发表文章 Publications

1. Shijie Zhao, Tami Lieberman, M. Poyet, K. Kauffman, S. Gibbons, M. Groussin, Ramnik Xavier, Eric Alm. Adaptive evolution within the gut microbiome of healthy people. 购宝钱包 Host & Microbe. 2019.

2.       Wenshan Zheng, Shijie Zhao, Yehang Yin, Huidan Zhang, …, Peter J. Lu, Eric J. Alm, David A. Weitz. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome, Science. 2022

3. Shijie Zhao, C. Dai, Z. Lu, E. Evans, Eric Alm. Tracking strains predicts personal microbiomes and reveals adaptive evolution within adult twins. BioRxiv. 2020

4.       Miles Richardson, Shijie Zhao, Ravi Sheth, Thomas Moody, …, Harris H. Wang. SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome. Nature Microbiology, 2025.

5.       Yiming Huang, Ravi U. Sheth, Shijie Zhao, …, Harris H. Wang. High-throughput microbial culturomics using automation and machine learning. Nature Biotechnology, 2022.

6.       I. Brito, T. Gurry, Shijie Zhao, K. Huang, S. Young, T. Shea, W. Naisilisili, A. Jenkins, S. Jupiter, D. Gevers, Eric Alm. Transmission of human-associated microbiota along family and social networks. Nature Microbiology, 2019.

7.       J. Schnitzbauer, Y. Wang, Shijie Zhao, M. Bakalar, T. Nuwal, B. Chen, Bo Huang. Correlation analysis framework for localization-based super-resolution microscopy. PNAS, 2018

8.       F. Wu, A. Xiao, …, Shijie Zhao, J. Thompson, Eric J Alm, SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases, Science of The Total Environment, 2022

9.       An-Ni Zhang, Jeffry M Gaston, Chengzhen L Dai, Shijie Zhao, …, Eric J Alm, Tong Zhang. An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nature Communications, 2021

10.   Xiaoqiong Gu, Jean XY Sim, …, Shijie Zhao, Zhanyi Lee, Janelle R Thompson, Eng Eong Ooi, Jenny G Low, Eric J Alm, Shirin Kalimuddin. Gut Ruminococcaceae Levels at Baseline Correlate with Risk of Antibiotic-associated Diarrhea. iScience, 2021

11.   Chenhao Li, Martin Stražar, Ahmed Mohamed, Julian Pacheco, Rebecca Walker, Shijie Zhao, …, Damian R Plichta, Ramnik J Xavier. Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria. 购宝钱包 , 2024

12.   An-Ni Zhang, Jeffry Gaston, Pablo Cárdenas, Shijie Zhao, Xiaoqiong Gu, Eric J Alm. CRISPR spacer acquisition is a rare event in human gut microbiome. 购宝钱包 Genomics, 2025.

13. M. Poyet, M. Groussin, S. Gibbons, …, Shijie Zhao, et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nature Medicine, 2019

14. Y. Shen, N.C. Harris, S. Skirlo, M. Prabhu, T. Baehr-Jones, M. Hochberg, X. Sun, Shijie Zhao, H. Larochelle, D. Englund, M. Soljačić. Deep Learning with coherent nanophotonic circuits. Nature Photonics, 2017