Publications

Selected publications

Samy Kefalopoulou^*, Pim M.J. Rullens^*, Kim L de Luca, Sandra S. de Vries, Korthout, Alexander van Oudenaarden, Peter Zeller⁺, Jop Kind⁺ *equal contribution ⁺jointly supervised
Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation
Nature Cell Biology 27, 1186–1198, 2025
https://www.nature.com/articles/s41556-025-01687-w
Marloes Blotenburg, Lianne Suurenbroek, Danique Bax, Joëlle de Visser, Vivek Bhardwaj, Luca Braccioli, Elzo de Wit, Antonius van Boxtel, Hendrik Marks, Peter Zeller
Stem cell culture conditions affect in vitro differentiation potential and efficiency of mouse gastruloid development
PLoS ONE 20(3): e0317309.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0317309
Peter Zeller*, Marloes Blotenburg*, Vivek Bhardwaj, Buys Anton de Barbanson, Fredrik Salmén, Alexander van Oudenaarden
T-ChIC: multi-omic detection of histone modifications and full-length transcriptomes in the same single cell
Biorxiv 13/05/2024
https://www.biorxiv.org/content/10.1101/2024.05.09.593364v1

Peter Zeller^*, Jake Yeung^*, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden.
Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
Nature Genetics 55, 333-345, 2023 *equal contributionhttps://www.nature.com/articles/s41588-022-01260-3
Jake Yeung^*, Maria Florescu^*, Peter Zeller*, Buys Anton de Barbanson, Max D. Wellenstein, Alexander van Oudenaarden.
scChIX-seq infers dynamic relationships between histone modifications in single cells.
Nature Biotechnology 02/01/2023 *equal contributionhttps://www.nature.com/articles/s41587-022-01560-3
Jan Padeken^*, Peter Zeller^*, Benjamin Towbin, Iskra Katic, Veronique Kalck, Stephen P Methot, Susan M Gasser. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression.
Genes Dev 33, 436-451, 2019 *equal contribution
http://genesdev.cshlp.org/content/33/7-8/436.long
Zeller P^*, Padeken J^*, Schendel R v, Kalck V, Tijsterman M, Gasser SM.
Repression by H3K9me is dispensable for C. elegans development, but suppresses RNA:DNA hybrid-associated repeat instability.
Nature Genetics 48, 1385–1395, 2016 *equal contributionhttp://www.nature.com/ng/journal/v48/n11/full/ng.3672.html

Publication list – other publications

Ning Qing Liu^*, Irene Paassen^*, Lars Custers, Peter Zeller, Hans Teunissen, Dilara Ayyildiz, Jiayou He, Juliane Laura Buhl, Eelco Wieger Hoving, Alexander van Oudenaarden, Elzo de Wit, Jarno Drost
SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors
Nat Commun 14, 7762, 2023 *equal contribution
https://pubmed.ncbi.nlm.nih.gov/38040699/
V. Bondarenko, M. Nikolaev, D. Kromm, R. Belousov, A. Wolny, M. Blotenburg, P. Zeller, S. Rezakhani, J. Hugger, V. Uhlmann, L. Hufnagel, A. Kreshuk, J. Ellenberg, A. van Oudenaarden, A. Erzberger, M. P Lutolf, T. Hiiragi
Embryo-uterine interaction coordinates mouse embryogenesis during implantation
The EMBO Journal e113280, 2023
https://www.embopress.org/doi/full/10.15252/embj.2022113280
Stephen P Methot^*, Jan Padeken^*, Giovanna Brancati, Peter Zeller, Colin E Delaney, Dimos Gaidatzis, Hubertus Kohler, Alexander van Oudenaarden, Helge Großhans, Susan M Gasser.
H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity.
Nat Cell Biol 23, 1163-1175, 2021 *equal contribution
https://www.nature.com/articles/s41556-021-00776-w
Jan Padeken, Stephen Methot, Peter Zeller, Colin E Delaney, Veronique Kalck, Susan M Gasser.
Argonaute NRDE-3 and MBT domain protein LIN-61 redundantly recruit an H3K9me3 HMT to prevent embryonic lethality and transposon expression.
Genes Dev 35, 82-101, 2020
http://genesdev.cshlp.org/content/35/1-2/82.long
Mintern JD, Macri C, Chin WJ, Panozza SE, Segura E, Patterson NL, Zeller P, Bourges D, Bedoui S, McMillan PJ, Idris A, Nowell CJ, Brown A, Radford KJ, Johnston APR, and Villadangos JA.
Differential use of autophagy by primary dendritic cells specialized in cross-presentation.
Autophagy 11(6): 906–917, 2015
http://www.tandfonline.com/doi/full/10.1080/15548627.2015.1045178

Reviews

Zeller P, Gasser SM. The Importance of Satellite Sequence Repression for Genome Stability.
Cold Spring Harb Symp Quant Biol 2017. 82: 15-24,
symposium.cshlp.org/content/82/15.abstract
Padeken J^*, Zeller P^*, Gasser SM. Repeat DNA in genome organization and stability.
Curr Opin Genet Dev. 2015 Apr;31:12-9
https://pubmed.ncbi.nlm.nih.gov/25917896/

Book chapter

Gaza HV, Bhardwaj V, Zeller P. Single-Cell Histone Modification Profiling with Cell Enrichment Using sortChIC Methods Mol Biol. 2024:2846:215-241
https://pubmed.ncbi.nlm.nih.gov/39141239/

Peer-reviewed publications from MBG

Sort by: Date | Author | Title

Kefalopoulou, S., Rullens, P. M. J., de Luca, K. L., de Vries, S. S., Korthout, T., van Oudenaarden, A., Zeller, P. & Kind, J. (2025). Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation. Nature Cell Biology, 27(7), 1186-1198. https://doi.org/10.1038/s41556-025-01687-w

van den Berg, J. & Zeller, P. (2025). Shining a light on cell biology of the nucleus with single-cell sequencing. Current Opinion in Cell Biology, 93, Article 102468. https://doi.org/10.1016/j.ceb.2025.102468

Blotenburg, M., Suurenbroek, L., Bax, D., de Visser, J., Bhardwaj, V., Braccioli, L., de Wit, E., van Boxtel, A., Marks, H. & Zeller, P. (2025). Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation. PLoS One, 20(3), Article e0317309. https://doi.org/10.1371/journal.pone.0317309

All publications by Pubmed search: Peter Zeller