Huan Fan

Education

2011 ~ 2016, Ph.D Department of Zoology, University of Wisconsin-Madison. Thesis: Assembly and Alignment Free Methods for Phylogenetic Reconstruction and Genome-Wide Association Studies
2015 ~ 2016, Data Science Specialization, Johns Hopkins University through Coursera
2008 ~ 2015, Ph.D Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. Thesis: Studies on the evolution of breeding systems in Ficus (Moraceae) powered by next-generation sequencing
2004 ~ 2008, B.S Biotechnology, Wu Yuzhang Honors College, Sichuan University, China.

Teaching (in English)

2019 ~ 2024, Lecturer, Advanced Statistics (Bayesian module), 2.5 credit, University of Chinese Academy of Sciences.
2021, Lecturer, Meta-barcoding Workshop, 1 credit, University of Chinese Academy of Sciences.
2020, Lecturer, Introduction to Python and Web Crawling, 1 credit, University of Chinese Academy of Sciences.
2015, Guest lecturer, Associated Colleges of the Chicago Area seminar series.
2014, Teaching assistant, Introductory Biology (Zoo152), University of Wisconsin-Madison
2012, Teaching assistant, Introductory Ecology (Zoo260), University of Wisconsin-Madison

Work Experience

2023 - , Research Scientist(again!), WIL@NUS Cooperate Lab, Wilmar International, Singapore
2020 - 2023, Postdoc(again!), Xishuangbanna Tropical Botanical Garden
2018 - 2019, Research Scientist, WIL@NUS Cooperate Lab, Wilmar International, Singapore
2017, Postdoc, Department of Bacteriology, University of Wisconsin-Madison
2015, Guest lecturer, Associated Colleges of the Chicago Area seminar series.
2014, Teaching assistant, Introductory Biology (Zoo152), UW-Madison
2012, Teaching assistant, Introductory Ecology (Zoo260), UW-Madison
2010, Intern, Botanical Garden Conservation International (London, UK, NGO)

Publication

Yang, J., Fan, H., He, Y., Wang, G., Cao, M., & Swenson, N. G*. (2024) Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought- and defence-related genes. Journal of Ecology, 112: 575–589.
Wang, X.¹, Fan, H^1*., Phoncharoen, W., Gélin, U., Tomlinson, K.W. (2023) Leaf chemistry of architecturally defended plants responds more strongly to soil phosphorus variation than non-architecturally defended ones. Physiologia Plantarum 175, e13856.
Nimalrathna, T.S., Fan, H., Quan, R.-C. & Nakamura, A*. (2023) Enhancing the dung beetle iDNA tool for mammalian biodiversity monitoring and ecological studies. Integrative Conservation, 2, 133–139.
Fan, H., Li, J.Y., Landrein, S*. (2022) Complete chloroplast genome of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae. Mitochondrial DNA Part B: Resources 7(6): 1035-1037.
Chen, B., Loo, B.Z.L., Cheng, Y.Y., Song, P., Fan, H., Latypov, O., Kittelmann, S*. (2022). Genome-wide high-throughput signal peptide screening via plasmid pUC256E improves protease secretion in Lactiplantibacillus plantarum and Pediococcus acidilactici. BMC Genomics 23(1): 48.
Silvaraju, S., Menon, N., Fan, H., Lim, K. and Kittelmann, S*. (2021). Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach. Applied and Environmental Microbiology, 87(1): e02191-20.
Zhao, J.B., Fan, H., Zhao, Y.B., Han, L.X.* (2021). Zebra Dove (Geopelia striata) Found in Mengla, Yunnan. Chinese Journal of Zoology. 56(6):870, 881(in Chinese with English abstract).
Fan, H., Ives, A., Surget-Groba, Y., Cannon, C. (2015). An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data, BMC Genomics, 16:522
Fan, H., Ives, A., Surget-Groba, Y. (2018). Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment, Molecular Ecology Resources, 18(6), 1482–1491 Full text
Carlos, C., Fan, H., and Currie, C. (2018). Substrate shift reveals roles for members of bacterial consortia in lignocellulose degradation. Frontiers in Microbiology, 9:364
Khadempour, L., Fan, H., Keefover-Ring, K., Carlos-Shanley, C., Nagamoto, N.S., Dam, M.A., Pupo, M.T. and Currie, C.R. (2020). Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass-and dicot-cutter ants. Frontiers in microbiology, 11.
Barcoto, M.O., Carlos-Shanley, C., Fan, H., Ferro, M., Nagamoto, N.S., Bacci, M., Currie, C.R. and Rodrigues, A. (2020). Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment. Scientific reports, 10(1), pp.1-13.
Silvaraju, S., Menon, N., Fan, H., Lim, K. and Kittelmann, S. (2020). Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach. Applied and Environmental Microbiology, AEM.02191–20.
Kozlowski, G., Gibbs, D., Fan, H., Frey, D., and Gratzfeld, J. (2012) Conservation of threatened relict trees through living ex situ collections: lessons from the global survey of the genus Zelkova (Ulmaceae). Biodiversity and Conservation, 21:671-685

Grant

2019-2021, International Postdoc Award, China
2019-2021, National Postdoc Research Grant (batch 66), China
2019-2021, Provincial Postdoc Grant, Yunnan, China
2019-2021, Postdoc Research Grant, Xishuangbanna Tropical Botanical Garden

Presentation

2020 Talk. Impact of seasonality on gut microbiota of free-ranging herbivores, Savanna Science Network Meeting, South Africa.
2017 Talk. Fantastic k-mers and where to find them, Evolution Seminar Series, UW-Madison
2015 Talk. A transcriptome analysis of the two types of female florets in Ficus fistulosa, Association of Tropical Biology and Conservation annual meeting, Cambodia.
2011 Poster. Reference-free phylogenomic analysis of the genus ficus using next-gen sequence data, OIST Summer School and Workshop “Quantitative Evolutionary and Comparative Genomics”, Okinawa Institute of Science and Technology, Japan.
2010 Poster. Digital rapid biodiverstiy assessment, Students Conference on Conservation Sciences, Cambridge University, UK.