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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13) Svea 36H Mouse Ann-Marie Mallon 1 , 4 , Laurens Wilming 2 , 4 , Joseph Weekes 1 , James G.R. Gilbert 2 , Jennifer Ashurst 2...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...important factors influencing the evolution of mammalian s. Yet little is known about its evolutionary rate or the fraction of the methylome that has undergone change. We compared whole-, single-CpG DNA methylation profiles in sperm of seven species—human, chimpanzee, gorilla, rhesus macaque, mouse, rat...
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Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
- Itai Yanai and
- Craig P. Hunter
Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
.... Protein evolution in the context of Drosophila development. J Mol Evol 60: 774–785. De S, Teichmann SA, BabuMM. 2009. The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res 19: 785–794. Denver DR, Morris K, Thomas WK. 2003. Phylogenetics in Caenorhabditis...
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Research: The frequent evolutionary birth and death of functional promoters in mouse and human
- Robert S. Young,
- Yoshihide Hayashizaki,
- Robin Andersson,
- Albin Sandelin,
- Hideya Kawaji,
- Masayoshi Itoh,
- Timo Lassmann,
- Piero Carninci,
- The FANTOM Consortium,
- Wendy A. Bickmore,
- Alistair R. Forrest,
- and Martin S. Taylor
Genome Res. October 2015 25: 1546-1557; Published in Advance July 30, 2015, doi:10.1101/gr.190546.115
....01, (∗∗∗) P < 0.001. Frequent promoter turnover in mouse and human Genome Research 1553 www..org and lost throughout mammalian evolution at an even higher rate than putative promoters in liver tissue (Villar et al. 2015). Measuring active enhancers across multiple matched tissues as we have done...
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Research: Functional and topological characteristics of mammalian regulatory domains
- Orsolya Symmons,
- Veli Vural Uslu,
- Taro Tsujimura,
- Sandra Ruf,
- Sonya Nassari,
- Wibke Schwarzer,
- Laurence Ettwiller,
- and François Spitz
Genome Res. March 2014 24: 390-400; Published in Advance January 7, 2014, doi:10.1101/gr.163519.113
..., MA 01938, USA Abstract Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene...
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Research: High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
- Penka Markova-Raina and
- Dmitri Petrov
Genome Res. June 2011 21: 863-874; Published in Advance March 10, 2011, doi:10.1101/gr.115949.110
...among all five aligners. (C ) v of AMAP vs. T-Coffee. 864 Genome Research www..org Markova-Raina and Petrov of the species. The impact of aligner choice in the presence of higher rates of protein evolution remains to be determined. Genes with positively selected sites Sites under positive selection were...

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