Publications

2025

• Spatio-temporal patterns of active epigenetic turnover

  Fabrizio Olmeda Misha Gupta Onurcan Bektas Steffen Rulands
  [arXiv:2505.13216]

• Self-propagating wave drives noncanonical antidurotaxis of skull bones in vivo

  Yiteng Dang Johanna Lattner Adrian Lahola-Chomiak Diana Alves-Afonso Elke Ulbricht Anna V Taubenberger Steffen Rulands Jacqueline Tabler
  Nature Communications 17, 4330 (2025).
  [bioRxiv:2023.07.10.547677]

• Transcriptional landscapes underlying Notch-induced lineage conversion and plasticity of mammary basal cells

  Candice Merle Calvin Rodrigues Atefeh Pourkhalili Langeroudi Robin Journot Fabian Rost Yiteng Dang Steffen Rulands Silvia Fre
  EMBO J (2025).

• Navigating Ethical Challenges across Professions: Insights from an Ethics Lab on Patient-derived Organoids

  Jeanette Bresson Ladegaard Knox Mie Seest Dam Sara Green Daniel E. Stange Franziska Baenke Bon-Kyoung Koo Steffen Rulands Tim Schmäche Vivian Mittné Ivan Terlizzi Beatrix Jahnke Mette N. Svendsen
  Med, in press (2025).

• A transcriptional clock of the human pluripotency transition

  Louis Coussement* Matteo Ciarchi* Aljona Kolmogorova Tim De Meyer Steffen Rulands+ Wolf Reik+ Maria Rostovskaya+
  submitted for publication.
  [bioRxiv:2025.03.13.643129]

• Controlling noise with self-organizedresetting

  Felix J. Meigel Steffen Rulands
  Communications Physics volume 8, 63.
  [arXiv:2312.09307]

• Emergent weight morphologies in deep neural networks

  Pascal de Jong* Felix Meige* Steffen Rulands
  submitted for publication.
  [arXiv:2501.05550]

• Universal quasi-particle kinetics control the cell death decision

  Felix Meige Lina Hellwig Harald Stachelscheid Philipp Mergenthaler Steffen Rulands
  submitted for publication.
  [arXiv:2501.04862]

• Collective dynamics of DNA methylation during ageing

  Aida Hashtroud Marc Bonder Oliver Stegle Ferdinand von Meyen Wolf Reik Steffen Rulands
  submitted for publication.
  [bioRxiv:2024.12.15.628564]

• Pre-cancerous Niche Remodelling Dictates Nascent Tumour Survival

  G. Skrupskelyte J. E. Rojo Arias Y. Dang S. Han M. T. Bejar B. Colom J. C. Fowler P. H. Jones S. Rulands B. D. Simons M. P. Alcolea
  submitted for publication.
  [bioRxiv:2024.07.04.602022]

2024

• scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood

  Marc Jan Bonder Stephen J. Clark Felix Krueger Siyuan Luo João Agostinho de Sousa Aida M. Hashtroud Thomas M. Stubbs Anne-Katrien Stark Steffen Rulands Oliver Stegle Wolf Reik Ferdinand von Meyenn
  Nature Communications 15, 7567 (2024).

• Field theory of enzyme-substrate systems with restricted long-range interactions

  Fabrizio Olmeda Steffen Rulands
  Physical Review E 110, 024404 (2024).
  [arXiv:2401.09827]

• Clonal dynamics of surface-driven growing tissues

  Ruslan Mukhamadiarov Matteo Ciarchi Fabrizio Olmeda Steffen Rulands
  Physical Review E 109, 064407 (2024).
  [arXiv.2312.01923]

• Statistical physics of biological aging

  Steffen Rulands Aida Hashtroud Matteo Ciarchi
  Bulletin of the American Physical Society, APS March Meeting 2024, W37.00009.

• Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

  N Cudak AC López-Delgado F Rost T Kurth M Lesche S Reinhardt A Dahl S Rulands F Knopf
  iScience 27, 108841 (2024).
  [bioRxiv:2023.06.04.543617]

• FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy

  Vera A. van der Weijden Maximilian Stötzel Dhanur P. Iyer Beatrix Fauler Elzbieta Gralinska Mohammed Shahraz David Meierhofer Martin Vingron Steffen Rulands Theodore Alexandrov Thorsten Mielke Aydan Bulut-Karslioglu
  Nature Cell Biology (2024).

• Long-range interactions and disorder facilitate pattern formation in spatial complex systems

  Fabrizio Olmeda Steffen Rulands
  submitted for publication.
  [arXiv:2303.12611]

• Single cell DNA methylation ageing in mouse blood

  Marc Jan Bonder Stephen J. Clark Felix Krueger Siyuan Luo João Agostinho de Sousa Aida M. Hashtroud Thomas M. Stubbs Anne-Katrien Stark Steffen Rulands Oliver Stegle Wolf Reik Ferdinand von Meyenn
  submitted for publication.
  [bioRxiv:2023.01.30.526343]

2022

• Making sense of fragmentation and merging in lineage tracing experiments

  Y. Dang S. Rulands
  Frontiers in Cell and Developmental Biology, 10 (2022).

• Self-organization of plasticity and specialization in a primitively social insect

  Solenn Patalano*+ Adolfo Alsina* Carlos Gregorio-Rodríguez Martin Bachman Stephanie Dreier Irene Hernando-Herraez Paulin Nana Shankar Balasubramanian Seirian Sumner Wolf Reik+ Steffen Rulands+
  Cell Syst. 13(9), 768-779 (2022).

• Metabolic enhancement of mammalian developmental pausing

  Vera A. van der Weijden Maximilian Stötzel Beatrix Fauler Dhanur Iyer Mohammed Shahraz David Meierhofer Steffen Rulands Theodore Alexandrov Thorsten Mielke Aydan Bulut-Karslioglu
  bioRxiv: 10.1101/2022.08.22.504730.

2021

• Four-pronged negative feedback of DSB machinery in meiotic DNA-break control in mice

  Ihsan Dereli Marcello Stanzione Fabrizio Olmeda Frantzeskos Papanikos Marek Baumann Sevgican Demir Fabrizia Carofiglio Julian Lange Bernard de Massy Willy M Baarends James Turner Steffen Rulands Attila Tóth
  Nucleic Acids Res. 49(5), 2609–2628 (2021).

• Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates

  Fabrizio Olmeda Tim Lohoff Stephen J Clark Laura Benson Felix Krüger Wolf Reik+ Steffen Rulands+
  bioRxiv:10.1101/2020.12.30.424823.

2020

• Active turnover of DNA methylation during cell fate decisions

  Aled Parry Steffen Rulands Wolf Reik
  Nat. Rev. Genet. 22, 59–66 (2020).

• Specialisation and plasticity in a primitively social insect

  Solenn Patalano+* Adolfo Alsina* Carlos Gregorio-Rodriguez Martin Bachman Stephanie Dreier Irene Hernando-Herraez Paulin Nana Shankar Balasubramanian Seirian Sumner Wolf Reik+ Steffen Rulands+
  bioRxiv: 10.1101/2020.03.31.007492.

• Lineage hierarchies and stochasticity ensure the long-term maintenance of adult neural stem cells

  Emmanuel Than-Trong Bahareh Kiani Nicolas Dray Sara Ortica Benjamin Simons Steffen Rulands Alessandro Alunni Laure Bally-Cuif
  Sci. Adv. 6(18) (2020).

• Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain

  Christian Lange Anja Machate Susanne Reinhardt Matthias Lesche Anke Weber Veronika Kuscha Andreas Dahl Steffen Rulands Michael Brand
  Development 147(1), dev185595 (2020).

2019

• Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool

  Nicole Prior Christopher J. Hindley Elena Meléndez Winnie W. Y. Lau Berthold Göttgens Steffen Rulands Benjamin D. Simons Meritxell Huch
  Development 146(12), dev174557 (2019).

2018

• Deterministic fate assignment of Müller glia cells in the zebrafish retina suggest a clonal backbone during development

  Steffen Rulands Ana Belen Iglesias-Gonzalez Henrik Boije
  Eur. J. Neurosci. 48(12), 3597-3605 (2018).

• Neurogenin3 phosphorylation controls reprogramming efficiency of pancreatic ductal organoids into endocrine cells

  Roberta Azzarelli Steffen Rulands Sonia Nestorowa John Davies Sara Campinoti Sébastien Gillotin Paola Bonfanti Berthold Göttgens Meritxell Huch Benjamin D. Simons Anna Philpott
  Sci. Rep. 8, 15374 (2018).

• Defining lineage potential and fate behavior of precursors during pancreas development

  Magdalena K. Sznurkowska Edouard Hannezo Roberta Azzarelli Steffen Rulands Sonia Nestorowa Christopher J. Hindley Jennifer Nichols Berthold Göttgens Meritxell Huch Anna Philpott Benjamin D. Simons
  Dev. Cell 46(3), 360-375 (2018).

• Genome-scale oscillations in DNA methylation during exit from pluripotency

  Steffen Rulands*+ Heather J. Lee*+ Stephen J. Clark Christof Angermueller Sébastien A. Smallwood Felix Krueger Hisham Mohammed Wendy Dean Jennifer Nichols Peter Rugg-Gunn Gavin Kelsey Oliver Stegle Benjamin D. Simons+ Wolf Reik+
  Cell Syst. 7(1), 63-76 (2018).

• Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland

  Anna M. Lilja* Veronica Rodilla* Mathilde Huyghe Edouard Hannezo Camille Landragin Olivier Renaud Olivier Leroy Steffen Rulands Benjamin D. Simons Silvia Fre
  Nat. Cell Biol. 20, 677–687 (2018).

• Universality of clone dynamics during tissue development

  Steffen Rulands+ Fabienne Lescroart Samira Chabab Christopher J. Hindley Nicole Prior Magdalena K. Sznurkowska Meritxell Huch Anna Philpott Cedric Blanpain Benjamin D. Simons+
  Nat. Phys. 14, 469-474 (2018).

• Muscle stem cells exhibit distinct clonal dynamics in response to tissue repair and homeostatic aging

  Matthew T. Tierney Michael J. Stec Steffen Rulands Benjamin D. Simons Alessandra Sacco
  Cell Stem Cell 22(1), 119-127 (2018).

2017

• Emergence and universality in the regulation of stem cell fate

  Steffen Rulands Benjamin D.Simons
  Curr. Opin. Syst. Biol. 5, 57-62 (2017).

• Multi-site Neurogenin3 phosphorylation controls pancreatic endocrine differentiation

  Roberta Azzarelli Christopher Hurley Magdalena K. Sznurkowska Steffen Rulands Laura Hardwick Ivonne Gamper Fahad Ali Laura McCracken Christopher Hindley Fiona McDuff Sonia Nestorowa Richard Kemp Kenneth Jones Berthold Göttgens Meritxell Huch Gerard Evan Benjamin D. Simons Douglas Winton Anna Philpott
  Dev. Cell 41(3), 274-286 (2017).

• Defining stem cell dynamics and migration during wound healing in mouse skin epidermis

  Mariaceleste Aragona* Sophie Dekoninck* Steffen Rulands Sandrine Lenglez Guilhem Mascré Benjamin D. Simons Cédric Blanpain
  Nat. Commun. 8, 14684 (2017).

2016

• Tracing cellular dynamics in tissue development, maintenance and disease

  Steffen Rulands Benjamin D. Simons
  Curr. Opin. Cell Biol. 43, 38-45 (2016).

• Quantitative lineage tracing strategies to resolve multipotency in tissue-specific stem cells

  Aline Wuidart* Marielle Ousset* Steffen Rulands Benjamin D. Simons Alexandra Van Keymeulen Cédric Blanpain
  Genes Dev. 30, 1261-1277 (2016).

• The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue

  Yinan Wan Alexandra D. Almeida Steffen Rulands Naima Chalour Leila Muresan Yunmin Wu Benjamin D. Simons Jie He William A. Harris
  Development 143(7), 1099–1107 (2016).

• Uncovering the number and clonal dynamics of Mesp1 progenitors during heart morphogenesis

  Samira Chabab* Fabienne Lescroart* Steffen Rulands* Navrita Mathiah Benjamin D. Simons Cédric Blanpain
  Cell Rep. 14 (1), 1-10 (2016).

2015

• The independent probabilistic firing of transcription factors: A paradigm for clonal variability in the zebrafish retina

  Henrik Boije Steffen Rulands Stefanie Dudczig Benjamin D. Simons William A. Harris
  Dev. Cell 34(5), 532-543 (2015).

• Clonal dynamics reveal two distinct populations of basal cells in slow turnover airway epithelium

  Julie K. Watson Steffen Rulands Adam C. Wilkinson Aline Wuidart Marielle Ousset Alexandra Van Keymeulen Berthold Göttgens Cédric Blanpain Benjamin D. Simons Emma L. Rawlins
  Cell Rep. 12 (1), 90-101 (2015).

2014

• Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development

  Fabienne Lescroart Samira Chabab Xionghui Lin Steffen Rulands Catherine Paulissen Annie Rodolosse Herbert Auer Younes Achouri Christine Dubois Antoine Bondue Benjamin D. Simons Cédric Blanpain
  Nat. Cell Biol. 16, 829–840 (2014).

• Specialization and Bet Hedging in Heterogeneous Populations

  Steffen Rulands David Jahn Erwin Frey
  Phys. Rev. Lett. 113, 108102 (2014).
  [arxiv:1408.4912]

• Range Expansion of Heterogeneous Populations

  Matthias Reiter* Steffen Rulands* Erwin Frey
  Phys. Rev. Lett. 112, 148103 (2014).
  [arxiv:1403.6333]

2013

• Global attractors and extinction dynamics of cyclically competing species

  Steffen Rulands Alejandro Zielinski Erwin Frey
  Phys. Rev. E 87, 052710 (2013).
  [arxiv:1305.0119]

• Stability of localized wave fronts in bistable systems

  Steffen Rulands Ben Klünder Erwin Frey
  Phys. Rev. Lett. 110, 038102 (2013).
  [arxiv:1212.1036]

2011

• Three-fold way to extinction in populations of cyclically competing species

  Steffen Rulands Tobias Reichenbach Erwin Frey
  J. Stat. Mech. 2011, L01003 (2011).
  [arXiv:1005.5704]