown CD, Ma L, Bristow CA, Miller SW, et al. (2011) A cis-regulatory map of the Drosophila genome. Nature 471: 527-531.
-
(2011)
Nature
, vol.471
, pp. 527-531
-
-
Negre, N.1
Brown, C.D.2
Ma, L.3
Bristow, C.A.4
Miller, S.W.5
-
15
-
-
80052771653
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, et al. (2010) A unique chromatin signature uncovers early developmental enhancers in humans. Nature.
-
(2010)
Nature
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Swigut, T.3
Brugmann, S.A.4
Flynn, R.A.5
-
16
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A.
-
(2010)
Proc Natl Acad Sci U S A
-
-
Creyghton, M.P.1
Cheng, A.W.2
Welstead, G.G.3
Kooistra, T.4
Carey, B.W.5
-
17
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
-
18
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465: 182-187.
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
-
19
-
-
77949977555
-
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages
-
Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, et al. (2010) Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32: 317-328.
-
(2010)
Immunity
, vol.32
, pp. 317-328
-
-
Ghisletti, S.1
Barozzi, I.2
Mietton, F.3
Polletti, S.4
de Santa, F.5
-
20
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
21
-
-
77956641239
-
ChIP-Seq identification of weakly conserved heart enhancers
-
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42: 806-810.
-
(2010)
Nat Genet
, vol.42
, pp. 806-810
-
-
Blow, M.J.1
McCulley, D.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
-
22
-
-
79955859947
-
An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation
-
Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W, et al. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nat Commun 2: 310.
-
(2011)
Nat Commun
, vol.2
, pp. 310
-
-
Tena, J.J.1
Alonso, M.E.2
de la Calle-Mustienes, E.3
Splinter, E.4
de Laat, W.5
-
23
-
-
39049147650
-
Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
-
McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, et al. (2008) Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res 18: 252-260.
-
(2008)
Genome Res
, vol.18
, pp. 252-260
-
-
McGaughey, D.M.1
Vinton, R.M.2
Huynh, J.3
Al-Saif, A.4
Beer, M.A.5
-
24
-
-
79951528195
-
Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events
-
Goode DK, Callaway HA, Cerda GA, Lewis KE, Elgar G, (2011) Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. Development 138: 879-884.
-
(2011)
Development
, vol.138
, pp. 879-884
-
-
Goode, D.K.1
Callaway, H.A.2
Cerda, G.A.3
Lewis, K.E.4
Elgar, G.5
-
25
-
-
4344636300
-
A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish
-
Kawakami K, Takeda H, Kawakami N, Kobayashi M, Matsuda N, et al. (2004) A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev Cell 7: 133-144.
-
(2004)
Dev Cell
, vol.7
, pp. 133-144
-
-
Kawakami, K.1
Takeda, H.2
Kawakami, N.3
Kobayashi, M.4
Matsuda, N.5
-
26
-
-
33746875570
-
Cracking the genome's second code: Enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos
-
Allende ML, Manzanares M, Tena JJ, Feijoo CG, Gómez-Skarmeta JL, (2006) Cracking the genome's second code: Enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos. Methods 39: 212-219.
-
(2006)
Methods
, vol.39
, pp. 212-219
-
-
Allende, M.L.1
Manzanares, M.2
Tena, J.J.3
Feijoo, C.G.4
Gómez-Skarmeta, J.L.5
-
27
-
-
34347244234
-
Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish
-
Fisher S, Grice EA, Vinton RM, Bessling SL, Urasaki A, et al. (2006) Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nat Protoc 1: 1297-1305.
-
(2006)
Nat Protoc
, vol.1
, pp. 1297-1305
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
Urasaki, A.5
-
28
-
-
33645833857
-
Conservation of RET regulatory function from human to zebrafish without sequence similarity
-
Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS, (2006) Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312: 276-279.
-
(2006)
Science
, vol.312
, pp. 276-279
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
McCallion, A.S.5
-
29
-
-
77649259719
-
Genome-wide discovery of human heart enhancers
-
Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, et al. (2010) Genome-wide discovery of human heart enhancers. Genome Res 20: 381-392.
-
(2010)
Genome Res
, vol.20
, pp. 381-392
-
-
Narlikar, L.1
Sakabe, N.J.2
Blanski, A.A.3
Arimura, F.E.4
Westlund, J.M.5
-
30
-
-
73349128469
-
Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
-
Gehrig J, Reischl M, Kalmar E, Ferg M, Hadzhiev Y, et al. (2009) Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nat Methods 6: 911-916.
-
(2009)
Nat Methods
, vol.6
, pp. 911-916
-
-
Gehrig, J.1
Reischl, M.2
Kalmar, E.3
Ferg, M.4
Hadzhiev, Y.5
-
31
-
-
77957225928
-
The importance of being cis: evolution of orthologous fish and mammalian enhancer activity
-
Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, et al. (2010) The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol 27: 2322-2332.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 2322-2332
-
-
Ritter, D.I.1
Li, Q.2
Kostka, D.3
Pollard, K.S.4
Guo, S.5
-
32
-
-
70349085853
-
Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish
-
Bessa J, Tena JJ, de la Calle-Mustienes E, Fernandez-Minan A, Naranjo S, et al. (2009) Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev Dyn 238: 2409-2417.
-
(2009)
Dev Dyn
, vol.238
, pp. 2409-2417
-
-
Bessa, J.1
Tena, J.J.2
de la Calle-Mustienes, E.3
Fernandez-Minan, A.4
Naranjo, S.5
-
33
-
-
60549097668
-
Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
-
Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, et al. (2009) Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 327: 526-540.
-
(2009)
Dev Biol
, vol.327
, pp. 526-540
-
-
Navratilova, P.1
Fredman, D.2
Hawkins, T.A.3
Turner, K.4
Lenhard, B.5
-
34
-
-
75649100190
-
Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish
-
Navratilova P, Fredman D, Lenhard B, Becker TS, (2010) Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol Genet Genomics 283: 171-184.
-
(2010)
Mol Genet Genomics
, vol.283
, pp. 171-184
-
-
Navratilova, P.1
Fredman, D.2
Lenhard, B.3
Becker, T.S.4
-
35
-
-
70449529760
-
Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split
-
Komisarczuk AZ, Kawakami K, Becker TS, (2009) Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split. Dev Biol 336: 301-312.
-
(2009)
Dev Biol
, vol.336
, pp. 301-312
-
-
Komisarczuk, A.Z.1
Kawakami, K.2
Becker, T.S.3
-
36
-
-
0029045033
-
Stages of embryonic development of the zebrafish
-
Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF, (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203: 253-310.
-
(1995)
Dev Dyn
, vol.203
, pp. 253-310
-
-
Kimmel, C.B.1
Ballard, W.W.2
Kimmel, S.R.3
Ullmann, B.4
Schilling, T.F.5
-
37
-
-
16644391315
-
Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element
-
Kawakami K, (2004) Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element. Methods Cell Biol 77: 201-222.
-
(2004)
Methods Cell Biol
, vol.77
, pp. 201-222
-
-
Kawakami, K.1
-
38
-
-
70349521671
-
Boundaries in vertebrate genomes: different solutions to adequately insulate gene expression domains
-
Molto E, Fernandez A, Montoliu L, (2009) Boundaries in vertebrate genomes: different solutions to adequately insulate gene expression domains. Brief Funct Genomic Proteomic 8: 283-296.
-
(2009)
Brief Funct Genomic Proteomic
, vol.8
, pp. 283-296
-
-
Molto, E.1
Fernandez, A.2
Montoliu, L.3
-
39
-
-
79958834622
-
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes
-
Martin D, Pantoja C, Minan AF, Valdes-Quezada C, Molto E, et al. (2011) Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol.
-
(2011)
Nat Struct Mol Biol
-
-
Martin, D.1
Pantoja, C.2
Minan, A.F.3
Valdes-Quezada, C.4
Molto, E.5
-
40
-
-
79952261267
-
Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
-
Roman AC, Gonzalez-Rico FJ, Molto E, Hernando H, Neto A, et al. (2011) Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch. Genome Res 21: 422-432.
-
(2011)
Genome Res
, vol.21
, pp. 422-432
-
-
Roman, A.C.1
Gonzalez-Rico, F.J.2
Molto, E.3
Hernando, H.4
Neto, A.5
-
41
-
-
50649125245
-
A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
-
Smith AM, Sanchez MJ, Follows GA, Kinston S, Donaldson IJ, et al. (2008) A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. Genome Res 18: 1422-1432.
-
(2008)
Genome Res
, vol.18
, pp. 1422-1432
-
-
Smith, A.M.1
Sanchez, M.J.2
Follows, G.A.3
Kinston, S.4
Donaldson, I.J.5
-
43
-
-
79151469568
-
When needles look like hay: how to find tissue-specific enhancers in model organism genomes
-
Haeussler M, Joly JS, (2011) When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 350: 239-254.
-
(2011)
Dev Biol
, vol.350
, pp. 239-254
-
-
Haeussler, M.1
Joly, J.S.2
-
44
-
-
0036668276
-
Iroquois genes: genomic organization and function in vertebrate neural development
-
Gómez-Skarmeta JL, Modolell J, (2002) iroquois genes: genomic organization and function in vertebrate neural development. Curr Opin Genet Dev 12: 403-408.
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 403-408
-
-
Gómez-Skarmeta, J.L.1
Modolell, J.2
-
45
-
-
67349245788
-
The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx
-
Rodriguez-Seguel E, Alarcon P, Gomez-Skarmeta JL, (2009) The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx. Dev Biol 329: 258-268.
-
(2009)
Dev Biol
, vol.329
, pp. 258-268
-
-
Rodriguez-Seguel, E.1
Alarcon, P.2
Gomez-Skarmeta, J.L.3
-
46
-
-
0034891325
-
Gene and cluster-specific expression of the Iroquois family members during mouse development
-
Houweling AC, Dildrop R, Peters T, Mummenhoff J, Moorman AFM, et al. (2001) Gene and cluster-specific expression of the Iroquois family members during mouse development. Mech Dev 107: 169-174.
-
(2001)
Mech Dev
, vol.107
, pp. 169-174
-
-
Houweling, A.C.1
Dildrop, R.2
Peters, T.3
Mummenhoff, J.4
Moorman, A.F.M.5
-
47
-
-
27544477666
-
Expression of the zebrafish Iroquois genes during early nervous system formation and patterning
-
Lecaudey V, Anselme I, Dildrop R, Ruther U, Schneider-Maunoury S, (2005) Expression of the zebrafish Iroquois genes during early nervous system formation and patterning. J Comp Neurol 492: 289-302.
-
(2005)
J Comp Neurol
, vol.492
, pp. 289-302
-
-
Lecaudey, V.1
Anselme, I.2
Dildrop, R.3
Ruther, U.4
Schneider-Maunoury, S.5
-
48
-
-
67549119096
-
CTCF: master weaver of the genome
-
Phillips JE, Corces VG, (2009) CTCF: master weaver of the genome. Cell 137: 1194-1211.
-
(2009)
Cell
, vol.137
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
49
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
|