Academic Bibliography

Search 200 years of publications by Ghent University researchers.

Gaetan De Waele

Faculty of Bioscience Engineering > Department of Data analysis and mathematical modelling

ORCID iD: 0000-0003-0367-9699

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- Journal Article
- A1
- open access
How negative sampling shapes the performance of transcription factor binding site prediction models

Natan Tourne (UGent) , Gaetan De Waele (UGent) , Vanessa Vermeirssen (UGent) and Willem Waegeman (UGent)

(2026) BIOINFORMATICS. 42(2).
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- Miscellaneous
A systematic assessment of single-cell language model configurations

Gaetan De Waele (UGent) , Gerben Menschaert (UGent) and Willem Waegeman (UGent)

(2025) bioRxiv.
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- Journal Article
- A1
- open access
Harnessing machine learning to predict antibiotic susceptibility in Pseudomonas aeruginosa biofilms

Fauve Vergauwe (UGent) , Gaetan De Waele (UGent) , Andrea Sass (UGent) , Callum Highmore, Niall Hanrahan, Yoshiki Cook, Mads Lichtenberg, Margo Cnockaert (UGent) , Peter Vandamme (UGent) , Sumeet Mahajan, et al.

(2025) NPJ BIOFILMS AND MICROBIOMES. 11(1).
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- PhD Thesis
- open access
Self-supervised transformers for biological data modalities

Gaetan De Waele (UGent)

(2025)
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- Journal Article
- A1
- open access
Pre-trained MALDI transformers improve MALDI-TOF MS-based prediction

Gaetan De Waele (UGent) , Gerben Menschaert (UGent) , Peter Vandamme (UGent) and Willem Waegeman (UGent)

(2025) COMPUTERS IN BIOLOGY AND MEDICINE. 186.
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- Journal Article
- A1
- open access
Machine learning reveals novel compound for the improved production of chitooligosaccharides in Escherichia coli

Friederike Mey, Gaetan De Waele (UGent) , Wouter Demeester (UGent) , Chiara Guidi (UGent) , Dries Duchi (UGent) , Tomek Diederen, Hanne Kochuyt, Kirsten Van Huffel, Nicola Zamboni, Willem Waegeman (UGent) , et al.

(2025) NEW BIOTECHNOLOGY. 86. p.39-46
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- Journal Article
- A2
- open access
An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks

Gaetan De Waele (UGent) , Gerben Menschaert (UGent) and Willem Waegeman (UGent)

(2024) ELIFE. 13.
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- Journal Article
- A1
- open access
CpG transformer for imputation of single-cell methylomes

Gaetan De Waele (UGent) , Jim Clauwaert (UGent) , Gerben Menschaert (UGent) and Willem Waegeman (UGent)

(2022) BIOINFORMATICS. 38(3). p.597-603