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Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila
Yongsheng Bai, Claudio Casola, Cédric Feschotte, Esther Betrán
Genome Biol. 2007; 8(1): R11. Published online 2007 January 18. doi: 10.1186/gb-2007-8-1-r11
PMCID:
PMC1839131
Abstract Full Text PDF–274K Supplementary Material

Is Cited by the Following 36 Articles in this Archive:

Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony
Mira V. Han, Matthew W. Hahn
Genetics. 2012 February; 190(2): 813–825. doi: 10.1534/genetics.111.135947
PMCID:
PMC3276645
Free in PMC on 2013/02/01
Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution
Yolanda Guillén, Alfredo Ruiz
BMC Genomics. 2012; 13: 53. Published online 2012 February 1. doi: 10.1186/1471-2164-13-53
PMCID:
PMC3355041
Abstract Full Text PDF–639K Supplementary Material
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
Daniel R. Schrider, Kristian Stevens, Charis M. Cardeño, Charles H. Langley, Matthew W. Hahn
Genome Res. 2011 December; 21(12): 2087–2095. doi: 10.1101/gr.116434.110
PMCID:
PMC3227099
Free in PMC on 2012/06/01
Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes
Hiroaki Sakai, Hiroshi Mizuno, Yoshihiro Kawahara, Hironobu Wakimoto, Hiroshi Ikawa, Hiroyuki Kawahigashi, Hiroyuki Kanamori, Takashi Matsumoto, Takeshi Itoh, Brandon S. Gaut
Genome Biol Evol. 2011; 3: 1357–1368. Published online 2011 October 31. doi: 10.1093/gbe/evr111
PMCID:
PMC3240961
Abstract Full Text PDF–655K
No Excess Gene Movement Is Detected off the Avian or Lepidopteran Z Chromosome
Melissa A. Toups, James B. Pease, Matthew W. Hahn
Genome Biol Evol. 2011; 3: 1381–1390. Published online 2011 October 24. doi: 10.1093/gbe/evr109
PMCID:
PMC3242482
Abstract Full Text PDF–143K
Molecular Evolution of Phosphoprotein Phosphatases in Drosophila
Márton Miskei, Csaba Ádám, László Kovács, Zsolt Karányi, Viktor Dombrádi
PLoS One. 2011; 6(7): e22218. Published online 2011 July 15. doi: 10.1371/journal.pone.0022218
PMCID:
PMC3137614
Abstract Full Text PDF–696K Supplementary Material
Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates
Ming Chen, Ming Zou, Beide Fu, Xin Li, Maria D. Vibranovski, Xiaoni Gan, Dengqiang Wang, Wen Wang, Manyuan Long, Shunping He
PLoS One. 2011; 6(7): e21466. Published online 2011 July 11. doi: 10.1371/journal.pone.0021466
PMCID:
PMC3136929
Abstract Full Text PDF–373K Supplementary Material
A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes
Yong E. Zhang, Maria D. Vibranovski, Benjamin H. Krinsky, Manyuan Long
Bioinformatics. 2011 July 1; 27(13): 1749–1753. Published online 2011 May 5. doi: 10.1093/bioinformatics/btr280
PMCID:
PMC3117337
Free in PMC on 2012/07/01
Intralocus sexual conflict resolved through gene duplication
Miguel Gallach, Esther Betrán
Trends Ecol Evol. Author manuscript; available in PMC 2012 May 1.
Published in final edited form as: Trends Ecol Evol. 2011 May; 26(5): 222–228. Published online 2011 March 11. doi: 10.1016/j.tree.2011.02.004
PMCID:
PMC3090214
Abstract Full Text PDF–241K
The rapid generation of chimerical genes expanding protein diversity in zebrafish
Beide Fu, Ming Chen, Ming Zou, Manyuan Long, Shunping He
BMC Genomics. 2010; 11: 657. Published online 2010 November 24. doi: 10.1186/1471-2164-11-657
PMCID:
PMC3091775
Abstract Full Text PDF–379K Supplementary Material
Age-dependent chromosomal distribution of male-biased genes in Drosophila
Yong E. Zhang, Maria D. Vibranovski, Benjamin H. Krinsky, Manyuan Long
Genome Res. 2010 November; 20(11): 1526–1533. doi: 10.1101/gr.107334.110
PMCID:
PMC2963816
Abstract Full Text PDF–453K
Analyses of Nuclearly Encoded Mitochondrial Genes Suggest Gene Duplication as a Mechanism for Resolving Intralocus Sexually Antagonistic Conflict in Drosophila
Miguel Gallach, Chitra Chandrasekaran, Esther Betrán
Genome Biol Evol. 2010; 2: 835–850. Published online 2010 October 29. doi: 10.1093/gbe/evq069
PMCID:
PMC2995371
Abstract Full Text PDF–328K
Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome
Yong E. Zhang, Maria D. Vibranovski, Patrick Landback, Gabriel A. B. Marais, Manyuan Long
PLoS Biol. 2010 October; 8(10): e1000494. Published online 2010 October 5. doi: 10.1371/journal.pbio.1000494
PMCID:
PMC2950125
Abstract Full Text PDF–1.3M Supplementary Material
Origins, evolution, and phenotypic impact of new genes
Henrik Kaessmann
Genome Res. 2010 October; 20(10): 1313–1326. doi: 10.1101/gr.101386.109
PMCID:
PMC2945180
Abstract Full Text PDF–630K
Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila
Jorge Ernesto Quezada-Díaz, Taniya Muliyil, Javier Río, Esther Betrán
Genetica. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Genetica. 2010 October; 138(9-10): 925–937. Published online 2010 August 8. doi: 10.1007/s10709-010-9474-8
PMCID:
PMC2998177
Abstract Full Text PDF–714K Supplementary Material
Convergently Recruited Nuclear Transport Retrogenes Are Male Biased in Expression and Evolving Under Positive Selection in Drosophila
Charles Tracy, Javier Río, Mansi Motiwale, Shawn M. Christensen, Esther Betrán
Genetics. 2010 April; 184(4): 1067–1076. doi: 10.1534/genetics.109.113522
PMCID:
PMC2865908
Abstract Full Text PDF–2.6M
Genome-wide analysis of YY2 versus YY1 target genes
Li Chen, Toshi Shioda, Kathryn R. Coser, Mary C. Lynch, Chuanwei Yang, Emmett V. Schmidt
Nucleic Acids Res. 2010 July; 38(12): 4011–4026. Published online 2010 March 9. doi: 10.1093/nar/gkq112
PMCID:
PMC2896514
Abstract Full Text PDF–5.9M Supplementary Material
Turnover and lineage-specific broadening of the transcription start site in a testis-specific retrogene
Mehran Sorourian, Esther Betrán
Fly (Austin) Author manuscript; available in PMC 2010 April 17.
Published in final edited form as: Fly (Austin). 2010 January; 4(1): 3–11. Published online 2010 January 30.
PMCID:
PMC2855778
Abstract Full Text PDF–2.4M Supplementary Material
Genetic conflict and sex chromosome evolution
Colin D Meiklejohn, Yun Tao
Trends Ecol Evol. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Trends Ecol Evol. 2010 April; 25(4): 215–223. Published online 2009 November 26. doi: 10.1016/j.tree.2009.10.005
PMCID:
PMC2843792
Abstract Full Text PDF–669K
Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes
Maria D. Vibranovski, Hedibert F. Lopes, Timothy L. Karr, Manyuan Long
PLoS Genet. 2009 November; 5(11): e1000731. Published online 2009 November 20. doi: 10.1371/journal.pgen.1000731
PMCID:
PMC2770318
Abstract Full Text PDF–611K Supplementary Material
An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications
Deng Pan, Liqing Zhang
PLoS One. 2009; 4(10): e7342. Published online 2009 October 23. doi: 10.1371/journal.pone.0007342
PMCID:
PMC2761543
Abstract Full Text PDF–348K Supplementary Material
Positive selection for the male functionality of a co-retroposed gene in the hominoids
Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, Liping Wei
BMC Evol Biol. 2009; 9: 252. Published online 2009 October 15. doi: 10.1186/1471-2148-9-252
PMCID:
PMC2773790
Abstract Full Text PDF–491K Supplementary Material
A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes
Richard P. Meisel, Mira V. Han, Matthew W. Hahn
Genome Biol Evol. 2009; 1: 176–188. Published online 2009 July 7. doi: 10.1093/gbe/evp018
PMCID:
PMC2817413
Abstract Full Text PDF–240K Supplementary Material
Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution
John K. Pace, II, Shurjo K. Sen, Mark A. Batzer, Cédric Feschotte
PLoS Genet. 2009 May; 5(5): e1000469. Published online 2009 May 8. doi: 10.1371/journal.pgen.1000469
PMCID:
PMC2671141
Abstract Full Text PDF–1.1M Supplementary Material
Burst of Young Retrogenes and Independent Retrogene Formation in Mammals
Deng Pan, Liqing Zhang
PLoS ONE. 2009; 4(3): e5040. Published online 2009 March 27. doi: 10.1371/journal.pone.0005040
PMCID:
PMC2657826
Abstract Full Text PDF–235K Supplementary Material
Molecular Evolution and Functional Diversification of Fatty Acid Desaturases after Recurrent Gene Duplication in Drosophila
Shu Fang, Chau-Ti Ting, Cheng-Ruei Lee, Kuang-Hsi Chu, Chuan-Chan Wang, Shun-Chern Tsaur
Mol Biol Evol. 2009 July; 26(7): 1447–1456. Published online 2009 March 23. doi: 10.1093/molbev/msp057
PMCID:
PMC2693736
Abstract Full Text PDF–276K Supplementary Material
Molecular Evolution of the Testis TAFs of Drosophila
Victor C. Li, Jerel C. Davis, Kapa Lenkov, Benjamin Bolival, Margaret T. Fuller, Dmitri A. Petrov
Mol Biol Evol. 2009 May; 26(5): 1103–1116. Published online 2009 February 25. doi: 10.1093/molbev/msp030
PMCID:
PMC2727373
Abstract Full Text PDF–504K Supplementary Material
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares
Genome Biol. 2008; 9(12): R176. Published online 2008 December 16. doi: 10.1186/gb-2008-9-12-r176
PMCID:
PMC2646280
Abstract Full Text PDF–550K Supplementary Material
Quality of regulatory elements in Drosophila retrogenes
Yongsheng Bai, Claudio Casola, Esther Betrán
Genomics. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Genomics. 2009 January; 93(1): 83–89. Published online 2008 October 23. doi: 10.1016/j.ygeno.2008.09.006
PMCID:
PMC2753227
Abstract Full Text PDF–708K Supplementary Material
On the origin of new genes in Drosophila
Qi Zhou, Guojie Zhang, Yue Zhang, Shiyu Xu, Ruoping Zhao, Zubing Zhan, Xin Li, Yun Ding, Shuang Yang, Wen Wang
Genome Res. 2008 September; 18(9): 1446–1455. doi: 10.1101/gr.076588.108
PMCID:
PMC2527705
Abstract Full Text PDF–400K
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