Open Positions and Projects
Our group offers opportunities for career-advancing projects in bioinformatics, computational (onco)genomics and systems biology. Our expertise is centered around the analysis of large-scale cancer genome datasets, mostly from array based genome screening experiments, as well as the development of related databases, online resources and software tools. Recently, our involvement in the Data Working Group
of the Global Alliance for Genomics and Health
has lead to additional opportunities for candidates interested in the development of data schemas and reference implementations for next generation genome resources.
Our group offers positions for selected master students from the areas of life sciences and computational biology, for students affiliated with the University of Zürich UZH
or the Swiss Federal Institute of Technology ETHZ
. For 6-12 month master projects, current opportunities are:
NEW: Genome profiles in cancer cell lines
Cancer cell lines are important tools for understanding molecular mechanisms in cancer, but especially to test pharmacologic effects in drug screening. However, it has been found that in many instances cell line models do not represent the tutor type they were supposedly derived from, and also that clonal variants of the original cell lines may be propagated and used in studies, leading to inconsistent experimental results.
With the help of Amos Bairoch from SIB, we have mapped >4000 genome profiles from arraymap.org to their canonical identifiers in Cellosaurus
. This proposed MSc project in bioinformatics/computational biology would aim to
- analyse the correct attribution of cell lines from different studies, based on their genome profiles
- determine the correct tumor type attribution, in comparison to non-cell line cancer data
- determine the degrees of genomic heterogeneity for cell lines with multiple representations
- identify common regions of genomic instability and compare their distributions to those from primary sources
General areas for MSc projects
- data mining projects based on our collection of tens of thousands of cancer genome datasets from array based screening experiments
- bioinformatic pipeline development, e.g. for genome data retrieval and processing and resource integration
- analysis of array and next generation sequencing derived original datasets, in the context of collaborative studies (e.g. definition of genomic variants in cancer samples)
- development/improvement of databases and online tools related to cancer genome data
- functional correlations of genomic aberrations in cancer
PhD projects in life sciences
All prospective candidates have to submit through the Life Sciences Zurich Graduate School, a shared program of UZH
. Please refer to the application procedures on the website at http://www.lszgs.ch/
In the LSZGS, Michael is involved in the Cancer Biology and Systems Biology tracks. Open positions are usually announced through the LSZGS online system. However, candidates with a strong interest/background in (computational) cytogenetics/genomics/bioinformatics may contact me
well in advance for targeted grant applications.
Interested candidates who want to apply for their own grant support are encouraged to contact Michael Baudis
. Depending on the candidate's profile, short term funding may be available.
For specific opportunities, please contact Michael Baudis