Searching journal content for articles similar to Loots et al. 12 (5): 832.

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  1. LETTER: Evolutionary turnover of mammalian transcription start sites
    • Martin C. Frith,
    • Jasmina Ponjavic,
    • David Fredman,
    • Chikatoshi Kai,
    • Jun Kawai,
    • Piero Carninci,
    • Yoshihide Hayshizaki,
    • and Albin Sandelin
    Genome Res. June 2006 16: 713-722; Published in Advance May 10, 2006, doi:10.1101/gr.5031006
    ...Evolutionary turnover of mammalian transcription start sites Evolutionary turnover of transcription start sites Martin C. Frith 1 , 3 , Jasmina Ponjavic 1 , 5 , David Fredman 4 , Chikatoshi Kai 1 , Jun Kawai 1 , Piero Carninci 1...
  2. RESOURCE: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
    • Eugene Berezikov,
    • Victor Guryev,
    • Ronald H.A. Plasterk,
    • and Edwin Cuppen
    Genome Res. January 2004 14: 170-178; Published in Advance December 12, 2003, doi:10.1101/gr.1642804
    ...comparisons. Science 288 : 136 -140. ↵ Loots, G.G., Ovcharenko, I., Pachter, L., Dubchak, I., and Rubin, E.M. 2002 . rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12 : 832...
  3. RESOURCE: zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Ross C. Hardison,
    • Webb Miller,
    • and Lisa Stubbs
    Genome Res. March 2004 14: 472-477; doi:10.1101/gr.2129504
    ...binding is a critical step for sequences-based discovery of noncoding regulatory elements. zPicture allows regulatory element analysis and transcription factor-binding sites (TFBS) visualization though the rVista tool portal ( Loots et al. 2002 ) available at the results page. The rVista tool combines...
  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
    ...of the GATA3 ORF in zebrafish. Multiple-sequence conservation of transcription factor binding sites The ability to accurately predict functional transcription factor binding sites (TFBS) is a powerful approach for sequence-based discovery of gene regulatory sequences and for elucidating gene regulation...
  5. Methods: Footer: A quantitative comparative genomics method for efficient recognition of cis-regulatory elements
    • David L. Corcoran,
    • Eleanor Feingold,
    • Jessica Dominick,
    • Marietta Wright,
    • Jo Harnaha,
    • Massimo Trucco,
    • Nick Giannoukakis,
    • and Panayiotis V. Benos
    Genome Res. June 2005 15: 840-847; doi:10.1101/gr.2952005
    ...sequence-based discovery of functional transcription factor binding sites. Genome Res. 12 : 832 -839. ↵ Mahony, S., Golden, A., Smith, T.J., and Benos, P.V. 2005 . Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Proc. Intell. Syst. Mol. Biol. (in press...
  6. Method: Genome-wide identification of conserved regulatory function in diverged sequences
    • Leila Taher,
    • David M. McGaughey,
    • Samantha Maragh,
    • Ivy Aneas,
    • Seneca L. Bessling,
    • Webb Miller,
    • Marcelo A. Nobrega,
    • Andrew S. McCallion,
    • and Ivan Ovcharenko
    Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
    ...without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functional noncoding orthologs at evolutionarily diverged loci...
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  7. Methods: Predicting tissue-specific enhancers in the human genome
    • Len A. Pennacchio,
    • Gabriela G. Loots,
    • Marcelo A. Nobrega,
    • and Ivan Ovcharenko
    Genome Res. February 2007 17: 201-211; Published in Advance January 8, 2007, doi:10.1101/gr.5972507
    ...( Ovcharenko et al. 2004b ; Prabhakar et al. 2006 ). Profiling putative TFBS in candidate gene regulatory elements Human–mouse ECR Brower alignments ( Ovcharenko et al. 2004a ) were processed by rVista 2.0 ( Loots and Ovcharenko 2004 ) to identify evolutionarily conserved putative TFBS in the human and mouse s...
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  8. LETTER: Computational identification and functional validation of regulatory motifs in cartilage-expressed genes
    • Sherri R. Davies,
    • Li-Wei Chang,
    • Debabrata Patra,
    • Xiaoyun Xing,
    • Karen Posey,
    • Jacqueline Hecht,
    • Gary D. Stormo,
    • and Linda J. Sandell
    Genome Res. October 2007 17: 1438-1447; Published in Advance September 4, 2007, doi:10.1101/gr.6224007
    ...is not yet available. We have taken a computational approach to identify cis -regulatory, transcription factor (TF) binding motifs in a set of cartilage characteristic genes to better define the transcriptional regulatory networks that regulate chondrogenesis. Our computational methods have identified...
  9. LETTER: Defining the mammalian CArGome
    • Qiang Sun,
    • Guang Chen,
    • Jeffrey W. Streb,
    • Xiaochun Long,
    • Yumei Yang,
    • Christian J. Stoeckert, Jr.,
    • and Joseph M. Miano
    Genome Res. February 2006 16: 197-207; Published in Advance December 19, 2005, doi:10.1101/gr.4108706
    ...uncovered >100 hypothetical SRF-dependent genes, including 10 previously identified SRF targets, harboring a conserved CArG element within 4000 bp of the annotated transcription start site (TSS). We PCR-cloned 89 hypothetical SRF targets and subjected each of them to at least two of several validations...
  10. LETTER: Conserved Noncoding Sequences in the Grasses
    • Dan Choffnes Inada,
    • Ali Bashir,
    • Chunghau Lee,
    • Brian C. Thomas,
    • Cynthia Ko,
    • Stephen A. Goff,
    • and Michael Freeling
    Genome Res. September 2003 13: 2030-2041; doi:10.1101/gr.1280703
    ...sequences do not result from selection alone and are not considered CNSs. Various algorithms and stringency schemes are currently employed to identify CNSs in mammals. Dubchak and coworkers ( 2000 ) and Loots and coworkers ( 2002 ) developed a global alignment (Avid) and scoring package called Vista (or rVista...
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