We are inteterested in the dynamic regulation of chromatin in stem cells and differentiation (e.g. Kumar et. al., Cell Reports, 2019; Navarro et. al., Nat Comms, 2020; Kumar et. al., Nat Cell Bio, 2 022, Weigert etl. al. Nat Cell Bio, 2023). We will further develop various genome-wide profiling methods (Kumar et. al., Nature Protocols, 2024, including single cell methods (Lyu et. al., manuscript in preparation), and expand a number of collaborations studying the role of epigenetic modifications and nuclear organization on the regulation of pluripotency, lineage commitment and cancer. We attempt to integrate various quantitative and singe-cell transcriptomic and epigenetic data modalities coming from single-cell RNA-Seq, single-cell ATAC-Seq and single-cell Cut&Tag experiments. The initial data matrices deriving from these techniques have high dimensionality, therefore the joint integrations and the downstream explorations by supervised and unsupervised machine learning tools are computationally challenging. We have also have various proteomics projects (Schlesinger et.al, iScience, in Press) for which we acquired an Exploris 120. Recent publications Schlesinger D, Dirks C, Navarro C, Lafranchi L, Eirich J, Elsässer SJ. A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function. iScience. (2025) - in press Kumar B, Navarro C, Kwong Yung PY, Lyu J, Salazar Mantero A, Katsori AM, Schwämmle H, Martin M, Elsässer SJ. Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors. Nature Protocols (2024). Lyu J, Segueni J, Hetey S, Elsässer SJ, Noordermeer D, “Matters Arising: Lack of evidence that G-quadruplexes promote CTCF binding in-vivo”, under review, Molecular Cell Lafranchi L, Spinner A, Hornisch M, Schlesinger D, Navarro C, Brinkenstråhle L, Shao R, Piazza I, Elsässer SJ. Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response. bioRxiv (2024) - in revisions.