Publications

• Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge.
  Sanchez-Quant E, Richter ML, Colomé-Tatché M and Martinez-Jimenez CP.
  Genome Biol. 2023 Oct 17;24(1):234. doi: 10.1186/s13059-023-03075-9.
  PubMed
  
  
• CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition.
  Swoboda AS, Arfelli VC, Danese A, Windisch R, Kerbs P, Redondo Monte E, Bagnoli JW, Chen-Wichmann L, Caroleo A, Cusan M, Krebs S, Blum H, Sterr M, Enard W, Herold T, Colomé-Tatché M, Wichmann C and Greif PA.
  Hemasphere 2023 Oct 11;7(10):e958. doi: 10.1097/HS9.0000000000000958. eCollection 2023 Oct.
  PubMed
• epiAneufinder identifies copy number alterations from single-cell ATAC-seq data.
  Ramakrishnan A, Symeonidi A, Hanel P, Schmid KT, Richter ML, Schubert M and Colomé-Tatché M.
  Nat Commun. 2023 Sept 14:5846. doi.org/10.1038/s41467-023-41076-1.
  Article
• CIARA: a cluster-independent algorithm for the identification of markers of rare cell types from single-cell sequencing data.
  Lubatti G, Stock M, Iturbide A, Ruiz Tejada Segura ML, Riepl M, Tyser RCV, Danese A, Colomé-Tatché M, Theis FJ, Srinivas S, Torres-Padilla M-E and A. Scialdone.
  Development 150 (11): dev201264 (2023).
  PubMed
• Benchmarking atlas-level data integration in single-cell genomics.
  Luecken MD, Büttner M, Chaichoompu K, Danese A, Interlandi M, Mueller MF, Strobl DC, Zappia L, Dugas M, Colomé-Tatché M and Theis FJ.
  Nat Methods. 2021 Dec 23. doi: 10.1038/s41592-021-01336-8.
  PubMed
• EpiScanpy: integrated single-cell epigenomic analysis
  Danese A, Richter ML, Chaichoompu K, Fischer DS, Theis FJ and Colomé-Tatché M.
  Nat Commun. 2021 Sep 1;12(1):5228. doi: 10.1038/s41467-021-25131-3.
  PubMed
• J. Denkena, F. Johannes and M. Colomé-Tatché*.
  Region-level Epimutation Rates in Arabidopsis thaliana.
  Heredity https://doi.org/10.1038/s41437-021-00441-w (2021).

• M.L. Richter, I.K. Deligiannis, A. Danese, E. Lleshi, P. Coupland, C.A. Vallejos, M. Colomé-Tatché* and C.P. Martinez-Jimenez*.
  Single-nucleus RNA-seq2 reveals a functional crosstalk between liver zonation and ploidy.
  Nat. Commun. Biorxiv doi: https://doi.org/10.1101/2020.07.11.193458

• A. Danese, M.L. Richter, D.S. Fischer, F.J. Theis* and M. Colomé-Tatché*.
  EpiScanpy: integrated single-cell epigenomic analysis.
  Nat. Commun. Biorxiv doi: https://doi.org/10.1101/648097

• M. Colomé-Tatché.
  Una visión más nítida de los secretos celulares.
  Investigación y Ciencia, September 2020.

• B. Hofmeister, J. Denkena, M. Colomé-Tatché, Y. Shahryary, R. Hazarika, J. Grimwood, S. Mamidi, J. Jenkins, P. Grabowski, A. Sreedasyam, S. Shu, K. Lail, A. Lipzen, C. Adam, K. Barry, R. Sorek, D. Kudrna, R. Wing, T. Jayson, D. Hall, G. Tuskan, J. Schmutz, F. Johannes, R.J. Schmitz.
  The rate of somatic genetic and epigenetic variation in wild long-lived perennial Populus trichocarp.
  Genome Biology 21, 259 (2020).

• Y. S. Dizaji, A. Symeonidi, R. R. Hazarika, J. Denkena, T. Mubeen, B. Hofmeister, T. van Gurp, M. Colomé-Tatché, K. Verhoeven, G. Tuskan, R. J. Schmitz, F. Johannes. AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.
  Genome Biology 21, 260 (2020).

• K.M. Schukken, Y-C. Lin, P.L. Bakker, M. Schubert, S.F. Preuss, J.E. Simon, H. van den Bos, Z. Storchova, M. Colomé-Tatché, H. Bastians, D.C.J. Spierings, F. Foijer.
  Altering microtubule dynamics is synergistically toxic with spindle assembly checkpoint inhibition.
  Life Science Alliance doi 10.26508/lsa.201900499 (2020).

• M. Schubert, M. Colomé-Tatché, F. Foijer.
  Gene networks in cancer are biased by aneuploidies and sample impurities.
  Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. DOI: 10.1016/j.bbagrm.2019.194444 (2019).

• C. W. Hanna, R. Pérez-Palacios, L. Gahurova, M. Schubert, F. Krueger, L. Biggins, S. Andrews, M. Colomé-Tatché, D. Bourc'his, W. Dean, G. Kelsey.
  Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues.
  Genome Biology 20, 225 (2019).

• W. Ricci, Z. Lu, L. Ji, A. P. Marand, C. L. Ethridge, N. G. Murphy, J. M. Noshay, M. Galli, M. K. Mejia-Guerra, M. Colomé-Tatché, F. Johannes, M. Jordan Rowley, V. G. Corces, J. Zhai, M. J. Scanlon, E. S. Buckler, A. Gallavotti, N. M. Springer, R. J. Schmitz, X. Zhang.
  Widespread Long-Range Cis-Regulatory Elements in the Maize Genome.
  Nature Plants 5, 1237-1249 (2019).

• D. Porubsky, A. D. Sanders, A. Taudt, M. Colomé-Tatché, P. M. Lansdorp, V. Guryev.
  breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.
  Bioinformatics https://doi.org/10.1093/bioinformatics/btz681 (2019).

• H. van den Bos, B. Bakker, A. Taudt, V. Guryev, M. Colomé-Tatché, P. M. Lansdorp, F. Foijer D. C. J. Spierings.
  Quantification of Aneuploidy in Mammalian Systems. In: Demaria M. (eds) Cellular Senescence.
  Methods in Molecular Biology, vol 1896. Humana Press, New York, NY (2019).

• M. Colomé-Tatché* and F.J. Theis*.
  Statistical single cell multi-omics integration.
  Current Opinion in Systems Biology, doi.org/10.1016/j.coisb.2018.01.003 (2018).

• C.W. Hanna, A. Taudt, J. Huang, L. Gahurova, A. Kranz, S. Andrews, W. Dean, A.F. Stewart, M. Colomé-Tatché, G. Kelsey.
  MLL2 conveys transcription-independent H3K4 trimethylation in oocytes.
  Nature Structural & Molecular Biology, 25(1):73-82 (2018).

• A. Taudt, D. Roquis, A. Vidalis, R. Wardenaar, F. Johannes, M. Colomé-Tatché*.
  METHimpute: Imputation-guided construction of complete methylomes from WGBS data.
  BMC Genomics 19:444 (2018).

• A.F. Kebede, A. Nieborak, L. Zorro Shahidian, S. Le Gras, F. Richter, D. Aguilar Gomez, M.P. Baltissen, G. Meszaros, H. de Fatima Magliarelli, A. Taudt, R. Margueron, M. Colomé-Tatché, R. Ricci, S. Daujat, M. Vermeulen, G. Mittler, R. Schneider.
  Histone propionylation is a novel mark of active chromatin.
  Nature Structural & Molecular Biology 24(12):1048-1056 (2017).

• C.L. Richards, C. Alonso, C. Becker, O. Bossdorf, E. Bucher, M. Colomé-Tatché, W. Durka, J. Engelhardt, B. Gaspar, A. Gogol-Doring, I. Grosse, T.P. van Gurp, K. Heer, I. Kronholm, C. Lampei, V. Latzel, M. Mirouze, L. Opgenoorth, O. Paun, S. Prohaska, S.A. Rensing, P. Stadler, E. Trucchi, K. Ullrich, KJ.F. Verhoeven.
  Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.
  Ecology Letters DOI:10.1111/ele.12858 (2017).

• P. Ferronika, H. van den Bos, A. Taudt, D.C.J. Spierings, A. Saber, T.J.N. Hiltermann, K. Kok, D. Porubsky, A.J. van der Wekken, W. Timens, F. Foijer, M. Colomé-Tatché, H.J.M. Groen, P.M. Lansdorp, A. van den Berg.
  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 (2017).

• B. Bakker, A. Taudt, M.E. Belderbos, D. Porubsky, D.C.J. Spierings, T.V. de Jong, N. Halsema, H.G. Kazemier, K. Hoekstra-Wakker, A. Bradley, E.S.J.M. de Bont, A. van den Berg, V. Guryev, P.M. Lansdorp, M. Colomé-Tatché*, F. Foijer*.
  Single cell sequencing reveals karyotype heterogeneity in murine and human malignancies.
  Genome Biology 17:115 (2016).

• H. van den Bos, D.C.J. Spierings, A. Taudt, B. Bakker, D. Porubsky, E. Falconer, C. Novoa, N. Halsema, I. Kazemier, K. Hoekstra-Wakker, V. Guryev, F. Foijer, M. Colomé-Tatché, E. Boddeke, P. Lansdorp.
  Single-cell whole genome sequencing reveals no evidence for increased aneuploidy in Alzheimer's disease.
  Genome Biology 17:116 (2016).

• A. Taudt, M. Colomé-Tatché, F. Johannes.
  Genetic sources of population epigenomic variation.
  Nature Reviews Genetics 17, 319 (2016).

• M. Colomé-Tatché* and F. Johannes*.
  Signatures of Dobzhansky-Muller incompatibilities in the genomes of recombinant inbred lines.
  Genetics 202, 825 (2016).

• A. vd Graaf, R. Wardenaar, D.A. Neumann, A. Taudt, R.G. Shaw, R.C. Jansen, R.J. Schmitz*, M. Colomé-Tatché*, F. Johannes*.
  Rate, spectrum and evolutionary dynamics of spontaneous epimutations.
  Proc. Natl. Acad. Sci. USA 112:6676-81 (2015).

• M. Heinig, M. Colomé-Tatché, A. Taudt, C. Rintisch, S. Schafer, M. Pravenec, N. Hubner, M. Vingron, F. Johannes.
  histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
  BMC Bioinformatics 16:60 (2015).

• C. Rintisch, M. Heinig, A. Bauerfeind, S. Schafer, C. Mieth, G. Patone, O. Hummel, W. Chen, S. Cook, E. Cuppen, M. Colomé-Tatché, F. Johannes, R.C. Jansen, H. Neil, M. Werner, M. Pravenec, M. Vingron, N. Hubner.
  Natural variation of histone modification and its impact on gene expression in the rat genome.
  Genome Research doi:10.1101/gr.169029.113 (2014).

• S. Cortijo†, R. Wardenaar†, M. Colomé-Tatché†, A. Gilly, M. Etcheverry, K. Labadie, E. Caillieux, F. Hospital, J-M. Aury, P. Wincker, F. Roudier, R. C. Jansen, V. Colot, F. Johannes.
  Mapping the epigenetic basis of complex traits.
  Science 343:1145-48 (2014).

• S. Cortijo, R. Wardenaar, M. Colomé-Tatché, F. Johannes, V. Colot.
  Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.
  Methods in Molecular Biology 1112:125-49 (2014).

• R. Wardenaar, H. Liu, V. Colot, M. Colomé-Tatché, F. Johannes.
  Evaluation of MeDIP-chip in the context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis.
  Methods in Molecular Biology 1067:203-24 (2013).

• M. Colomé-Tatché, S. Cortijo, R. Wardenaar, B. Lahouze, M. Etcheverry, A. Martin, S. Feng, E. Duvernois-Berthet, K. Labadie, P. Wincker, S. E. Jacobsen, R. C. Jansen, V. Colot, F. Johannes.
  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 (2012).

• M. Seifert, S. Cortijo, M. Colomé-Tatché, F. Johannes, F. Roudier, V. Colot.
  MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.
  Bioinformatics doi: 10.1093/bioinformatics/bts562 (2012).

• F. Roux†, M. Colomé-Tatché†, C. Edelist, R. Wardenaar, P.Guerche, F. Hospital, V. Colot, R. C. Jansen, F. Johannes.
  Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.
  Genetics 188, 1015 (2011).
• F. Johannes and M. Colomé-Tatché.
  Concerning epigenetics and inbreeding (correspondence).
  Nature Reviews Genetics 12, 376 (2011).

• F. Johannes and M. Colomé-Tatché.
  Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines.
  Genetics 188, 215 (2011).

• M. Colomé-Tatché, C. Klempt, L. Santos, T. Vekua.
  Adiabatic spin cooling using high-spin Fermi gases.
  New Journal of Physics 13, 113021 (2011).

• M. Colomé-Tatché and D.S. Petrov.
  Parametric excitation of a 1D gas in integrable and nonintegrable cases.
  Physical Review Letters 106, 125302 (2011).

• F. Johannes, R. Wardenaar, M. Colomé-Tatché, F. Mousson, P. de Graaf, M. Mokry, V. Guryev, M.H.Th. Timmers, E. Cuppen, R.C. Jansen.
  Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
  Bioinformatics 26, 1000 (2010).

• K. Rodríguez, A. Argüelles, M. Colomé-Tatché, T. Vekua, L. Santos.
  Mott-insulator phases of spin-3/2 fermions in the presence of quadratic Zeeman coupling.
  Physical Review Letters 105, 050402 (2010).

• M. Colomé-Tatché, S. I. Matveenko, G.V. Shlyapnikov.
  Finite size effects for the gap in the excitation spectrum of the one-dimensional Hubbard model.
  Physical Review A 81, 013611 (2010).

• M. Colomé-Tatché*.
  Two-component repulsive Fermi gases with population imbalance in elongated harmonic traps.
  Physical Review A 78, 033612 (2008).

*(co-)corresponding author(s);
† these authors contributed equally.