| A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants R Shahan, CW Hsu, TM Nolan, BJ Cole, IW Taylor, L Greenstreet, ... Developmental cell 57 (4), 543-560. e9, 2022 | 212 | 2022 |
| Toward a mathematical theory of trajectory inference H Lavenant, S Zhang, YH Kim, G Schiebinger The Annals of Applied Probability 34 (1A), 428-500, 2024 | 53 | 2024 |
| Optimal transport analysis reveals trajectories in steady-state systems S Zhang, A Afanassiev, L Greenstreet, T Matsumoto, G Schiebinger PLoS computational biology 17 (12), e1009466, 2021 | 31 | 2021 |
| Trajectory Inference via Mean-field Langevin in Path Space L Chizat*, S Zhang*, M Heitz, G Schiebinger Advances in Neural Information Processing Systems, 35, 16731-16742., 2022 | 23 | 2022 |
| Manifold learning with sparse regularised optimal transport S Zhang, G Mordant, T Matsumoto, G Schiebinger arXiv preprint arXiv:2307.09816, 2023 | 14* | 2023 |
| Persistent exclusion processes: Inertia, drift, mixing, and correlation S Zhang, A Chong, BD Hughes Physical Review E 100 (4), 042415, 2019 | 9 | 2019 |
| Learning cell-specific networks from dynamics and geometry of single cells SY Zhang, MPH Stumpf bioRxiv, 2023.01. 08.523176, 2023 | 6* | 2023 |
| A unified framework for non-negative matrix and tensor factorisations with a smoothed Wasserstein loss SY Zhang Proceedings of the IEEE/CVF International Conference on Computer Vision …, 2021 | 5 | 2021 |
| Joint trajectory and network inference via reference fitting SY Zhang arXiv preprint arXiv:2409.06879, 2024 | 2 | 2024 |
| Approximate Bayesian computation for inferring Waddington landscapes from single-cell data Y Liu, SY Zhang, IT Kleijn, MPH Stumpf Royal Society Open Science 11 (7), 231697, 2024 | 2 | 2024 |
| LoxCode in vivo barcoding resolves epiblast clonal fate to fetal organs TS Weber, C Biben, DC Miles, S Glaser, S Tomei, S Zhang, PPL Tam, ... bioRxiv, 2023.01. 02.522501, 2023 | 2 | 2023 |
| Hematopoiesis at single cell resolution spanning human development and maturation H Li, J Ezike, A Afanassiev, L Greenstreet, S Zhang, J Whangbo, VL Butty, ... bioRxiv, 2021.08. 25.457678, 2021 | 2 | 2021 |
| The dynamics of hematopoiesis over the human lifespan H Li, P Côté, M Kuoch, J Ezike, K Frenis, A Afanassiev, L Greenstreet, ... Nature Methods, 1-13, 2024 | 1 | 2024 |
| Topological Optimal Transport for Geometric Cycle Matching SY Zhang, MPH Stumpf, T Needham, A Barbensi arXiv preprint arXiv:2403.19097, 2024 | 1 | 2024 |
| A multi-track landscape of haematopoiesis informed by cellular barcoding and agent-based modelling D Lin, S Zhang, J Schreuder, J Tran, D Metcalf, T Sargeant, AP Ng, ... bioRxiv, 2024.03. 28.587126, 2024 | 1 | 2024 |
| The Topological Properties of the Protein Universe CD Madsen, A Barbensi, SY Zhang, L Ham, A David, DEV Pires, ... bioRxiv, 2023.09. 25.559443, 2023 | 1 | 2023 |
| Identifying Drift, Diffusion, and Causal Structure from Temporal Snapshots V Guan, J Janssen, H Rahmani, A Warren, S Zhang, E Robeva, ... arXiv preprint arXiv:2410.22729, 2024 | | 2024 |
| Geometry of the Space of Partitioned Networks: A Unified Theoretical and Computational Framework SY Zhang, F Lan, Y Zhou, A Barbensi, MPH Stumpf, B Wang, T Needham arXiv preprint arXiv:2409.06302, 2024 | | 2024 |
| OptimalTransport.jl S Zhang, D Widmann, DS Barreira https://zenodo.org/records/5920148, 2022 | | 2022 |
| Dynamical inference for biological processes through the lens of optimal transport SY Zhang University of British Columbia, 2021 | | 2021 |
