Eivind Valen

Summary

Affiliation: University of Copenhagen
Country: Denmark

Publications

  1. pmc Discovery of regulatory elements is improved by a discriminatory approach
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    PLoS Comput Biol 5:e1000562. 2009
  2. doi Genomic and chromatin signals underlying transcription start-site selection
    Eivind Valen
    The Bioinformatics Centre, Department of Biology, Ole Maaløes Vej 5, Copenhagen University, DK 2200, Denmark
    Trends Genet 27:475-85. 2011
  3. pmc Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
    Yun Chen
    The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, Ole Maaloes Vej 5, DK 2200 Denmark
    BMC Genomics 12:544. 2011
  4. pmc Systematic clustering of transcription start site landscapes
    Xiaobei Zhao
    Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
    PLoS ONE 6:e23409. 2011
  5. doi Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    Nat Struct Mol Biol 18:1075-82. 2011
  6. pmc Asap: a framework for over-representation statistics for transcription factor binding sites
    Troels T Marstrand
    Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 3:e1623. 2008
  7. pmc Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK 2200, Denmark
    Genome Res 19:255-65. 2009

Detail Information

Publications7

  1. pmc Discovery of regulatory elements is improved by a discriminatory approach
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    PLoS Comput Biol 5:e1000562. 2009
    ..Using a large background set of real promoters instead of a simplified model leads to higher discriminatory power and markedly reduces the need for repeat masking; a common pre-processing step for other pattern finders...
  2. doi Genomic and chromatin signals underlying transcription start-site selection
    Eivind Valen
    The Bioinformatics Centre, Department of Biology, Ole Maaløes Vej 5, Copenhagen University, DK 2200, Denmark
    Trends Genet 27:475-85. 2011
    ..We review here the genomic and chromatin features that underlie TSS selection and usage, focusing on the differences between the major classes of core promoters...
  3. pmc Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
    Yun Chen
    The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, Ole Maaloes Vej 5, DK 2200 Denmark
    BMC Genomics 12:544. 2011
    ....
  4. pmc Systematic clustering of transcription start site landscapes
    Xiaobei Zhao
    Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Copenhagen, Denmark
    PLoS ONE 6:e23409. 2011
    ..Thus, previous two-class separations of promoter based on TSS distributions are motivated, but the ultra-sharp TSS distributions will confound downstream analyses if not removed...
  5. doi Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and the Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    Nat Struct Mol Biol 18:1075-82. 2011
    ..We also reveal new AGO1/2-associated RNAs derived from 3' ends of introns and from mRNA 3' UTRs that appear to draw from noncanonical microRNA biogenesis pathways...
  6. pmc Asap: a framework for over-representation statistics for transcription factor binding sites
    Troels T Marstrand
    Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre BRIC, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 3:e1623. 2008
    ..However there is little or no information available for guiding the end users choice of method. Furthermore it would be necessary to obtain several different software programs from various sources to make a well-founded choice...
  7. pmc Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
    Eivind Valen
    The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK 2200, Denmark
    Genome Res 19:255-65. 2009
    ..Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue...