Associated member since March 2017
Maria Colomé Tatché is interested in the development of new computational methods for the analysis of genome-wide epigenetic data, as well as in the development of mathematical models to describe epigenetic processes. In particular, she works on the development and application of methods for the analysis of histone modification data in many samples with large numbers of histone modifications and/or transcription factors experiments (both low-input and bulk sequencing), as well as for the analysis of DNA methylation data in large populations (of individuals and of single cells). She also works on the development of methods for the integration of different ‘omics’ levels from bulk and/or single cell populations (genomics, epigenomics and transcriptomics). Finally, her research also focuses on the development of mathematical models of epigenetic processes, such as the inheritance of epigenetic states (meiotic/mitotic) or the estimation of the rates of stochastic gains and losses of epigenetic marks (epimutation rates).
10 Major publications related to project
Ferronika P, van den Bos H, Taudt A, Spierings DCJ, Saber A, Hiltermann TJN, Kok K, Porubsky D, van der Wekken AJ, Timens W, Foijer F, Colomé-Tatché M, Groen HJM, Lansdorp PM, van den Berg A. (2017). Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small cell lung cancer patient. Annals of oncology, doi: 10.1093/annonc/mdx182.
Taudt A, Nguyen MA, Heinig M, Johannes F, Colomé-Tatché M* (*corresponding author) (2016). chromstaR: Tracking combinatorial chromatin state dynamics in space and time, biorxiv doi: https://doi.org/10.1101/038612.
Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ES, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M*, Foijer F* (*corresponding authors) (2016). Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biology, 17:115.
Taudt A, Colomé-Tatché M and Johannes F (2016). Genetic sources of population epigenomic variation. Nature Reviews Genetics, 17, 319.
vd Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ*, Colomé-Tatché M* and Johannes F* (*corresponding authors) (2015). Rate, spectrum and evolutionary dynamics of spontaneous epimutations. Proc. Natl. Acad. Sci. USA, 112:6676-81.
Heinig M, Colome-Tatche M, Rintisch C, Schäfer S, Pravenec M, Hubner N, Vingron M, Johannes F. (2015). histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics, 16:60.
Cortijo S*, Wardenaar R*, Colomé-Tatché M*, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury J-M, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F (*equal contributions) (2014). Mapping the epigenetic basis of complex traits. Science, 343:1145-48.
Colomé-Tatché M, Cortijo S, Wardenaar R, Lahouze B, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, V Colot and Johannes F. (2012). Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc. Natl. Acad. Sci. USA, doi: 10.1073/pnas.1212955109.
Roux F*, Colomé-Tatché M*, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F (*equal contributions) (2011). Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics, 188, 1015.
Johannes F and Colomé-Tatché M. (2011). Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines. Genetics, 188, 215.