Morten Beck Rye

Summary

Affiliation: Norwegian University of Science and Technology
Country: Norway

Publications

  1. doi request reprint Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P, O, Box 8905, NO 7491 Trondheim, Norway
    BMC Genomics 15:120. 2014
  2. pmc Cell-type specificity of ChIP-predicted transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491, Trondheim, Norway
    BMC Genomics 13:372. 2012
  3. pmc The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
    Karl Kornacker
    Division of Sensory Biophysics, Ohio State University, Columbus, OH, USA
    BMC Bioinformatics 13:176. 2012
  4. pmc A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
    Morten Beck Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    Nucleic Acids Res 39:e25. 2011
  5. pmc Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Biol 9:80. 2011
  6. pmc A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS ONE 6:e18430. 2011
  7. doi request reprint A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis
    Morten Beck Rye
    Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1359-68. 2008
  8. doi request reprint A multivariate spot filtering model for two-dimensional gel electrophoresis
    Morten Beck Rye
    Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1369-81. 2008
  9. doi request reprint An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis
    Morten Beck Rye
    Chemometrics and Bioinformatics Group, Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1382-93. 2008

Collaborators

Detail Information

Publications9

  1. doi request reprint Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P, O, Box 8905, NO 7491 Trondheim, Norway
    BMC Genomics 15:120. 2014
    ..Here we investigate chromatin features around a comprehensive set of transcription start sites in four cell lines by integrating data from these two projects...
  2. pmc Cell-type specificity of ChIP-predicted transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7491, Trondheim, Norway
    BMC Genomics 13:372. 2012
    ..But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding?..
  3. pmc The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
    Karl Kornacker
    Division of Sensory Biophysics, Ohio State University, Columbus, OH, USA
    BMC Bioinformatics 13:176. 2012
    ..However, the profiles are normally noisy, making it challenging to identify all significantly enriched regions in a reliable way and with an acceptable false discovery rate...
  4. pmc A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
    Morten Beck Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO 7489 Trondheim, Norway
    Nucleic Acids Res 39:e25. 2011
    ..Our results showed that ChIP-seq peaks should be narrowed down to 100-400 bp, which is sufficient to identify unique peaks and binding sites. Based on these results, we propose a meta-approach that gives improved peak definitions...
  5. pmc Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements
    Morten Rye
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    BMC Biol 9:80. 2011
    ....
  6. pmc A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites
    Tony Håndstad
    Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
    PLoS ONE 6:e18430. 2011
    ..Also, it is believed that information about sequence conservation across different genomes can generally improve accuracy of motif-based predictors, but it is not clear under what circumstances use of conservation is most beneficial...
  7. doi request reprint A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis
    Morten Beck Rye
    Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1359-68. 2008
    ..Conclusions based on the visual inspection are that the spot density method identifies partly overlapping spots and low-intensity spots better than the synthetic gel approach...
  8. doi request reprint A multivariate spot filtering model for two-dimensional gel electrophoresis
    Morten Beck Rye
    Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1369-81. 2008
    ..The model successfully managed to separate segments caused by noise, artefacts and cracks from image segments representing true protein spots. The classification method used is discriminant partial least squares regression...
  9. doi request reprint An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis
    Morten Beck Rye
    Chemometrics and Bioinformatics Group, Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
    Electrophoresis 29:1382-93. 2008
    ..Results are compared with software using a common spot boundary approach on an experiment consisting of 35 full size gel images. Gel alignment is required before analysis...