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

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