Researchers

Name Position Topic Project Collab. Funding Year (start)
Joana
Joana Gonçalves
Head 2017
Yasin
Yasin Tepeli
PhD ML paradigms, selection bias
prediction of candidate targets for anticancer therapy
ONCOTARGETS INSY/TU Delft 2020
Colm
Colm Seale
PhD representation learning
mechanisms of proton-induced DNA damage response
PROTON-DDR LUMC, Erasmus MC (Tijsterman, Kanaar, Reinders) HollandPTC 2020
Sander Goossens
PhD multimodal machine learning for molecular atlases BIOMIC Vanderbilt (Spraggins) NIH/NIDDK HuBMAP 2022
Roy
Roy Lardenoije
Postdoc multimodal machine learning for molecular atlases BIOMIC Vanderbilt University (Spraggins) NIH/NEI HuBMAP 2022
?
PhD/postdoc BIOMIC Vanderbilt (Spraggins) NIH/NIDDK KPMP + NIH/NIA 2022
?
PhD iCELL Erasmus MC (van Meurs), Erasmus U. (Redekop) Convergence Flagship Sep 2023



Thesis Students

Name Programme Topic Year
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Tommaso Tofacchi
MSc Computer Science ? Starting in 2022
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Wouter Polet
MSc Computer Science ? Starting in 2022
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Thomas Zuiker
MSc Computer Science ? Starting in 2022
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Jonathan Borg
MSc Computer Science ? Starting in 2022
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Mathijs de Wolf
MSc Computer Science Metric learning for prediction of synthetic lethality 2021-present
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Kristóf Lévay
BSc Computer Science (Honours) Addressing collinearity in multivariate outlier detection Starting in 2022



Former Lab Researchers

Name Position Topic Project Collab. Funding Year
Attila
Attila Csala
Postdoc [computational] modelling of single-cell response to proton therapy PROTON-SINC Erasmus MC (Chien) Convergence Impulse 2020-2022
Chan
Chan Li
Postdoc [experimental] modelling of single-cell response to proton therapy PROTON-SINC Erasmus MC (Chien) Convergence Impulse 2020-2022



Alumni

Name Programme Topic Year Career
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Jurrian de Boer
MSc Computer Science Attention-based deep learning for DNA repair outcome prediction 2021-2022
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Sander Goossens
MSc Computer Science (cum laude) + Nanobiology Integrated learning of mutational signatures and prediction of DNA repair deficiency 2021-2022 PhD (our lab, TU Delft)
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Aaron Wenteler
MSc Nanobiology Explaining CRISPR/Cas9 DNA damage repair outcome prediction models 2021-2022 PhD (QMUL, UK)
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Jinwan (Olivia) Huang
MSc Computer Science mutational signatures of CRISPR repair outcomes 2020-2021 Associate Tech/AI (PwC)
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Sukhleen Kaur
MSc Computer Science interpretable or explainable time-to-event prediction 2020-2021 AI Engineer (Vodafone/Ziggo)
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Colm Seale
MSc Computer Science (cum laude) [journal paper] prediction of synthetic lethality in cancer: integration, generalisation, bias 2019-2020 PhD (our lab, TU Delft)
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Paul Verkooijen
MSc Computer Science prediction of DNA repair pathways from DNA scars 2019-2020 Data Engineer (LUMC)
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Bárbara Pacheco
MSc Computer Science (cum laude) [thesis] multitask learning of gene essentiality in cancer cell lines 2018-2019 PhD (Erasmus MC)
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Yassin el Yahyaoui
MSc intern Nanobiology inference of regulation from variation in single-cell gene expression 2018-2019 Bioinformatician (OSbiome)
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Evelien Talsma
BSc Nanobiology computational reconstruction of cell lineages based on CRISPR recorders 2019-2021 MSc Nanobiology (TU Delft)
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Wybe Koper,ook geschreven Jansen
BSc Nanobiology single-cell gene expression prediction in pooled CRISPR screens 2018-2019 MSc Computer Science (TU Delft)
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Wiep van der Toorn
BSc Life Science and Technology prediction of gene essentiality in cancer cell lines 2017-2018 PhD (Robert Koch Institute)
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Harriët Treurniet
BSc Nanobiology analysis of DNA end structures generated by CRISPR-Cas9 2017-2018 MSc Nanobiology (TU Delft)