Searching journal content for articles similar to Verhasselt and Volckaert 4 (2): 129.

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  1. Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
    • Peter O. Mulhair,
    • Liam Crowley,
    • Douglas H. Boyes,
    • Amber Harper,
    • Owen T. Lewis,
    • Darwin Tree of Life Consortium,
    • and Peter W.H. Holland
    Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
    ...or to genomic organization. To a large degree, this is a consequence of the limited number of high-quality chromosomal-level assemblies available until very recently. With advances in DNA sequencing technology, coupled with scaffolding using Hi-C, this limitation is being overcome (The Darwin Tree of Life...
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  2. Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
    • Marin Volarić,
    • Evelin Despot-Slade,
    • Damira Veseljak,
    • Brankica Mravinac,
    • and Nevenka Meštrović
    Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
    ...and assemble, and therefore, they are underrepresented or absent even in the best assemblies (for review, see Miga 2015; Lower et al. 2018). However, with the improvement of long-read sequencing technology, especially the Oxford Nanopore platform, it has recently been demonstrated that genomic loci made of satDNAs...
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  3. Research: Patching gaps in plant genomes results in gene movement and erosion of colinearity
    • Thomas Wicker,
    • Jan P. Buchmann,
    • and Beat Keller
    Genome Res. September 2010 20: 1229-1237; Published in Advance June 7, 2010, doi:10.1101/gr.107284.110
    ...colinearity through repair Genome Research 1233 www..org internal domain with many low-complexity motifs at the border of the captured fragment (Supplemental Fig. 1). We speculate that, whatever primary function these regions have for the transposon, theymay accidentally trigger the uptake of foreign DNA...
  4. LETTER: Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
    • Jianxin Ma,
    • Katrien M. Devos,
    • and Jeffrey L. Bennetzen
    Genome Res. May 2004 14: 860-869; Published in Advance April 12, 2004, doi:10.1101/gr.1466204
    ...Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice Jianxin Ma 1 , 2 , Katrien M. Devos 1 , 3 , and Jeffrey L. Bennetzen 1 , 2 , 4 1 Department of Biological Sciences, Purdue University, West...
  5. Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
    • Steven G. Kuntz,
    • Erich M. Schwarz,
    • John A. DeModena,
    • Tristan De Buysscher,
    • Diane Trout,
    • Hiroaki Shizuya,
    • Paul W. Sternberg,
    • and Barbara J. Wold
    Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
    ...W. Diane Trout Schwarz ErichM Schwarz Steven G Kuntz J DeModena Wold, B Erich Sternberg, PW Kuntz Erich M Kuntz Steven G. De Buysscher, Tristan B Wold DeModena SG Kuntz Erich M Schwarz genome;gr.085472.108 10.1101/gr.085472.108 1088-9051 Multigenome DNA sequence conservation identifies Hox cis...
  6. LETTER: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution
    • Graham R. Bignell,
    • Thomas Santarius,
    • Jessica C.M. Pole,
    • Adam P. Butler,
    • Janet Perry,
    • Erin Pleasance,
    • Chris Greenman,
    • Andrew Menzies,
    • Sheila Taylor,
    • Sarah Edkins,
    • Peter Campbell,
    • Michael Quail,
    • Bob Plumb,
    • Lucy Matthews,
    • Kirsten McLay,
    • Paul A.W. Edwards,
    • Jane Rogers,
    • Richard Wooster,
    • P. Andrew Futreal,
    • and Michael R. Stratton
    Genome Res. September 2007 17: 1296-1303; Published in Advance August 3, 2007, doi:10.1101/gr.6522707
    ...). Complete sequencing of a single BAC revealed a patchwork of genomic DNA fragments ( Volik et al. 2003 ). Using this strategy, we have now conducted a detailed investigation of the structure at sequence-level resolution of somatic rearrangements in multiple amplified regions in cancer. We have shown...
  7. Letter: Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability
    • Mark D. Pertile,
    • Alison N. Graham,
    • K.H. Andy Choo,
    • and Paul Kalitsis
    Genome Res. December 2009 19: 2202-2213; Published in Advance September 8, 2009, doi:10.1101/gr.092080.109
    ...Ymin array. (C ) PFGE Southern hybridization of genomic DNAs probed with Ymin exhibits malespecific fragment lengths of predicted size (arrow) in five strains carrying a M.m. molossinus Y chromosome after digestion with enzymes BamHI (90.7 kb expected) and PacI (124 kb expected) (HindIII and XbaI data...
  8. ARTICLE: Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris
    • Wei Qian,
    • Yantao Jia,
    • Shuang-Xi Ren,
    • Yong-Qiang He,
    • Jia-Xun Feng,
    • Ling-Feng Lu,
    • Qihong Sun,
    • Ge Ying,
    • Dong-Jie Tang,
    • Hua Tang,
    • Wei Wu,
    • Pei Hao,
    • Lifeng Wang,
    • Bo-Le Jiang,
    • Shenyan Zeng,
    • Wen-Yi Gu,
    • Gang Lu,
    • Li Rong,
    • Yingchuan Tian,
    • Zhijian Yao,
    • Gang Fu,
    • Baoshan Chen,
    • Rongxiang Fang,
    • Boqin Qiang,
    • Zhu Chen,
    • Guo-Ping Zhao,
    • Ji-Liang Tang,
    • and Chaozu He
    Genome Res. June 2005 15: 757-767; Published in Advance May 17, 2005, doi:10.1101/gr.3378705
    ...and annotation Genomic DNA was sheared by sonication. The blunt-ends were created by mung bean nuclease, and 1.5-3.0 kb fragments were cloned into pUC18 digested with SmaI. The 8-10-kb inserts generated by Sau3AI/MboI were ligated into pUC18 digested with BamHI. Approximately 55,000 clones were sequenced from...
  9. LETTER: An intermediate grade of finished genomic sequence suitable for comparative analyses
    • Robert W. Blakesley,
    • Nancy F. Hansen,
    • James C. Mullikin,
    • Pamela J. Thomas,
    • Jennifer C. McDowell,
    • Baishali Maskeri,
    • Alice C. Young,
    • Beatrice Benjamin,
    • Shelise Y. Brooks,
    • Bradley I. Coleman,
    • Jyoti Gupta,
    • Shi-Ling Ho,
    • Eric M. Karlins,
    • Quino L. Maduro,
    • Sirintorn Stantripop,
    • Cyrus Tsurgeon,
    • Jennifer L. Vogt,
    • Michelle A. Walker,
    • Catherine A. Masiello,
    • Xiaobin Guan,
    • NISC Comparative Sequencing Program,
    • Gerard G. Bouffard,
    • and Eric D. Green
    Genome Res. November 2004 14: 2235-2244; Published in Advance October 12, 2004, doi:10.1101/gr.2648404
    ...are typically performed in two broad phases. In the initial “shotgun” phase, highly redundant sequence data are obtained by generating sequence reads from one or both insert ends of randomly selected subclones derived from the starting DNA (large-insert clone or whole ). This phase involves high...
  10. RESEARCH: Ataxia-Telangiectasia Locus: Sequence Analysis of 184 kb of Human Genomic DNA Containing the Entire ATM Gene
    • Matthias Platzer,
    • Galit Rotman,
    • David Bauer,
    • Tamar Uziel,
    • Kinneret Savitsky,
    • Anat Bar-Shira,
    • Shlomit Gilad,
    • Yosef Shiloh,
    • and André Rosenthal
    Genome Res. June 1, 1997 7: 592-605; doi:10.1101/gr.7.6.592
    ...previous results from cDNA sequencing and long-distance PCR using human DNA as the template ( Uziel et al. 1996 ). It also proves the colinearity of the cosmid and genomic sequence. View larger version: In this window In a new window Figure 2. Schematic representation of the sequenced ATM locus. Boxes...
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