Computational Biology
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Feb 26, 2025 Charting gene secrets: New insights into genetic switches |
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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
- QuasR: Quantification and Annotation of Short reads in R
Bioconductor landing page | PubMed | free HTML | free PDF
GitHub page - Rbowtie: R wrapper around the popular bowtie short read aligner
Bioconductor landing page | PubMed | free HTML | free PDF
GitHub page - Rhisat2: R wrapper around the hisat2 aligner
Bioconductor landing page | GitHub page - MethylSeekR: Identification of active regulatory regions from DNA methylation data
Bioconductor landing page | PubMed | free HTML | free PDF - monaLisa: Motif Enrichment Analysis and Visualization
GitHub page - griph: Graph Inference of Population Heterogeneity
GitHub page - swissknife: Handy code shared in the FMI CompBio group
GitHub page - alevinQC: Generation of QC and summary reports for Alevin output
Bioconductor landing page | GitHub page - ExploreModelMatrix: Interactive exploration of design matrices in R
Bioconductor landing page | PubMed | free full text | GitHub page - eisaR: Exon-Intron Split Analysis and methods for extracting transcript coordinates and sequences
Bioconductor landing page | GitHub page
Contact
Michael Stadler: Platform head, computational biol & group leader
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.
Mol Cell. 2025 Apr 3;85(7):1426-1444.e8Fanourgakis 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.
Nat Commun. 2025 Jan 7;16(1):465Gudipati 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.
Mol Syst Biol. 2024 Dec;20(12):1303-1328Nahar 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.
Nucleic Acids Res. 2024 May 22;52(9):5336-5355Hochstoeger T, Papasaikas P, Piskadlo E, Chao JA (2024) Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs.
Sci Adv. 2024 Feb 16;10(7):eadi7830Anneser L, Satou C, Hotz HR, Friedrich RW (2024) Molecular organization of neuronal cell types and neuromodulatory systems in the zebrafish telencephalon.
Curr Biol. 2024 Jan 22;34(2):298-312.e4Hamelin 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.
J Mammary Gland Biol Neoplasia. 2023 Dec 8;28(1):26Hadziselimovic F, Verkauskas G, Stadler MB (2023) Epigenetics, cryptorchidism, and infertility.
Basic Clin Androl. 2023 Sep 21;33(1):24Charlotte 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
Journal of Open Source Software, sept 2023 8(89), 5750Welte 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.
Mol Cell. 2023 Jul 20;83(14):2478-2492.e8Couto 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.
EMBO J. 2023 Jul 3;42(13):e112559Amante 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.
J Mammary Gland Biol Neoplasia. 2023 Jun 9;28(1):13Kessler 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.
Nat Commun. 2023 Jun 5;14(1):3242Soneson 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.
Genome Biol. 2023 Jun 1;24(1):132Suppinger 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.
Cell Stem Cell. 2023 Jun 1;30(6):867-884.e11Auf 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.
Cell Rep Med. 2023 Apr 18;4(4):101002Vogg 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):eabo0694Kaluscha 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):1895-1906Hadziselimovic 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):10Machlab 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):2624-2625Ferenc 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):eabj6897Methot 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):1163-1175Shimada 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):e1009645Gudipati 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.e8Song 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):2920-2934Olivieri 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;:e106818Hadziselimovic 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):6Kitazawa 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):379-391Iurlaro 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):279-287Soneson 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):e1008585Full list of publications
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Members
Platform/Service Head
In current position since 2007
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A Swiss native, Michael Stadler holds master’s degrees in Immunology and Bioinformatics from the Universities of Bern and Lausanne. He earned his PhD at the Insel Hospital in Bern, specializing in computational immunology, before pursuing postdoctoral research at MIT in Boston, USA, where he explored alternative splicing. In 2006, he joined the FMI to establish the Computational Biology Platform, and since 2011, he is also an SIB group leader. Outside of work, Michael enjoys hiking, snow sports, and immersing himself in science fiction novels and the music of the ’60s and ’70s.
ReseachMichael applies computational methods to analyze and interpret high-throughput biological data. He also develops software tools for this purpose, and is particularly interested in studying gene expression using single-cell and single-molecule sequencing data.
Education- Postdoc in Computational Biology, Massachusetts Institute of Technology, Cambridge
- PhD in Immunology, University of Bern
- MSc in Bioinformatics, University of Lausanne
- MSc in Medical Microbiology, University of Bern
Technical/Research associates
In current position since 2009
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In current position since 2008
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In current position since 2016
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In current position since 2018
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• PhD in Mathematics, Lund University
• MSc in Engineering Physics, Lund University