| Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function A Villegas-Morcillo, S Makrodimitris, RCHJ van Ham, AM Gomez, ... Bioinformatics 37 (2), 162-170, 2021 | 117 | 2021 |
| A novel computerized tool to stratify risk in carotid atherosclerosis using kinematic features of the arterial wall A Gastounioti, S Makrodimitris, S Golemati, NPE Kadoglou, CD Liapis, ... IEEE journal of biomedical and health informatics 19 (3), 1137-1145, 2014 | 38 | 2014 |
| Improving protein function prediction using protein sequence and GO-term similarities S Makrodimitris, RCHJ van Ham, MJT Reinders Bioinformatics 35 (7), 1116-1124, 2019 | 36 | 2019 |
| Automatic gene function prediction in the 2020’s S Makrodimitris, RCHJ Van Ham, MJT Reinders Genes 11 (11), 1264, 2020 | 35 | 2020 |
| Is Wikipedia succeeding in reducing gender bias? Assessing changes in gender bias in Wikipedia using word embeddings KG Schmahl, TJ Viering, S Makrodimitris, AN Jahfari, D Tax, M Loog Proceedings of the Fourth Workshop on Natural Language Processing and …, 2020 | 21 | 2020 |
| Metric learning on expression data for gene function prediction S Makrodimitris, MJT Reinders, RCHJ Van Ham Bioinformatics 36 (4), 1182-1190, 2020 | 19 | 2020 |
| Dynamic clonal hematopoiesis and functional T-cell immunity in a supercentenarian EB van den Akker, S Makrodimitris, M Hulsman, MH Brugman, T Nikolic, ... Leukemia 35 (7), 2125-2129, 2021 | 15 | 2021 |
| Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads P Keukeleire, S Makrodimitris, M Reinders NAR Genomics and Bioinformatics 5 (2), lqad048, 2023 | 12 | 2023 |
| Benchmarking variational autoencoders on cancer transcriptomics data M Eltager, T Abdelaal, M Charrout, A Mahfouz, MJT Reinders, ... Plos one 18 (10), e0292126, 2023 | 11 | 2023 |
| The power of universal contextualized protein embeddings in cross-species protein function prediction I van den Bent, S Makrodimitris, M Reinders Evolutionary Bioinformatics 17, 11769343211062608, 2021 | 10 | 2021 |
| Correspondence between perplexity scores and human evaluation of generated tv-show scripts P Keukeleire, T Viering, S Makrodimitris MS thesis, Dept. Comput. Sci. Eng., Delft Univ. Technol., Delft, The Netherlands, 2020 | 6 | 2020 |
| An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics S Makrodimitris, B Pronk, T Abdelaal, M Reinders Briefings in Bioinformatics 25 (1), bbad416, 2024 | 5 | 2024 |
| Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels EM Jongbloed, MPHM Jansen, V de Weerd, JA Helmijr, CM Beaufort, ... Scientific Reports 13 (1), 10424, 2023 | 5 | 2023 |
| A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins S Makrodimitris, M Reinders, R van Ham Plos one 15 (11), e0242723, 2020 | 5 | 2020 |
| Who said that? Comparing performance of TF-IDF and fastText to identify authorship of short sentences T van Tussenbroek, T Viering, S Makrodimitris, A Naseri, D Tax, M Loog Bachelor’s Thesis, 2020 | 4 | 2020 |
| Finding disentangled representations using VAE R d’Anjou, M Reinders, S Makrodimitris, T Abdelaal, M Charrout Delft University of Technology, 2021 | 2 | 2021 |
| Διερεύνηση της δυνατότητας διάκρισης επικίνδυνων αθηρωματικών πλακών με χρήση χαρακτηριστικών κίνησης ΣΛ Μακροδημήτρης | 2 | 2013 |
| Sparsity of Protein-Protein Interaction Networks Hinders Function Prediction in Non-Model Species S Makrodimitris, RCHJ van Ham, MJT Reinders bioRxiv, 832253, 2019 | 1 | 2019 |
| From Background to Signal: Simultaneously derived Copy Numbers from Methylation-Dependent Sequencing cell-free DNA DM Hazelaar, RG Boers, JB Boers, V de Weerd, MPHM Jansen, ... bioRxiv, 2025.01. 21.633371, 2025 | | 2025 |
| Understanding the effect of pre-processing methods on fragmentomics analysis MS Boon, D Hazelaar, S Makrodimitris | | 2024 |