I am an independent Research Fellow based at Oxford Population Health studying the evolution of microbes, particularly pathogenic bacteria and viruses. My current research focuses on developing novel computational methods and software tools to build genetic genealogies and applying them to large-scale genomic datasets to learn about the emergence, transmission, and adaptation of pathogens. I have diverse interests in statistical/population genetics, phylogenetics, and community ecology.
Ancestral recombination graphs
- Jeffery B, Wong Y, Thornton K, Tsambos G, ..., Zhan SH*, et al. 2025. Population-scale Ancestral Recombination Graphs with tskit 1.0. *Joint second. Nat Methods. In press. arXiv. https://arxiv.org/abs/2602.09649
- Deng Y, Zhan SH*, Zhang Y*, Zhang C, Chen B. 2025. Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species. *Equal contribution. In revision. arXiv. https://arxiv.org/abs/2512.05499
- Zhan SH, Wong Y*, Ignatieva A*, Eaton K, Guthrie I, Jeffery B, Palmer DS, Murall CL, Otto SP, Kelleher J. 2025. A Pandemic-Scale Ancestral Recombination Graphs for SARS-CoV-2. *Equal contribution. In revision. bioRxiv. https://www.biorxiv.org/content/10.1101/2023.06.08.544212v3
- Zhan SH, Ignatieva A*, Wong Y*, Eaton K, Jeffery B, Palmer DS, Murall CL, Otto SP, Kelleher J. 2023. Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2. *Equal contribution. bioRxiv. https://www.biorxiv.org/content/10.1101/2023.06.08.544212v1
Chromosomal evolution
- Li Z*, Kinosian SP*, Zhan SH, Barker MS. Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns. *Equal contribution. In revision. https://www.biorxiv.org/content/10.1101/2024.09.23.614530v1
- Zhan SH, Otto SP, Barker MS. Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification. In revision. https://www.biorxiv.org/content/10.1101/2021.03.30.436382v1
- Zhan SH, Drori M, Goldberg EE, Otto SP, Mayrose I. 2016. Phylogenetic evidence for cladogenetic polyploidization in land plants. Am. J. Bot. https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1600108
- Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I. 2014. Comparative analysis reveals that polyploidy does not decelerate diversification in fish. J. Evol. Biol. https://academic.oup.com/jeb/article-abstract/27/2/391/7318530
- Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP. 2011. Recently formed polyploid plants diversify at lower rates. Science https://www.science.org/doi/abs/10.1126/science.1207205
Community ecology
- Zhan SH, Huang YT, Liao CP, Liou CY, Liu SL. 2026. Sedimentation-driven environmental filtering shapes community assembly of cryptic coralline algae. EcoSphere. https://doi.org/10.1002/ecs2.70686 Highlighted on social media by the Ecological Society of America (https://www.instagram.com/p/DadRrDHmvZx).
- Zhan SH, et al. 2022. Geographic distance, sedimentation, and substrate shape cryptic crustose coralline algal assemblages in the world’s largest subtropical intertidal algal reef. Mol. Ecol. On the Cover. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16455
- Zhan SH, Hsieh TY, Yeh LW, Kuo TC, Suda S, Liu SL. 2020. Hidden introductions of freshwater red algae via the aquarium trade exposed by DNA barcodes. Environ. DNA. https://doi.org/10.1002/edn3.139
- Zhan SH, Shih CC, Liu SL. 2020. Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era. Ecol. Evol. https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5984
- Hsieh CJ*, Zhan SH*, Liao CP*, et al. 2018. The effects of contemporary selection and dispersal limitation on the community assembly of acidophilic microalgae. J. Phycol. https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12771
- Hsieh CJ, Zhan SH, Lin Y, Tang SL, Liu SL. 2015. Analysis of rbcL sequences reveals the global biodiversity, community structure, and biogeographical pattern of thermoacidophilic red algae (Cyanidiales). J. Phycol. https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12310