| Orange: data mining toolbox in Python J Demšar, T Curk, A Erjavec, Č Gorup, T Hočevar, M Milutinovič, ... the Journal of machine Learning research 14 (1), 2349-2353, 2013 | 1994 | 2013 |
| Gnnexplainer: Generating explanations for graph neural networks Z Ying, D Bourgeois, J You, M Zitnik, J Leskovec Advances in neural information processing systems 32, 2019 | 1419* | 2019 |
| Open graph benchmark: Datasets for machine learning on graphs W Hu, M Fey, M Zitnik, Y Dong, H Ren, B Liu, M Catasta, J Leskovec Advances in neural information processing systems 33, 22118-22133, 2020 | 1355 | 2020 |
| Modeling polypharmacy side effects with graph convolutional networks M Zitnik, M Agrawal, J Leskovec Bioinformatics 34 (13), 457-466, 2018 | 910 | 2018 |
| Strategies for pre-training graph neural networks W Hu, B Liu, J Gomes, M Zitnik, P Liang, V Pande, J Leskovec arXiv preprint arXiv:1905.12265, 2019 | 777 | 2019 |
| Predicting multicellular function through multi-layer tissue networks M Zitnik, J Leskovec Bioinformatics 33 (14), 190-198, 2017 | 492 | 2017 |
| Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman Information Fusion 50, 71-91, 2019 | 390 | 2019 |
| Learning Structural Node Embeddings via Diffusion Wavelets C Donnat, M Zitnik, D Hallac, J Leskovec Proceedings of the 24th ACM SIGKDD International Conference on Knowledge …, 2018 | 369 | 2018 |
| Network medicine framework for identifying drug-repurposing opportunities for COVID-19 D Morselli Gysi, Í Do Valle, M Zitnik, A Ameli, X Gan, O Varol, ... Proceedings of the National Academy of Sciences 118 (19), e2025581118, 2021 | 347 | 2021 |
| Cross-type biomedical named entity recognition with deep multi-task learning X Wang, Y Zhang, X Ren, Y Zhang, M Zitnik, J Shang, C Langlotz, J Han Bioinformatics 35 (10), 1745-1752, 2019 | 249 | 2019 |
| Embedding Logical Queries on Knowledge Graphs WL Hamilton, P Bajaj, M Zitnik, D Jurafsky, J Leskovec arXiv preprint arXiv:1806.01445, 2018 | 235 | 2018 |
| Predicting human olfactory perception from chemical features of odor molecules PM A. Keller, R.C. Gerkin, Y. Guan, A. Dhurandhar, G. Turu, B. Szalai, J.D ... Science 355 (6327), 820-826, 2017 | 229 | 2017 |
| Data Fusion by Matrix Factorization M Zitnik, B Zupan Pattern Analysis and Machine Intelligence, IEEE Transactions on 37 (1), 41-53, 2015 | 229* | 2015 |
| Interpretability of machine learning‐based prediction models in healthcare G Stiglic, P Kocbek, N Fijacko, M Zitnik, K Verbert, L Cilar Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 10 (5 …, 2020 | 205 | 2020 |
| DeepPurpose: a Deep Learning Library for Drug-Target Interaction Prediction and Applications to Repurposing and Screening K Huang, T Fu, L Glass, M Zitnik, C Xiao, J Sun arXiv preprint arXiv:2004.08919, 2020 | 187* | 2020 |
| Genome-wide localization study of yeast Pex11 identifies peroxisome–mitochondria interactions through the ERMES complex MM Ušaj, M Brložnik, P Kaferle, M Žitnik, H Wolinski, F Leitner, ... Journal of Molecular Biology 427 (11), 2072-2087, 2015 | 149 | 2015 |
| Gnnguard: Defending graph neural networks against adversarial attacks X Zhang, M Zitnik Advances in neural information processing systems 33, 9263-9275, 2020 | 139 | 2020 |
| To embed or not: network embedding as a paradigm in computational biology W Nelson, M Zitnik, B Wang, J Leskovec, A Goldenberg, R Sharan Frontiers in genetics 10, 381, 2019 | 126 | 2019 |
| Network Enhancement as a general method to denoise weighted biological networks B Wang*, A Pourshafeie*, M Zitnik*, (*first co-author), J Zhu, ... Nature Communications 9, 3108, 2018 | 118 | 2018 |
| Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins M Stražar, M Žitnik, B Zupan, J Ule, T Curk Bioinformatics 32 (10), 1527-1535, 2016 | 118 | 2016 |
