K. S. Xue

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

This study investigates gut microbiome colonization dynamics after antibiotic use, finding prolonged delays in microbial transmission and ecological barriers to colonization.

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

The paper constructs an ordered mutant collection of Bacteroides thetaiotaomicron using transposon-insertion and barcode sequencing, identifies factors limiting coverage, and demonstrates phenotypic screening for growth defects and cell shape changes.

Linking influenza virus evolution within and between human hosts

This study links influenza virus evolution within and between human hosts, finding that synonymous mutations accumulate globally while nonsynonymous mutations are purged, except at antigenic sites where selection favors them.

Reconciling disparate estimates of viral genetic diversity during human influenza infections

The paper re-analyzes sequencing data from four studies to resolve discrepancies in estimates of viral genetic diversity during human influenza infections, identifying technical issues in one study as the source of inflated diversity measurements.

Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo

The paper shows that sera from humans with narrowly focused influenza virus antibodies select for single HA escape mutations in ovo, reducing antibody binding.

Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples

The paper investigates whether a cooperative mutation in H3N2 influenza virus, observed in cell culture, is present in unpassaged clinical samples using deep sequencing.