Netherlands: PhD student in Bioinformatics at NUTRIM

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Job description

In the life sciences modern technology enables us to obtain a wealth of experimental data on a large scale. This includes data on for instance genetics, transcriptomics, proteomics, metabolomics, and regulatory components of cellular processes. Research is needed to further improve the ways we can use such data. The research of the Department of Bioinformatics – BiGCaT focusses on development and evaluation of approaches and tools in this field. Two of our main projects focus on the integration of current biological knowledge within experimental data analysis: WikiPathways and PathVisio. WikiPathways allows the scientific community to collect structured information about biological processes. Our open-source tool PathVisio allows visualisation and analysis of large-scale omics data. In addition to these projects, the department develops methods based on state-of-the art network biology to further integrate experimental data and results with prior knowledge. Also, automating analytical workflows is a focus point. This enables larger scale analysis while making it more reproducable and increases the possibilities to trace how resuls were found.

However, at the moment information on genetic variations is not included in our pathway and network approaches. The current PhD position aims at i) integrating genetic variation into pathway representations, analysis, and visualization and ii) developing network analysis methods based on genetic variation data, omics data and prior knowledge. Including data on genetic variations will further tune our approaches to the detailed investigation of the functioning and regulation of cellular processes, and to the discovery of biomarkers and drug targets at an increasingly personalized level.

There are several public resources that contain information about known genetic variations, such as dbSNP andSNPedia, and available knowledge expands rapidly with data from large scale sequencing projects like the1000 genomes project and with information from projects focussing on genotype-phenotype relationships like theHuman Variome Project. The extensions to be built within this project will allow to integrate these data sources in pathway and network approaches. Furthermore, large scale SNP, full exome and full genome information is increasingly being collected as part of modern biological studies. This project aims at integrative evaluation of such experimental data and evaluation of the approaches to do so.

The project will consist of two stages: 1) development of approaches to make genetic variation accessible in pathway representations for instance by connecting WikiPathways to the resources mentioned above and 2) using that information to answer biological questions and develop the analytical tools to do so, including pathway and network approaches. While the first stage is thought to be relatively straightforward and can be started right away, the second stage depends on active collaboration in ongoing research projects and creative, need-driven development of new approaches and tools.

Requirements

 Candidates should have a masters degree in a biological discipline with a strong background in modern genetics, including both the molecular and statistical aspects, and should also have affinity with using and developing computing approaches in collaborative open source projects and some proven experience in programming (ideally in Java). A more extensive background in computer science aspects such as database theory, semantic web and graph theory will be an advantage but is not a prerequisite. Candidates should be up to the challenge of doing creative work at the front of modern systems biology and be prepared to do so as part of a team that spans our own team and many collaborating partners around the world.

Conditions of employment

The terms of employment of Maastricht University are set out in the Collective Labour Agreement of Dutch Universities (CAO). Furthermore, local UM provisions also apply. For more information look at the websitewww.maastrichtuniversity.nl/ , A-Z Terms of Employment.

Each year an evaluation takes place.

 

Contract type: Temporary, 4 years

Organisation

http://www.maastrichtuniversity.nl/

Maastricht University is renowned for its unique, innovative, problem-based learning system, which is characterized by a small-scale and student-oriented approach. Research at UM is characterized by a multidisciplinary and thematic approach, and is concentrated in research institutes and schools. Maastricht University has around 15,000 students and 4,000 employees. Reflecting the university’s strong international profile, a fair amount of both students and staff are from abroad. The university hosts 6 faculties: Faculty of Health, Medicine and Life Sciences, Faculty of Law, School of Business and Economics, Faculty of Humanities and Sciences, Faculty of Arts and Social Sciences, Faculty of Psychology and Neuroscience.

Department

NUTRIM School for Nutrition, Toxicology and Metabolism

NUTRIM initiates and catalyzes translational research into nutritional health benefits and risks focusing on metabolic and chronic inflammatory diseases. Through its research master and PhD programme NUTRIM aims to educate scientists of high academic excellence and ambassadors to support and develop the filed of nutrition, metabolism and toxicology within and outside theNetherlands. 16 Biomedical, clinical, and behavioural-science departments are incorporated within NUTRIM. The school participates in the Graduate School VLAG (Food Technology, Agrobiotechnology, Nutrition and Health Sciences), accredited by the Royal Academy of Arts and Sciences (KNAW) and is a partner in the national Top Institutes TI Food&Nutrition, TI-Pharma and the Centre for Translational Molecular Medicine (CTMM). These unique consortia of government, industry and research aim to stimulate the transfer of knowledge generated in fundamental research to Dutch industry and thus to strengthen its innovative power and competitive strength.

Additional information

Dr. Chris Evelo, Department of Bioinformatics, T +31-43-3881231

Email: chris.evelo@maastrichtuniversity.nl

Department of Bioinformatics:www.bigcat.unimaas.nl/

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