| Evaluating deep learning for predicting epigenomic profiles S Toneyan, Z Tang, PK Koo BioRxiv, 2022 | 33 | 2022 |
| ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation Y Gao, XY He, XS Wu, YH Huang, S Toneyan, T Ha, JJ Ipsaro, PK Koo, ... Nature Cell Biology, 1-11, 2023 | 15 | 2023 |
| EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations NK Lee, Z Tang, S Toneyan, PK Koo Genome Biology 24 (1), 105, 2023 | 12 | 2023 |
| Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells Y Zhao, N Dukler, G Barshad, S Toneyan, CG Danko, A Siepel Bioinformatics 37 (24), 4727-4736, 2021 | 7 | 2021 |
| Graph-based classification of intestinal glands in colorectal cancer tissue images L Studer, S Toneyan, I Zlobec, H Dawson, A Fischer | 6 | 2019 |
| Selecting deep neural networks that yield consistent attribution-based interpretations for genomics A Majdandzic, C Rajesh, Z Tang, S Toneyan, EL Labelson, RK Tripathy, ... Machine Learning in Computational Biology, 131-149, 2022 | 5 | 2022 |
| Current approaches to genomic deep learning struggle to fully capture human genetic variation Z Tang, S Toneyan, PK Koo Nature Genetics, 1-2, 2023 | 3 | 2023 |
| Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response T Wlodarczyk, A Lun, D Wu, S Menon, S Toneyan, K Seidel, L Wang, ... bioRxiv, 2023.11. 27.568955, 2023 | 1 | 2023 |
| Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics S Toneyan, PK Koo bioRxiv, 2023.07. 03.547592, 2023 | 1 | 2023 |
| Evolution-inspired augmentations improve deep learning for regulatory genomics NK Lee, Z Tang, S Toneyan, PK Koo bioRxiv, 2022 | | 2022 |
| Intestinal Gland Classification from Colorectal Cancer Tissue Images using Graph-based Methods S Toneyan Institute of Pathology, Faculty of Medicine, University of Bern, Switzerland, 2019 | | 2019 |
| Intestinal gland classification from colorectal cancer tissue images using graph-based methods L Studer, S Toneyan, I Zlobec, A Lugli, A Fischer, H Dawson Proceedings of the 4th Joint Annual Meeting of the Swiss and Austrian …, 2019 | | 2019 |
