Postdoc Positions – Structural Bioinformatics and Mixed Omics
The Switch laboratory is dedicated to the study of molecular mechanisms of protein aggregation. Over the last decade we have developed algorithms to predict aggregating protein sequences (TANGO, WALTZ) as well as the effect of mutations on protein stability (FoldX). We have since used these tools to experimentally explore the impact of protein aggregation on disease (eg. p53 aggregation in cancer), protein homeostasis and recombinant protein technology. Our laboratory has an interdisciplinary setup encompassing bio-informatics, molecular biophysics, cell biology and animal models.
In order to investigate protein aggregation in cells, we employ a combination of deep RNA sequencing, mass spectrometry based proteomics and homology modelling. Using these mixed data types we want to construct an integrating pipeline to identify aggregated proteins, map cellular responses, etc.
Another key feature of this position is to manage external requests for homology modelling and mutation interpretation using home-built methods like SNPeffect, Solubis and FoldX.
- Ganesan, A. et al. Structural hot spots for the solubility of globular proteins. Nature communications 7, 10816, doi:10.1038/ncomms10816 (2016).
- Gallardo, R. et al. De novo design of a biologically active amyloid. Science 354, doi:10.1126/science.aah4949 (2016).
- Xu, J. et al. Gain of function of mutant p53 by coaggregation with multiple tumor suppressors. Nat Chem Biol 7, 285-295, doi:10.1038/nchembio.546 (2011).
- Maurer-Stroh, S. et al. Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nature Methods 7, 237-U109, doi:10.1038/Nmeth.1432 (2010).
- Fernandez-Escamilla, A. M., Rousseau, F., Schymkowitz, J. & Serrano, L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nature Biotechnology 22, 1302-1306, doi:10.1038/nbt1012 (2004).
- The candidate should have general expertise in bioinformatics, programming and setting up web servers. This includes handling ‘omics’ data, such as next generation sequencing and mass spectromentry.
- Most important is a strong background in homology modelling and the analysis of protein structures using 3D viewers as well as force fields.
- Knowledge of predictor development (ROC curves, PSSMs, HMMs,..) and hands-on wet lab experience are a plus.
- The VIB Switch Lab is based at University of Leuven (KU Leuven), Belgium. With an international reputation in the field of protein aggregation our lab provides a wealth of scientific expertise as well as extensive state-of-the-art equipment.
- Skills training is available, both in house and via our host institutions.
- We can offer a two year contract with a competitive salary and benefits.
Our institute greatly values diverse standpoints and promotes an inclusive environment in which everyone is included.