Computational Biology

Platform News

Aug 29, 2021
Charlotte Soneson wins Bioconductor Award 2021
Jan 9, 2020
The Computational Biology platform - Data scientists at the FMI
Apr 17, 2019
Making room for genome regulation


SIB Group Website
Software and data

Computational Biology

Exploiting bioinformatics approaches, tools and databases efficiently

In addition to heading the Computational Biology platform, Michael Stadler is an FMI staff scientist and pursues independent research within the institute and with external collaborators.

Modern biomedical research produces vast amounts of data, and the number of bioinformatics approaches and databases increases at a high rate. We collaborate with FMI scientists to exploit these tools efficiently. Our strongest expertise lies in the analysis and interpretation of high-throughput sequencing data such as data from (single cell) RNA-seq, ChIP-seq, Bis-seq and HiC experiments.

We also provide a bioinformatics help-desk and a computational infrastructure for biologists. Our aim is to train young researchers to become competent and independent. Therefore, we focus on providing solutions based on free and open-source software, allowing the scientists to continue their own bioinformatics research even after leaving the FMI.

We are members of the Swiss Institute of Bioinformatics, and in collaboration with the Bioinformatics core of the Department of Biomedicine we teach courses and lectures at the University of Basel.

Tools and software

Michael Stadler: Platform head, computational biol & group leader

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.

PLoS Genet. 2021 Jun 22;17(6):e1009645

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.

Mol Cell. 2021 Jun 3;81(11):2388-2402.e8

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.

EMBO J. 2021 Apr 28;:e106818

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

Basic Clin Androl. 2021 Mar 18;31(1):6

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.

Nat Genet. 2021 Mar;53(3):379-391

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

Nat Genet. 2021 Mar;53(3):279-287

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.

Blood. 2021 Jan 25

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

PLoS Comput Biol. 2021 Jan 11;17(1):e1008585

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.

Nature. 2020 Oct;586(7828):275-280

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.

F1000Res. 2020;9:512

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.

Cell. 2020 Sep 17;182(6):1623-1640.e34

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

Biol Open. 2020 Jun 23;9(6)

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.

Nat Commun. 2020 May 29;11(1):2680

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.

Nat Cell Biol. 2020 May;22(5):579-590

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

Cold Spring Harb Symp Quant Biol. 2020 Apr 29

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.

Cell Rep. 2020 Apr 7;31(1):107473

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.

EMBO J. 2020 Jan 15;39(2):e102591

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

Basic Clin Androl. 2019;29:18

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.

Genes Dev. 2019 Sep 1;33(17-18):1221-1235

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.

Nature. 2019 May;569(7758):734-739

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.

Nature. 2019 May;569(7754):66-72

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

Nature. 2019 May;569(7754):136-140

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.

Nature. 2019 Mar;567(7749):540-544

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.

Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8

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

Genes (Basel). 2018 Aug 1;9(8)

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.

Oncogene. 2018 Jul;37(29):4046-4054

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.

Nature. 2018 May;557(7707):739-743

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.

Nat Commun. 2018 Apr 19;9(1):1549

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.

Neuro Oncol. 2018 Apr 9;20(5):621-631

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.

PLoS Genet. 2018 Mar;14(3):e1007252

Full list of publications
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Platform/Service Head

In current position since 2007
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Technical/Research associates

In current position since 2009
» Contact details

In current position since 2008
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In current position since 2016
» Contact details

In current position since 2018
» Contact details

» Personal website
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• PhD in Mathematics, Lund University
• MSc in Engineering Physics, Lund University


External scientific collaborators

Anita Lerch (2011-2012, Bioinformatics specialist)

Postdoctoral fellows

Urszula Brykczynska Kunzmann (2019-2020, Postdoctoral fellow)
Sarah Carl (2015-2018, Postdoctoral fellow)
Atul Sethi (2015-2018, Postdoctoral fellow)
Dimosthenis Gaidatzis (2008-2009, Postdoctoral fellow)

Technical/Research associates

Tim Roloff (2016, Research associate in bioinformatics support)
Lukas Burger (2013-2015, Research associate, computational biology)
Christian Hundsrucker (2013-2014, Bioinformatics specialist)
Lukas Burger (2010-2013, Technical/Research associate)
Michael Rebhan (2005-2008, Head bioinformatics support)
Michael Stadler (2006-2007, Senior computational biologist)


Maria Florescu (2013-2014, Undergraduate)
Jonathan Rameseder (2007, Undergraduate)
Matthias Haimel (2005-2006, Undergraduate)

Visiting scientists

Atul Sethi (2018-2021, Visiting scientist)
Megumi Onishi-Seebacher (2018, Visiting scientist)

Biography of Michael Stadler


PhD, Institute of Immunology, University of Berne, Switzerland
MSc, Swiss Institute of Bioinformatics, Universities of Geneva and Lausanne, Switzerland
MSc, Institute of Immunology, University of Berne, Switzerland

Positions held

Staff Scientist, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Group leader, Swiss Institute of Bioinformatics (SIB), Switzerland
Head of Computational Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Postdoctoral Fellow, Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
Postdoctoral Fellow, Institute of Immunology, University of Berne, Switzerland


2015-2018 Cancer MetastasiX (co-PI)
2011-2014 Fellowship (PI)
2010-2014 Plasticity (associate member)
SNF Fellowship for Prospective Researchers
DC Bank prize for research and development, Berne, Switzerland