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  Close sequence comparisons are sufficient to identify human cis-regulatory elements

  • Shyam Prabhakar,
  • Francis Poulin,
  • Malak Shoukry,
  • Veena Afzal,
  • Edward M. Rubin,
  • Olivier Couronne,
  • and Len A. Pennacchio

  Genome Res. July 2006 16: 855-863; Published in Advance June 12, 2006, doi:10.1101/gr.4717506
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  Functional noncoding sequences derived from SINEs in the mammalian genome

  • Hidenori Nishihara,
  • Arian F.A. Smit,
  • and Norihiro Okada

  Genome Res. July 2006 16: 864-874; Published in Advance May 22, 2006, doi:10.1101/gr.5255506
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  Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

  • Daniel L. Halligan and
  • Peter D. Keightley

  Genome Res. July 2006 16: 875-884; Published in Advance June 2, 2006, doi:10.1101/gr.5022906
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  Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

  • Elfar Torarinsson,
  • Milena Sawera,
  • Jakob H. Havgaard,
  • Merete Fredholm,
  • and Jan Gorodkin

  Genome Res. July 2006 16: 885-889; Published in Advance June 2, 2006, doi:10.1101/gr.5226606
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  Suz12 binds to silenced regions of the genome in a cell-type-specific manner

  • Sharon L. Squazzo,
  • Henriette O’Geen,
  • Vitalina M. Komashko,
  • Sheryl R. Krig,
  • Victor X. Jin,
  • Sung-wook Jang,
  • Raphael Margueron,
  • Danny Reinberg,
  • Roland Green,
  • and Peggy J. Farnham

  Genome Res. July 2006 16: 890-900; Published in Advance June 2, 2006, doi:10.1101/gr.5306606
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  Identification of clustered YY1 binding sites in imprinting control regions

  • Jeong Do Kim,
  • Angela K. Hinz,
  • Anne Bergmann,
  • Jennifer M. Huang,
  • Ivan Ovcharenko,
  • Lisa Stubbs,
  • and Joomyeong Kim

  Genome Res. July 2006 16: 901-911; Published in Advance June 7, 2006, doi:10.1101/gr.5091406
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  Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription

  • Ian A. Swinburne,
  • Clifford A. Meyer,
  • X. Shirley Liu,
  • Pamela A. Silver,
  • and Alexander S. Brodsky

  Genome Res. July 2006 16: 912-921; Published in Advance June 12, 2006, doi:10.1101/gr.5211806
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  Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity

  • Miao Sun,
  • Laurence D. Hurst,
  • Gordon G. Carmichael,
  • and Jianjun Chen

  Genome Res. July 2006 16: 922-933; Published in Advance June 12, 2006, doi:10.1101/gr.5210006
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  Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes

  • Brian C. Thomas,
  • Brent Pedersen,
  • and Michael Freeling

  Genome Res. July 2006 16: 934-946; Published in Advance June 7, 2006, doi:10.1101/gr.4708406
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