Gaidatzis D, Graf-Landua M, Methot SP, Wölk M, Brancati G, Hauser YP, Meeuse MWM, Nahar S, Braun K, van der Does M, Aluri S, Kohler H, Smallwood S, Großhans H (2025) A scheduler for rhythmic gene expression.

Kawamura YK, Ozonov EA, Papasaikas P, Kondo T, Nguyen NV, Stadler MB, Smallwood SA, Koseki H, Peters AHFM (2025) Preventing CpG hypermethylation in oocytes safeguards mouse development.

Ferenc J, Bonvin M, Papasaikas P, Ferralli J, Nuninger C, Tsiairis CD (2025) A transcription factor toggle switch determines differentiated epidermal cell identities in Hydra.

Durdu S, Iskar M, Isbel L, Hoerner L, Wirbelauer C, Burger L, Hess D, Iesmantavicius V, Schübeler D (2025) Chromatin-dependent motif syntax defines differentiation trajectories.

Bocker MT, Fanourgakis G, Wetzel K, Komarov PA, Royo H, Rohmer A, Chun S, Liang CY, Kohler H, Chen T, Mao X, Labow MA, Valdez RA, Stadler MB, de Rooij DG, Capodieci P, Tallarico J, Peters AHFM, Nicholson TB (2025) The histone H3 lysine 36 demethylase KDM2A/FBXL11 controls Polycomb-mediated gene repression and germ cell development in male mice.

Skribbe M, Soneson C, Stadler MB, Schwaiger M, Suma Sreechakram VN, Iesmantavicius V, Hess D, Moreno EPF, Braun S, Seebacher J, Smallwood SA, Bühler M (2025) A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.

Fanourgakis G, Gaspa-Toneu L, Komarov PA, Papasaikas P, Ozonov EA, Smallwood SA, Peters AHFM (2025) DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos.

Williams TD, Michalak EM, Carey KT, Lam EYN, Anderson A, Griesbach E, Chan YC, Papasaikas P, Tan VWT, Ngo L, MacPherson L, Gilan O, Rucinski A, Rutkowska-Klute A, Zinn N, Grandi P, Bantscheff M, Prinjha RK, Dawson SJ, Chao JA, Wickramasinghe VO, Dawson MA (2025) mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.

Gudipati RK, Gaidatzis D, Seebacher J, Muehlhaeusser S, Kempf G, Cavadini S, Hess D, Soneson C, Großhans H (2024) Deep quantification of substrate turnover defines protease subsite cooperativity.

Shimada K, Tarashev CVD, Bregenhorn S, Gerhold CB, van Loon B, Roth G, Hurst V, Jiricny J, Helliwell SB, Gasser SM (2024) TORC2 inhibition triggers yeast chromosome fragmentation through mis regulated Base Excision Repair of clustered oxidation events.

Ohsawa S, Schwaiger M, Iesmantavicius V, Hashimoto R, Moriyama H, Matoba H, Hirai G, Sodeoka M, Hashimoto A, Matsuyama A, Yoshida M, Yashiroda Y, Bühler M (2024) Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast.

Grand RS, Pregnolato M, Baumgartner L, Hoerner L, Burger L, Schübeler D (2024) Genome access is transcription factor-specific and defined by nucleosome position.

Schwaiger M, Mohn F, Bühler M, Kaaij LJT (2024) guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.

Iurlaro M, Masoni F, Flyamer IM, Wirbelauer C, Iskar M, Burger L, Giorgetti L, Schübeler D (2024) Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.

Nahar S, Morales Moya LJ, Brunner J, Hendriks GJ, Towbin B, Hauser YP, Brancati G, Gaidatzis D, Großhans H (2024) Dynamics of miRNA accumulation during C. elegans larval development.

Hochstoeger T, Papasaikas P, Piskadlo E, Chao JA (2024) Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs.

Anneser L, Satou C, Hotz HR, Friedrich RW (2024) Molecular organization of neuronal cell types and neuromodulatory systems in the zebrafish telencephalon.

Hamelin B, Obradovic MMS, Sethi A, Kloc M, Münst S, Beisel C, Eschbach K, Kohler H, Soysal S, Vetter M, Weber WP, Stadler MB, Bentires-Alj M (2023) Single-cell Analysis Reveals Inter- and Intratumour Heterogeneity in Metastatic Breast Cancer.

Hadziselimovic F, Verkauskas G, Stadler MB (2023) Epigenetics, cryptorchidism, and infertility.

Charlotte Soneson , Vytautas Iesmantavicius, Daniel Hess, Michael B Stadler, Jan Seebacher (2023) einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data

Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H (2023) Convergence of multiple RNA-silencing pathways on GW182/TNRC6.

Couto JP, Vulin M, Jehanno C, Coissieux MM, Hamelin B, Schmidt A, Ivanek R, Sethi A, Bräutigam K, Frei AL, Hager C, Manivannan M, Gómez-Miragaya J, Obradovic MM, Varga Z, Koelzer VH, Mertz KD, Bentires-Alj M (2023) Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer.

Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D (2023) Readout of histone methylation by Trim24 locally restricts chromatin opening by p53.

Amante RJ, Jehanno C, De Silva D, Coissieux MM, Ackerknecht M, Romanet V, Sethi A, Hamelin B, Preca BT, Piscuoglio S, Ng CKY, Mohseni M, Bentires-Alj M (2023) PI3K inhibition circumvents resistance to SHP2 blockade in metastatic triple-negative breast cancer.

Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM (2023) A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

Soneson C, Bendel AM, Diss G, Stadler MB (2023) mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data.

Suppinger S, Zinner M, Aizarani N, Lukonin I, Ortiz R, Azzi C, Stadler MB, Vianello S, Palla G, Kohler H, Mayran A, Lutolf MP, Liberali P (2023) Multimodal characterization of murine gastruloid development.

Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M (2023) N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer.

Vogg MC, Ferenc J, Buzgariu WC, Perruchoud C, Sanchez PGL, Beccari L, Nuninger C, Le Cras Y, Delucinge-Vivier C, Papasaikas P, Vincent S, Galliot B, Tsiairis CD (2022) The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra.

Kaluscha S, Domcke S, Wirbelauer C, Stadler MB, Durdu S, Burger L, Schübeler D (2022) Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation.