Stem Cell Center

Epigenetics and Stem Cells

At the Institute of Epigenetics and Stem Cells (IES),  we aim to unlock a cell's full potential by understanding how a single cell can give rise to all the cells in our body at the beginning of life.

At the Institute of Epigenetics and Stem Cells (IES), we aim to unlock a cell's full potential by understanding how a single cell can give rise to all the cells in our body at the beginning of life.

microscope of human stem cells, 3d rendering.

About Our Research

Research Groups

GFP-labelled early mouse embryos

Torres-Padilla Lab

Epigenetics and cell-fate in early mammalian development

We combine high-resolution microscopy with single-cell genomics to study the epigenetic principles underlying cellular reprogramming in the mouse embryo.

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Transcription-Replication Conflicts under different temperatures

Hamperl Lab

Chromosome dynamics and genome stability

We study how DNA replication and transcription can occur simultaneously without major accidents that cause DNA damage and genome instability.

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Cellular Decision Making

Scialdone Lab

Physics and Data-Based Modeling of Cellular Identity Changes

We aim to understand the molecular bases of cell identity changes by combining single-cell and spatial omics data analysis with physical modeling.

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Battich Lab

Quantitative Cell Biology

We are interested in the strategies that cells use to control gene expression levels and variability during differentiation.

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News & Highlights

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The DNA is packaged into chromatin

IES, IFE,

Empowering Young Scientists: Applications Open for 2026 Chromatin Summer School

Talented PhD students are encouraged to apply for the upcoming Chromatin Summer School taking place from 17 - 29 August 2026

Verleihung des Bayerischen Maximiliansordens

Awards & Grants, Stem Cells, IES,

Maria-Elena Torres-Padilla Honored With the Maximiliansorden

Prof. Maria-Elena Torres-Padilla, this year’s Leibniz Prize winner, has received the Bavarian Maximiliansorden for Science and Art. Minister-President Dr. Markus Söder presented the distinguished state honor to her at the State Chancellery,…

Talent Forum Welcome

Events, Stem Cells, IES,

A Platform for Emerging Talent: The Helmholtz Munich Talent Forum 2025

The Helmholtz Munich Talent Forum took place on November 18–19, 2025, at the Helmholtz Munich Conference Center, bringing together eight outstanding early-career scientists from around the world working in the fields of Epigenetics and Nucleic Acids…

Exhibition Stem Cells at Deutsches Museum_For Website

Events, Stem Cells, IES, Molecular Targets and Therapeutics, IFE,

Exhibition on Cell Identity at the Deutsches Museum

How do the many different cells in the human body emerge from a single stem cell – and what makes each one unique? The Epigenetics Community at Helmholtz Munich explores these questions in a special exhibition at the Deutsches Museum. From 14. to 16.…

Cellular Reprogramming Necklace by Anna Dumitriu photo credit Audrey Rose Mizzi large_QUER

Public Engagement, IES,

Science Through an Artistic Lens

In a world where scientific innovation is increasingly interconnected, the RepliFate-Artist in Residence program seeks to further unite the realms of art and science. Led by Prof. Maria-Elena Torres-Padilla at Helmholtz Munich and supported by…

Develop a protocol for the generation of induced pluripotent stem cells (iPSCs) from somatic cells in the in vitro laboratory _AdobeStock_760802337

Stem Cells, IES, ISF,

Interview Maria-Elena Torres-Padilla and Magdalena Götz: The Power of Stem Cells

Stem cells are transforming the way we think about treating disease, repairing damaged tissues, and even regenerating entire organs. As a cornerstone of regenerative medicine, they offer hope for conditions previously thought untreatable. In their…

IES Members

Portrait Maria-Elena Torres-Padilla_freigestellt
Prof. Dr. Maria-Elena Torres-Padilla

Director of the Stem Cell Center, Director of the Institute for Epigenetics and Stem Cells, Group Leader, Director of the Stem Cell Center (rotating)

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Portrait Stephan Hamperl
Dr. Stephan Hamperl

Group Leader

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Portrait Antonio Scialdone
Dr. Antonio Scialdone

Group Leader

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Nicoals Battich_freigestellt
Dr. Nicolas Battich

Group Leader

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Portrait Jonathan Adam Burton
Dr. Jonathan Adam Burton

Deputy Head of Institute for Epigenetics and Stem Cells

Portrait Andreas Ettinger
Dr. Andreas Ettinger

Head of Microscopy Core

Tamas Schauer
Dr. Tamas Schauer

Senior Computational Biologist

Portrait Marlies Oomen
Dr. Marlies Oomen

Postdoc

Portrait Antoine Canat
Dr. Antoine Canat

Postdoc

Portrait Maxime Lalonde
Dr. Maxime Lalonde

Postdoc

Clare_ShukKwan.png
Dr. Clare Shuk Kwan Lee

Postdoc

Portrait of Martin Miranda
Dr. Martin Miranda

Postdoc

Portrait Federico Pecori
Dr. Federico Pecori

Postdoc

Ioannis Tsirkas Portrait
Dr. Ioannis Tsirkas

Postdoc

JiezhenMo_selfportrait_personnel
Dr. Jiezhen Mo

Postdoc

Yuki Oyama self-portrait
Dr. Yuki Oyama

Postdoc

JoseBautistaPictureNoBG
Dr. José Terrón-Bautista

Postdoc

Gofur Mohammad Wasiful

Doctoral Researcher, IES/HPC

Portrait Marco Stock
Marco Stock

Doctoral Researcher

Veronica Finazzi self-portrait (personnel)
Veronica Finazzi

Doctoral Researcher

Yicong Chen
Yicong Chen

Doctoral Researcher

Atiqa Sajid photo
Atiqa Sajid

Doctoral Researcher

Porträt Iliya Nadelson
Iliya Nadelson

Doctoral Researcher, Torres-Padilla lab

Porträt David von Bonin
David von Bonin

Doctoral Researcher

Portrait_selfie_Elizabeth_Gomez
Elizabeth Marquez Gomez

Research Assistant – Bioinformatics

Portrait Margarita Cespedes Borroso
Margarita Cespedes Barroso

Lab Manager

Xanthoula Karypidou self portrait
Xanthoula Karypidou

Lab Manager

Untitled design - 1
Melissa Mayen Quiroz

Intern

Portrait Thomas Gerling
Thomas Gerling

Administrative Assistant

Our Institute in Numbers

39
Employees
24
Nationalities
4467
Cups of Coffee
4
IES Sport Events
12
Languages

Latest Publications

Nature 650, 1025-1034 (2026)

Uruci, S. ; Boer, D.E.C. ; Chrystal, P. ; Lalonde, M. ; Panagopoulos, A. ; Yakoub, G. ; Kirdök, I. ; Lint, K.d. ; Woude, M.v.d. ; Wendel, T.J. ; Brussee, S. ; Wondergem, A.P. ; Overbeek, N.v. ; Schotman, N. ; Lingeman, J. ; Ljungman, M. ; Vidal, M. ; Attikum, H.v. ; Vertegaal, A.C.O. ; Noordermeer, S.M. ; Wolthuis, R.M.F. ; Altmeyer, M. ; Hamperl, S. ; Tropepe, V. ; Berg, J.v.d. ; Heuvel, D.v.d. ; Luijsterburg, M.S.

CFAP20 salvages arrested RNAPII from the path of co-directional replisomes.
Mol. Cell 86, 24-40.e10 (2026)

Nitsch, S. ; Coraor, A.E. ; Schauer, T. ; Wu, Y. ; Sun, J. ; Möritz, N. ; Funke, J.J. ; Nagpal, H. ; Chua, G.N.L. ; Battistini, F. ; Lauberth, S.M. ; Richard, E.M. ; Orozco, M. ; Liu, S. ; Desviat, L.R. ; Fierz, B. ; Dietz, H. ; Roeder, R.G. ; de Pablo, J.J. ; Schneider, R.

H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.
Nat. Commun. 16:11334 (2025)

Oak, M.S. ; Stock, M. ; Janeva, A. ; Mezes, M. ; Hynes-Allen, A.M. ; Straub, T. ; Forné, I. ; Ettinger, A. ; Hamperl, S. ; Imhof, A. ; van den Ameele, J. ; Scialdone, A. ; Hörmanseder, E.

Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.
EMBO Rep. 26, 4691-4722 (2025)

Ummethum, H. ; Murriello, A.C. ; Werner, M. ; Márquez-Gómez, E. ; König, A.-C. ; Kruse, E. ; Lalonde, M. ; Trauner, M. ; Chanou, A. ; Weiß, M. ; Lee, C.S.K. ; Ettinger, A. ; Erhard, F. ; Hauck, S.M. ; Hamperl, S.

The CGG triplet repeat binding protein 1 counteracts R-loop induced transcription-replication stress.
Cell Rep. 44:116565 (2025)

Wagner, C.B. ; Longaretti, M. ; Sergi, S.G. ; Singh, N. ; Tsirkas, I. ; Bento, F. ; Wong, R.P. ; Wilkens, M. ; Hamperl, S. ; Butter, F. ; Aharoni, A. ; Ulrich, H.D. ; Luke, B.

Rad53 regulates RNase H1, which promotes DNA replication through sites of transcription-replication conflict.
Nucleic Acids Res. 53:gkaf1087 (2025)

Apostolou, Z. ; Venkatasubramani, A.V. ; Kopp, L.C. ; Kars, G. ; Scacchetti, A. ; Campos-Sparr, A. ; Schauer, T. ; Imhof, A. ; Becker, P.B.

The Tip60 acetylome is a hallmark of the proliferative state in Drosophila.
Development 152:dev205224 (2025)

Ewe, C.K. ; Farnworth, M.S. ; Miller, A. ; Navajas Acedo, J. ; Oomen, M.E. ; Paci, G. ; Widen, S.A. ; Yamada, T.

Pathway to Independence: A forecast for the future of developmental biology.
Nat. Cell Biol. 27, 1603-1604 (2025)

Fratton, A. ; Bonev, B.

Deciphering glioma susceptibility.
2025 in
München, Technische Universität, Naturwissenschaften, Diss., 2025, 92 S.

Stock, M.

Incorporation of prior knowledge to improve gene regulatory network inference from single-cell transcriptomics data.
Nat. Struct. Mol. Biol. 32, 2128-2129 (2025)

Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Ruiz-Morales, E.R. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.

Addendum: Retinoic acid signaling is critical during the totipotency window in early mammalian development.
Curr. Opin. Cell Biol. 95:102530 (2025)

Fukagawa, T. ; Torres-Padilla, M.E.

Exploring the cell nucleus: From chromosome structure to single-cell omics.
Cancer Res. 85, SY23 - 01 (2025)

Hains, A.E. ; Marques, J.G. ; Chetal, K. ; Nakatani, T. ; Ettinger, A. ; Biagi, C.A.O.d. ; Gonzalez‐Sandoval, A. ; Pillai, R. ; Gatto, A. ; Torres-Padilla, M.E. ; Sadreyev, R.I. ; Filbin, M.G. ; Rechem, C.V.

Abstract SY23-01: Diffuse midline gliomas: From cell cycle to therapeutic opportunities.
Stem Cell Rep. 20:102447 (2025)

Zikmund, T. ; Fiorentino, J. ; Penfold, C. ; Stock, M. ; Shpudeiko, P. ; Agarwal, G. ; Langfeld, L. ; Petrova, K. ; Peshkin, L. ; Hamperl, S. ; Scialdone, A. ; Hörmanseder, E.

Differentiation success of reprogrammed cells is heterogeneous in vivo and modulated by somatic cell identity memory.

Networks and Affiliations

Logo epigenetics@HelmholtzMunich

Epigenetics@HelmholtzMunich

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Chromdesign

Chromdesign

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Epigenesys

Epigene3sys

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Logo CRC Chromatin Dynamics

CRC Chromatin Dynamics

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Logo Ludwig-Maximilians-Universität München LMU

Ludwig-Maximilians-Universität München

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Logo LifeTime Initiative

LifeTime Initiative

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ITN RepliFate

RepliFate

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ArtTheIES_Workshop_1

Art the IES

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Contact

Portrait Thomas Gerling
Thomas Gerling

Administrative Assistant

Epigenetics@HelmholtzMunich Banner

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

Researchers at the IES also belong to epigenetics@HelmholtzMunich

Infinite Cells,

Infinite Innovation, Infinite Potential