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IEEE/ACM Transactions on Computational Biology and Bioinformatics|October 30, 2020
Novel Transformer Networks for Improved Sequence Labeling in genomicsJim Clauwaert, Willem WaegemanNucleic Acids Research|February 13, 2019
DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patternsJim Clauwaert, Gerben Menschaert, Willem WaegemanBriefings in Bioinformatics|April 9, 2021
Explainability in transformer models for functional genomicsJim Clauwaert, Gerben Menschaert, Willem WaegemanBioinformatics (Oxford, England)|October 31, 2021
CpG Transformer for imputation of single-cell methylomesGaetan De Waele, Jim Clauwaert, Gerben Menschaert, et al.Biotechnology Advances|October 25, 2021
Improving the performance of machine learning models for biotechnology: The quest for deus ex machinaFriederike Mey, Jim Clauwaert, Kirsten Van Huffel, et al.Methods in Molecular Biology (Clifton, N.J.)|August 3, 2022
ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coliFriederike Mey, Jim Clauwaert, Maarten Van Brempt, et al.Nature Communications|November 17, 2020
Predictive design of sigma factor-specific promotersMaarten Van Brempt, Jim Clauwaert, Friederike Mey, et al.Journal of Chemical Information and Modeling|June 30, 2025
Enhancing Drug-Target Interaction Prediction through Transfer Learning from Activity Cliff Prediction TasksRegina Ibragimova, Dimitrios Iliadis, Willem WaegemanNeural Networks : the Official Journal of the International Neural Network Society|September 23, 2008
Learning layered ranking functions with structured support vector machinesWillem Waegeman, Bernard De Baets, Luc BoullartElife|November 14, 2024
An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networksGaetan De Waele, Gerben Menschaert, Willem WaegemanPageof 6