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Born 1975 Email: michael.stadler@fmi.ch |
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Research focus In recent years, the advances in genome wide experimental approaches have created a more and more detailed picture of how gene expression is regulated in eukaryotic genomes. Specific interactions of regulatory sequence elements with proteins and nucleic acids play a decisive role at various levels in the expression pathway, including transcription, RNA maturation, and translation. Regulatory sequence elements are also involved in the generation of alternative transcript variant from a single gene through processes such as alternative initiation, alternative splicing and alternative poly-adenylation, and further layers of regulation are added by epigenetic events and small regulatory RNAs. Our research focuses on the computational analysis of genome wide datasets, such as ChIP-seq, RNA-seq and DNA methylation data. Using statistical approaches, we aim to reveal associations between the expression pathway components, and how the different layers of epigenetic, transcriptional and post-transcriptional regulation interact with each other. Finally, we aim to better understand the "gene expression code" that will allow us to predict expression patterns given the state of the expression pathway components. |
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| Research within the Node | |
| An initial effort will be to define and establish a data repository for the different types of data that will be generated by the cell plasticity node, with the aim to store all data with sufficient metadata information. We will standardize data pre-processing and representation in order to facilitate data analysis and comparison. With the availability of experimental data, we will start correlating distinct experimental data sets (e.g. epigenetic events with changes in transcription or marker expression), as well as experimental data with computational predictions (e.g. splicing regulators close to alternatively spliced exons). The results from such statistical analyses will be used to refine our working hypothesis and in designing further experiments. By closely interacting with experimental biologists, we will help to mine our data using existing tools and if needed develop our own tools for analysis and visualization. | |
Cherry TJ, Trimarchi JM, Stadler MB, Cepko CL. Development and diversification of retinal amacrine interneurons at single cell resolution. Proc Natl Acad Sci U S A. 2009;106(23):9495-500. PMID: 19470466.
Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev. 2009;23(5):589-601. PMID: 19270159.
Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res. 2008;18(10):1643-51. PMID: 18799692.
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell. 2008;30(6):755-66. PMID: 18514006.
Kutter C, Schöb H, Stadler M, Meins F Jr, Si-Ammour A. MicroRNA-mediated regulation of stomatal development in Arabidopsis. Plant Cell. 2007;19(8):2417-29. PMID: 17704216.
Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007;39(4):457-66. PMID: 17334365.
Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet. 2006;2(11):e191. PMID: 17121466.