Publications
Academic publications
Shijie Zhao, Tami D Lieberman, Mathilde Poyet, Kathryn M Kauffman, Sean M Gibbons, Mathieu Groussin, Ramnik J Xavier, Eric J Alm.
“Adaptive evolution within gut microbiomes of healthy people.”
Cell Host & Microbe (2019). doi: 10.1016/j.chom.2019.03.007. BioRxiv.
Associated github: shijiezhao/gut-evolution.
News reports: MIT News.
M Poyet, M Groussin, SM Gibbons, J Avila-Pacheco, X Jiang, SM Kearney, AR Perrotta, B Berdy, Shijie Zhao, TD Lieberman, PK Swanson, M Smith, S Roesemann, JE Alexander, SA Rich, J Livny, H Vlamakis, C Clish, K Bullock, A Deik, J Scott, KA Pierce, RJ Xavier, EJ Alm.
“A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.”
Nature Medicine (2019). doi: doi.org/10.1038/s41591-019-0559-3.
Ilana L Brito, Thomas Gurry, Shijie Zhao, Katherine Huang, Sarah K Young, Terrence P Shea, Waisea Naisilisili, Aaron P Jenkins, Stacy D Jupiter, Dirk Gevers, Eric J Alm.
“Transmission of human-associated microbiota along family and social networks.”
Nature Microbiology (2019). doi: doi.org/10.1038/s41564-019-0409-6. BioRxiv.
Fuqing Wu, Amy Xiao, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas, Richard Bonneau, Megan A Brown, Mary Bushman, Peter R Chai, Claire Duvallet, Timothy B Erickson, Katelyn Foppe, Newsha Ghaeli, Xiaoqiong Gu, William P Hanage, Katherine H Huang, Wei Lin Lee, Mariana Matus, Kyle A McElroy, Jonathan Nagler, Steven F Rhode, Mauricio Santillana, Joshua A Tucker, Stefan Wuertz, Shijie Zhao, Janelle Thompson, Eric J Alm.
“SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases.”
MedRxiv (2020). doi: doi.org/10.1101/2020.06.15.20117747.
Joerg Schnitzbauer, Yina Wang, Shijie Zhao, Matthew Bakalar, Tulip Nuwal, Baohui Chen, Bo Huang.
“Correlation analysis framework for localization-based superresolution microscopy.”
Proceedings of the National Academy of Sciences (2018). doi: doi.org/10.1073/pnas.1711314115.
Yichen Shen, Nicholas C Harris, Scott Skirlo, Mihika Prabhu, Tom Baehr-Jones, Michael Hochberg, Xin Sun, Shijie Zhao, Hugo Larochelle, Dirk Englund, Marin Soljačić.
“Deep learning with coherent nanophotonic circuits.”
Nature Photonics (2017). doi: doi.org/10.1038/nphoton.2017.93.