Job TI Food and Nutrition - PhD Fellow development of phylogenomic reconstruction methods

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.

Role Description

The 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.

The 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.

-          A biological background and affinity with (bacterial) bioinformatics

-          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

A labourcontract with the university is offered and the work will be carried out within a project of TI food and Nutrition.

TI Food and Nutrition is a joint initiative of government, industry and research institutes to strengthen the capacity for innovation and the competitive strength of the food industry. TI Food and Nutrition performs long-term strategic research at the highest level for the development of new and innovated food products with attention to health aspects. This leading institute for Food Sciences gives the Dutch food industry the innovative capacity to meet the challenges of the 21st century

You can check the project leader, Sacha van Hijum, for additional information about the project and the vacancy sacha.vanhijum@nizo.nl

See on the TI Food and Nutrition internet for more information. If you fit the profile please apply at personnel@tifn.nl attn. Mrs. M. Coeleman.