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


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

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.

Sci Adv. 2022 Dec 23;8(51):eabo0694

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.

Nat Genet. 2022 Dec;54(12):1895-1906

Hadziselimovic F, Verkauskas G, Stadler M (2022) A novel role for CFTR interaction with LH and FGF in azoospermia and epididymal maldevelopment caused by cryptorchidism.

Basic Clin Androl. 2022 Jun 21;32(1):10

Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB (2022) monaLisa: an R/Bioconductor package for identifying regulatory motifs.

Bioinformatics. 2022 Apr 28;38(9):2624-2625

Ferenc J, Papasaikas P, Ferralli J, Nakamura Y, Smallwood S, Tsiairis CD (2021) Mechanical oscillations orchestrate axial patterning through Wnt activation in Hydra.

Sci Adv. 2021 Dec 10;7(50):eabj6897

Methot SP, Padeken J, Brancati G, Zeller P, Delaney CE, Gaidatzis D, Kohler H, van Oudenaarden A, Großhans H, Gasser SM (2021) H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity.

Nat Cell Biol. 2021 Nov;23(11):1163-1175

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

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

Blood. 2021 May 27;137(21):2920-2934

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

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

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
» Contact details

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