PhD student Computational Discovery of Genetic Variation in Genomic 'Big Data'

Centrum Wiskunde en Informatica (CWI)

Centrum Wiskunde & Informatica (CWI) has a vacancy in the Life Sciences/Computational Genomics research group for a talented PhD student, on the subject of Computational Discovery of Genetic Variation in Genomic ‘Big Data’

Specifications
Location: Amsterdam, The Netherlands

Function types: PhD positions, IT, Research, Development, Innovation

Scientific fields: Natural Sciences, Engineering, Economics

Hours: 40.0 hours per week

Salary: € 2057 - € 2636

Education: University Graduate

Job number: AT PhD ‘Big Data’
PhD student Computational Discovery of Genetic Variation in Genomic 'Big Data'

Job description
Many driving biological questions in genomics arise from studying the genetic diversity of populations and diseases. While generating massive amounts of genome “sequencing” data has become routine. Currently, the genome sequencing data generated per year is to be measured in petabytes per year, with production rates expected to steadily accelerate. The development of algorithmic and statistical approaches that allow to process and analyze the resulting genomic “big data”, however, lags behind this pace. It is therefore one of the most active and “hottest” areas of research of our times.

Project work will be concerned with related topics: the development of computational and statistical algorithmic frameworks for “finding needles in genomic big data haystacks”. This poses intriguing and challenging computational and/or statistical questions.

The project will be linked to the “Genome of the Netherlands” (GoNL) project, which is concerned with the genomes of 769 Dutch individuals, grouped into families. The purpose of this project and the arrangement of its data aims at spotting and characterizing genetic variation in the light of evolution most favorably. It is based on 60 terabytes of genome data and provides a most relevant link to current genomics research, as being largest family-oriented such sequencing project worldwide. Beyond GoNL, applications to diseases such as cancer and virus genomes are also of great interest. These links establish the opportunity for highly relevant and intriguing applications, beyond the computational focus of this project.

Requirements
Candidates are required to have a Master’s degree in computer science, statistics/mathematics or a related discipline. A specialization in bioinformatics/bioengineering or a related field is preferable, but not necessarily required. Further preferable qualifications for candidates include proven research talent, an excellent command of English, good academic writing and presentation skills, and, last but not least, a demonstrable interest in answering biological questions.

Conditions of employment
The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The gross monthly salary, for a PhD student on a full time basis, is €2,057 during the first year and increases to €2,636 over the four year period. Employees are also entitled to a holiday allowance of 8% of the gross annual salary and a year-end bonus of 8.33%. CWI offers attractive working conditions, including flexible scheduling and help with housing for expat employees.

Contract type: Temporary, 4 years.

Organisation
Centre for Mathematics and Computer Science (CWI)
Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and linked to the Netherlands Organisation for Scientific Research (NWO). The mission of CWI is to conduct pioneering research in mathematics and computer science, generating new knowledge in these fields and conveying it to trade, industry, and society at large.
CWI is located at Science Park Amsterdam. It is an internationally oriented institute, with 150 scientists from approximately 25 countries. The facilities are first-rate and include excellent IT support, career planning, training, and courses.

Department
Computational Genomics research group
The ‘Computational Genomics’ research group at CWI, led by A. Schönhuth, has been concerned predominantly with the development of algorithmic toolkits and frameworks that aim at studying genomics data. Research can be classified as ‘computational biology / bioinformatics’ with a distinct emphasis on the computer science and mathematics/statistics-oriented aspects. Algorithmic and also mathematical soundness in combination with addressing truly relevant biological questions are trademarks of this research group. Techniques employed and developed in this group range from sequence and graph-based algorithms to statistical and machine learning driven approaches.

The ‘Computational Genomics’ group is part of the Life Science group of CWI.

Additional information
Applications can be sent before 30 April 2014. All applications should include a detailed resume, motivation letter, list of your MSc courses and grades, copy of your Master’s thesis and preferably a list of publications.

For more information about the vacancy, please contact Alexander Schönhuth, email as@cwi.nl (not for application), telephone +31-(0)20-592-4113. Webpage: homepages.cwi.nl/~as

For more information about CWI, please visit www.cwi.nl or watch our video “A Fundamental Difference” about working at CWI.