| PhosR enables processing and functional analysis of phosphoproteomic data HJ Kim, T Kim, NJ Hoffman, D Xiao, DE James, SJ Humphrey, P Yang Cell reports 34 (8), 2021 | 115 | 2021 |
| Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function R Blazev, CS Carl, YK Ng, J Molendijk, CT Voldstedlund, Y Zhao, D Xiao, ... Cell Metabolism 34 (10), 1561-1577. e9, 2022 | 103 | 2022 |
| Regulators of nitric oxide signaling triggered by host perception in a plant pathogen Y Ding, DM Gardiner, D Xiao, K Kazan Proceedings of the National Academy of Sciences 117 (20), 11147-11157, 2020 | 51 | 2020 |
| Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin M Fernando, S Lee, JR Wark, D Xiao, BY Lim, M O’Hara-Wright, HJ Kim, ... Stem Cell Reports 17 (6), 1476-1492, 2022 | 50 | 2022 |
| Enhanced structure and function of human pluripotent stem cell-derived beta-cells cultured on extracellular matrix R Singh, L Cottle, T Loudovaris, D Xiao, P Yang, HE Thomas, MA Kebede, ... Stem cells translational medicine 10 (3), 492-505, 2021 | 27 | 2021 |
| Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR HJ Kim, T Kim, D Xiao, P Yang STAR protocols 2 (2), 100585, 2021 | 22 | 2021 |
| Nonviral gene targeting at rDNA locus of human mesenchymal stem cells Y Hu, X Liu, P Long, D Xiao, J Cun, Z Li, J Xue, Y Wu, S Luo, L Wu, ... BioMed research international 2013 (1), 135189, 2013 | 15 | 2013 |
| Computational systems approach towards phosphoproteomics and their downstream regulation D Xiao, C Chen, P Yang Proteomics 23 (3-4), 2200068, 2023 | 13 | 2023 |
| Phosphoproteomics uncovers exercise intensity-specific skeletal muscle signaling networks underlying high-intensity interval training in healthy male participants NJ Hoffman, J Whitfield, D Xiao, BE Radford, V Suni, R Blazev, P Yang, ... Sports Medicine, 1-22, 2025 | 10 | 2025 |
| Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis D Xiao, M Caldow, HJ Kim, R Blazev, R Koopman, D Manandi, BL Parker, ... Iscience 25 (6), 2022 | 9 | 2022 |
| Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities D Xiao, HJ Kim, I Pang, P Yang Bioinformatics 38 (7), 1956-1963, 2022 | 7 | 2022 |
| SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data D Xiao, M Lin, C Liu, TA Geddes, JG Burchfield, BL Parker, SJ Humphrey, ... NAR Genomics and Bioinformatics 5 (4), lqad099, 2023 | 3 | 2023 |
| Multitask benchmarking of single-cell multimodal omics integration methods C Liu, S Ding, HJ Kim, S Long, D Xiao, S Ghazanfar, P Yang Nature Methods, 1-12, 2025 | 2 | 2025 |
| SwitchClass: dissecting attenuated and escalated molecular features via a label-switch classification framework D Xiao, P Yang bioRxiv, 2025.10. 29.685265, 2025 | | 2025 |
| Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion D Xiao, S Sahadevan, MM Mangala, HJ Kim, A Fredericks, H Huang, ... bioRxiv, 2025 | | 2025 |
