Searching journal content for articles similar to Paten et al..

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  1. Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • Jakob Skou Pedersen,
    • Eivind Valen,
    • Amhed M. Vargas Velazquez,
    • Brian J. Parker,
    • Morten Rasmussen,
    • Stinus Lindgreen,
    • Berit Lilje,
    • Desmond J. Tobin,
    • Theresa K. Kelly,
    • Søren Vang,
    • Robin Andersson,
    • Peter A. Jones,
    • Cindi A. Hoover,
    • Alexei Tikhonov,
    • Egor Prokhortchouk,
    • Edward M. Rubin,
    • Albin Sandelin,
    • M. Thomas P. Gilbert,
    • Anders Krogh,
    • Eske Willerslev,
    • and Ludovic Orlando
    Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
    ...G dinucleotides, as experimental evidence supports the longterm survival of methylated cytosines (5mC) in aDNA fragments (Briggs et al. 2010; Llamas et al. 2012). Genome-wide methylationmaps of the human have already been reconstructed using high-throughput sequencing in combination with a variety of approaches...
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  2. Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Benedict Paten,
    • Javier Herrero,
    • Kathryn Beal,
    • Stephen Fitzgerald,
    • and Ewan Birney
    Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
    ...Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs Benedict Paten 1 , 3 , 4 , Javier Herrero 2 , 3 , Kathryn Beal 2 , Stephen Fitzgerald 2 , and Ewan Birney 2 , 4 1 Center...
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  3. 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
    ...or absence of a nucleotide is much higher than confidence in which base pair existed in an ancestor (Supplemental Fig. 4b). This is not surprising given that these are reconstructions across diverse mammalian species and that parts of the alignment are problematic due to low conservation and/or alignment...
  4. Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
    • Chun-Long Chen,
    • Aurélien Rappailles,
    • Lauranne Duquenne,
    • Maxime Huvet,
    • Guillaume Guilbaud,
    • Laurent Farinelli,
    • Benjamin Audit,
    • Yves d'Aubenton-Carafa,
    • Alain Arneodo,
    • Olivier Hyrien,
    • and Claude Thermes
    Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
    ...Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes Chun-Long Chen 1 , Aurélien Rappailles 2 , Lauranne Duquenne 1 , 6 , Maxime Huvet 1 , 7 , Guillaume Guilbaud 2 , Laurent Farinelli 3...
  5. Methods: Reconstructing contiguous regions of an ancestral genome
    • Jian Ma,
    • Louxin Zhang,
    • Bernard B. Suh,
    • Brian J. Raney,
    • Richard C. Burhans,
    • W. James Kent,
    • Mathieu Blanchette,
    • David Haussler,
    • and Webb Miller
    Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
    ...predicted ancestral run of segments a “contiguous ancestral region,” abbreviated CAR. We found 29 CARs in total from the data we used (see Fig. 4 and Table 2 ). If we add the human sequence between conserved segments that are adjacent in both human and the ancestor (since a nucleotide-level reconstruction...
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  6. Method: Short template switch events explain mutation clusters in the human genome
    • Ari Löytynoja and
    • Nick Goldman
    Genome Res. June 2017 27: 1039-1049; Published in Advance April 6, 2017, doi:10.1101/gr.214973.116
    ...detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human s. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also...
  7. Method: Quantification of GC-biased gene conversion in the human genome
    • Sylvain Glémin,
    • Peter F. Arndt,
    • Philipp W. Messer,
    • Dmitri Petrov,
    • Nicolas Galtier,
    • and Laurent Duret
    Genome Res. August 2015 25: 1215-1228; Published in Advance May 20, 2015, doi:10.1101/gr.185488.114
    ...machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%–2% of the human is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences...
  8. RESOURCE: The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
    • Matthew M. Hill,
    • Karl W. Broman,
    • Elia Stupka,
    • William C. Smith,
    • Di Jiang,
    • and Arend Sidow
    Genome Res. August 2008 18: 1369-1379; Published in Advance June 2, 2008, doi:10.1101/gr.078576.108
    .... intestinalis . Sensitive nucleotide-level alignments between these two species were previously generated using a combination of global and local (glocal) alignment ( Brudno et al. 2007 ). To enrich for high-quality and putatively orthologous alignments, only reciprocal best alignments were used in our analyses...
  9. ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
    • Stephen Richards,
    • Yue Liu,
    • Brian R. Bettencourt,
    • Pavel Hradecky,
    • Stan Letovsky,
    • Rasmus Nielsen,
    • Kevin Thornton,
    • Melissa J. Hubisz,
    • Rui Chen,
    • Richard P. Meisel,
    • Olivier Couronne,
    • Sujun Hua,
    • Mark A. Smith,
    • Peili Zhang,
    • Jing Liu,
    • Harmen J. Bussemaker,
    • Marinus F. van Batenburg,
    • Sally L. Howells,
    • Steven E. Scherer,
    • Erica Sodergren,
    • Beverly B. Matthews,
    • Madeline A. Crosby,
    • Andrew J. Schroeder,
    • Daniel Ortiz-Barrientos,
    • Catharine M. Rives,
    • Michael L. Metzker,
    • Donna M. Muzny,
    • Graham Scott,
    • David Steffen,
    • David A. Wheeler,
    • Kim C. Worley,
    • Paul Havlak,
    • K. James Durbin,
    • Amy Egan,
    • Rachel Gill,
    • Jennifer Hume,
    • Margaret B. Morgan,
    • George Miner,
    • Cerissa Hamilton,
    • Yanmei Huang,
    • Lenée Waldron,
    • Daniel Verduzco,
    • Kerstin P. Clerc-Blankenburg,
    • Inna Dubchak,
    • Mohamed A.F. Noor,
    • Wyatt Anderson,
    • Kevin P. White,
    • Andrew G. Clark,
    • Stephen W. Schaeffer,
    • William Gelbart,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
    ...sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis -regulatory sequences are more conserved than random and nearby sequences between the species—but the difference is slight, suggesting that the evolution of cis -regulatory elements...
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