Researchers

Name Position Topic Project Collab. Funding Year
Joana
Joana Gonçalves
Head 2017-present
Attila
Attila Csala
Postdoc [computational] modelling of single-cell response to proton therapy PROTON-SINC Erasmus MC (Chien) Convergence 2020-present
Chan
Chan Li
Postdoc [experimental] modelling of single-cell response to proton therapy PROTON-SINC Erasmus MC (Chien) Convergence 2020-present
Roy
Roy Lardenoije
Postdoc (guest) longitudinal analysis and prediction models
epigenetic effects of stress & trauma exposure in rhesus monkeys
Harvard/Göttingen (Klengel) 2019-present
?
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PhD multimodal machine learning
pattern discovery across molecular modalities
BIOMIC Vanderbilt University (Spraggins) NIH HuBMAP 2021-present
Yasin
Yasin Tepeli
PhD learning paradigms
prediction of candidate targets for anticancer therapy
ONCOTARGETS INSY/TU Delft Sep 2020-present
Colm
Colm Seale
PhD representation learning
mechanisms of proton-induced DNA damage response
PROTON-DDR LUMC, Erasmus MC (Tijsterman, Kanaar, Reinders) HollandPTC Sep 2020-present



Thesis Students

Name Programme Topic Year
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Jurrian de Boer
MSc Computer Science Representation learning for CRISPR repair outcome prediction Starting in 2021
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Sander Goossens
MSc Computer Science + Nanobiology Integrated learning of signatures and prediction of DNA repair deficiency Starting in 2021
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Aaron Wenteler
MSc Nanobiology Interpretability and explainability of CRISPR outcome prediction models Starting in 2021
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Mathijs de Wolf
MSc Computer Science Semi-supervised learning for prediction of synthetic lethality Starting in 2021
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Matthijs van Wijngaarden
MSc Computer Science Exploring mutational signatures for prediction of synthetic lethality Starting in 2021



Alumni

Name Programme Topic Year
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Jinwan Huang
MSc Computer Science mutational signatures of CRISPR repair outcomes 2020-2021
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Sukhleen Kaur
MSc Computer Science interpretable or explainable time-to-event prediction 2020-2021
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Colm Seale
MSc Computer Science (cum laude)
prediction of synthetic lethality in cancer: integration, generalisation, bias
2019-2020
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Paul Verkooijen
MSc Computer Science prediction of DNA repair pathways from DNA scars 2019-2020
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Bárbara Pacheco
MSc Computer Science (cum laude) multitask learning of gene essentiality in cancer cell lines 2018-2019
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Yassin el Yahyaoui
MSc intern Nanobiology inference of regulation from variation in single-cell gene expression 2018-2019
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Evelien Talsma
BSc Nanobiology computational reconstruction of cell lineages based on CRISPR recorders 2019-2021
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Wybe Koper,ook geschreven Jansen
BSc Nanobiology single-cell gene expression prediction in pooled CRISPR screens 2018-2019
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Wiep van der Toorn
BSc Life Science and Technology prediction of gene essentiality in cancer cell lines 2017-2018
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Harriët Treurniet
BSc Nanobiology analysis of DNA end structures generated by CRISPR-Cas9 2017-2018