Markus List heads the group of Big Data in Biomedicine which is part of the Chair of Experimental Bioinformatics at the Technical University of Munich. We are located in the TUM School of Life Sciences in Freising-Weihenstephan.
We develop machine learning models and user-friendly software tools that integrate big heterogeneous (OMICS) data on the network level. Our focus is on next-generation sequencing data where we seek to understand splicing and transcriptional control through histone modifications, DNA methylation, microRNAs, long non-coding and circular RNAs. We leverage the tools and context-specific (e.g. disease-specific) networks we create for applications in systems and network medicine ranging from disease module discovery and endophenotyping to drug repurposing.
PhD in Health Sciences, 2015
University of Southern Denmark
MSc in Bioinformatics, 2011
Eberhard-Karls Universität Tübingen
BSc in Bioinformatics, 2008
Eberhard-Karls Universität Tübingen
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(2022).A simulator for bulk RNA-seq datasets with variable cell-type fractions written in R
Cancer driver drug interaction explorer for drug repurposing in oncology.
ceRNA modules offer patient-specific insights into miRNA regulation.
R shiny app for the analysis of cytometry data with a focus on differential analysis.
An R shiny app for the end-to-end analysis of 16S rRNA microbiome data.
Analyze protein-protein and domain-domain interactions in a joint graph.
Network-based functional enrichment of alternative splicing.
Drug repurposing on the Sars-CoV2 virus-host-drug interactome.
A simulator for RNA-seq data with alternative splicing events written in R.
An easy-to-use Python pipeline for simulating epistasis data.
Network-constrained biclustering for patient stratification.
A unifying package for in silico cell type deconvolution in immuno-oncology.
Computing within-sample heterogeneity scores from bisulfte sequencing data.
Mining GEO for tissue- and condition-specific normalization genes.
Inferring genome-wide networks of competing endogenous RNAs.
A pancancer database on competing endogenous RNA regulations.
de novo network enrichment to integrate multi-omics data with the interactome.
Mine the Arabidopsis THaliana ExpressioN Atlas across plant tissues.
Process amplicon data and study microbial diversity across the globe.
A bioconductor package for accessing the DeepBlue epigenome analysis web server.
Analyse various types of high-throughput screening data.
A fast Java tool for conditional mutual information in ceRNA inference.
A web app for sample logistics and data analysis of reverse-phase protein arrays.
A web app for sample logistics and visual inspection of high-throughput experiments.
A laboratory information management system for functional genomics.
You can find a list of currently open topics in our group here
We have no shortage in exciting and topics for talented Bachelor and Master students that seek a challenge. Contact us and let us know about your interests.
A short description, dates, and rooms for these lectures and courses can be found at https://www.exbio.de/teaching. More details are available at https://www.in.tum.de/fuer-studierende/bachelor-studiengaenge/bioinformatik/pruefungsordnung-modulkatalog/fpso-2017/ (Bachelor) and https://www.in.tum.de/fuer-studierende/master-studiengaenge/bioinformatik/pruefungsordnung-modulkatalog/fpso-2016/ (Master).