Searching journal content for articles similar to Catchen et al. 19 (8): 1497.

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  1. Methods: Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
    • Michael Brudno,
    • Alexander Poliakov,
    • Asaf Salamov,
    • Gregory M. Cooper,
    • Arend Sidow,
    • Edward M. Rubin,
    • Victor Solovyev,
    • Serafim Batzoglou,
    • and Inna Dubchak
    Genome Res. April 2004 14: 685-692; doi:10.1101/gr.2067704
    ...downloaded. ↵ http://pipeline.lbl.gov/downloads.shtml ; Download page for whole alignments and other materials. ↵ http://www.softberry.com/berry.phtml?topic=human-mouse-rat ; Three-way gene-based synteny. Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human Michael Brudno 1 , Alexander Poliakov...
  2. Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
    • Karin S. Kassahn,
    • Vinh T. Dang,
    • Simon J. Wilkins,
    • Andrew C. Perkins,
    • and Mark A. Ragan
    Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
    ...Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates Karin S. Kassahn 1 , Vinh T. Dang 1 , Simon J. Wilkins 2 , Andrew C. Perkins 2 and Mark A. Ragan 1 , 3 1...
  3. Resource: Multiple whole-genome alignments without a reference organism
    • Inna Dubchak,
    • Alexander Poliakov,
    • Andrey Kislyuk,
    • and Michael Brudno
    Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
    ...on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric...
  4. Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
    • Tim Downing,
    • Hideo Imamura,
    • Saskia Decuypere,
    • Taane G. Clark,
    • Graham H. Coombs,
    • James A. Cotton,
    • James D. Hilley,
    • Simonne de Doncker,
    • Ilse Maes,
    • Jeremy C. Mottram,
    • Mike A. Quail,
    • Suman Rijal,
    • Mandy Sanders,
    • Gabriele Schönian,
    • Olivia Stark,
    • Shyam Sundar,
    • Manu Vanaerschot,
    • Christiane Hertz-Fowler,
    • Jean-Claude Dujardin,
    • and Matthew Berriman
    Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
    ...Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance Tim Downing 1 , 10 , Hideo Imamura 2 , 10 , Saskia Decuypere 2 , Taane G. Clark 3...
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  5. LETTER: Improvement of whole-genome annotation of cereals through comparative analyses
    • Wei Zhu and
    • C. Robin Buell
    Genome Res. March 2007 17: 299-310; Published in Advance February 6, 2007, doi:10.1101/gr.5881807
    ...Improvement of whole-genome annotation of cereals through comparative analyses Wei Zhu and C. Robin Buell 1 The Institute for Genomic Research, Rockville, Maryland 20850, USA Abstract Rice is an important model species for the Poaceae and other...
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  6. LETTER: Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
    • Mulu Ayele,
    • Brian J. Haas,
    • Nikhil Kumar,
    • Hank Wu,
    • Yongli Xiao,
    • Susan Van Aken,
    • Teresa R. Utterback,
    • Jennifer R. Wortman,
    • Owen R. White,
    • and Christopher D. Town
    Genome Res. April 2005 15: 487-495; doi:10.1101/gr.3176505
    ..., we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering 283 Mb (0.44×) of the estimated 650 Mb Brassica genome were searched against...
  7. Methods: Identification of transposable elements using multiple alignments of related genomes
    • Anat Caspi and
    • Lior Pachter
    Genome Res. February 2006 16: 260-270; Published in Advance December 14, 2005, doi:10.1101/gr.4361206
    ...on the host genome, and improve the quality of assembled genomes. Using the availability of several nearly complete Drosophila genomes and developments in whole genome alignment methods, we introduce a large-scale comparative method for identifying repetitive mobile DNA regions. These regions are highly...
  8. LETTER: An ~140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival
    • John C. Fyfe,
    • Marilyn Menotti-Raymond,
    • Victor A. David,
    • Lars Brichta,
    • Alejandro A. Schäffer,
    • Richa Agarwala,
    • William J. Murphy,
    • William J. Wedemeyer,
    • Brittany L. Gregory,
    • Bethany G. Buzzell,
    • Meghan C. Drummond,
    • Brunhilde Wirth,
    • and Stephen J. O'Brien
    Genome Res. September 2006 16: 1084-1090; Published in Advance August 9, 2006, doi:10.1101/gr.5268806
    ...-onset SMA similar to human SMA type III. Here we report results of a whole-genome scan for linkage in the feline SMA pedigree using recently developed species-specific and comparative mapping resources. We identified a novel SMA gene candidate, LIX1 , in an ~140-kb deletion on feline chromosome A1q...
  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
    ...of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25–55 million years (Myr) since the pseudoobscura / melanogaster divergence. Genes expressed in the testes had higher amino acid...
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  10. Resource: The genome of the pear (Pyrus bretschneideri Rehd.)
    • Jun Wu,
    • Zhiwen Wang,
    • Zebin Shi,
    • Shu Zhang,
    • Ray Ming,
    • Shilin Zhu,
    • M. Awais Khan,
    • Shutian Tao,
    • Schuyler S. Korban,
    • Hao Wang,
    • Nancy J. Chen,
    • Takeshi Nishio,
    • Xun Xu,
    • Lin Cong,
    • Kaijie Qi,
    • Xiaosan Huang,
    • Yingtao Wang,
    • Xiang Zhao,
    • Juyou Wu,
    • Cao Deng,
    • Caiyun Gou,
    • Weili Zhou,
    • Hao Yin,
    • Gaihua Qin,
    • Yuhui Sha,
    • Ye Tao,
    • Hui Chen,
    • Yanan Yang,
    • Yue Song,
    • Dongliang Zhan,
    • Juan Wang,
    • Leiting Li,
    • Meisong Dai,
    • Chao Gu,
    • Yuezhi Wang,
    • Daihu Shi,
    • Xiaowei Wang,
    • Huping Zhang,
    • Liang Zeng,
    • Danman Zheng,
    • Chunlei Wang,
    • Maoshan Chen,
    • Guangbiao Wang,
    • Lin Xie,
    • Valpuri Sovero,
    • Shoufeng Sha,
    • Wenjiang Huang,
    • Shujun Zhang,
    • Mingyue Zhang,
    • Jiangmei Sun,
    • Linlin Xu,
    • Yuan Li,
    • Xing Liu,
    • Qingsong Li,
    • Jiahui Shen,
    • Junyi Wang,
    • Robert E. Paull,
    • Jeffrey L. Bennetzen,
    • Jun Wang,
    • and Shaoling Zhang
    Genome Res. February 2013 23: 396-408; Published in Advance November 13, 2012, doi:10.1101/gr.144311.112
    ...of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When...
    OPEN ACCESS ARTICLE
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