Searching journal content for articles similar to Ovcharenko et al. 14 (6): 1191.

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  1. 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
    ...two or more sequences are simultaneously aligned to each other) for comparative studies. It has been shown that comparisons of multiple closely related sequences through the phylogenetic shadowing approach are capable of identifying primate specific exons and enhancers ( Boffelli et al. 2003...
  2. Methods: Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells
    • Dan Xie,
    • Jun Cai,
    • Na-Yu Chia,
    • Huck H. Ng,
    • and Sheng Zhong
    Genome Res. August 2008 18: 1325-1335; Published in Advance May 15, 2008, doi:10.1101/gr.072769.107
    ...-regulatory elements have been explored. Comparative sequence analysis is one of the best strategies known for finding functional sequences in animal s. The basic idea is to look for sequences that are conserved across species (e.g., Loots et al. 2000 ; Boffelli et al. 2003 ; Hardison et al. 2003 ; Kellis et...
  3. LETTER: Identifying Candidate Causal Variants Responsible for Altered Activity of the ABCB1 Multidrug Resistance Gene
    • Nicole Soranzo,
    • Gianpiero L. Cavalleri,
    • Michael E. Weale,
    • Nicholas W. Wood,
    • Chantal Depondt,
    • Richard Marguerie,
    • Sanjay M. Sisodiya,
    • and David B. Goldstein
    Genome Res. July 2004 14: 1333-1344; Published in Advance June 14, 2004, doi:10.1101/gr.1965304
    ...>T site ( Fig. 4A ), and (2) the intronic sequences surrounding the IVS 25+5231 T>C and IVS 26+80 T>C sites ( Fig. 4B ), using the HMM Islands model no-parameter optimization. All analyses were implemented using eShadow ( http://eshadow.dcode.org ). Acknowledgments We thank Alice Smith and Mari Wyn...
  4. Letter: The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression
    • Alan M. Pittman,
    • Silvia Naranjo,
    • Emily Webb,
    • Peter Broderick,
    • Esther H. Lips,
    • Tom van Wezel,
    • Hans Morreau,
    • Kate Sullivan,
    • Sarah Fielding,
    • Philip Twiss,
    • Jayaram Vijayakrishnan,
    • Fernando Casares,
    • Mobshra Qureshi,
    • José Luis Gómez-Skarmeta,
    • and Richard S. Houlston
    Genome Res. June 2009 19: 987-993; Published in Advance April 24, 2009, doi:10.1101/gr.092668.109
    ...functional enhancer assays (green and red blocks). Note that this region contains an evolutionarily-conserved noncoding peak. ( c ) eShadow view (ClustalW multiple sequence alignments presented as percent mismatch) of the SMAD7 construct showing regions of sequence conservation amongst primates (Human, Chimp...
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