-
1
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
DOI 10.1038/nature06341, PII NATURE06341
-
Clark, A.G., Eisen, M.B., Smith, D.R., Bergman, C.M., Oliver, B., Markow, T.A., Kaufman, T.C., Kellis, M., Gelbart, W., Iyer, V.N. et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203-218. (Pubitemid 351972300)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 203-218
-
-
Clark, A.G.1
Eisen, M.B.2
Smith, D.R.3
Bergman, C.M.4
Oliver, B.5
Markow, T.A.6
Kaufman, T.C.7
Kellis, M.8
Gelbart, W.9
Iyer, V.N.10
Pollard, D.A.11
Sackton, T.B.12
Larracuente, A.M.13
Singh, N.D.14
Abad, J.P.15
Abt, D.N.16
Adryan, B.17
Aguade, M.18
Akashi, H.19
Anderson, W.W.20
Aquadro, C.F.21
Ardell, D.H.22
Arguello, R.23
Artieri, C.G.24
Barbash, D.A.25
Barker, D.26
Barsanti, P.27
Batterham, P.28
Batzoglou, S.29
Begun, D.30
Bhutkar, A.31
Blanco, E.32
Bosak, S.A.33
Bradley, R.K.34
Brand, A.D.35
Brent, M.R.36
Brooks, A.N.37
Brown, R.H.38
Butlin, R.K.39
Caggese, C.40
Calvi, B.R.41
Bernardo De Carvalho, A.42
Caspi, A.43
Castrezana, S.44
Celniker, S.E.45
Chang, J.L.46
Chapple, C.47
Chatterji, S.48
Chinwalla, A.49
Civetta, A.50
Clifton, S.W.51
Comeron, J.M.52
Costello, J.C.53
Coyne, J.A.54
Daub, J.55
David, R.G.56
Delcher, A.L.57
Delehaunty, K.58
Do, C.B.59
Ebling, H.60
Edwards, K.61
Eickbush, T.62
Evans, J.D.63
Filipski, A.64
Findeiss, S.65
Freyhult, E.66
Fulton, L.67
Fulton, R.68
Garcia, A.C.L.69
Gardiner, A.70
Garfield, D.A.71
Garvin, B.E.72
Gibson, G.73
Gilbert, D.74
Gnerre, S.75
Godfrey, J.76
Good, R.77
Gotea, V.78
Gravely, B.79
Greenberg, A.J.80
Griffiths-Jones, S.81
Gross, S.82
Guigo, R.83
Gustafson, E.A.84
Haerty, W.85
Hahn, M.W.86
Halligan, D.L.87
Halpern, A.L.88
Halter, G.M.89
Han, M.V.90
Heger, A.91
Hillier, L.92
more..
-
2
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
DOI 10.1126/science.287.5461.2185
-
Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195. (Pubitemid 30177013)
-
(2000)
Science
, vol.287
, Issue.5461
, pp. 2185-2195
-
-
Adams, M.D.1
Celniker, S.E.2
Holt, R.A.3
Evans, C.A.4
Gocayne, J.D.5
Amanatides, P.G.6
Scherer, S.E.7
Li, P.W.8
Hoskins, R.A.9
Galle, R.F.10
George, R.A.11
Lewis, S.E.12
Richards, S.13
Ashburner, M.14
Henderson, S.N.15
Sutton, G.G.16
Wortman, J.R.17
Yandell, M.D.18
Zhang, Q.19
Chen, L.X.20
Brandon, R.C.21
Rogers, Y.C.22
Blazej, R.G.23
Champe, M.24
Pfeiffer, B.D.25
Wan, K.H.26
Doyle, C.27
Baxter, E.G.28
Helt, G.29
Nelson, C.R.30
Gabor Miklos, G.L.31
Abril, J.F.32
Agbayani, A.33
An, H.-J.34
Andrews-Pfannkoch, C.35
Baldwin, D.36
Ballew, R.M.37
Basu, A.38
Baxendale, J.39
Bayraktaroglu, L.40
Beasley, E.M.41
Beeson, K.Y.42
Benos, P.V.43
Berman, B.P.44
Bhandari, D.45
Bolshakov, S.46
Borkova, D.47
Botchan, M.R.48
Bouck, J.49
Brokstein, P.50
Brottier, P.51
Burtis, K.C.52
Busam, D.A.53
Butler, H.54
Cadieu, E.55
Center, A.56
Chandra, I.57
Cherry, J.M.58
Cawley, S.59
Dahlke, C.60
Davenport, L.B.61
Davies, P.62
De Pablos, B.63
Delcher, A.64
Deng, Z.65
Mays, A.D.66
Dew, I.67
Dietz, S.M.68
Dodson, K.69
Doup, L.E.70
Downes, M.71
Dugan-Rocha, S.72
Dunkov, B.C.73
Dunn, P.74
Durbin, K.J.75
Evangelista, C.C.76
Ferraz, C.77
Ferriera, S.78
Fleischmann, W.79
Fosler, C.80
Gabrielian, A.E.81
Garg, N.S.82
Gelbart, W.M.83
Glasser, K.84
Glodek, A.85
Gong, F.86
Gorrell, J.H.87
Gu, Z.88
Guan, P.89
Harris, M.90
Harris, N.L.91
Harvey, D.92
Heiman, T.J.93
Hernandez, J.R.94
Houck, J.95
Hostin, D.96
Houston, K.A.97
Howland, T.J.98
Wei, M.-H.99
more..
-
3
-
-
58149199579
-
FlyBase: Enhancing Drosophila gene ontology annotations
-
Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R. et al. (2009) FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res., 37, D555-D559.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Tweedie, S.1
Ashburner, M.2
Falls, K.3
Leyland, P.4
McQuilton, P.5
Marygold, S.6
Millburn, G.7
Osumi-Sutherland, D.8
Schroeder, A.9
Seal, R.10
-
4
-
-
67649292737
-
Unlocking the secrets of the genome
-
Celniker, S.E., Dillon, L.A., Gerstein, M.B., Gunsalus, K.C., Henikoff, S., Karpen, G.H., Kellis, M., Lai, E.C., Lieb, J.D., MacAlpine, D.M. et al. (2009) Unlocking the secrets of the genome. Nature, 459, 927-930.
-
(2009)
Nature
, vol.459
, pp. 927-930
-
-
Celniker, S.E.1
Dillon, L.A.2
Gerstein, M.B.3
Gunsalus, K.C.4
Henikoff, S.5
Karpen, G.H.6
Kellis, M.7
Lai, E.C.8
Lieb, J.D.9
MacAlpine, D.M.10
-
5
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
The modENCODE Consortium
-
The modENCODE Consortium, Roy, S., Ernst, J., Kharchenko, P.V., Kheradpour, P., Negre, N., Eaton, M.L., Landolin, J.M., Bristow, C.A., Ma, L. et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330, 1787-1797.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
Kheradpour, P.4
Negre, N.5
Eaton, M.L.6
Landolin, J.M.7
Bristow, C.A.8
Ma, L.9
-
6
-
-
12744263842
-
Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
Berman, B.P., Pfeiffer, B.D., Laverty, T.R., Salzberg, S.L., Rubin, G.M., Eisen, M.B. and Celniker, S.E. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol., 5, R61.
-
(2004)
Genome Biol.
, vol.5
-
-
Berman, B.P.1
Pfeiffer, B.D.2
Laverty, T.R.3
Salzberg, S.L.4
Rubin, G.M.5
Eisen, M.B.6
Celniker, S.E.7
-
7
-
-
77956830473
-
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials
-
Kazemian, M., Blatti, C., Richards, A., McCutchan, M., Wakabayashi-Ito, N., Hammonds, A.S., Celniker, S.E., Kumar, S., Wolfe, S.A., Brodsky, M.H. et al. (2010) Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol., 8, e1000456.
-
(2010)
PLoS Biol.
, vol.8
-
-
Kazemian, M.1
Blatti, C.2
Richards, A.3
McCutchan, M.4
Wakabayashi-Ito, N.5
Hammonds, A.S.6
Celniker, S.E.7
Kumar, S.8
Wolfe, S.A.9
Brodsky, M.H.10
-
8
-
-
13244271362
-
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
-
Sinha, S., Schroeder, M.D., Unnerstall, U., Gaul, U. and Siggia, E.D. (2004) Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics, 5, 129.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 129
-
-
Sinha, S.1
Schroeder, M.D.2
Unnerstall, U.3
Gaul, U.4
Siggia, E.D.5
-
10
-
-
70349996336
-
Motif-blind genome-wide discovery of cis-regulatory modules in Drosophila and mouse
-
Kantorovitz, M.R., Kazemian, M., Kinston, S., Miranda- Saavedra, D., Zhu, Q., Robinson, G.E., Gottgens, B., Halfon, M.S. and Sinha, S. (2009) Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev. Cell, 17, 568-579.
-
(2009)
Dev. Cell
, vol.17
, pp. 568-579
-
-
Kantorovitz, M.R.1
Kazemian, M.2
Kinston, S.3
Miranda- Saavedra, D.4
Zhu, Q.5
Robinson, G.E.6
Gottgens, B.7
Halfon, M.S.8
Sinha, S.9
-
11
-
-
46249100442
-
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
-
Ivan, A., Halfon, M.S. and Sinha, S. (2008) Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol., 9, R22.
-
(2008)
Genome Biol.
, vol.9
-
-
Ivan, A.1
Halfon, M.S.2
Sinha, S.3
-
12
-
-
78651321628
-
FlyFactorSurvey: A database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
-
Zhu, L.J., Christensen, R.G., Kazemian, M., Hull, C.J., Enuameh, M.S., Basciotta, M.D., Brasefield, J.A., Zhu, C., Asriyan, Y., Lapointe, D.S. et al. (2011) FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res, 39, D111-D117.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Zhu, L.J.1
Christensen, R.G.2
Kazemian, M.3
Hull, C.J.4
Enuameh, M.S.5
Basciotta, M.D.6
Brasefield, J.A.7
Zhu, C.8
Asriyan, Y.9
Lapointe, D.S.10
-
13
-
-
78651335916
-
REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila
-
Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M. and Halfon, M.S. (2010) REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res., 39, D118-D123.
-
(2010)
Nucleic Acids Res.
, vol.39
-
-
Gallo, S.M.1
Gerrard, D.T.2
Miner, D.3
Simich, M.4
Des Soye, B.5
Bergman, C.M.6
Halfon, M.S.7
-
14
-
-
1042264827
-
A probabilistic method to detect regulatory modules
-
Sinha, S., van Nimwegen, E. and Siggia, E.D. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19(Suppl. 1), i292-i301.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Sinha, S.1
Van Nimwegen, E.2
Siggia, E.D.3
-
15
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
DOI 10.1101/gr.403602
-
Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610. (Pubitemid 35175099)
-
(2002)
Genome Research
, vol.12
, Issue.10
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.3
Caudy, M.4
Mangone, M.5
Day, A.6
Nickerson, E.7
Stajich, J.E.8
Harris, T.W.9
Arva, A.10
Lewis, S.11
-
16
-
-
43349107222
-
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
-
DOI 10.1093/nar/gkn048
-
Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H. and Wolfe, S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res., 36, 2547-2560. (Pubitemid 351659570)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.8
, pp. 2547-2560
-
-
Noyes, M.B.1
Meng, X.2
Wakabayashi, A.3
Sinha, S.4
Brodsky, M.H.5
Wolfe, S.A.6
-
17
-
-
68849103482
-
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
-
MacArthur, S., Li, X.Y., Li, J., Brown, J.B., Chu, H.C., Zeng, L., Grondona, B.P., Hechmer, A., Simirenko, L., Keranen, S.V. et al. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol., 10, R80.
-
(2009)
Genome Biol.
, vol.10
-
-
MacArthur, S.1
Li, X.Y.2
Li, J.3
Brown, J.B.4
Chu, H.C.5
Zeng, L.6
Grondona, B.P.7
Hechmer, A.8
Simirenko, L.9
Keranen, S.V.10
-
18
-
-
65749087932
-
An integrated approach to identifying cis-regulatory modules in the human genome
-
Won, K.J., Agarwal, S., Shen, L., Shoemaker, R., Ren, B. and Wang, W. (2009) An integrated approach to identifying cis-regulatory modules in the human genome. PLoS ONE, 4, e5501.
-
(2009)
PLoS ONE
, vol.4
-
-
Won, K.J.1
Agarwal, S.2
Shen, L.3
Shoemaker, R.4
Ren, B.5
Wang, W.6
-
19
-
-
78651230601
-
Assessing computational methods of cis-regulatory module prediction
-
Su, J., Teichmann, S.A. and Down, T.A. (2010) Assessing computational methods of cis-regulatory module prediction. PLoS Comput. Biol., 6, e1001020.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Su, J.1
Teichmann, S.A.2
Down, T.A.3
-
20
-
-
50949131215
-
PhyloGibbs-MP: Module prediction and discriminative motif-finding by Gibbs sampling
-
Siddharthan, R. (2008) PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PLoS Comput. Biol., 4, e1000156.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Siddharthan, R.1
-
21
-
-
17044431033
-
The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila
-
Ochoa-Espinosa, A., Yucel, G., Kaplan, L., Pare, A., Pura, N., Oberstein, A., Papatsenko, D. and Small, S. (2005) The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc. Natl Acad. Sci. USA, 102, 4960-4965.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4960-4965
-
-
Ochoa-Espinosa, A.1
Yucel, G.2
Kaplan, L.3
Pare, A.4
Pura, N.5
Oberstein, A.6
Papatsenko, D.7
Small, S.8
|