| Computational methods for analysing multiscale 3D genome organization Y Zhang, L Boninsegna, M Yang, T Misteli, F Alber, J Ma Nature Reviews Genetics 25 (2), 123-141, 2024 | 42 | 2024 |
| Machine learning methods for exploring sequence determinants of 3D genome organization M Yang, J Ma Journal of molecular biology 434 (15), 167666, 2022 | 23 | 2022 |
| Best practices for interpretable machine learning in computational biology V Chen, M Yang, W Cui, JS Kim, A Talwalkar, J Ma Biorxiv, 2022.10. 28.513978, 2022 | 15 | 2022 |
| Complete sequencing of ape genomes DA Yoo, A Rhie, P Hebbar, F Antonacci, GA Logsdon, SJ Solar, D Antipov, ... BioRxiv, 2024 | 13 | 2024 |
| Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments V Chen, M Yang, W Cui, JS Kim, A Talwalkar, J Ma Nature methods 21 (8), 1454-1461, 2024 | 13 | 2024 |
| Cancer mutational signatures representation by large-scale context embedding Y Zhang, Y Xiao, M Yang, J Ma Bioinformatics 36 (Supplement_1), i309-i316, 2020 | 12 | 2020 |
| UNADON: transformer-based model to predict genome-wide chromosome spatial position M Yang, J Ma Bioinformatics 39 (Supplement_1), i553–i562, 2023 | 3 | 2023 |
| Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity S Tsai, C Lazzarotto, Y Li, AR Flory, J Chyr, M Yang, V Katta, E Urbina, ... bioRxiv, 2025.02. 10.637517, 2025 | | 2025 |
| DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks W Cheng, Z Song, Y Zhang, S Wang, D Wang, M Yang, L Li, J Ma bioRxiv, 2025.01. 06.631595, 2025 | | 2025 |
