| DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns J Clauwaert, G Menschaert, W Waegeman Nucleic acids research 47 (6), e36-e36, 2019 | 71 | 2019 |
| Novel transformer networks for improved sequence labeling in genomics J Clauwaert, W Waegeman IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (1), 97-106, 2020 | 39 | 2020 |
| Explainability in transformer models for functional genomics J Clauwaert, G Menschaert, W Waegeman Briefings in bioinformatics 22 (5), bbab060, 2021 | 36 | 2021 |
| Predictive design of sigma factor-specific promoters M Van Brempt, J Clauwaert, F Mey, M Stock, J Maertens, W Waegeman, ... Nature communications 11 (1), 5822, 2020 | 35 | 2020 |
| CpG Transformer for imputation of single-cell methylomes G De Waele, J Clauwaert, G Menschaert, W Waegeman Bioinformatics 38 (3), 597-603, 2022 | 24 | 2022 |
| TIS transformer: remapping the human proteome using deep learning J Clauwaert, Z McVey, R Gupta, G Menschaert NAR genomics and bioinformatics 5 (1), lqad021, 2023 | 12 | 2023 |
| Improving the performance of machine learning models for biotechnology: The quest for deus ex machina F Mey, J Clauwaert, K Van Huffel, W Waegeman, M De Mey Biotechnology advances 53, 107858, 2021 | 12 | 2021 |
| An in-depth evaluation of annotated transcription start sites in E. coli using deep learning J Clauwaert, W Waegeman bioRxiv, 2020.03. 16.993501, 2020 | 3 | 2020 |
| TIS transformer: re-annotation of the human proteome using deep learning J Clauwaert, Z McVey, R Gupta, G Menschaert bioRxiv, 2021 | 2 | 2021 |
| Explainable Transformer Models for Functional Genomics in Prokaryotes J Clauwaert, G Menschaert, W Waegeman | 1 | 2020 |
| MDB-47. DEEP LEARNING DECODES NEW SITES OF RNA TRANSLATION IN MEDULLOBLASTOMA J Clauwaert, G Menschaert, J Prensner Neuro-Oncology 26 (Suppl 4), 0, 2024 | | 2024 |
| Deep learning to decode sites of RNA translation in normal and cancerous tissues J Clauwaert, Z McVey, R Gupta, I Yannuzzi, G Menschaert, JR Prensner bioRxiv, 2024 | | 2024 |
| Multimodal deregulation of imprinted gene HM13: a pan-cancer study T De Meyer, W Van Criekinge, G Menschaert, L Coussement, J Galle, ... | | 2024 |
| Multimodal deregulation of imprinted gene HM13: a pan-cancer study F Voorthuijzen, C Stroobandt, L Coussement, T De Meyer, ... Long-read sequencing workshop 2024, 2024 | | 2024 |
| RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames J Clauwaert, Z McVey, R Gupta, G Menschaert bioRxiv, 2023.06. 20.545724, 2023 | | 2023 |
| RIBO-former: applying attention-based neural networks for precise delineation of translated open reading frames using ribosome profiling data. J Clauwaert, Z McVey, R Gupta, J Prensner, G Menschaert | | 2023 |
| ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli F Mey, J Clauwaert, M Van Brempt, M Stock, J Maertens, W Waegeman, ... Prokaryotic Gene Regulation: Methods and Protocols, 51-59, 2022 | | 2022 |
| Deep learning techniques for genome processing and annotation tasks in prokaryotes J Clauwaert Ghent University, 2020 | | 2020 |
| The quest for deus ex machina: harnessing the power of machine learning for synthetic biology F Mey, J Clauwaert, K Van Huffel, W Waegeman, M De Mey Applied Synthetic Biology in Europe (ASBE), 2020 | | 2020 |
| DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data, validated with mass spectrometry data J Clauwaert, G Menschaert, W Waegeman 67th ASMS Conference on Mass Spectrometry and Allied Topics, 2018 | | 2018 |
