-
1
-
-
0033866762
-
Duplication, dicistronic transcription, and subsequent evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in Drosophila
-
Betran, E., and M. Ashburner, 2000 Duplication, dicistronic transcription, and subsequent evolution of the alcohol dehydrogenase and alcohol dehydrogenase2related genes in Drosophila. Mol. Biol. Evol. 17: 1344- 1352.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 1344-1352
-
-
Betran, E.1
Ashburner, M.2
-
2
-
-
0032103829
-
1998 Gene clusters and polycistronic transcription in eukaryotes
-
Blumenthal, T., 1998 Gene clusters and polycistronic transcription in eukaryotes. BioEssays 20: 480-487.
-
BioEssays
, vol.20
, pp. 480-487
-
-
Blumenthal, T.1
-
3
-
-
84904259668
-
2014 Comparative validation of the D. melanogaster modENCODE transcriptome annotation
-
Chen, Z. X., D. Sturgill, J. Qu, H. Jiang, S. Park et al., 2014 Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 24: 1209-1223.
-
Genome Res
, vol.24
, pp. 1209-1223
-
-
Chen, Z.X.1
Sturgill, D.2
Qu, J.3
Jiang, H.4
Park, S.5
-
4
-
-
84866150022
-
2012 Unconstrained evolution in short introns? An analysis of genome-wide polymorphism and divergence data from Drosophila
-
Clemente, F., and C. Vogl, 2012 Unconstrained evolution in short introns? An analysis of genome-wide polymorphism and divergence data from Drosophila. J. Evol. Biol. 25: 1975-1990.
-
J. Evol. Biol.
, vol.25
, pp. 1975-1990
-
-
Clemente, F.1
Vogl, C.2
-
5
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Drosophila Twelve Genomes Consortium, 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
-
6
-
-
34548013932
-
2007 The evolution of sex-biased genes and sexbiased gene expression
-
Ellegren, H., and J. Parsch, 2007 The evolution of sex-biased genes and sexbiased gene expression. Nat. Rev. Genet. 8: 689-698.
-
Nat. Rev. Genet.
, vol.8
, pp. 689-698
-
-
Ellegren, H.1
Parsch, J.2
-
7
-
-
0032545933
-
1998 Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
-
Fire, A., S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver et al., 1998 Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
-
Nature
, vol.391
, pp. 806-811
-
-
Fire, A.1
Xu, S.2
Montgomery, M.K.3
Kostas, S.A.4
Driver, S.E.5
-
8
-
-
79960264362
-
2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr, M. G., B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644-652.
-
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
-
9
-
-
84880266648
-
2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
Haas, B. J., A. Papanicolaou, M. Yassour, M. Grabherr, P. D. Blood et al., 2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8: 1494-1512.
-
Nat. Protoc.
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
-
10
-
-
37249039910
-
2007 Evolution in the fast lane: rapidly evolving sex-related genes in Drosophila
-
Haerty, W., S. Jagadeeshan, R. J. Kulathinal, A. Wong, K. Ravi Ram et al., 2007 Evolution in the fast lane: rapidly evolving sex-related genes in Drosophila. Genetics 177: 1321-1335.
-
Genetics
, vol.177
, pp. 1321-1335
-
-
Haerty, W.1
Jagadeeshan, S.2
Kulathinal, R.J.3
Wong, A.4
Ravi Ram, K.5
-
11
-
-
36048950933
-
2007 Gene family evolution across 12 Drosophila genomes
-
Hahn, M. W., M. V. Han, and S. G. Han, 2007 Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3: e197.
-
PLoS Genet
, vol.3
-
-
Hahn, M.W.1
Han, M.V.2
Han, S.G.3
-
12
-
-
33745612972
-
2006 Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
-
Halligan, D. L., and P. D. Keightley, 2006 Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res. 16: 875-884.
-
Genome Res
, vol.16
, pp. 875-884
-
-
Halligan, D.L.1
Keightley, P.D.2
-
13
-
-
84871958299
-
2013 A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
-
Hu, T. T., M. B. Eisen, K. R. Thornton, and P. Andolfatto, 2013 A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res. 23: 89-98.
-
Genome Res
, vol.23
, pp. 89-98
-
-
Hu, T.T.1
Eisen, M.B.2
Thornton, K.R.3
Andolfatto, P.4
-
14
-
-
84865070369
-
2012 A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
Jinek, M., K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna et al., 2012 A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816-821.
-
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
Chylinski, K.2
Fonfara, I.3
Hauer, M.4
Doudna, J.A.5
-
15
-
-
84876996918
-
2013 TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., G. Pertea, C. Trapnell, H. Pimentel, R. Kelley et al., 2013 TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14: R36.
-
Genome Biol
, vol.14
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
-
16
-
-
62349130698
-
2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
-
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
17
-
-
38849101777
-
2007 Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
-
Lin, M. F., J. W. Carlson, M. A. Crosby, B. B. Matthews, C. Yu et al., 2007 Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res. 17: 1823-1836.
-
Genome Res
, vol.17
, pp. 1823-1836
-
-
Lin, M.F.1
Carlson, J.W.2
Crosby, M.A.3
Matthews, B.B.4
Yu, C.5
-
18
-
-
38349083274
-
2008 Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression
-
Mank, J. E., L. Hultin-Rosenberg, M. Zwahlen, and H. Ellegren, 2008 Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. Am. Nat. 171: 35-43.
-
Am. Nat.
, vol.171
, pp. 35-43
-
-
Mank, J.E.1
Hultin-Rosenberg, L.2
Zwahlen, M.3
Ellegren, H.4
-
19
-
-
0026428610
-
1991 Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald, J. H., and M. Kreitman, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
-
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
20
-
-
79957479702
-
2011 Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution
-
Meisel, R. P., 2011 Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution. Mol. Biol. Evol. 28: 1893-1900.
-
Mol. Biol. Evol.
, vol.28
, pp. 1893-1900
-
-
Meisel, R.P.1
-
21
-
-
33845878246
-
2007 Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana
-
Nakamura, Y., T. Itoh, and W. Martin, 2007 Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Mol. Biol. Evol. 24: 110-121.
-
Mol. Biol. Evol.
, vol.24
, pp. 110-121
-
-
Nakamura, Y.1
Itoh, T.2
Martin, W.3
-
22
-
-
0346460960
-
2003 Paucity of genes on the Drosophila X chromosome showing male-biased expression
-
Parisi, M., R. Nuttall, D. Naiman, G. Bouffard, J. Malley et al., 2003 Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299: 697-700.
-
Science
, vol.299
, pp. 697-700
-
-
Parisi, M.1
Nuttall, R.2
Naiman, D.3
Bouffard, G.4
Malley, J.5
-
23
-
-
4844222675
-
2004 A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults
-
Parisi, M., R. Nuttall, P. Edwards, J. Minor, D. Naiman et al., 2004 A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 5: R40.
-
Genome Biol
, vol.5
-
-
Parisi, M.1
Nuttall, R.2
Edwards, P.3
Minor, J.4
Naiman, D.5
-
24
-
-
77952800173
-
2010 On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
-
Parsch, J., S. Novozhilov, S. S. Saminadin-Peter, K.M. Wong, and P. Andolfatto, 2010 On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol. Biol. Evol. 27: 1226-1234.
-
Mol. Biol. Evol.
, vol.27
, pp. 1226-1234
-
-
Parsch, J.1
Novozhilov, S.2
Saminadin-Peter, S.S.3
Wong, K.M.4
Andolfatto, P.5
-
25
-
-
0037504137
-
2003 Sex-dependent gene expression and evolution of the Drosophila transcriptome
-
Ranz, J. M., C. I. Castillo-Davis, C. D. Meiklejohn, and D. L. Hartl, 2003 Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
-
Science
, vol.300
, pp. 1742-1745
-
-
Ranz, J.M.1
Castillo-Davis, C.I.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
26
-
-
35348827911
-
2007 Sugar receptors in Drosophila
-
Slone, J., J. Daniels, and H. Amrein, 2007 Sugar receptors in Drosophila. Curr. Biol. 17: 1809-1816.
-
Curr. Biol.
, vol.17
, pp. 1809-1816
-
-
Slone, J.1
Daniels, J.2
Amrein, H.3
-
27
-
-
1242352089
-
2004 Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
-
Tamura, K., S. Subramanian, and S. Kumar, 2004 Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21: 36-44.
-
Mol. Biol. Evol.
, vol.21
, pp. 36-44
-
-
Tamura, K.1
Subramanian, S.2
Kumar, S.3
-
28
-
-
65449136284
-
2009 TopHat: discovering splice junctions with RNA-Seq
-
Trapnell, C., L. Pachter, and S. L. Salzberg, 2009 TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
29
-
-
84859885816
-
2012 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell, C., A. Roberts, L. Goff, G. Pertea, D. Kim et al., 2012 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7: 562-578.
-
Nat. Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
-
30
-
-
77749292824
-
2010 The genetic signature of conditional expression
-
Van Dyken, J. D., and M. J. Wade, 2010 The genetic signature of conditional expression. Genetics 184: 557-570.
-
Genetics
, vol.184
, pp. 557-570
-
-
Van Dyken, J.D.1
Wade, M.J.2
-
31
-
-
77957243009
-
2010 The Drosophila melanogaster sperm proteome-II (DmSP-II)
-
Wasbrough, E. R., S. Dorus, S. Hester, J. Howard-Murkin, K. Lilley et al., 2010 The Drosophila melanogaster sperm proteome-II (DmSP-II). J. Proteomics 73: 2171-2185.
-
J. Proteomics
, vol.73
, pp. 2171-2185
-
-
Wasbrough, E.R.1
Dorus, S.2
Hester, S.3
Howard-Murkin, J.4
Lilley, K.5
-
32
-
-
36049041622
-
2007 Constraint and turnover in sex-biased gene expression in the genus Drosophila
-
Zhang, Y., D. Sturgill, M. Parisi, S. Kumar, and B. Oliver, 2007 Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450: 233-237.
-
Nature
, vol.450
, pp. 233-237
-
-
Zhang, Y.1
Sturgill, D.2
Parisi, M.3
Kumar, S.4
Oliver, B.5
-
33
-
-
84893906285
-
Origin and spread of de novo genes in Drosophila melanogaster populations
-
Zhao, L., P. Saelao, C. D. Jones, and D. J. Begun, 2014 Origin and spread of de novo genes in Drosophila melanogaster populations. Science 343: 769-772.
-
(2014)
Science
, vol.343
, pp. 769-772
-
-
Zhao, L.1
Saelao, P.2
Jones, C.D.3
Begun, D.J.4
|