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Research: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus
- Julie E. Horvath,
- Christina B. Sheedy,
- Stephanie L. Merrett,
- Abdoulaye Banire Diallo,
- David L. Swofford,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- and Huntington F. Willard
Genome Res. June 2011 21: 850-862; Published in Advance April 25, 2011, doi:10.1101/gr.111849.110
.... This comparative evolutionary genomics approach reveals significant expansion in genomic size across the XIC region in higher primates, with minimal size alterations across the XIST locus itself. Reconstructed primate ancestral XIC sequences show that the most dramatic changes during the past 80 million years...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...species. Similar to nucleotide variation, different types of elements show differing rates of turnover (Fig. 2B). Because DNA transposons, as opposed to retrotransposons, lost their activity early in the primate and rodent lineages (Mouse Genome Sequencing Consortium 2002; Pace and Feschotte 2007), we...
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Research: Discovery of a new repeat family in the Callithrix jacchus genome
- Miriam K. Konkel,
- Brygg Ullmer,
- Erika L. Arceneaux,
- Sreeja Sanampudi,
- Sarah A. Brantley,
- Robert Hubley,
- Arian F.A. Smit,
- and Mark A. Batzer
Genome Res. May 2016 26: 649-659; Published in Advance February 25, 2016, doi:10.1101/gr.199075.115
...; The Chimpanzee Sequencing and Analysis Consortium 2005; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007; Locke et al. 2011; Carbone et al. 2014; The Marmoset Genome Sequencing and Analysis Consortium 2014). The major drivers of repeat-driven expansion in primate s are retrotransposons. They move...
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LETTER: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications
- Xinwei She,
- Ge Liu,
- Mario Ventura,
- Shaying Zhao,
- Doriana Misceo,
- Roberta Roberto,
- Maria Francesca Cardone,
- Mariano Rocchi,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Nicoletta Archidiacano,
- and Evan E. Eichler
Genome Res. May 2006 16: 576-583; Published in Advance April 10, 2006, doi:10.1101/gr.4949406
....E. ( 2003 ) Analysis of primate genomic variation reveals a repeat-driven expansion of the human . Genome Res. 13 : 358 – 368 . ↵ Murphy W.J. , Larkin D.M. , Everts-van der Wind A. , Bourque G. , Tesler G. , Auvil L. , Beever J.E. , Chowdhary B.P. , Galibert F. , Gatzke L. , et al. ( 2005 ) Dynamics...
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Letter: Comparative analysis of Alu repeats in primate genomes
- George E. Liu,
- Can Alkan,
- Lu Jiang,
- Shaying Zhao,
- and Evan E. Eichler
Genome Res. May 2009 19: 876-885; doi:10.1101/gr.083972.108
..., K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human . Nature 409: 860– 921. Liu, G., Zhao, S., Bailey, J.A., Sahinalp, S.C., Alkan, C., Tuzun, E., Green, E.D., and Eichler, E.E. 2003. Analysis of primate genomic variation reveals a repeat-driven...
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Letter: Mobile elements create structural variation: Analysis of a complete human genome
- Jinchuan Xing,
- Yuhua Zhang,
- Kyudong Han,
- Abdel Halim Salem,
- Shurjo K. Sen,
- Chad D. Huff,
- Qiong Zhou,
- Ewen F. Kirkness,
- Samuel Levy,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. September 2009 19: 1516-1526; Published in Advance May 13, 2009, doi:10.1101/gr.091827.109
...Mobile elements create structural variation: Analysis of a complete human genome Jinchuan Xing 1 , Yuhua Zhang 1 , Kyudong Han 2 , Abdel Halim Salem 2 , 3 , 5 , Shurjo K. Sen 2 , 6 , Chad D. Huff 1 , Qiong Zhou 1...
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LETTER: A genome-wide survey of structural variation between human and chimpanzee
- Tera L. Newman,
- Eray Tuzun,
- V. Anne Morrison,
- Karen E. Hayden,
- Mario Ventura,
- Sean D. McGrath,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005
...A genome-wide survey of structural variation between human and chimpanzee Tera L. Newman 1 , Eray Tuzun 1 , V. Anne Morrison 1 , Karen E. Hayden 2 , Mario Ventura 3 , Sean D. McGrath 1 , Mariano Rocchi 3 , and Evan E...
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LETTER: Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes
- Aaron T. Hamilton,
- Stuart Huntley,
- Mary Tran-Gyamfi,
- Daniel M. Baggott,
- Laurie Gordon,
- and Lisa Stubbs
Genome Res. May 2006 16: 584-594; Published in Advance April 10, 2006, doi:10.1101/gr.4843906
...expression differences between species and the evolution of novel primate traits. Footnotes 1 ↵ 1 Corresponding author. ↵ 1 E-mail stubbs5@llnl.gov ; fax (925) 422-2099. [Supplemental material is available online at www.genome.org .] Article published online before print...
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Research: DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation
- Anne Y. Lai,
- Deepak Mav,
- Ruchir Shah,
- Sara A. Grimm,
- Dhiral Phadke,
- Katerina Hatzi,
- Ari Melnick,
- Cissy Geigerman,
- Steve E. Sobol,
- David L. Jaye,
- and Paul A. Wade
Genome Res. December 2013 23: 2030-2041; Published in Advance September 6, 2013, doi:10.1101/gr.155473.113
..., AY Deepak Paul A Mav David Grimm, S.A Steve E Hatzi Katerina Steve E Sobol Grimm Anne Y Lai SaraA Grimm S Sobol Wade, P Hatzi, Katerina Phadke, D AnneY Lai David L, Jaye PA Wade Lai, A.Y genome;gr.155473.113 1088-9051 10.1101/gr.155473.113 DNA methylation profiling in human B cells reveals immune...
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ARTICLE: Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23
- Anna Antonell,
- Oscar de Luis,
- Xavier Domingo-Roura,
- and Luis Alberto Pérez-Jurado
Genome Res. September 2005 15: 1179-1188; doi:10.1101/gr.3944605
.... As the differences at the level of genomic DNA sequence are very low among primates ( Chen and Li 2001 ), many relevant phenotypic differences might be due to chromosomal rearrangements and insertion/deletion events ( Frazer et al. 2003 ; Locke et al. 2003 ). Karyotype analysis of the primate s reveals just a few...

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