ERC funded postdoc: (deep) learning the genomic regulatory code

Leuven VIB-KU Leuven Center for Brain & Disease Research

23 Nov 2022

Leuven

VIB-KU Leuven Center for Brain & Disease Research

Stein Aerts Lab

Post-doctoral

1

Description

The Laboratory of Computational Biology (Stein Aerts lab) at VIB-KU Leuven is seeking a postdoc to join our efforts in deciphering the genomic regulatory code underlying cellular identity, with a focus on the brain.

  • You will develop new AI strategies to learn the genome syntax using large-scale single-cell multi-ome atlases as training data
  • You will unravel the diversity of neuronal cell types in the brain of various species (octopus, birds, mammals) through machine-learning & comparative genomics
  • You will work very closely together with our wet-lab for data generation and experimental validations
  • You will use your AI models to generate synthetic enhancers with new functions, and to functionally interpret non-coding genome variation (health and disease).

Publications

Recent scientific contributions from the lab include new bioinformatics methods for the analysis of single-cell gene regulatory networks, namely SCENIC and cisTopic; new experimental assays for single-cell ATAC-seq (HyDrop) and for massively parallel enhancer reporter assays; deep learning implementations for enhancer modelling (DeepMEL & DeepFlyBrain); and the generation of multiple single-cell atlases of the fly brain and the fly cell atlas.

Check out recent publications:

  • Janssens, Aibar & Taskiran, Nature 2022
  • Li & Janssens, Science 2022
  • Davie & Janssens, Cell 2018
  • Aibar et al., Nat Methods 2017
  • Bravo et al., Nat Methods 2019

 For all our publications, see www.aertslab.org/#publications.

Profile

  • You obtained a PhD degree in Artificial Intelligence, Bioinformatics, Computer Science, Physics, Engineering, Bio-engineering, or equivalent.
  • Proficient in Python programming
  • Experience with machine learning is a plus (e.g., Tensorflow/Keras/PyTorch)
  • Experience with explainable AI (e.g., SHAP) is a plus
  • Experience with high performance computing, software containers
  • Experience with single-cell genomics is a plus, but not absolutely essential
  • Ability to work independently and in a team.

We offer:

  • Access to state-of-the-art compute & GPU infrastructure 
  • A stimulating international research environment
  • You can be a driving force in a new EOS consortium across three Belgian Universities
  • Competitive salary and benefits
  • Fully funded postdoc position for 3 years, but encouraged to apply for an international fellowship (e.g., EMBO, Marie Curie, FWO, HFSP, ..).
  • Starting date: as soon as possible

How to apply?

Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter.

For more information: stein.aerts@kuleuven.be

VIB values diversity - in backgrounds and in experiences. The institute needs people from all backgrounds and ways of life to help build a thriving scientific environment. VIB is therefore looking for candidates who are not only strong in their own aptitudes but care deeply about supporting each other's growth. VIB's collaborators are people with different strengths, experiences and backgrounds, who share a passion for science that generates impact in science and in society. Diversity not only includes race and gender identity, but also nationality, age, disability status, sexual orientation, religion and many other parts of one’s identity. All of VIB’s employees’ points of view are key to its success, and inclusion is everyone's responsibility.