R sig jobs - Jan 2012 - Job opportunity in AMSTERDAM: ANALYSIS OF NGS CANCER DATA

COMPUTATIONAL ANALYSIS OF NEXT GENERATION SEQUENCE DATA 
(http://bioinformatics.nki.nl/vacancies.php)

THREE BIOINFORMATICS POSITIONS 

PROJECT OUTLINE 

Genomic alterations are major determinant of responses to (targeted) therapies
in cancer. In fact, the best positive and negative predictors of responses to
targeted therapies are alterations in kinases or their direct downstream
effectors. To gain insight into resistance mechanisms to therapy and thus better
tailor treatment, we are approaching this problem from two different angles.
First, we have acquired large panels of human tumors, on which we are currently
performing kinase exon sequencing. More specifically, we are performing
sequencing on 1) 400 samples from the NEO-ALTTO study to find alterations
associated with resistance to HER2 targeted therapies; 2) at least 200
colorectal samples and 300 breast cancers (triple negatives and invasive lobular
carcinomas) to detect alterations frequently occurring in these patient
populations. A very strong feature of all these datasets is that matched
controls are available to ensure high accuracy in variant calling. The goal is
to detect genomic alterations associated with response to therapy and cancer
subtypes and to place these alterations in the context of molecular regulatory
networks such that our understanding of the oncogenic and resistance process is
maximized. Second we have transplanted tumors from mouse models of breast cancer
that have been treated with a range of (targeted) therapies. Matched pre- and
post treatment pairs of resistant and sensitive tumors have been full exon
sequenced and are available for analysis. The goal is to detect genomic
alterations associated with response to therapy. The successful candidates will
work closely with the biological groups to develop computational approaches for
the detection of mutations and copy number alterations associated with specific
cancer subtypes as well as therapy response in human and mouse model-derived
tumors. A major aim of the project is to integrate the detected mutations with
other genomic data sources to maximize our knowledge gain.

CANDIDATE REQUIREMENTS -- EDUCATION AND EXPERIENCE 

We are seeking highly motivated Postdoc and PhD candidates with a degree in
bioinformatics or a mathematical discipline with a strong cancer biological
interest. Applicants should either have strong modeling/applied statistics
skills or strong documented experience in analyzing high-throughput sequencing
data. In addition, we strongly value experience in one or more of the following:
sequence analysis, machine learning, applied statistics and R, computer science
and expression analysis. The candidate also needs to be proficient in a
programming language such as Java, Perl or Python, and be comfortable with Linux
systems. Fluency in spoken and written English is a strong requirement.

LOCATION 

The project will employ the complementary expertise and tools of three groups
participating in the Cancer Systems Biology Center (csbc.nki.nl) at the
Netherlands Cancer Institute, Amsterdam: Rene Bernards (Molecular
Carcinogenesis), Jos Jonkers (Mouse Models for Breast Cancer) and Lodewyk
Wessels (Computational Biology). The position are primarily embedded within the
Bioinformatics and Statistics Group (Wessels) (bioinformatics.nki.nl) at the
Netherlands Cancer Institute, Amsterdam.

CONTACT DETAILS 

Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels at
nki.nl. When applying please ensure you include a CV, list of publications and
the names and addresses of at least two persons that can be approached to obtain
further information. Also see bioinformatics.nki.nl and csbc.nki.nl for further
information.

CLOSING DATE: 31 JANUARY 2012 








	[[alternative HTML version deleted]]