Project Supervisor

Judith Zaugg


Judith Zaugg heads the Systems Epigenetics group at EMBL (Germany) ( Prior to joining EMBL, Judith did her postdoctoral work at Stanford University (US) and obtained her PhD from EMBL-EBI and Cambridge University (UK). Her current research aims at understanding how cells integrate genetic information, epigenetic make-up, and extrinsic signals from their microenvironment, to give rise to complex cellular phenotypes, including differentiation, function, and cellular cross-talk.

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For this the group combines (single cell) multiomics profiling with advanced computational modelling of gene regulatory networks. A specific system of interest is the bone marrow stem cell niche and immune cells. Judith was recently awarded the prestigious ERC consolidator grant. In addition to her research, Judith serves on the institutional scientific advisory boards of the Nordic Centre of Molecular Medicine and the Hungarian Centre of Excellence in Molecular Medicine, and on the editorial advisory board of the journal Molecular Systems Biology (EMBO press), and on the GSK-EMBL Alliance advisory board.

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OUR VISION is to understand how cells integrate genetic and epigenetic information with extrinsic signals from their microenvironment, and how these molecular layers contribute to cellular phenotypes that ultimately define complex disease phenotypes. Our system of interest is the bone marrow and immune system, where we aim to understand how hematopoietic stem cells are affected by intrinsic (mutations) and extrinsic (microenvironment) factors, and how these interactions are disrupted in malignancies and inborn errors of immunity. In the context of IMMERGE we aim to delineate cell-type specific effect of germline mutations in immune cells, and how they affect function, cross-talk and differentiation.

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Approach: We employ a systems biology framework that combines deep molecular profiling and advanced computational modelling, applied to clinical samples from patient cohorts. Briefly, we combine cutting-edge single cell multiomics profiling (RNA, chromatin) and predictive computational models, and collaborate with consortium partners for functional studies, to shed light on cellular and molecular disease mechanism driven by the disease mutations.

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Kamal A, Arnold C, Claringbould A, Moussa R, Servaas NH, Kholmatov M, Daga N, Nogina D, Mueller-Dott S, Reyes-Palomares A, Palla G, Sigalova O, Bunina D, Pabst C, Zaugg JB. (2023) GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks. Mol Syst Biol. Apr 19:e11627. doi: 10.15252/msb.202311627. Epub ahead of print. PMID: 37073532.

Sigalova OM, Shaeiri A, Forneris M, Furlong EE, Zaugg JB. (2020). Predictive features of gene expression variation reveal mechanistic link with differential expression. Mol Syst Biol 16 (8), e9539. doi:10.15252/msb.20209539.

Reyes-Palomares A, Gu M, Grubert F, Berest I, Sa S, Kasowski M, Arnold C, Shuai M, Srivas R, Miao S, Li D, Snyder MP, Rabinovitch M, Zaugg JB. (2020). Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nat Commun 11 (1), 1-14. doi:10.1038/s41467-020-15463-x.

Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H,  Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. (2019) Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Rep. 29, 3147–3159.e12. doi:10.1016/j.celrep.2019.10.106.

Ranzoni AM Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada, Mohorianu I, Zaugg JB, Cvejic A (2021) Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 28, 472-487.e7. doi:10.1016/j.stem.2020.11.015.