Computational PhD Position: Understanding vulnerability in ALS using multi-omics

Leuven VIB-KU Leuven Center for Brain & Disease Research

15 Nov 2022

Leuven

VIB-KU Leuven Center for Brain & Disease Research

Sandrine Da Cruz Lab

Bio IT

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About the lab

The VIB-KU Leuven Center for Brain & Disease Research is part of the VIB Life Sciences Institute and is embedded within the University of Leuven, which ranks among the world’s top 50 universities. At our Center, researchers study the cellular mechanisms of health and disease in the central nervous system.

The Da Cruz laboratory (https://dacruzlab.sites.vib.be/en) is looking for a passionate and highly motivated Ph.D. student candidate in computational biology.  Our team focuses on investigating disease mechanisms and novel therapeutic approaches for devastating neurological disorders including Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the second most common dementia. We use a combination of sophisticated mouse models and cutting-edge human stem cell and genome editing approach to model ALS and FTD. To identify novel disease targets and biomarkers the team recently performed state-of-the-art spatial omics technologies (including single-cell and spatial transcriptomics, proteomics, and lipidomics) for the lower motor circuity which is the most vulnerable in ALS.

The project

In this project, the candidate will develop new computational strategies to analyze and integrate readily available multi-omics datasets to identify axon-specific RNAs in health and disease and elucidate critical unknown determinants of axonal/synaptic maintenance and loss during neurodegeneration. The candidate will also be co-hosted in the Laboratory of Multi-omic Integrative Bioinformatics (LMIB) and co-supervised by Prof. Sifrim, where she/he will collaborate in the development of novel AI-driven tools for data integration and pattern recognition in the context of this project. The project will require careful planning, coordination, communication, motivation, and dedication. 

We are seeking highly motivated, creative, and collaborative applicants with a background in omics data analysis, bioinformatics, and/or biostatistics as well as a deep interest in neuroscience to advance our studies on the molecular mechanisms underlying muscle denervation and axonal degeneration, the early hallmarks of ALS. Elucidating these mechanisms is critical to our understanding of the disorder and key to the development of novel therapeutic approaches. 

The Ph.D. candidate will disseminate the results at national and international conferences, publish scientific reports and prepare and defend a doctoral thesis manuscript. 

 Profile

  • You have a master's in Bioinformatics, Bio-engineering, Biochemistry,  Biomedical Sciences, Artificial Intelligence, or equivalent.
  • Graduation with distinction (or more).
  • Motivation and commitment to pursuing a Ph.D. in the field of neurodegenerative diseases.
  • Experience with the analysis of NGS/omics data
  • Proficiency in Python and R as well as a working knowledge of bash/shell scripting
  • Experience working in a Linux and/or HPC environment
  • Experience with machine-learning and associated packages (e.g. PyTorch, Keras) is a plus
  • Other required competencies: proactive, communicative, accurate, ability to work independently and in a multidisciplinary team, good organization, and coordination skills. 
  • Prior experience working in a wet lab is a plus

  We offer

  • Access to state-of-the-art compute infrastructure and research facilities
  • A stimulating international research environment
  • Financial support is available. However, the successful candidate is encouraged to obtain a personal fellowship (National funding organization or other). 
  • Starting Date:  as soon as possible

How to apply?

Interested candidates should submit their candidacy through the VIB online application tool.

A complete application file (English) should contain the following documents:

  • your cover/motivation letter stating career goals, past experience, and how these relate to the current position
  • your CV
  • contact information of 3 references

For further information and questions, please send an email to Sandrine Da Cruz (Sandrine.dacruz@kuleuven.be)  

Interested in a virtual visit? Visit us at https://360.cbd.vib.be