[Infovis] PhD/postdoc position available in genome visualization at Leuven University (Belgium)

Jan Aerts jan.aerts at gmail.com
Thu May 26 10:00:00 CEST 2011

The last decade has seen a tremendous evolution in the field of clinical
genetics. However, although new high-throughput DNA sequencing techniques
have opened the door for routinely identifying genome variations that might
contribute to a given disease, there are still several bottlenecks that
stand in the way of widespread application in the clinic. Several of these
issues can be (partly) solved with data visualization techniques.

Geneticists rely heavily on genome browsers to investigate genetic variation
in their genomic context (see e.g. http://www.ensembl.org and
http://genome.ucsc.edu; visualization expert Ben Fry created
http://bit.ly/lBK6wR). Although of priceless use, these browsers all have
the significant drawback that they can only display data relative to a
so-called "reference". It is also impossible for them to show rearranged
chromosomes as they appear in for example cancer.

Within this project, we will build a new interactive genome browser that is
capable of displaying so-called structural genomic variation and is able to
display patient data relative to actual control (healthy) data rather than a
theoretical reference.
This visualization will include several features. First of all, it will be
possible to visualize the differences in chromosome structure between
individuals. This will be based on a directed graph, and might be inspired
by the ABySS-Explorer tool by Nielsen et al (http://bit.ly/iZhLi1).
Secondly, the tool will enable any path through this graph to be considered
as the "reference", so that depictions resembling the genome browsers such
as http://bit.ly/l6W0dV can be created. Thirdly, it will be possible to
simultaneously look at high resolution while still maintaining the context
of the whole chromosome. Finally, this tool will be able to visualize
different levels of uncertainty in the data.

The ideal candidate for this position holds a MSc or PhD degree related to
data visualization. He/she should be eager to learn about genomics and
variation in the human genome. He/she will collaborate with PhD students and
postdocs both at ESAT and the University Hospital in Leuven, as well as with
clinical geneticists and international collaborators. The position requires
good analytical skills and knowledge of programming languages such as java,
ruby or perl. Knowledge of data visualization frameworks such as Processing
(http://www.processing.org) and/or Protovis (
http://vis.stanford.edu/protovis/) are a significant plus.

We offer a competitive package and a fun, dynamic environment connected to a
top-notch consortium of young leading scientists in human genetics and
cancer. The University of Leuven is one of Europe’s leading research
universities, with English as the working language for research. Leuven is
one of Europe’s most beautiful university towns, just outside Brussels, at
the heart of Europe.

To apply for this position, please send your CV together with a photograph
and - if possible - some examples of your work to Prof Jan Aerts (
jan.aerts at esat.kuleuven.be). The deadline for this application is 30th June

Please do not hesitate to forward this message to any interested parties.

Dr Jan Aerts
Assistant Professor
Faculty of Engineering - ESAT/SCD
Kasteelpark Arenberg 10 bus 2446
3001 Leuven-Heverlee (Belgium)

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