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Centre for Epigenetics
  1. Centre for Epigenetics
  2. About us
  3. Kaplan

Kaplan lab

We are a computational group, studying DNA methylation across the human body, in health and disease. We integrate genetic, epigenetic, and gene expression data to understand the role of DNA sequence and packaging in gene regulation and in ageing, and to develop multimodal cell-free DNA applications for liquid biopsy.

Selected Publications

BCI page: https://www.bci.qmul.ac.uk/team/profile/tommy-kaplan

Google Scholar page: https://scholar.google.com/citations?user=Zqqw2FQAAAAJ

 

  • Loyfer, N., Magenheim, J., Darwish, A., . . . Dor, Y.*, & Kaplan, T.* (2026). Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity. bioRxiv, doi:10.64898/2026.03.24.713040
  • Masika, H., Ruppo, S., Clark, S. J., . . . Kaplan, T.*, & Cedar, H.* (2026). Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging. Nature Communications, doi:10.1038/s41467-026-74118-5
  • Wang, W., Mennea, P. D., McAndrew, G., . . .  Kaplan, T., Cooper, W. N., Zhao, H.*, & Rosenfeld, N.* (2026). A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing. Science Advances, 12:28, doi:10.1126/sciadv.ady9432
  • Loyfer, N., Rosenski, J., & Kaplan, T. (2026). wgbstools: a computational suite for DNA methylation sequencing data analysis. LSA, 9(4). doi:10.26508/lsa.202503514
  • Patel, T., Schwarz, R., Riege, K., . . .  Kaplan, T., Hoffmann, S.*, & van Bömmel, A* (2026). Enhancing the performance and interpretability of epigenetic clocks. NAR, 54:13, doi:10.1093/nar/gkag661
  • Rosenski, J., Sabag, O., Marcus, E., Loyfer, N., Dor, Y., Cedar, H.*, & Kaplan, T.* (2025). The genetic basis for DNA methylation variation across tissues and development. Nature Communications, doi:10.1038/s41467-026-71693-5
  • Rosenski, J., Peretz, A., Magenheim, J., . . . Dor, Y.,* & Kaplan, T.* (2025). Atlas of imprinted and allele-specific DNA methylation in the human body. Nature Communications, 16(1). doi:10.1038/s41467-025-57433-1
  • Ochana, B. L., Nudelman, D., Cohen, D., Peretz, A., Piyanzin, S., Gal Rosenberg, O., . . . Dor, Y.,* Kaplan, T.*, Shemer, R.* (2025). Time is encoded by methylation changes at clustered CpG sites. Cell Reports, 44(7). doi:10.1016/j.celrep.2025.115958
  • Loyfer, N., Magenheim, J., Peretz, A., . . . Kaplan, T.* (2023). A DNA methylation atlas of normal human cell types. Nature, 613(7943), 355-364. doi:10.1038/s41586-022-05580-6
  • Varshavsky, M., Harari, G., Glaser, B., Dor, Y.*, Shemer, R.*, & Kaplan, T.* (2023). Accurate age prediction from blood using a small set of DNA methylation sites and a cohort-based machine learning algorithm. Cell Reports Methods, 3(9). doi:10.1016/j.crmeth.2023.100567
  • Sadeh, R., Sharkia, I., Fialkoff, G., . . . Friedman, N. (2021). ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nature Biotechnology, 39(5), 586-598. doi:10.1038/s41587-020-00775-6
  • Habib, N., McCabe, C., Medina, S., . . . Schwartz, M. (2020). Disease-associated astrocytes in Alzheimer’s disease and aging. Nature Neuroscience, 23(6), 701-706. doi:10.1038/s41593-020-0624-8
  • Moss, J., Magenheim, J., Neiman, D., . . . Kaplan, T.* & Dor, Y.* (2018). Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nature Communications, 9(1). doi:10.1038/s41467-018-07466-6
  • Ron, G., Globerson, Y., Moran, D., & Kaplan, T. (2017). Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. Nature Communications, 8(1). doi:10.1038/s41467-017-02386-3
  • Malka, Y., Steiman-Shimony, A., Rosenthal, E., . . . Kaplan, T.*, & Berger, M.* (2017). Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments. Nature Communications. doi:10.1038/s41467-017-02099-7
  • Klutstein, M., Moss, J., Kaplan, T., & Cedar, H. (2017). Contribution of epigenetic mechanisms to variation in cancer risk among tissues. PNAS, 114(9), 2230-2234. doi:10.1073/pnas.1616556114
  • May, D., Blow, M. J., Kaplan, T., . . . Visel, A. (2012). Large-scale discovery of enhancers from human heart tissue. Nature Genetics, 44(1), 89-93. doi:10.1038/ng.1006
  • Capaldi, A. P., Kaplan, T., Liu, Y., Habib, N., Regev, A., Friedman, N., & O’shea, E. K. (2008). Structure and function of a transcriptional network activated by the MAPK Hog1. Nature Genetics, 40(11), 1300-1306. doi:10.1038/ng.235
  • Dion, M. F.*, Kaplan, T.*, Kim, M., Buratowski, S., Friedman, N., & Rando, O. J. (2007). Dynamics of replication-independent histone turnover in budding yeast. Science, 315(5817), 1405-1408. doi:10.1126/science.1134053
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