M Inmaculada Barrasa

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression
    M Inmaculada Barrasa
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    BMC Genomics 8:21. 2007
  2. pmc A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 22:2535-49. 2008
  3. pmc Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 18:2005-15. 2008
  4. pmc The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
    John S Reece-Hoyes
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 37:3689-98. 2009
  5. pmc A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors
    Christian A Grove
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 138:314-27. 2009
  6. pmc Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex
    Tomoko M Tabuchi
    Program in Molecular Medicine and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
    PLoS Genet 7:e1002074. 2011
  7. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nat Methods 4:659-64. 2007
  8. pmc The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans
    Maria C Ow
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 22:2520-34. 2008
  9. pmc Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 17:1061-71. 2007

Collaborators

Detail Information

Publications9

  1. pmc EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression
    M Inmaculada Barrasa
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    BMC Genomics 8:21. 2007
    ..The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration...
  2. pmc A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 22:2535-49. 2008
    ..This "high flux capacity" suggests that loops provide a mechanism of high information flow for the coordinate and adaptable control of miRNA and TF target regulons...
  3. pmc Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 18:2005-15. 2008
    ..Finally, our data suggest that post-transcriptional mechanisms contribute to differential miRNA expression. The data and strains described here will provide a valuable guide and resource for the functional analysis of C. elegans miRNAs...
  4. pmc The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
    John S Reece-Hoyes
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 37:3689-98. 2009
    ..Together, our data indicate that there are at least two types of CES-1 target genes and, therefore, that the molecular function of Snail-type TFs is more plastic than previously appreciated...
  5. pmc A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors
    Christian A Grove
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell 138:314-27. 2009
    ..For a video summary of this article, see the PaperFlick file available with the online Supplemental Data...
  6. pmc Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex
    Tomoko M Tabuchi
    Program in Molecular Medicine and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
    PLoS Genet 7:e1002074. 2011
    ..Sex chromosome gene regulation may thus have profound evolutionary effects on genome organization and transcriptional regulatory networks...
  7. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nat Methods 4:659-64. 2007
    ..Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well...
  8. pmc The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans
    Maria C Ow
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 22:2520-34. 2008
    ..Therefore, the FLH-1 and FLH-2 proteins likely play a more general role in regulating gene expression in embryos...
  9. pmc Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 17:1061-71. 2007
    ..Taken together, we show that a core neuronal C. elegans protein-DNA interaction network possesses TF modules that relate to different functional aspects of the complete network...