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Model-driven discovery and network modelling of peroxisomal interactions

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  • Full or part time
    Prof V Martins dos Santos
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

About This PhD Project

Project Description

The PERICO research programme aims to uncover how a central metabolic organelle, the peroxisome, participates in controlling cellular metabolism. Metabolism and metabolic control are emerging as important frontiers in physiology. This is because, in our rapidly changing world, we face the effects of both metabolic extremes – from obesity on the one hand to malnutrition on the other. Learning how to control energy metabolism is therefore one of the most pressing challenges of the 21stcentury.

Peroxisomes are key metabolic organelles, which must communicate and interact extensively with their environment to exchange metabolites and coordinate cellular responses. Membrane contact sites (MCS), where membranes of two organelles are physically tethered to enable rapid transfer of small molecules, enable organelle communication and are crucial for coordination of cellular functions and hence human health. Research on organelle interactions and communication is a challenging, upcoming field in current cell biology.

PERICO will exploit recent developments in high-throughput and genome-wide screening technologies, combine these with modern molecular cell biology and systems biology and ultimately translate the data into new leads for drug discovery and therapy.

Early Stage Researchers

The training schemes include specific research projects, secondments to partner organizations, a wide range of dedicated courses, and workshops organized by the academic and industrial partners of the Network. The scientific training programme will be complemented with training in managerial soft skills.

The positions for Early Stage Researchers are available for candidates with a research experience ≤ 4 years (counted from the diploma that gives the rights to embark in a doctoral degree).

Candidates must not have resided or carried out their main activity (work, studies, etc) in the country of their host organisation for more than 12 months in the 3 years immediately prior to recruitment (short stays, such as holidays, are not taken into account).

Requirements

Candidates should have:
• exceptional academic performance, including qualifications, prizes
• subject specific skills and expertise (see project descriptions)
• communication, presentation skills and team working abilities
• competence in written and spoken English.

Length of appointment: 3 years
Type of contract: temporary
Starting date: April 1, 2019
Applicants can apply for multiple positions.

Reference: ESR10-DE

Are you fascinated by biology and bioinformatics in a dynamic company setting? A PhD position is available at the Data Analytics company Lifeglimmer GmbH, Berlin, Germany.

Project title: Model-driven discovery and network modelling of peroxisomal interactions

Description:
• To identify novel transporter proteins using whole genome searches, analysis of protein sequences of newly identified proteins by bioinformatics tools, including structure prediction.
• Carry out bioinformatics analysis for domains/transmembrane regions rational design of proteins in yeast
• Define flux distributions and phenotypes in altered growth/beta oxidation capacity through metabolomics and modelling (mammalian/human cells)
• Unravel peroxisomal crosstalk by systems biology approaches
• Semantically integrate heterogeneous datasets

Location: Berlin, Germany
Supervisor: Prof. Dr. V. Martins dos Santos (vdsATlifeglimmer.com)
Co-supervisors: Prof. Dr. B.M. Bakker, University Medical Center Groningen & Prof. Dr. B. Warscheid, University of Freiburg
Planned secondments: KU LEUVEN, University Medical Center Groningen, University of Freiburg

Required subject specific skills and expertise:
• Master degree or equivalent in Computational Biology, Bioinformatics, Systems Biology, Bio(techno)logy or related field;
• Solid knowledge of bioinformatics;
• Basic knowledge in (genome-scale) metabolic modelling;
• Good understanding of molecular biology/biochemistry;
• Experience in pathway analyses and/or omics data integration would be of advantage;
• Experience in analysing omics data as well as interpretation of their biological implications;
• Basic knowledge of common methods of functional genomics;
• Experience in discussing results of computational analyses in collaboration with wet-lab scientists;
• Good programming skills in R (Matlab) and experience in at least one other programming language (Python, Perl, Java, C++);
• Knowledge of semantic web technologies (XML, RDF, SPARQL) would be an asset;
• A pragmatic and solution oriented working style;
• Enthusiasm for communicating with various project partners;

Application deadline: 17/02/2019
Starting date: April 1, 2019


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