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

Leuven VIB-KU Leuven Center for Brain & Disease Research

27 Mar 2023

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

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