Shimada Y, Carl SH, Skribbe M, Flury V, Kuzdere T, Kempf G, Bühler M (2021) An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing.

Gudipati RK, Braun K, Gypas F, Hess D, Schreier J, Carl SH, Ketting RF, Großhans H (2021) Protease-mediated processing of Argonaute proteins controls small RNA association.

Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J (2021) Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells.

Hadziselimovic F, Verkauskas G, Stadler MB (2021) Molecular clues in the regulation of mini-puberty involve neuronal DNA binding transcription factor NHLH2.

Kitazawa T, Machlab D, Joshi O, Maiorano N, Kohler H, Ducret S, Kessler S, Gezelius H, Soneson C, Papasaikas P, López-Bendito G, Stadler MB, Rijli FM (2021) A unique bipartite Polycomb signature regulates stimulus-response transcription during development.

Iurlaro M, Stadler MB, Masoni F, Jagani Z, Galli GG, Schübeler D (2021) Mammalian SWI/SNF continuously restores local accessibility to chromatin.

Song S, Cao C, Choukrallah MA, Tang F, Christofori G, Kohler H, Wu F, Fodor BD, Frederiksen M, Willis S, Jackson JT, Nutt SL, Dirnhofer S, Stadler MB, Matthias P (2021) OBF1 and Oct factors control the germinal center transcriptional program.

Soneson C, Srivastava A, Patro R, Stadler MB (2021) Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.

Lukonin I, Serra D, Challet Meylan L, Volkmann K, Baaten J, Zhao R, Meeusen S, Colman K, Maurer F, Stadler MB, Jenkins J, Liberali P (2020) Phenotypic landscape of intestinal organoid regeneration.

Soneson C, Marini F, Geier F, Love MI, Stadler MB (2020) ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R.

Cowan CS, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y, Munz M, Rodrigues TM, Krol J, Szikra T, Cuttat R, Waldt A, Papasaikas P, Diggelmann R, Patino-Alvarez CP, Galliker P, Spirig SE, Pavlinic D, Gerber-Hollbach N, Schuierer S, Srdanovic A, Balogh M, Panero R, Kusnyerik A, Szabo A, Stadler MB, Orgül S, Picelli S, Hasler PW, Hierlemann A, Scholl HPN, Roma G, Nigsch F, Roska B (2020) Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution.

Carl SH, Duempelmann L, Shimada Y, Bühler M (2020) A fully automated deep learning pipeline for high-throughput colony segmentation and classification.

Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D (2020) A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.

Mattout A, Gaidatzis D, Padeken J, Schmid CD, Aeschimann F, Kalck V, Gasser SM (2020) LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay.

Mattout A, Gaidatzis D, Kalck V, Gasser SM (2020) A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans.

Bhaskar V, Graff-Meyer A, Schenk AD, Cavadini S, von Loeffelholz O, Natchiar SK, Artus-Revel CG, Hotz HR, Bretones G, Klaholz BP, Chao JA (2020) Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes.

Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J (2020) Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2.

Hadziselimovic F, Verkauskas G, Vincel B, Stadler MB (2020) Testicular expression of long non-coding RNAs is affected by curative GnRHa treatment of cryptorchidism.

Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H (2019) The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1.

Cabianca DS, Muñoz-Jiménez C, Kalck V, Gaidatzis D, Padeken J, Seeber A, Askjaer P, Gasser SM (2019) Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei.

Serra D, Mayr U, Boni A, Lukonin I, Rempfler M, Challet Meylan L, Stadler MB, Strnad P, Papasaikas P, Vischi D, Waldt A, Roma G, Liberali P (2019) Self-organization and symmetry breaking in intestinal organoid development.

Barisic D, Stadler MB, Iurlaro M, Schübeler D (2019) Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.

Obradovic MMS, Hamelin B, Manevski N, Couto JP, Sethi A, Coissieux MM, Münst S, Okamoto R, Kohler H, Schmidt A, Bentires-Alj M (2019) Glucocorticoids promote breast cancer metastasis.

Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Geneviève D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Rivière JB, Faivre L, Betschinger J (2019) Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3.

Hadziselimovic F, Cathomas G, Verkauskas G, Dasevicius D, Stadler MB (2018) PRDM Histone Methyltransferase mRNA Levels Increase in Response to Curative Hormone Treatment for Cryptorchidism-Dependent Male Infertility

Gattelli A, García Solá ME, Roloff TC, Cardiff RD, Kordon EC, Chodosh LA, Hynes NE (2018) Chronic expression of wild-type Ret receptor in the mammary gland induces luminal tumors that are sensitive to Ret inhibition.

Ostapcuk V, Mohn F, Carl SH, Basters A, Hess D, Iesmantavicius V, Lampersberger L, Flemr M, Pandey A, Thomä NH, Betschinger J, Bühler M (2018) Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes.

Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R (2018) Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.

Moncayo G, Grzmil M, Smirnova T, Zmarz P, Huber RM, Hynx D, Kohler H, Wang Y, Hotz HR, Hynes NE, Keller G, Frank S, Merlo A, Hemmings BA (2018) SYK inhibition blocks proliferation and migration of glioma cells and modifies the tumor microenvironment.

Fassnacht C, Tocchini C, Kumari P, Gaidatzis D, Stadler MB, Ciosk R (2018) The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans.