* Corresponding or co-corresponding author 

+ Undergraduate student lab member

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Bioluminescent fungi:

R.C. Rabara, X. Xie*. 2025. Decoding the Bioluminescent and Non-Bioluminescent Traits of Panellus stipticus: A Genomic and Phenotypic Perspective. Journal of Fungi, 11, 774. https://doi.org/10.3390/jof11110774

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Microbiome research:

The BioDIGS Consortium, T. Alberts, ..., AC Egwu+, ..., A.M. Horton+, ..., M. Marone, ..., X. Xie*, ...L. Zirkle. 2025. Unearthing soil biodiversity through collaborative genomic research and education. Nature Genetics: https://doi.org/10.1038/s41588-025-02442-5

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Mentewab Ayalew, ..., X. Xie. 2026. Microbiome education at under-resourced institutions: current status, barriers, and approaches to successful implementation. Journal of Microbiology and Biology Education: https://journals.asm.org/doi/epdf/10.1128/jmbe.00288-25

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The Genomic Data Science Community Network, ..., X. Xie. 2022. Diversifying the genomic data science research community. Genome Research: https://genome.cshlp.org/content/early/2022/07/18/gr.276496.121

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Protein structural evolution:   

Zheng, L., W. Niu, X. Xie, T. Vu, G. Du. 2026. A Redox-Sensitive Phosphatase Regulates Glycolysis as a Metabolic Switch in the Bacterial Inner Membrane. Science Advances (In press).

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Virus evolution:   

Xie, X.*, T.-J. Lewis+, N. Green+, and Z. Wang. 2021. Phylogenetic network analysis revealed the recombinant origin of the SARS-CoV-2 VOC202012/01 (B.1.1.7) variant first discovered in U.K.. bioRxiv doi: 10.1101/2021.06.24.449840.

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Population genomics and comparative epigenomic and transciptomic study of rice domestication:

Li, X., J. Zhu, F. Hu, S. Ge, M. Ye, H. Xiang, G. Zhang, X. Zheng, H. Zhang, S. Zhang, Q. Li, R. Luo, C. Yu, J. Yu, J. Sun, X. Zou, X. Cao, X. Xie*, J. Wang*, W. Wang*. 2012. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics13, 300. [read the paper]

 

Xie, X.*, J. Molina, R. Hernandez, A. Reynolds, A.R. Boyko, C.D. Bustamante, and M. Purugganan. 2011. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection. PLoS One 6, e20670. [read the paper]

 

Yeast molecular evolution:   

Xie, X.*, W. Qiu, and P. Lipke. 2011. Accelerated and adaptive evolution of yeast sexual adhesins. Molecular Biology and Evolution 2, 3127-3137. [read the paper]

 

Xie, X.* and P. Lipke. 2010. The evolution of fungal and yeast cell walls. Yeast 27, 479-488. [read the paper]

 

Speciation in the model system Rhagoletis pomonella species complex (the "true fruit fly"):   

Xie, X., A. P. Michel, D. Schwarz, J. Rull, S. Velez, A. A. Forbes, M. Aluja, and J. Feder*. 2008. Radiation and divergence in the Rhagoletis pomonella species complex: Inferences from DNA sequence data. Journal of Evolutionary Biology 21, 900-913. [read the paper]

 

Xie, X., J. Rull, S. Velez, A. Forbes, A. P. Michel, S. Velez, A. A. Forbes, N. Lobo, M. Aluja, and J. Feder*. 2007. Hawthorn-infesting populations of Rhagoletis pomonella in Mexico and speciation mode plurality. Evolution 61, 1091–1105. [read the paper]

 

Feder, J.L.*, X. Xie, J. Rull, S. Velez, A. Forbes, B. Leung, H. Dambroski, K. Filchak, and M. Aluja. 2005. Mayr, Dobzhansky and Bush: A golden braid of biogeography, inversions, differential introgression, clines, and sympatric speciation? Proceedings of the National Academy of Sciences USA 102, 6573-6580. [read the paper]