Searching journal content for articles similar to Hufton et al. 18 (10): 1582.

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  1. Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    • Harsh G. Shukla,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
    ...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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  2. Research: Large haplotypes highlight a complex age structure within the maize pan-genome
    • Jianing Liu and
    • R. Kelly Dawe
    Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
    ...) Perform pairwise whole- alignment, (2) chain aligned segments with LIS in a two-step process, where the first step identified syntenic (collinear) segments and the second step resolved locally rearranged regions, and (3) characterize structural variants through identifying alignment gaps. Refer to https://github.com/dawelab/Age_Structure/tree/master/SV-calling.AlignmentGenome...
  3. LETTER: The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage
    • John K. Pace II and
    • Cédric Feschotte
    Genome Res. April 2007 17: 422-432; Published in Advance March 5, 2007, doi:10.1101/gr.5826307
    ...(∼33 Mb) in the human genome, have been active in the primate lineage. There was a cessation in the transpositional activity of DNA transposons during the later phase of the primate radiation, with no evidence of elements younger than ∼37 My. This data points to intense activity of DNA transposons...
  4. ARTICLE: Complex Evolution of 7E Olfactory Receptor Genes in Segmental Duplications
    • Tera Newman and
    • Barbara J. Trask
    Genome Res. May 1, 2003 13: 781-793; doi:10.1101/gr.769003
    ...of Washington, Seattle, Washington 98195, USA Abstract Large segmental duplications (SDs) constitute at least 3.6% of the human genome and have increased its size, complexity, and diversity. SDs can mediate ectopic sequence exchange resulting in gross chromosomal rearrangements that could contribute...
  5. LETTER: The Human Hox-bearing Chromosome Regions Did Arise by Block or Chromosome (or Even Genome) Duplications
    • Dan Larhammar,
    • Lars-Gustav Lundin,
    • and Finn Hallböök
    Genome Res. December 1, 2002 12: 1910-1920; doi:10.1101/gr.445702
    ...contributed to the expansion of the vertebrate has been debated intensely during the past few years ( Pennisi 2001 ). A recent article in Genome Research by Hughes et al. (2001) aimed to test the chromosome/ duplication hypothesis by studying gene families with members on two or more of the human Hox...
  6. LETTER: Segmental Duplications in Euchromatic Regions of Human Chromosome 5: A Source of Evolutionary Instability and Transcriptional Innovation
    • Anouk Courseaux,
    • Florence Richard,
    • Josiane Grosgeorge,
    • Christine Ortola,
    • Agnes Viale,
    • Claude Turc-Carel,
    • Bernard Dutrillaux,
    • Patrick Gaudray,
    • and Jean-Louis Nahon
    Genome Res. March 1, 2003 13: 369-381; Published in Advance February 12, 2003, doi:10.1101/gr.490303
    ...in the Hominidae lineage has fully reshaped the SMA locus during primate evolution. Although a direct connection is yet to be established, it is particularly tempting to speculate that there is a link between the dynamic duplicative nature of genomic duplicons and the rearrangements mediating the SMA disease (e...
  7. Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
    • Barbara Dunn,
    • Chandra Richter,
    • Daniel J. Kvitek,
    • Tom Pugh,
    • and Gavin Sherlock
    Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
    ..., and also in new yeast species via interspecific hybridization, autopolyploidization, gene duplication, gene transfer, and other large-scale changes (for review, see Sicard and Legras 2011). Using aCGH on a custom multispecies array platform, we show that different genomic locations have differing levels...
  8. Research: Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
    • Takashi Makino and
    • Aoife McLysaght
    Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111
    ..., Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. 2007. Ensembl 2007. Nucleic Acids Res 35: D610–D617. Hufton AL, Groth D, Vingron M, Lehrach H, Poustka AJ, Panopoulou G. 2008. Early vertebrate whole duplications were predated by a period of intense rearrangement. Genome Res...
  9. Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
    • Florent Murat,
    • Jian-Hong Xu,
    • Eric Tannier,
    • Michael Abrouk,
    • Nicolas Guilhot,
    • Caroline Pont,
    • Joachim Messing,
    • and Jérôme Salse
    Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
    .... Abstract The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms...
  10. Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
    • Andrew L. Hufton,
    • Susanne Mathia,
    • Helene Braun,
    • Udo Georgi,
    • Hans Lehrach,
    • Martin Vingron,
    • Albert J. Poustka,
    • and Georgia Panopoulou
    Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
    ...that the strong conservation of these sequences may affect the evolution of the surrounding genome, both by repressing rearrangement, and possibly by promoting duplicate gene retention. Conflicting data, however, have made the validity of these propositions unclear. Here, we use a new computational method...
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