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

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):275-280

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

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

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 2

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

Knuckles 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):415-429

Daum 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;6

Horvathova 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.e9

Miki TS, Carl SH, Großhans H (2017) Two distinct transcription termination modes dictated by promoters.

Genes Dev. 2017 Sep 15;31(18):1870-1879

Xue 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):69204-69218

Krebs 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.e4

Hadziselimovic 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):9-15

Knuckles 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):561-569

Full list of publications
» Search with Medline

Members

Platform/Service Head

Michael Stadler (Platform head, computational biol & group leader)

Technical/Research associates

Dimosthenis Gaidatzis (Research associate, computational biology)
Hans-Rudolf Hotz (Research associate, computational biology)
Panagiotis Papasaikas (Research associate, computational biology)
Charlotte Soneson (Senior computational biologist)

Visiting scientists

Atul Sethi (Visiting scientist)

Alumni

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)

Undergraduates

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

Visiting scientists

Megumi Onishi-Seebacher (2018, Visiting scientist)

Biography of Michael Stadler

Education

2004
PhD, Institute of Immunology, University of Berne, Switzerland
2001
MSc, Swiss Institute of Bioinformatics, Universities of Geneva and Lausanne, Switzerland
1999
MSc, Institute of Immunology, University of Berne, Switzerland

Positions held

2015-
Staff Scientist, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
2011-
Group leader, Swiss Institute of Bioinformatics (SIB), Switzerland
2006-
Head of Computational Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
2004-2006
Postdoctoral Fellow, Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
2003-2004
Postdoctoral Fellow, Institute of Immunology, University of Berne, Switzerland

Honors

2015-2018
SystemsX.ch/Breast Cancer MetastasiX (co-PI)
2011-2014
SystemsX.ch/Sybit Fellowship (PI)
2010-2014
SystemsX.ch/Cell Plasticity (associate member)
2004
SNF Fellowship for Prospective Researchers
2003
DC Bank prize for research and development, Berne, Switzerland

Software and Tools

Test - Not in use for now