Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation. - Carey D. Nadell; Kevin R. Foster; João B. Xavier (PLoS Comput. Biol., 2010)

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota. - Vanni Bucci; Serena Bradde; Giulio Biroli; João B. Xavier (PLoS Comput. Biol., 2012)

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota. - Richard R. Stein; Vanni Bucci; Nora C. Toussaint; Charlie G. Buffie; Gunnar Rätsch; Eric G. Pamer; Chris Sander; João B. Xavier (PLoS Comput. Biol., 2013)

Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait. - Kerry E. Boyle; Hilary Monaco; Dave van Ditmarsch; Maxime Deforet; João B. Xavier (PLoS Comput. Biol., 2015)

Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. - Jinyuan Yan; Maxime Deforet; Kerry E. Boyle; Rayees Rahman; Raymond Liang; Chinweike Okegbe; Lars E. P. Dietrich; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2017)

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. - Jinyuan Yan; Henri Estanbouli; Chen Liao; Wook Kim; Jonathan M. Monk; Rayees Rahman; Mini Kamboj; Bernhard O. Palsson; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2019)

Compositional Lotka-Volterra describes microbial dynamics in the simplex. - Tyler A. Joseph; Liat Shenhav; João B. Xavier; Eran Halperin; Itsik Pe'er (PLoS Comput. Biol., 2020)

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. - Chen Liao; Tong Wang 033; Sergei Maslov; João B. Xavier (PLoS Comput. Biol., 2020)