Publications (*: equal contribution)
Review Paper Preprint - Artificial intelligence for microbiology and microbiome research
Xu-Wen Wang, Tong Wang, Yang-Yu Liu, Under Review at Cell Systems, 2024
November 2024
![]()
Article - Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments
Tong Wang, Yuanqing Fu, Menglei Shuai, Ju-Sheng Zheng, Lu Zhu, Qi Sun, Frank B. Hu, Scott T. Weiss, Yang-Yu Liu, Nature Communications, 2024
October 2024
![]()
Preprint - Predicting metabolic response to dietary intervention using deep learning
Tong Wang, Hannah D. Holscher, Sergei Maslov, Frank B. Hu, Scott T. Weiss, Yang-Yu Liu, In Press at Nature Communications, 2024
September 2024
![]()
Preprint - Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations
Tong Wang, Ashish B. George, Sergei Maslov, Under Review at Cell Systems, 2024
May 2024
![]()
Article - Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes
Tong Wang*, Leyuan Li*, Daniel Figeys, Yang-Yu Liu, ISME Communications, 2024
May 2024
![]()
Article - Data-driven prediction of colonization outcomes for complex microbial communities
Lu Wu, Xu-Wen Wang, Zining Tao, Tong Wang, Wenlong Zuo, Yu Zeng, Yang-Yu Liu, Lei Dai, Nature Communications, 2024
March 2024
![]()
Article - Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites
Zheng Sun, Jiang Liu, Meng Zhang, Tong Wang, Shi Huang, Scott T. Weiss, Yang-Yu Liu, Nature Communications, 2023
September 2023
![]()
Article - Feasibility in MacArthur’s consumer-resource model
Andrea Aparicio, Tong Wang, Serguei Saavedra, Yang-Yu Liu, Scott T. Weiss, Theoretical Ecology, 2023
July 2023
![]()
Article - Functional convergence in slow-growing microbial communities arises from thermodynamic constraints
Ashish George, Tong Wang, Sergei Maslov, ISME Journal, 2023
June 2023
![]()
Article - Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics
Leyuan Li*, Tong Wang*, Zhibin Ning, Xu Zhang, James Butcher, Caitlin Simopoulos, Janice Mayne, Alain Stintzi, David R. Mack, Yang-Yu Liu, Daniel Figeys, Nature Communications, 2023
June 2023
![]()
Article - Predicting metabolomic profiles from microbial composition through neural ordinary differential equations
Tong Wang, Xu-Wen Wang, Augusto A. Litonjua, Kathleen Lee-Sarwar, Scott T. Weiss, Yizhou Sun, Sergei Maslov, Yang-Yu Liu, Nature Machine Intelligence, 2023
March 2023
![]()
Article - Benchmarking omics-based prediction of asthma development in children
Xu-Wen Wang, Tong Wang, Darius P. Schaub, Can Chen, Zheng Sun, Shanlin Ke, Julian Hecker, Anna Maaser-Hecker, Oana A. Zeleznik, Roman Zeleznik, Augusto A. Litonjua, Dawn L. DeMeo, Jessica Lasky-Su, Edwin K. Silverman, Yang-Yu Liu, Scott T. Weiss, Respiratory Research, 2023
February 2023
![]()
Article - Mitigation of SARS-CoV-2 transmission at a large public university
Diana Rose Ranoa, Robin Holland, Fadi Alnaji, Kelsie Green, Leyi Wang, Richard Fredrickson, Tong Wang, George Wong, Johnny Uelmen, Sergei Maslov, et al., Nature Communications, 2022
June 2022
![]()
Article - Complementary resource preferences spontaneously emerge in diauxic microbial communities
Zihan Wang, Akshit Goyal, Veronika Dubinkina, Ashish George, Tong Wang, Yulia Fridman, Sergei Maslov, Nature Communications, 2021
November 2021
![]()
Article - Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state
Alexei Tkachenko, Sergei Maslov, Tong Wang, Ahmed Elbanna, George Wong, Nigel Goldenfeld, eLife, 2021
November 2021
![]()
Article - Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Akshit Goyal*, Tong Wang*, Veronika Dubinkina, Sergei Maslov, Nature Communications, 2021
February 2021
![]()
Article - The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
Shai Pilosof, Sergio A. Alcala-Corona, Tong Wang, Ted Kim, Sergei Maslov, Rachel Whitaker, Mercedes Pascual, Nature Ecology and Evolution, 2020
October 2020
![]()
Article - Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
Chen Liao, Tong Wang, Sergei Maslov, Joao Xavier, PLoS Computational Biology, 2020
August 2020
![]()
Article - Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations
Derek Ping*, Tong Wang*, David T Fraebel, Sergei Maslov, Kim Sneppen, Seppe Kuehn, ISME Journal, 2020
May 2020
![]()
Article - Evidence for a multi-level trophic organization of the human gut microbiome
Tong Wang*, Akshit Goyal*, Veronika Dubinkina, Sergei Maslov, PLoS Computational Biology, 2019
December 2019
![]()