Epigenetics@HelmholtzMunich

Dozens of researchers at Helmholtz Munich joined forces to reveal the myriad of secrets of Epigenetics.

Dozens of researchers @Helmholtz Munich join forces to reveal the myriad of secrets of Epigenetics.

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The Epigenetics@HelmholtzMunich Community Research consists of almost 30 labs from 17 Helmholtz Munich institutes, committed to performing ground-breaking research in the field of epigenetics. These groups are pioneers in their respective disciplines, utilizing cutting edge techniques to answer the complex questions of today.

The topics studied by the community include: stem cells, cellular plasticity, metabolism, diabetes, computational biology, epidemiology, immunology, development, and systems biology. 

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Beads on a string
chromatin visualized using 3D-printed nucleosomes (by Igor Kukhtevich) and crochet yarn

Epigenetics in Numbers

28
Research Groups
16
Institutes
6
Departments

Key Activities

News & Highlights

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Medical diagnostic systems using ai to analyze patient data

IFE,

From pixels to discovery: microscopy image analysis with SpotMAX

What if analysing thousands of microscopic signals could be done in minutes rather than hours? Researchers at Helmholtz Munich have developed SpotMAX, a new AI-powered open-source framework that automates the detection and quantification of…

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Science as Art

Events, Public Engagement, Stem Cells, IES,

“In Formation”: Helmholtz Munich Brings Science as Art to Muffatwerk

From 5 to 8 July 2026, Munich’s Muffatwerk will become a unique space where the worlds of scientific research and artistic creation converge. The exhibition “In Formation” brings together four international artists – Anna Dumitriu, Solveig Lill,…

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A new study clarifies the role of the RNA methyltransferase METTL5, showing that it does not modify mRNA in living cells but is instead restricted to rRNA.

IFE,

Defining the Role of METTL5 in m6A Deposition: No Evidence for mRNA Methylation In Vivo

A new study clarifies the role of the RNA methyltransferase METTL5, showing that it does not modify mRNA in living cells but is instead restricted to rRNA.

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12.07.2023, Neuherberg: Helmholtz Pioneer Campus Opening. Foto: Matthias Balk/Helmholtz Zentrum München

Stem Cells, IES, Computational Health, ICB, Bioengineering, IBMI, Pioneer Campus,

Three Helmholtz Munich Researchers Elected to Bavarian Academy

At its most recent plenary session, the Bavarian Academy of Sciences and Humanities (BAdW) elected 13 distinguished scholars as new members. Among them are three researchers from Helmholtz Munich: Prof. Maria-Elena Torres-Padilla, Prof. Fabian Theis,…

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photosynthesis green pattern

Environmental Health, EPI, Molecular Targets and Therapeutics, IFE,

More Than Waste: Photorespiration Shapes the Plant Epigenome

Photorespiration has long been regarded as an energetically costly side reaction of photosynthesis, reducing plants’ net carbon gain. Now, researchers at Helmholtz Munich, in collaboration with Heidelberg University and the Technical University of…

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When Metabolism Meets Chromatin: Histone Acylations Tune Gene Expression

IFE,

When Metabolism Meets Chromatin: Histone Acylations Tune Gene Expression

Metabolic dysfunction is a hallmark of numerous diseases, including diabetes and other metabolic disorders. But how do changes in our metabolism affect our cells and the way they function? How do they influence our genes?

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Businessmen shaking hands to seal a deal with his partner. Business and entrepreneurship award ceremony theme.

Recent Publications

Diabetologia, DOI: 10.1007/s00125-026-06906-z (2026)

Valla, L. ; Schwager, M.F. ; Cohrs, C.M. ; Stöckl, J.B. ; Karampelias, C. ; Shashikadze, B. ; Rathkolb, B. ; Lindner, R. ; Kraetzl, M. ; Renner, S. ; Molina van Den Bosch, M. ; Yang, K. ; Sterr, M. ; Böttcher, A. ; Hrabě de Angelis, M. ; Speier, S. ; Fröhlich, T. ; Theis, F.J. ; Lickert, H. ; Wolf, E. ; Kemter, E.

Pregestational maternal diabetes primes neonatal beta cell dysfunction with structural remodelling, impaired calcium buffering and altered mTORC2–Gαq–PKCα signalling in a pig model.
Cardiovasc. Res., DOI: 10.1093/cvr/cvag258 (2026)

Horstmann, H. ; Wolfram, C. ; De Vore, L. ; Abdelwahed, Y.S. ; Amend, A. ; Meteva, D. ; Heiser, M. ; Stapmanns, P. ; Seppelt, C. ; Zanders, L. ; Nelles, G. ; Peters, D. ; Wientjens, C. ; Zimmermann, F. ; Yücel, D. ; Franitza, M. ; Becker, K. ; Losert, C. ; Heinig, M. ; Stark, K. ; Joner, M. ; Lang, A. ; Riffelmacher, T. ; Gerdes, N. ; Baldus, S. ; Giannarelli, C. ; Wolf, D. ; Landmesser, U. ; Kränkel, N. ; Leistner, D.M. ; Winkels, H. ; Gerhardt, T.

Divergent T cell programs in plaque rupture and erosion revealed by single-cell multiomics in the OPTICO-ACS study.
EMBO J., DOI: 10.1038/s44318-026-00949-z (2026)

Basille, A. ; Bawadi, Y. ; Lin, Y. ; Kirke, C. ; Bourgeay, C. ; Cluet, D. ; Vachez, L. ; Dervieux, V. ; Guiguettaz, L. ; Bernard, P. ; Hamperl, S. ; Pasero, P. ; Ricci, E.P. ; Vanoosthuyse, V.

The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids.
Sci. Data 13:1457 (2026)

Kardoost, A. ; Ghanem, N. ; Li, T. ; Kolter, J. ; Marr, C.

A large-scale expert-annotated 3D image dataset of dermal tissue macrophages.
In:. 2026. 306 - 315 (Lect. Notes Comput. Sc. ; 16885 LNCS)

Dasdelen, M.F. ; Ozlugedik, F. ; Looser, I. ; Umer, R.M. ; Pohlkamp, C. ; Marr, C.

Genetically Aligned Patient Representations Improve Hematological Diagnosis.
J. Cell Biol. 225:e202410020 (2026)

Chadha, Y. ; Kukhtevich, I. ; Stegmaier, T. ; Padovani, F. ; Schneider, R. ; Schmoller, K.M.

Single-cell imaging reveals a key role of Bck2 in yeast cell size adaptation to nutrient challenges.
EMBO J., DOI: 10.1038/s44318-026-00928-4 (2026)

Stępień, A. ; Pulimamidi, D. ; Plens-Gałąska, M. ; Lalonde, M. ; Kopczyńska, M. ; Ostatek, K. ; Kapeliukha, M. ; Kimurâ, H. ; Irshad, S. ; Gdula, M.R. ; Hamperl, S. ; Kamieniarz-Gdula, K.

Proximity of pre-mRNA 3′ end processing and transcription termination is associated with enhanced gene expression.
Nucleic Acids Res. 54:gkag949 (2026)

Munoz-Barrera, M. ; Mata-Cabana, A. ; Moreno-Rivero, A. ; Piubeli, F.A. ; Ren-Barroso, B. ; Al-Refaie, N. ; Gutierrez, G. ; Cabianca, D.S. ; Olmedo, M.

HLH-30/TFEB is necessary for chromatin reorganization and maintenance of cell quiescence during starvation in C. elegans.
In: (Computer Vision – ECCV 2026). 2026. 76-94 (Lect. Notes Comput. Sc. ; 17074 LNCS)

Grashei, C. ; Brechenmacher, C. ; Umer, R.M. ; Liu, J. ; Marr, C. ; Schüffler, P. ; Szczurek, E.

Pathryoshka: Compressing Pathology Foundation Models via Multi-teacher Knowledge Distillation with Nested Embeddings.
Nat. Commun. 17:10651 (2026)

Schütze, T.M. ; Kolodziejczyk, A. ; Ditzer, N. ; Vangelisti, S. ; Capra, E. ; Lee, J. ; Chiaradia, I. ; Kufrin, V. ; Yamada, S. ; Peters, J. ; Krause, M. ; Oegema, C.E. ; Derihaci, R.P. ; Birdir, C. ; Namba, T. ; Wurm, A.A. ; Martin, U. ; Wimberger, P. ; Long, K.R. ; Lancaster, M.A. ; Kalebic, N. ; Bonev, B. ; Albert, M.

Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution.
In:. 2026. 665-684 (Lect. Notes Comput. Sc. ; 17002 LNCS)

Riel, J. ; Singh, V.M. ; Aryasomayajula, S.A. ; Chinbat, A. ; Leonhard, H. ; Ladenburger, M. ; Alexander, F. ; Choudhary, V. ; Laredo, F. ; Masserdotti, G. ; Prein, T. ; Marr, C. ; Kardoost, A.

HASSL: Hierarchy-Aware Self-supervised Learning Framework for Single Cell Microscopy.
Cell, DOI: 10.1016/j.cell.2026.09.021 (2026)

Schmacke, N.A. ; Mädler, S.C. ; Wallmann, G. ; Metousis, A. ; Varlamova, V. ; Steigerwald, S. ; Christ, S.B. ; Bérouti, M. ; Harz, H. ; Leonhardt, H. ; Theis, F.J. ; Mann, M. ; Hornung, V.

SPARCS enables scalable recovery of complex image-based phenotypes for genetic screening.
Cancer Res., DOI: 10.1158/0008-5472.CAN-25-3126 (2026)

Leonhardt, L. ; Mei, J. ; Hendley, A.M. ; Ansari, S.A. ; Ashe, S. ; Berrios, D.I. ; Joost, L.-H. ; Fadel, L. ; Yigin, M. ; Wirth, J. ; Lewandowski-Hoppe, N. ; Maachi, H. ; Schicktanz, F. ; Remke, M. ; Lindner, R. ; Li, L.Y. ; Gbenedio, O.M. ; Hui, Y. ; Ghabi, E. ; Luchini, C. ; Malleo, G. ; He, J. ; Graham, R.P. ; Roose, J.P. ; Dawson, D.W. ; Uhlenhaut, N.H. ; Feuchtinger, A. ; Steiger, K. ; Kim, G.E. ; Hebrok, M.

KDM6 histone demethylases tune pancreatic cancer plasticity.
J. Clin. Immunol. 46, 1113-1119 (2026)

Hamad, S.G. ; Makhlouf, M. ; Agrebi, N. ; Kaddourah, A. ; Abu-Hasan, M. ; Al‐Adba, B. ; Sadoun, A. ; Hubrack, S.Z. ; Aamer, W. ; Ruiz Tejada Segura, M.L. ; Scialdone, A. ; Machaca, K. ; Saraiva, L.R. ; Bout-Tabaku, S. ; Lo, B.

Unraveling immune dysregulation in ZNFX1 deficiency: From interferonopathies to macrophage activation syndrome.
iScience 29:117314 (2026)

Solovey, M. ; Celik, M.A. ; Salcher, F. ; Gülec, C. ; Abdalfattah, M. ; Ali, M.I.H ; Heinig, M. ; Scialdone, A. ; Ziemann, F. ; Colomé-Tatché, M.

Community: Component based differential cell communication analysis in large multi-sample case-control scRNAseq datasets.
Nat. Genet. 58, 2469–2473 (2026)

Lotfollahi, M. ; Bright, C. ; Skorobogat, R. ; Dehkordi, M.M. ; George, X. ; Richter, S. ; Shitov, V.A. ; Topalova, A. ; Melcher, H. ; Nussbaumer, N. ; Fomm, A. ; Luecken, M. ; Theis, F.J.

ArchMap is a web-based platform for reference-based analysis of single-cell datasets.
Plant Biol., DOI: 10.1111/plb.70291 (2026)

Behr, R. ; Gallo-Franco, J.J. ; Hazarika, R.R. ; Zhang, Z. ; Wilming, F. ; Schnitzler, J.-P. ; Lindermayr, C. ; Johannes, F.

DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis.
Angiogenesis 29:74 (2026)

Gogiraju, R. ; Moiko, K. ; Bochenek, M.L. ; Greulich, F. ; Witzler, C. ; Schmitz, W. ; Zifkos, K. ; Derieux, C. ; Ghasemi, I. ; Guliani, P. ; Sun, B. ; Espinola-Klein, C. ; Uhlenhaut, N.H. ; Bock, A. ; Ruf, W. ; Madhusudhan, T. ; Lurz, P. ; Schäfer, K.

Lysed erythrocyte membranes metabolically prime endothelial cells for angiogenesis.

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Epigenetics Coordination Office
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