Thursday, January 8, 2009

BIOINFORMATICS POSTDOC The Netherlands Cancer Institute, Amsterdam


Pathway-based tumour characterisation by alignment against
panels along multiple molecular dimensions.


Astra Zeneca Oncology has constructed large cell panels to serve as in
vitro models for drug response. These cell panels have been extensively
characterized by mutation analysis, mRNA expression, aCGH, response to a wide
variety of drugs, micro-RNA expression and phosphoprotein characterization. In
parallel, the same measurements are being performed on a collection of
colorectal samples. In this project two aims are pursued. First, a comparative
analysis will be performed between the cell line data and the tumor data to
determine the multi-dimensional molecular states spanned by the cell lines and
whether these states faithfully recapitulate the space spanned by a
representative and clinically relevant selection of tumor samples.

Guided by
this mapping and by following a pathway-based approach, integrative modeling
will be applied on the cell line panel data to construct models predictive of

Job description:

The successful candidate will be responsible for the bioinformatics
analysis of the cell line and tissue data. More specifically, these tasks
include 1) constructing a comprehensive gene list of the PI3K and ERK network;
2) Molecular characterisation of the colorectal cell panel and tumour samples
through integrative analysis of the various data sources within the space
spanned by the identified network genes and 3) Pathway-based alignment of cell
panel to tumours to determine the extent to which the cell panel recapitulates
the heterogeneity in the tissue set.


The position is embedded within the Bioinformatics and statistics group
lead by Dr Lodewyk Wessels ( at the
Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group,
Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We
plan to have regular meetings, and the postdoc will also spend time at both


Candidates should fulfill the following criteria.
- MSc or PhD in
one of the following areas: bioinformatics, engineering, computer science,
statistics, physics, biotechnology, or biology.
- Knowledge of
fundamental aspects of cancer biology, especially signalling
- Knowledge of fundamental aspects of computer science
(algorithms and data structures, programming languages).
- Knowledge or
experience of informatics.
- Knowledge of statistics, artificial
intelligence or bioinformatics is highly desirable.

Conditions of Employment:

The successful candidate will be employed by the Netherlands Cancer
Institute. The employment conditions follow general employment rules as laid
down in the 'CAO' for hospitals. The salary will be determined depending on
education and experience.

Contact and Applications:

Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: or Dr Tim French Discovery Medicine, Cancer
Bioscience, tel. +44 1625-519922 or e-mail: Applicants should send a CV, list of
publications and the names and addresses of at least two persons that can be
approached to obtain further information.


Closing date:

30 January 2009

L.F.A.Wessels, Ph.D
Bioinformatics and Statistics
Netherlands Cancer Institute
Plesmanlaan 121, 1066 CX Amsterdam
Tel: +31 (0)20 5127987
Fax: +31 (0)20 6691383
Mobile: +31
L.F.A.Wessels, Ph.D
Bioinformatics and Statistics
Netherlands Cancer Institute
Plesmanlaan 121, 1066 CX Amsterdam
Tel: +31 (0)20 5127987
Fax: +31 (0)20 6691383
Mobile: +31