I'm an NDPH Intermediate Fellow at the University of Oxford. I study the evolutionary, ecological, and epidemiological dynamics of pathogens using a variety of approaches, methods, and tools from genomics, population genetics, phylogenetics, and community ecology. My work involves developing novel computational methodologies and applying them to large-scale genomic datasets which are publicly available or generated through collaborations.
Ancestral recombination graphs
Zhan SH, et al. 2023. Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2. bioRxiv. https://www.biorxiv.org/content/10.1101/2023.06.08.544212v1.abstract
Phylogenetic tools and methods
TODO
Chromosomal evolutionary dynamics
- Li Z, Kinosian SP, Zhan SH, Barker MS. Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns. https://www.biorxiv.org/content/10.1101/2024.09.23.614530v1.abstract
- Zhan SH, Otto SP, Barker MS. Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification. https://www.biorxiv.org/content/10.1101/2021.03.30.436382v1.abstract
- 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?login=false
- 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 of extremophiles
- Zhan SH, Huang YT, Liao CP, Liou CY, Liu SL. 2024. Environmental filtering of cryptic coralline algal diversity. In prep.
- 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, 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