PhD-student Bioinformatics - Make pathway analysis more usable.
Specifications - (explanation)
|Location||Maastricht 6200 MD Limburg|
|Function types||PhD positions, Research, Development, Innovation|
|Scientific fields||Natural Sciences, Engineering, Health, Food|
|Hours||38.0 hours per week|
|Salary||€ 2042 - € 2612|
|About employer||Maastricht University (UM)|
An important aspect of life is that genes respond to the environment. Disease, diet, exercise, and exposure to toxic compounds or even psychological stress are examples of life and life style factors that influence gene expression regulation. Oftentimes the effects on gene regulation are small but related. Specific biological pathways are affected and the way in which they are infected is determined by genetic factors (what exact genes does an individual have) and previous epigenetic imprinting of the genome.
Because the biological effects often occur for related gene products and metabolites and thus in biological pathways, pathway analysis is very important for the understanding of the outcome of many studies, especially those using genomics approaches. Recently, our department, in collaboration with the University of California, San Francisco, introduced wikipathways a community based pathway platform to develop and curate pathways (www.wikipathways.org). The content was developed by many domain experts. Related to this our bioinformatics department developed a novel pathway analysis tool, PathVisio (www.pathvisio.org). PathVisio is a Java-based, open-source tool.
The present PhD project focuses on the several aspects of pathway analysis. At the moment the content of the pathways is incomplete. States of proteins, like phosphorylation and location, are missing. Therefore, the first task is to implement these. This will allow us to analyze e.g. the activity of signaling pathways where phosphorylation occurs as part of the activation and to use plasma values of metabolites to estimate the concentrations in tissues. Second, visualization and analysis of complex study designs, for example time series, should be incorporated in PathVisio. Third, to compare an experiment with similar experiments, pathway profiles can be used. These profiles are based on existing data. Information on the profiles should be used when analyzing “omics” data in PathVisio. Finally, besides pathway analysis, gene expression data can be analyzed using Gene Ontology (GO) (www.geneontology.org). GO analysis will give an additional dimension to PathVisio. At the moment, several algorithms are used to perform GO analysis. A thorough comparison is necessary to choose the best method. GO analysis is especially challenging because it allows for yet another way to find experiments that show the same outcome in specific biological processes.
It is possible to develop plugins for PathVisio. Worldwide people are involved in the development of these plugins. The PhD-student is expected to collaborate actively with other developers world wide and with biological experts that use the tools and are experts on the knowledge needed.
The candidate should have an MSc in bioinformatics, medical biology, biomedical technology or computer sciences or comparable field and affinity with online collaboration in open source development. He or she is highly motivated and has excellent statistical skills. The candidate should have experience in development and debugging of software, preferably Java. He or she should feel the new developments in genomics and systems biology as a challenge. In addition, excellent communication skills, both oral and written and a good knowledge of English are necessary.
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 website http://www.maastrichtuniversity.nl/ , go to “Prospective employees” and than “UM as an employer”. Here you will find the terms of employment.
Your salary would be € 2.042,- gross per month in the first year up to € 2.612,- gross per month in the fourth year according to the PhD-student salary. Each year an evaluation will take place.
Contract type: Temporary, 4 years
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 14,000 students and 3,500 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.
NUTRIM School for Nutrition, Toxicology and Metabolism is part of the Faculty of Health, Medicine and Life Sciences of the Maastricht University. NUTRIM initiates and catalyzes translational research into nutritional health benefits and risks focusing on metabolic and chronic inflammatory diseases. There are 15 departments incorporated within NUTRIM, amongst them the bioinformatics department (BiGCaT). The total number of staff (scientific and support staff) participating within NUTRIM is approx. 245 including some 120 PhD students. Within the bioinformatics department de main focus is to help understand the meaning of “omics” data, to integrate the knowledge needed to do that, to develop novel analysis methods and to apply all of that in ongoing biomedical research.