Frank Johannes

Summary

Affiliation: University of Groningen
Country: The Netherlands

Publications

  1. doi request reprint Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
    Frank Johannes
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, Biologisch Centrum, 9751 NN Haren, The Netherlands
    Bioinformatics 26:1000-6. 2010
  2. pmc Quantitative epigenetics through epigenomic perturbation of isogenic lines
    Frank Johannes
    University of Groningen, Nijenborgh 7, AG Groningen, The Netherlands
    Genetics 188:215-27. 2011
  3. doi request reprint Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis
    René Wardenaar
    Faculty of Mathematics and Natural Sciences, Groningen Bioinformatics Centre, University of Groningen, AG Groningen, The Netherlands
    Methods Mol Biol 1067:203-24. 2013
  4. pmc Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia
    Agnes Lendvai
    Department of Gynaecological Oncology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
    Epigenetics 7:1268-78. 2012
  5. doi request reprint Epigenome dynamics: a quantitative genetics perspective
    Frank Johannes
    Frank Johannes and Ritsert C Jansen are at the Groningen Bioinformatics Centre, University of Groningen, NL 9751 NN, Haren, The Netherlands
    Nat Rev Genet 9:883-90. 2008
  6. pmc Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
    Maria Colomé-Tatché
    Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 109:16240-5. 2012
  7. doi request reprint MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
    Michael Seifert
    Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Gatersleben, Germany
    Bioinformatics 28:2930-9. 2012
  8. doi request reprint Undifferentiated embryonic cell transcription factor 1 regulates ESC chromatin organization and gene expression
    Susanne M Kooistra
    Department of Developmental Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Stem Cells 28:1703-14. 2010
  9. doi request reprint System-wide molecular evidence for phenotypic buffering in Arabidopsis
    Jingyuan Fu
    Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands
    Nat Genet 41:166-7. 2009

Collaborators

Detail Information

Publications9

  1. doi request reprint Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
    Frank Johannes
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, Biologisch Centrum, 9751 NN Haren, The Netherlands
    Bioinformatics 26:1000-6. 2010
    ..This shortcoming presents a bottleneck in biological interpretations of multiple sample data...
  2. pmc Quantitative epigenetics through epigenomic perturbation of isogenic lines
    Frank Johannes
    University of Groningen, Nijenborgh 7, AG Groningen, The Netherlands
    Genetics 188:215-27. 2011
    ....
  3. doi request reprint Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis
    René Wardenaar
    Faculty of Mathematics and Natural Sciences, Groningen Bioinformatics Centre, University of Groningen, AG Groningen, The Netherlands
    Methods Mol Biol 1067:203-24. 2013
    ..We conclude that MeDIP-chip is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies...
  4. pmc Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia
    Agnes Lendvai
    Department of Gynaecological Oncology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
    Epigenetics 7:1268-78. 2012
    ..In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and are candidate biomarkers for early detection...
  5. doi request reprint Epigenome dynamics: a quantitative genetics perspective
    Frank Johannes
    Frank Johannes and Ritsert C Jansen are at the Groningen Bioinformatics Centre, University of Groningen, NL 9751 NN, Haren, The Netherlands
    Nat Rev Genet 9:883-90. 2008
    ..Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits...
  6. pmc Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
    Maria Colomé-Tatché
    Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 109:16240-5. 2012
    ..This level of robustness is remarkable, considering that this population represents an extreme with key recombination barriers having been forced to a minimum...
  7. doi request reprint MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
    Michael Seifert
    Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research IPK, Gatersleben, Germany
    Bioinformatics 28:2930-9. 2012
    ..Therefore, a method for the identification of more than two methylation states is highly desirable...
  8. doi request reprint Undifferentiated embryonic cell transcription factor 1 regulates ESC chromatin organization and gene expression
    Susanne M Kooistra
    Department of Developmental Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Stem Cells 28:1703-14. 2010
    ....
  9. doi request reprint System-wide molecular evidence for phenotypic buffering in Arabidopsis
    Jingyuan Fu
    Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands
    Nat Genet 41:166-7. 2009
    ..We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs...