Bio


I work on understanding the statistical physics and optimization principles of organized biological systems. Specifically, I use planarian as model system to study cell collective behavior and the molecular mechanisms of adaption.

I am interested in a lot of things: development, evolution, ecology, statistical physics, dynamic systems, and biophysics. I also spend time on sequencing and fluorescence imaging technology required for depicting concrete biological systems.

Education & Certifications


  • Master of Science, Stanford University, BIOE-MS (2020)
  • B.S., Zhejiang University, Mathematics and Applied Mathematics (2018)

All Publications


  • Mechanical expansion microscopy. Methods in cell biology Fan, Y. n., Lim, Y. n., Wyss, L. S., Park, S. n., Xu, C. n., Fu, H. n., Fei, J. n., Hong, Y. n., Wang, B. n. 2021; 161: 125–46

    Abstract

    This chapter describes two mechanical expansion microscopy methods with accompanying step-by-step protocols. The first method, mechanically resolved expansion microscopy, uses non-uniform expansion of partially digested samples to provide the imaging contrast that resolves local mechanical properties. Examining bacterial cell wall with this method, we are able to distinguish bacterial species in mixed populations based on their distinct cell wall rigidity and detect cell wall damage caused by various physiological and chemical perturbations. The second method is mechanically locked expansion microscopy, in which we use a mechanically stable gel network to prevent the original polyacrylate network from shrinking in ionic buffers. This method allows us to use anti-photobleaching buffers in expansion microscopy, enabling detection of novel ultra-structures under the optical diffraction limit through super-resolution single molecule localization microscopy on bacterial cells and whole-mount immunofluorescence imaging in thick animal tissues. We also discuss potential applications and assess future directions.

    View details for DOI 10.1016/bs.mcb.2020.04.013

    View details for PubMedID 33478686

  • Deciphering functional redundancy in the human microbiome. Nature communications Tian, L. n., Wang, X. W., Wu, A. K., Fan, Y. n., Friedman, J. n., Dahlin, A. n., Waldor, M. K., Weinstock, G. M., Weiss, S. T., Liu, Y. Y. 2020; 11 (1): 6217

    Abstract

    Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.

    View details for DOI 10.1038/s41467-020-19940-1

    View details for PubMedID 33277504

  • Phase transitions in mutualistic communities under invasion PHYSICAL BIOLOGY Bray, S. R., Fan, Y., Wang, B. 2019; 16 (4)
  • Horizontal gene transfer can help maintain the equilibrium of microbial communities. Journal of theoretical biology Fan, Y. n., Xiao, Y. n., Momeni, B. n., Liu, Y. Y. 2018; 454: 53–59

    Abstract

    Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. Yet, the evolutionary advantage of horizontal gene transfer has not been well understood and is constantly being debated. Here we propose a simple population dynamics model based on frequency-dependent genotype interactions to evaluate the influence of horizontal gene transfer on microbial communities. In particular, we examine the structural stability of coexistence (i.e., the capability of the system to maintain species coexistence in response to small changes in parameters), as well as the robustness (defined as the maximal degree of perturbation the system can sustain around a stable coexistence steady state) of microbial communities. We find that both structural stability of coexistence and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stabilize the ecosystem, helping it recover from disturbance and maintain the species coexistence.

    View details for DOI 10.1016/j.jtbi.2018.05.036

    View details for PubMedID 29859211

  • Game among interdependent networks: The impact of rationality on system robustness EPL Fan, Y., Cao, G., He, S., Chen, J., Sun, Y. 2016; 116 (6)