PUBLICATIONS

“The joy of discovery is certainly the liveliest that the mind of man can ever feel.”

- Claude Bernard -

Research Publications

*The list reflects our diverse research interests. While the teaching load and other circumstances have severely curtailed publication recently, we are still striving for innovative research even under limiting conditions for research, and advocating for a more inclusive research environment.

Research education in genomics and bioinformatics:

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

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.

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 "true fruit fly" Rhagoletis species complex:

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]

* Corresponding author