Research Groups

Quantitative Epigenetics

The functional differences between cells across tissue types are determined by epigenetic factors that alter gene expression patterns without changing the underlying DNA sequence. The unique assembly and distribution of these epigenetic factors along the genome gives rise to specific gene expression programs that define the functional state of a cell. Clearly their faithful maintenance during mitotic cell divisions is crucial for the functional integrity of tissues over time. However, this process is not always perfect. Epigenetic factors can be stochastically gained or lost and ultimately lead to progressive functional heterogeneity among cells within a given tissue, causing the emergence of phenotypes typically observed during ageing.
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  • Maria Colomé Tatché Visit
    Position

    Group Leader of the Laboratory of Quantitative Epigenetics

    Research fields

    Quantitative epigenetics, theoretical biology, bioinformatics, computational biology, ageing

    PhD Students
  • The core aim of our research is to understand the role of combinatorial epigenetic changes involved in the process of ageing. To achieve this, we provide both a computational and a theoretical framework to study and quantify these epigenetic changes on a genome-wide scale. From the computational point of view, we work on the development of algorithms for the analysis and integration of different types of genome-wide next generation sequencing epigenetic data. From the theoretical point of view, we develop formal models of epigenetic dynamical processes during cell development and division.
    • Taudt A, Colomé-Tatché M, Johannes F. (2016) Genetic sources of population epigenomic variation. Nature Reviews Genetics.
    • Colomé-Tatché M, Johannes F. (2015) Signatures of Dobzhansky-Muller Incompatibilities in the Genomes of Recombinant Inbred Lines. Genetics.
    • vd Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG,  Jansen RC, Schmitz RJ, Colomé-Tatché M , Johannes F. (2015) Rate, spectrum and evolutionary dynamics of spontaneous epimutations. PNAS.
    • Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F. (2015) histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics.
    • Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. (2014) Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research.
    • Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. (2014) Mapping the Epigenetic Basis of Complex Traits. Science.
    • Cortijo S, Wardenaar R, Colomé-Tatché M, Johannes F, Colot V. (2014) Genome-Wide Analysis of DNA Methylation in Arabidopsis Using MeDIP-Chip. Methods in molecular biology.
    • Wardenaar R, Liu H, Colot V, Colomé-Tatché M, Johannes F. (2013) Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis. Methods in molecular biology.
    • Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F. (2012) Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. PNAS.
    • Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V. (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics.
    • Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F. (2011) Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics.
    • Johannes F, Colomé-Tatché M. (2011) Concerning epigenetics and inbreeding. Nature reviews Genetics.
    • Johannes F, Colomé-Tatché M. (2011) Quantitative epigenetics through epigenomic perturbation of isogenic lines. Genetics.
    • Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC. (2010) Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics.
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