Searching journal content for articles similar to Ghanem et al. 13 (4): 533.

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  1. ARTICLE: De novo discovery of a tissue-specific gene regulatory module in a chordate
    • David S. Johnson,
    • Qing Zhou,
    • Kasumi Yagi,
    • Nori Satoh,
    • Wing Wong,
    • and Arend Sidow
    Genome Res. October 2005 15: 1315-1324; Published in Advance September 16, 2005, doi:10.1101/gr.4062605
    ..., J.L., and Ekker, M. 2003 . Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res. 13 : 533 -543. ↵ GuhaThakurta, D., Schriefer, L.A., Waterston, R.H., and Stormo, G.D. 2004 . Novel transcription regulatory elements in Caenorhabditis elegans muscle genes...
  2. LETTER: A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts
    • Elisa de la Calle-Mustienes,
    • Cármen Gloria Feijóo,
    • Miguel Manzanares,
    • Juan J. Tena,
    • Elisa Rodríguez-Seguel,
    • Annalisa Letizia,
    • Miguel L. Allende,
    • and José Luis Gómez-Skarmeta
    Genome Res. August 2005 15: 1061-1072; Published in Advance July 15, 2005, doi:10.1101/gr.4004805
    ...cis -regulatory elements can be one of the reasons for the evolutionary conservation of their peculiar organization in gene clusters ( Duboule 1998 ). Furthermore, such work has also highlighted the power of comparative genomics to identify cis -elements and the regulatory networks that act upon them...
  3. Method: Discriminative prediction of mammalian enhancers from DNA sequence
    • Dongwon Lee,
    • Rachel Karchin,
    • and Michael A. Beer
    Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
    ...is that the SVM can be subsequently used to scan the for novel enhancers not in the original training set. The results of scanning a well-studied region near Dlx1/2 is shown in Figure 1B 2168 Genome Research www..org Lee et al. and detects novel and experimentally confirmed enhancers, as discussed in detail below...
  4. Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Belinda M. Giardine,
    • Minmei Hou,
    • Jian Ma,
    • Ross C. Hardison,
    • Lisa Stubbs,
    • and Webb Miller
    Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
    ...that identifies evolutionarily conserved transcription factor binding sites (TFBSs) shared by all analyzed species, allowing for the decoding of the sequence structure of regulatory elements that are functionally conserved among different species. Mulan is publicly available at http://mulan.dcode.org . Results...
  5. LETTER: A novel olfactory receptor gene family in teleost fish
    • Luis R. Saraiva and
    • Sigrun I. Korsching
    Genome Res. October 2007 17: 1448-1457; Published in Advance August 23, 2007, doi:10.1101/gr.6553207
    ...of intron-exon structure may indicate the existence of regulatory elements within these introns. The size distribution of the exons is rather conserved between species and intron/exon borders are accurately maintained. Interestingly, none of these four intron/exon borders are found in the monoexonic Xenopus...
  6. RESOURCE: eShadow: A Tool for Comparing Closely Related Sequences
    • Ivan Ovcharenko,
    • Dario Boffelli,
    • and Gabriela G. Loots
    Genome Res. June 2004 14: 1191-1198; doi:10.1101/gr.1773104
    ...., Long, Q., Hatch, G., Park, B.K., Rubenstein, J.L., and Ekker, M. 2003 . Regulatory roles of conserved intergenic domains in vertebrate dlx bigene clusters. Genome Res. 13 : 533 –543. ↵ Gilligan, P., Brenner, S., and Venkatesh, B. 2002 . Fugu and human sequence comparison identifies novel human genes...
  7. ARTICLE: Distribution and intensity of constraint in mammalian genomic sequence
    • Gregory M. Cooper,
    • Eric A. Stone,
    • George Asimenos,
    • Eric D. Green,
    • Serafim Batzoglou,
    • and Arend Sidow
    Genome Res. July 2005 15: 901-913; Published in Advance June 17, 2005, doi:10.1101/gr.3577405
    ...). This small fraction of the includes most known protein-coding exons and the majority of known transcriptional regulatory elements ( Rat Genome Sequencing Project Consortium 2004 ). Considering such estimates, as well as recent studies that successfully leveraged sequence conservation to identify regions...
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