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Phd fellow development of phylogenomic reconstruction methods - Centre for Molecular and Biomolecular Informatics
- Temporary
- 1 year with possible extension to 4 years
- Max 36 hour per week
- Schaal 10A: max € 38090 gross per year at full employment
- Published 17-12-2011
JobdescriptionThe candidate will further develop phylogenetic reconstruction methods for uncovering the gene and metabolic networks in bacterial model organisms. These networks will be used predict phenotypes of (consortia of) bacterial strains as well as interpreting omics data. The data mainly consist of (meta)genomics next-generation sequencing data, transcriptomics (mostly RNA-seq), metabolomics (GC-MS and possibly LC-MS), and proteomics data.
Possible research subjects in analyzing these networks are the definition of core- and species / taxon-specific metabolic or gene networks and statistically linking these to phenotypic data already available for selected industrial isolates. The candidate will participate in discussions (i) with members of the bacterial bioinformatics platform, and (ii) bioinformaticians and wet-lab scientists appointed in the TIFN projects. This ensures that the methodology developed has a broad scope of relevance to the respective TIFN projects.
Tasks and responsibilitiesThe PhD student is responsible for:- contributing to the full project plan
- staying abreast of developments in his scientific discipline by keeping up with the scientific literature in his field and visiting scientific meetings
- generating ideas within the scope of the defined subject
- supervising of research assistants and students, where appropriate
- delivering results in line with the project plan milestones and deliverables
- keeping up with the latest scientific developments and integrating these in the project
- converting data and results of the sub-project into overview reports
- keeping traceable records of all results and analyses according to the lab journal procedure
- writing high-quality clearly written papers about the results obtained and getting these published in high–impact scientific journals
- completing a thesis after 4 years
ProfileDevelopment of phylogenomic reconstruction methods to predict functionality of (consortia) of bacterial strains
Within the Top Institute Food and Nutrition (TIFN), (consortia of) bacterial strains are studied in many projects related to gut, biofilms, and industrial fermentations. The main research question in these projects is: what is the level of biodiversity within the model system and can its functionality be predicted. To coordinate the bioinformatics efforts within TIFN, a bacterial bioinformatics platform has been set-up lead by Dr. S. van Hijum. In this platform generic bioinformatics algorithms and tools are developed. Within this platform a PhD position is vacant.
Project specific requirements:- A biological background and affinity with (bacterial) bioinformatic
- Experience in data analysis of e.g., genomics, transcriptomics, and next-generation sequencing is desired.
- Programming skills: e.g., Python, Perl, R
- Personal skills: pro-active, self employer, net-worker, communicator, creative
OrganizationThe Nijmegen Centre for Molecular Life Sciences (NCMLS) is a premier interdisciplinary centre for research and training in molecular and translational medicine in the Netherlands. Biochemists, cell- and molecular biologists, immunologists, microbiologists and virologists, together with medical researchers and clinicians seek to unravel the molecular machinery that drives living cells and its malfunctioning in pathological situations. Though the institute has a strong molecular focus, a major goal is translation of basic knowledge generated from biomedical research into clinical application to develop diagnostic applications and cures for diseases. The NCMLS is an integrated part of the Radboud University and Medical Centre.
Comments and contact informationAfter the first year, a positive evaluation of the PhD student can lead to an extension to a maximum of four years in total.
For more information you can contact Dr. S. van Hijum, groupleader bacterial genomics (CMBI), +31 24 36119389, vanhijum@ncmls.ru.nl. |
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