Videos on our research：
https://www.chinagut.cn/talks/s/756ebd5ca2a34243b83edfb1da7e62f5
https://www.bilibili.com/video/BV1bq4y1H7c7/
Lab members in bold #Co-first +Co-second *Co-corresponding
In process:
Sisi Huang et al... Chao Jiang*. evoSIR-Seeding-Spreading (evoSSS): A Predictive Model for Competitive Evolution and Transmission Dynamics of SARS-CoV-2 and Emerging Viral Pathogens. In submission
Qiong Chen#, Boliang Zhang#, Chen Peng, Jiajun Huang, Xiaotao Shen, Chao Jiang*. Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all. In submission
Silan Gu#, Xin Wei#, Xiaohan Huang#, Xindie Ren, Wei Wu, Guojun He, Jun Xu, Xuewu Zhang, Hongliu Cai*, Chao Jiang*, Lingtong Huang*. Pneumocystis jirovecii colonization and infection are associated with virome in the lungs of patients with severe pneumonia. In submission
Qiong Chen#, Mengyi Yuan#, Liuyiqi Jiang#, Xin Wei#, Zhen Liu+, Chen Peng+, Zinuo Huang+, Dongmei Tang+, Xiangrong Wu, Jing Sun, Cunqi Ye, Qing Liu, Xiaowei Zhu, Peng Gao, Laibin Huang, Mingkai Jiang, Chao Jiang*. Progressive multifaceted soil microbiome and metabolome remodeling underpins long-term desert ecosystem restoration. In preparation
Cai et al., Shanghai Metro Air Exposome: An Integrated Study Using Metagenomics, Metatranscriptomics, and Chemical Profiling. In submission
Qing Liu#, Haodi Wu#, Qing-Jun Luo, Chao Jiang, Zhana Duren, Kevin Van Bortle, Ming-tao Zhao, Bingqing Zhao, Jun Liu, David P Marciano, Brittany Lee-McMullen, Chenchen Zhu, Anil M Narasimha, Joshua J Gruber, Andrew M Lipchik, Hongchao Guo, Nathaniel K Watson, Ming-Shian Tsai, Takaaki Furihata, Lei Tian, Eric Wei, Yingxin Li, Lars M Steinmetz, Wing Hung Wong, Mark A Kay, Joseph C Wu, Michael P Snyder*. Tyrosine kinase inhibitors induce mitochondrial dysfunction during cardiomyocyte differentiation through alteration of GATA4-mediated networks. In submission
Published：
Yueer Li#, Chen Peng#, Fei Chi, Zinuo Huang, Mengyi Yuan, Xin Zhou, Chao Jiang*.The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees. Accepted, Briefings in Bioinformatics(2024)
Chen Q, Wei X, Xie R, Jiang C. Beyond physical particles: A holistic assessment of human health risks from real-world micro-nanoplastic exposure. The Innovation Medicine (2024)
Minghui Cheng#, Yingjie Xu#, Xiao Cui#, Xin Wei#, Yundi Chang#, Jun Xu, Cheng Lei, Lei Xue, Yifan Zheng, Zhang Wang, Lingtong Huang, Min Zheng, Hong Luo*, Yuxin Leng*, Chao Jiang*. Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness. Nature Communications (2024)
Qiong Chen*, Chen Peng, Haoteng Xu, Zhuojie Su, Gulimire Yilihan, Xin Wei, Sen Yang, Yueran Shen, Cunqi ye, Chao Jiang*. Placental and fetal enrichment of microplastics from disposable paper cups: implications for metabolic and reproductive health during pregnancy. Journal of Hazardous Materials (2024)
Reported by various domestic media, including 潮新闻、丁香园、科技网 with more than 500,000 views.
Xin Wei#, Li Guo#, Hongliu Cai#, Silan Gu#, Lingling Tang#, Yuxin Leng#.... Lili Ren*, Jianwei Wang*, Chao Jiang*, Lingtong Huang*. MASS Cohort: Multicenter, Longitudinal, and Prospective Study of the Role of Microbiome in Severe Pneumonia and Host Susceptibility. iMeta (2024)
Xin Wei#, Xiaohan Huang#, Silan Gu, Hongliu Cai, Mingqiang Wang, Hongyu Wang, Shengfeng Wang, Chao Jiang*, Lingtong Huang*. Landscape of fungal detection in the lungs of patients with severe pneumonia in the ICU, a multicenter study based on clinical metagenomics. Journal of Infection (2024)
Xin Wei#, Ming-Shian Tsai#, Liang Liang#, Liuyiqi Jiang, Chia-Jui Hung, Laura Jelliffe-Pawlowski, Larry Rand*, Michael Snyder*, Chao Jiang*. Vaginal microbiomes show ethnic evoluti.onary dynamics and positive selectionof Lactobacillus adhesins driven by a long-term niche-specific process. Cell Reports (2024）
Qiong Chen, Feng-Qi Zhao, Bingqing Hana, Jianxin Liua, Chao Jiang*, Hongyun Liu*. Methionyl-Methionine Dipeptide Improves Mammogenesis and Lactogenesis over Free Methionine by Suppressing the Expression of a Novel Long Non-coding RNA MGPNCR that Promotes Dephosphorylation of eIF4B. Journal of Agricultural and Food Chemistry（2024）
Chen Peng, Qiong Chen, Shangjin Tan, Xiaotao Shen, Chao Jiang*. Generalized Reporter Score-based Enrichment Analysis for Omics Data. Briefings in Bioinformatics (2024)
Zinuo Huang#, Chen Peng#, ZixinRong, Liuyiqi Jiang, Yueer Li, Yue Feng, Shuanghong Chen, Changyong Xie*, Chao Jiang*. Longitudinal mapping of personal biotic and abiotic exposomes and transcriptome in underwater confined space using wearable passive samplers. Environmental Science and Technology (2024)
Peng Gao*, Feng Ju*, Chao Jiang*. Editorial: Mapping the exposome and investigating its role in human and environmental health. Frontiers in Microbiology (2024)
Editorial piece for the special exposome collection.
Rong-min Zhang#, Xin-lei Lian#, Li-wei Shi#, Liuyiqi Jiang, Shan-shan Chen, Wen-qing Haung, Jia-en Wu, Fei-jing Wu, Jian Sun, Xiao-ping Liao, Yun-xiao Chong, Ya-hong Liu, Chao Jiang*. Dynamic human exposure to airborne bacteria-associated antibiotic resistomes revealed by longitudinal personal monitoring data. STOTEN (2023)
Liuyiqi Jiang#, Xiao Mu#*, Qing-Qing Liao#, Luqian Zheng#*, Chunyan Li, Yuemei Liu, Bing Yang*, Aiming Ren*, Chao Jiang*, and Xin-Hua Feng*. High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA. mSystems (2023)
Xin Wei, Zinuo Huang+, Liuyiqi Jiang+, Yueer Li, Xinyue Zhang, Yuxin Leng, Chao Jiang*. Charting the landscape of the environmental exposome. iMeta (2022)
Systematically summarized the environmental exposome in air, soil, and water environment and discussed how physical, biological, and chemical exposomes are interacting.
Fang Li#, Liuyiqi Jiang#, Shuming Pan#, Tengjiao Zhu, Shaowei Jiang, Yiwen Fan, Chao Jiang*, Chengjin Gao*, and Yuxin Leng*. Multi-omic Profiling Reveals that Intra-abdominal-Hypertension-Induced Intestinal Damage Can Be Prevented by Microbiome and Metabolic Modulations with 5-Hydroxyindoleacetic Acid as a Diagnostic Marker. mSystems (2022)
Jiang, C.*#, Zhang, X. Y.#, Gao, P.#, Chen, Q., & Snyder, M*. Decoding personal biotic and abiotic airborne exposome. Nature Protocols (2021)
Featured by Nature Protocols as the protocol of the week
Huang, S. and Jiang, C. eLetter RE: Timing the SARS-CoV-2 index case in Hubei province. Science (2021)
Yao, H. P.#, Lu, X. G.#, Chen, Q.#, Xu K. J, Chen, Y., Cheng, M. H., Chen, K. D., Cheng, L. F., Weng, T. H., Shi, D. R., Liu, F. M., Wu, Z. G., Xie, M. J., Wu, H. B., Jin, C. Z., Zheng, M.*, Wu, N. P.*, Jiang, C.*, & Li, L. J.*. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discovery (2020)
Reported by Science Tranlsational Medicine. One of the first papers to report the effect of mutations on the viral biology.
Jiang, C.*#,Wang, X.*#, Li, X.#, Jingga, I.#, Wang, T.#, Liu, Q., & Snyder, M*. Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Cell (2018)
Reported by Nature Medicine, Scientific American, Wired, BBC, and Seeker. Recommended by F1000.
Jiang, C., Brown, P. J., Ducret, A., & Brun, Y. V. Sequential evolution of bacterial morphology by co-option of a developmental regulator. Nature (2014)
Reported by Cell and Current Biology.
Jiang, C., Caccamo, P., & Brun, Y. V. Mechanisms of bacterial morphogenesis: Evolutionary cell biology approaches provide new insights. Bioessays (2015)
Cover Story; Invited review
Zhou and Shen et al., Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host & Microbe (2024)
Liu et al., Multi-omics studies reveal gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL. Microbiome (2023)
Jiang et al., Mitochondrial EglN1 drives breast cancer progression by controlling metabolic adaptation to hypoxic stress. The EMBO Jounrnal (2023)
Xihao Du, Yixuan Jiang, Huichu Li, Qingli Zhang, Xinlei Zhu, Yang Zhang, Cong Liu, Yue Niu, John Ji, Chao Jiang, Jing cai, Renjie Chen*, Haidong Kan*. Dynamic Molecular Choreography Induced by Traffic Exposure: A Randomized, Crossover Trial using Multi-Omics Profiling. Journal of Hazardous Materials (2021)
Lu Chen#, Yanan Zhang#, Xin Shu, Qiong Chen, Tiantian Wei, Heman Wang, Xiaorong Wang, Qirou Wu, Xiaomei Zhang, Xiaoyan Liu, Suya Zheng, Lan Huang, Junyu Xiao, Chao Jiang, Bing Yang, Zhiping Wang* & Xing Guo*. Proteasome regulation by reversible tyrosine phosphorylation at the membrane. Oncogene (2021)
Cissé, O. H., Ma, L., Jiang, C., Snyder, M., & Kovacs, J. A. Humans are selectively exposed to pneumocystis jirovecii. mBio (2020)
Liu, Q., Bortle, K.V., Zhang, Y., Zhao, M., Zhang, J., Geller, B., Gruber, J., Jiang, C.,Wu, J., & Snyder, M. Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. Scientific Report (2018)
Liu, Q., Jiang, C., Xu, J., Zhao, M., Bortle, K.V., Cheng, X., Wang, G., Wu, J., & Snyder, M. Genome-Wide Temporal Profiling of Transcriptome and Open-Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circulation Research (2017)
Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., & Snyder, M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nature Biotechnology (2016)
Hughes, V., Jiang, C., & Brun, Y. V. Caulobacter crescentus. Current Biology (2012) (Invited Review)