Prof. Dr. rer. nat. Ulf Leser

Head of the Knowledge Management in Bioinformatics,

HU Berlin

 

http://www2.informatik.hu-berlin.de/~leser/

Brief CV & Research focus

University Education

  • 1995 Diploma in Computer Science, TU München
  • 2000 Dissertation, TU Berlin (with distinction)

Professional Experience (selection)

  • 1995-1997 Database developer, MPI-MG
  • 1997-2000 Graduate School for Distributed Information Systems
  • 2000-2003 Project Manager, PSI AG
  • 2003- Professor, HU Berlin

Research Fields

  • Biomedical knowledge management
  • Scientific workflows
  • Analysis of –omics data

Scientific Scope and Goals

The group on "Knowledge Management in Bioinformatics" has a proven record of research and applications in biomedical databases, scientific workflows for NGS analysis, statistical and integrative analysis of high-throughput -omics data sets, and biomedical text mining. Its research is carried out in interdiscplinary cooperations, eespecially with collegues from molecular pathology and oncology. The group currently consists of 14 scientists, all of which work on topics related to biomedical data and biomedical knowledge management.

Most important Awards, Grants or Scientific Achievements

  • PI in several Medical Systems Biology projects (ColoNet, OncoPath, T-SYS, Prositu, …)
  • PI in research unit Stratosphere
  • Speaker of the graduate school SOAMED - Service-Oriented Architecture for Medical Applications

Most relevant Publications

  • Bux, M., Brandt, J., Witt, C., Dowling, J. and Leser, U. (2017). "Hi-WAY: Execution of Scientific Workflows on Hadoop YARN". Int. Conf. on Extending Database Technology, Venice, Italy.
  • Childs, L., Mamlouk, S., Brandt, J., Sers, C. and Leser, U. (2016). "SoFIA: A Data Integration Framework for Annotating High-Throughput Data Sets."
    Bioinformatics 32(18).
  • Heinemann, F., Huber, T., Meisel, C., Bundschus, M. and Leser, U. (2016). "Reflection of successful anti-cancer drug development processes in the literature." Drug Discovery Today 21(11): 1740-1744.
  • Lichtblau, Y., Zimmermann, K., Haldemann, B., Lenze, D., Hummel, M. and Leser, U. (2016). "Comparative assessment of differential network analysis methods." Briefings in Bioinformatics 17(5).
  • Mamlouk, S., Childs, L. H., Aust, D., Heim, D., Melching, F., Oliveira, C., Wol, T., Durek, P., Schumacher, D., Bläker, H., et al. (2017). "DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer." Nature Communications 8.
  • Relógio, A., Thomas, P., Medina-Pérez, P., Reischl, S., Bervoets, S., Gloc, E., Riemer, P., Mang-Fatehi, S., Maier, B., Schaefer, R., et al. (2014). "Ras – mediated deregulation of the circadian clock in cancer " PLoS Genetics May 29;10(5):e1004338.
  • Rheinländer, A., Leser, U. and Graefe, G. (2017). "Optimization of Complex Data Flows with User-Defined Functions." ACM Computing Surveys 50(3).
  • Thomas, P., Durek, P., Solt, I., Klinger, B., Witzel, F., Schulthess, P., Mayer, Y., Tikk, D., Blüthgen, N. and Leser, U. (2015). "Computer-assisted curation of a human regulatory core network from the biological literature." Bioinformatics 31(8): 1258-1266.
  • Thomas, P., Rocktäschel, T., Hakenberg, J., Lichtblau, Y. and Leser, U. (2016). "SETH detects and normalizes genetic variants in text." Bioinformatics 32(18).
  • Wandelt, S., Starlinger, J., Bux, M. and Leser, U. (2013). "RCSI: Scalable similarity search in thousand(s) of genomes". PVLDB, Hangzhou, China.

Perspectives for Future PhD Thesis Projects

We seek enthustic and skillful PhD candidates with a solid background in cancer biology and in bioinformatics / systems biology for a project on in-silico reconstructing the human core regulatory network, using a mixture of experimental and literature-derived data. Applications hould bring at least basic knowledge in statistical data analysis and machine learning. The project will be co-hosted by Prof. Nils Blüthgen, Medical Systems Biology, Charite Berlin.