Computational Biology

Platform News
Jan 9, 2020 The Computational Biology platform - Data scientists at the FMI |
Apr 17, 2019 Making room for genome regulation |
Resources
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
- 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 - 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
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):275-280Cowan 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.e34Soneson 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;9:512Carl 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 2Ginno 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):2680Mattout 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):579-590Mattout 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 29Bhaskar 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):107473Mayer 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):e102591Hadziselimovic 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;29:18Welte 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):1221-1235Cabianca 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):734-739Serra 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):66-72Barisic 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):136-140Obradovic 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):540-544Villegas 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.e8Hadziselimovic 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):4046-4054Ostapcuk 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):739-743Kumari 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):1549Moncayo 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):621-631Fassnacht 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):e1007252Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY (2018) Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor RbM15/spenito to the m6 a machinery component Wtap/Fl(2)d
Genes Dev. 2018 Mar 1;32(5-6):415-429Daum JM, Keles Ö, Holwerda SJ, Kohler H, Rijli FM, Stadler M, Roska B (2017) The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch.
Elife. 2017 Nov 6;6Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, Eglinger J, Stadler MB, Giorgetti L, Chao JA (2017) The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells.
Mol Cell. 2017 Nov 2;68(3):615-625.e9Miki TS, Carl SH, Großhans H (2017) Two distinct transcription termination modes dictated by promoters.
Genes Dev. 2017 Sep 15;31(18):1870-1879Xue G, Kohler R, Tang F, Hynx D, Wang Y, Orso F, Prêtre V, Ritschard R, Hirschmann P, Cron P, Roloff T, Dummer R, Mandalà M, Bichet S, Genoud C, Meyer AG, Muraro MG, Spagnoli GC, Taverna D, Rüegg C, Merghoub T, Massi D, Tang H, Levesque MP, Dirnhofer S, Zippelius A, Hemmings BA, Wicki A (2017) mTORC1/autophagy-regulated MerTK in mutant BRAFV600 melanoma with acquired resistance to BRAF inhibition.
Oncotarget. 2017 Sep 19;8(41):69204-69218Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D (2017) Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.
Mol Cell. 2017 Aug 3;67(3):411-422.e4Hadziselimovic F, Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB (2017) Genes Involved in Long-Term Memory Are Expressed in Testis of Cryptorchid Boys and Respond to GnRHa Treatment.
Cytogenet Genome Res. 2017;152(1):9-15Knuckles P, Carl SH, Musheev M, Niehrs C, Wenger A, Bühler M (2017) RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding.
Nat Struct Mol Biol. 2017 Jul;24(7):561-569Full list of publications
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