Selected Publications

* equal contribution, † equal senior contribution. Full list on Google Scholar.

2026

• 
  Prehistoric Global Migration of Vanishing Gut Microbes with Humans

  Matthew M. Carter*, Zhiru Liu*, Matthew R. Olm*, …, Benjamin H. Good†, Justin L. Sonnenburg† (15 authors)

  Nature, 2026

  Coverage: New York Times · NPR · Stanford Medicine

2025

• 
  Dynamics of dN/dS within Recombining Bacterial Populations

  Zhiru Liu, Benjamin H. Good

  bioRxiv (preprint), 2025

  Code: dNdS_dynamics

2024

• 
  Linkage Equilibrium between Rare Mutations

  Anastasia S. Lyulina*, Zhiru Liu*, Benjamin H. Good

  Genetics, 2024

  Featured article · Cover art (Anastasia Lyulina)
• 
  Dynamics of Bacterial Recombination in the Human Gut Microbiome

  Zhiru Liu, Benjamin H. Good

  PLOS Biology, 2024

  Code: CP-HMM

2020

• 
  Scale-Invariant Topology and Bursty Branching of Evolutionary Trees Emerge from Niche Construction

  Chi Xue, Zhiru Liu, Nigel Goldenfeld

  Proceedings of the National Academy of Sciences, 2020