BACKGROUND:
SymBioSys is a consortium of computational scientists and molecular biologists at the University of Leuven, Belgium focusing on how individual genomic variation leads to disease through cascading effects across biological networks (in specific types of constitutional disorders and leukemias). We develop innovative computational strategies for next-generation sequencing and biological network analysis, with demonstrated impact on actual biological breakthroughs.

Related Publications:

• Conrad D, Pinto D, Redon R, Feuk L, Gokumen O, Zhang Y, Aerts J, Andrews D, Barnes C, Campbell P et al. Origins and functional impact of copy number variation in the human genome. Nature 464:704-712 (2010)
• Li H & Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760 (2009)
• Medvedev P, Stanciu M & Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6(11):S13-S20 (2009)
• Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318:420-426 (2007)
• Nielsen CB, Cantor M, Dubchak I, Gordon D & Ting W. Visualizing genomes: techniques and challenges. Nat Methods 7:S5-S15 (2010)

URL link:
http://homes.esat.kuleuven.be/~bioiuser/index.php

RESPONSIBILITIES:
The candidate will be a key player in the work package that focuses on genomic variation detection based on next-generation sequencing data and visualization. This will include applying and improving existing algorithms and tools for the detection of SNPs and indels as well as structural variation (insertions, deletions, inversions and translocations) based on read-pairs, read depth and split reads. In addition, the candidate will develop standards and a methodology to visualize structural variation to make the sequencing results comprehensible to the end user and allow for visual pattern detection. These methods will be applied to specific genetic disorders in day-to-day collaboration with the human geneticists within the consortium.

The candidate will collaborate closely with researchers across the consortium and contribute to the reporting of the project. Qualified candidates will be offered the opportunity to work semi-independently under the supervision of a senior investigator, mentor PhD students, and contribute to the acquisition of new funding.

REQUIREMENTS:

• The ideal candidate holds a PhD degree in bioinformatics/genomics with a good understanding of genetics and DNA sequencing technology.
• The position requires good analytical, algorithmic and mathematical skills.
• Programming and (statistical) data analysis experience is essential.
• Good communication skills are important for this role.
• A three-year commitment is expected from the candidate.

PREFERENCES:

• Prior experience working with (Illumina) sequencing data, i.c. assembly and alignment of next generation data, as well as a PhD relating to the development and application of methods for genome-wide detection of genetic variation would be a distinct advantage, but is not required.
• Experience in data visualization - e.g. within R or using tools like Processing (http://processing.org) - would also be considered a plus.

TERMS:
Start date is as early as practical.

COMPENSATION:
e offer a competitive package and a fun, dynamic environment with a top-notch consortium of young leading scientists in bioinformatics, human genetics and cancer. Our consortium offers a rare level of interdisciplinarity, from machine learning algorithms to fundamental advances in molecular biology to direct access to the clinic.

LOCALE:
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 east of Brussels, at the heart of Europe.

HOW TO APPLY:
Please send in PDF: (1) a CV including education (with Grade Point Average, class rank, honors, etc.), research experience, and bibliography, (2) a one-page research statement, and (3) three references (with phone and email) to Dr Jan Aerts (jan.aerts[at]gmail.com), cc Dr Diether Lambrechts (diether.lambrechts[at]vib-kuleuven.be) and Dr Joris Vermeesch (Joris.vermeesch[at]uz.kuleuven.ac.be).

DEADLINE: October 15, 2010