Publications

Identifying keystone species in microbial communities using deep learning

Wang, Xu-Wen, Sun, Zheng, Jia, Huijue, Michel-Mata, Sebastian, Angulo, Marco Tulio, Dai, Lei, He, Xuesong, Weiss, Scott T, Liu, Yang-Yu

Nature Ecology & Evolution

Data-driven prediction of colonization outcomes for complex microbial communities

Wu, Lu^#, Wang, Xu-Wen^#, Tao, Zining, Wang, Tong, Zuo, Wenlong, Zeng, Yu, Liu, Yang-Yu, Dai, Lei

Nature Communications

Stability of ecological systems: A theoretical review

Chen, Can, Wang, Xu-Wen, Liu, Yang-Yu

Physics Reports

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

Wang, Tong, Wang, Xu-Wen, Lee-Sarwar, Kathleen A, Litonjua, Augusto A, Weiss, Scott T, Sun, Yizhou, Maslov, Sergei, Liu, Yang-Yu

Nature Machine Intelligence

Ecological dynamics imposes fundamental challenges in community-based microbial source tracking

Wang, Xu-Wen, Wu, Lu, Dai, Lei, Yin, Xiaole, Zhang, Tong, Weiss, Scott T, Liu, Yang-Yu

iMeta

Origins of scaling laws in microbial dynamics

Wang, Xu-Wen, Liu, Yang-Yu

Physical Review Research

Benchmarking omics-based prediction of asthma development in children

Wang, Xu-Wen, Wang, Tong, Schaub, Darius P, Chen, Can, Sun, Zheng, Ke, Shanlin, Hecker, Julian, Maaser-Hecker, Anna, Zeleznik, Oana A, Zeleznik, Roman, and others

Respiratory Research

Nutritional redundancy in the human diet and its application in phenotype association studies

Wang, Xu-Wen, Hu, Yang, Menichetti, Giulia, Grodstein, Francine, Bhupathiraju, Shilpa N, Sun, Qi, Zhang, Xuehong, Hu, Frank B, Weiss, Scott T, Liu, Yang-Yu

Nature Communications

A statistical physics approach for disease module detection

Wang, Xu-Wen, Qiao, Dandi, Cho, Michael H, DeMeo, Dawn L, Silverman, Edwin K, Liu, Yang-Yu

Genome Research

Predicting microbiome compositions from species assemblages through deep learning

Michel-Mata, Sebastian, Wang, Xu-Wen, Liu, Yang-Yu, Angulo, Marco Tulio

iMeta

Association Rule Mining of the Human Gut Microbiome

Zhang, Yiyan, Ke, Shanlin, Wang, Xu-Wen, Liu, Yang-Yu

bioRxiv

Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

Wang, Xu-Wen, Liu, Yang-Yu

bioRxiv

Integrating gut microbiome and host immune markers to understand the pathogenesis of Clostridioides difficile infection

Ke, Shanlin, Pollock, Nira R, Wang, Xu-Wen, Chen, Xinhua, Daugherty, Kaitlyn, Lin, Qianyun, Xu, Hua, Garey, Kevin W, Gonzales-Luna, Anne J, Kelly, Ciarán P, and others

Gut Microbes

Link prediction through deep generative model

Wang, Xu-Wen, Chen, Yize, Liu, Yang-Yu

Iscience

Deciphering Functional Redundancy in the Human Microbiome

Tian, Liang, Wang, Xu-Wen, Wu, Ang-Kun, Fan, Yuhang, Friedman, Jonathan, Dahlin, Amber, Waldor, Matthew K, Weinstock, George, Weiss, Scott T, Liu, Yang-Yu

Nature Communications

Comparative study of classifiers for human microbiome data

Wang, Xu-Wen, Liu, Yang-Yu

Medicine in Microecology

Structural feedback in the control of complex networks

Nie, Sen, Stanley, H Eugene, Chen, Shi-Ming, Wang, Bing-Hong, Wang, Xu-Wen^#

Europhysics Letters

Control energy of complex networks towards distinct mixture states

Nie, Sen, Stanley, H Eugene, Chen, Shi-Ming, Wang, Bing-Hong, Wang, Xu-Wen^*

Scientific Reports

The influence of panic on the efficiency of escape

Shen, Jia-Quan and Wang, Xu-Wen^* and Jiang, Luo-Luo>

Physica A: Statistical Mechanics and its Applications

Role of delay-based reward in the spatial cooperation

Wang, Xu-Wen, Nie, Sen, Luo-Luo, Wang, Wang, Bing-Hong, Chen, Shi-Ming

Physica A: Statistical Mechanics and its Applications

Cooperation in spatial evolutionary games with historical payoffs

Wang, Xu-Wen, Nie, Sen, Jiang, Luo-Luo, Wang, Bing-Hong, Chen, Shi-Ming

Physics Letters A

Promoting cooperation through fast response to defection in spatial games

Wang, Xu-Wen, Jiang, Luo-Luo, Nie, Sen, Chen, Shi-Ming, Wang, Bing-Hong

New Journal of Physics

Cooperation transition of spatial public goods games

Wang, Xu-Wen, Nie, Sen, Jiang, Luo-Luo, Wang, Bing-Hong

Journal of Statistical Mechanics: Theory and Experiment

Effect of correlations on controllability transition in network control

Nie, Sen, Wang, Xu-Wen, Wang, Bing-Hong, Jiang, Luo-Luo

Scientific Reports

Effect of degree correlation on exact controllability of multiplex networks

Nie, Sen, Wang, Xu-Wen^*, Wang, Bing-Hong

Physica A: Statistical Mechanics and its Applications

Controlling complex networks with conformity behavior

Wang, Xu-Wen, Nie, Sen, Wang, Wen-Xu, Wang, Bing-Hong

Europhysics Letters

Dependency links can hinder the evolution of cooperation in the prisoner’s dilemma game on lattices and networks

Wang, Xu-Wen, Nie, Sen, Wang, Bing-Hong

PLoS One

Impact of keeping silence on spatial reciprocity in spatial games

Wang, Xu-Wen, Wang, Zheng, Nie, Sen, Jiang, Luo-Luo, Wang, Bing-Hong

Applied Mathematics and Computation

Effects of aspiration-induced adaptation and migration on the evolution of cooperation

Peng, Yu, Wang, Xu-Wen^*, Lu, Qian, Zeng, Qin-Ke, Wang, Bing-Hong

International Journal of Modern Physics C

Robustness of controllability for networks based on edge-attack

Nie, Sen, Wang, Xu-Wen^*, Zhang, Hai-Feng, Li, Qi-Lang, Wang, Bing-Hong

PLoS One