Publications

Members of the Xue lab are listed in bold.

SELECTED PUBLICATIONS

Xue, K.S.^†, Walton, S.J., Goldman, D.A., Morrison, M.L., Verster, A.J., Parrott, A.B., Yu, F.B., Neff, N.F., Rosenberg, N.A., Ross, B.D., Petrov, D.A., Huang, K.C., Good, B.H.^†, Relman, D.A.^† Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. bioRxiv (2023). DOI: 10.1101/2023.09.26.559480 ^†corresponding authors

Goldman, D.A.*, Xue, K.S.*^,†, Parrott, A.B., Jeeda, R.R., Lopez, J.G., Vila, J.C.C., Petrov, D.A., Good, B.H., Relman, D.A., Huang, K.C^†. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. Proceedings of the National Academy of Sciences 122 (11) e2322440122 (2025). DOI: 10.1073/pnas.2322440122 *equal contribution, ^†corresponding authors

Xue, K.S., Stevens-Ayers, T., Campbell, A.P., Englund, J.A., Pergam, S.A., Boeckh, M., Bloom, J.D. Parallel evolution of influenza across multiple spatiotemporal scales. eLife 6: e26875 (2017). DOI: 10.7554/eLife.26875
press coverage: The Atlantic, Wired, and Science News; public lecture at Seattle Town Hall

ALL PUBLICATIONS

Lopez, M.L., Kang, T., Espeleta, A., Rubtsova, V.I., Baek, J., Songcuan, J., Moyer, E.M., Kim, J., Song, W.S., Jung, S., D’Sa, N., Anica, A., Tran, E., Chun, Y., Choi, W., Jang, K.H., Kelly, M.E., Tamburini, I.J., Alam, Y.H., Le, J., Ramirez, C.B., Kataru, R.P., Hong, S.P., Nicholas, D.A., Xue, K.S., Lee, G., Bae, H., Jang, C. Intestinal catabolism of dietary fructose promotes obesity and insulin resistance via ileal lacteal remodeling. bioRxiv (2025). DOI: 10.1101/2025.08.18.670963

Fischer, M.T., Xue, K.S., Costello, E.K., Dvorak, M., Raboisson, G., Robaczewska, A., Caty, S.N., Relman, D.A., O’Connell, L.A. Effects of parental care on skin microbial community composition in poison frogs. eLife 14:RP103331 (2025). DOI: 10.7554/eLife.103331.1

Morrison, M.L., Xue, K.S., and Rosenberg, N.A. Quantifying compositional variability in microbial communities with FAVA. Proceedings of the National Academy of Sciences 122 (11) e2322440122 (2025). DOI: 10.1073/pnas.2322440122

Arjes, H.A., Sun, J., Liu, H., Nguyen, T.H., Culver, R.N., Celis, A.I., Walton, S.J., Vasquez, K.S., Yu, F.B., Xue, K.S., Newton, D., Zermeno, R., Weglarz, M., Deutschbauer, A., Huang, K.C., Shiver, A.L. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotamicron. BMC Biology 20:285 (2022). DOI: 10.1186/s12915-022-01481-2

Celis, A.I., Aranda-Díaz, A., Culver, R., Xue, K.S., Relman, D.A., Shi, H., Huang, K.C. Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals. iScience 25(4). (2022). DOI: 10.1016/j.isci.2022.103907

Xue, K.S., Bloom, J.D. Linking influenza virus evolution within and between human hosts. Virus Evolution 6(1): veaa010. (2020). DOI: 10.1093/ve/veaa010

Xue, K.S., Bloom, J.D. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nature Genetics 51:1298-1301(2019). DOI: 10.1038/s41588-019-0349-3

Xue, K.S., Moncla, L.H., Bedford, T., Bloom, J.D. Within-host evolution of human influenza virus. Trends in Microbiol. 26(8):781-793(2018). DOI: 10.1016/j.tim.2018.02.007

Davis, A.K.F., McCormick, K., Gumina, M.E., Petrie, J.G., Martin, E.T., Xue, K.S., Bloom, J.D., Monto, A.S., Bushman, F.D., Hensley, S.E. Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo. J. Virol.:00859-18 (2018). DOI: 10.1128/JVI.00859-18

Xue, K.S., Greninger, A.L., Pérez-Osorio, A., Bloom, J.D. Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples. mSphere 3: e00552-17 (2017). DOI: 10.1128/mSphereDirect.00552-17

Xue, K.S., Hooper, K.A., Ollodart, A.R., Dingens, A., Bloom, J.D. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. eLife 5: e13974 (2016). DOI: 10.7554/eLife.13974

Wright, K.M., Arnold, B.J., Xue, K.S., Surinova, M., O’Connell, J., Bomblies, K. Selection on meiosis genes in diploid and tetraploid Arabidopsis arenosa. Mol. Biol. Evol. 32(4): 944-955 (2015). DOI: 10.1093/molbev/msu398

Carroll, S.M., Xue, K.S., Marx, C.J. Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance. BMC Microbiol. 14:2 (2014). DOI: 10.1186/1471-2180-14-2

Hollister, J.D., Arnold, B.J., Svedin, E., Xue, K.S., Dilkes, B.P., Bomblies, K. Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Gen 8(12): e1003093 (2012). DOI: 10.1371/journal.pgen.1003093