Shanghai Institute of Material Medical Chinese Academy of Sciences

Biography

Dr. Xiangwu Ju earned his Ph.D. from Peking Union Medical College (PUMC) and completed postdoctoral training at The Rockefeller University. He is a Principal Investigator at the Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences (CAS), where he leads the Bacterial Gene Regulation and Antimicrobial Resistance Research Group.

Dr. Ju studies bacterial gene regulation, transcription dynamics, and antimicrobial resistance using customized, high-resolution omics approaches. He developed SEnd-seq, a full-length RNA sequencing technology for transcriptome-wide profiling of RNA molecules at single-nucleotide resolution. Using SEnd-seq, his research has revealed previously unrecognized features of bacterial transcription, including bidirectional termination in Escherichia coli and pervasive transcriptional pausing in Mycobacterium tuberculosis (Mtb).

Dr. Ju has published as a first or co-first author in journals including Nature, Nature Microbiology, Journal of Virology, Respiratory Research, and Molecular Psychiatry. His work advances understanding of bacterial gene regulation and the mechanisms underlying antimicrobial resistance.

Education Experience：

2003.09 - 2007.06 B.S. in Pharmacy, Shenyang Pharmaceutical University (SPU)

2007.09 - 2012.07 Ph.D. in Biochemistry and Molecular Biology, Peking Union Medical College (PUMC) / Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

Work Experience：

2012.10 - 2015.12 Postdoctoral Researcher, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

2016.02 - 2021.01 Postdoctoral Fellow, Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University

2021.02 - 2023.11 Research Associate, Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University

2023.12 - 2025.03 Senior Research Associate, Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University

2025.04 - present Principal Investigator, Bacterial Gene Regulation and Drug Resistance Research Group, Shanghai Institute of Materia Medica, Chinese Academy of Sciences

Research Directions

Rapid, precise gene regulation enables bacteria to survive environmental changes and cause disease. Our laboratory investigates how bacteria coordinate transcription, translation, and RNA turnover, and how these processes contribute to antimicrobial tolerance and resistance. We combine genomics, transcriptomics, biochemistry, and computational approaches to study Mtb and other clinically important pathogens.

Our research focuses on:

1.Gene expression regulation: How transcriptional pausing, transcription–translation coupling, and RNA degradation shape Mtb transcription output.

2.Drug tolerance and persistence: How Mtb adapt to antibiotic stress and how these mechanisms may reveal new therapeutic targets.

3.Transcriptome technologies: Developing and applying cutting-edge genomic methods to study pathogen responses to infection and environmental change.

Grants & Research Projects

National Natural Science Foundation of China (NSFC) General Program, 2026.01–2028.12

Achievements

morefold

Social Titles

morefold

Awards & Honors

morefold

Publications

Selected Publications

Recent publications：

Ju X#, Liu S#. High-resolution profiling of bacterial transcriptomes by SEnd-seq. Biochemical Journal. 2026 Sep 2;483(9):1713-1727. https://doi: 10.1042/BCJ20250251.

Kim S, Zhang Y, Ju X, Hassan A, Wang YH, Liu S, Kim S. Spatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria. Nature Microbiology 11, 1920–1933 (2026). https://doi.org/10.1038/s41564-026-02374-8

Eckartt KA, Munsamy-Govender V, Quiñones-Garcia S, DeJesus MA, Ju X, et al. Transcription attenuation amplifies collateral vulnerabilities in rifampicin-resistant Mycobacterium tuberculosis. Nature Microbiology 11, 1696–1710 (2026). https://doi.org/10.1038/s41564-026-02357-9

Watters JW, Mueller AU, Ju X, Chuquimarca SJ, Ye HJ, Darst SA, et al. Structural principles of transcriptional collisions. bioRxiv (2026).

Representative first-author publications：

Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S. Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. Nature. 2024;627:424–430. https://doi: 10.1038/s41586-024-07105-9.

Ju X, Li D, Liu S. Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. Nature Microbiology. 2019;4:1907–1918. https://doi: 10.1038/s41564-019-0500-z

Li S*, Ju X*, Liu Q, Yan Y, Zhang C, Qin Y, et al. Ambient atmospheric particulate matter worsens influenza A virus-induced lung injury through lysosomal dysfunction. Respiratory Research. 2023;24:306. https://doi: 10.1186/s12931-023-02618-9

Ju X*, Yan Y*, Liu Q, Li N, Sheng M, Zhang L, et al. Neuraminidase of influenza A virus binds LAMPs directly and induces lysosome rupture. Journal of Virology. 2015;89:10347–10358. https://doi: 10.1128/JVI.01411-15

Xu C*, Ju X*, Song D*, Huang F*, Tang D, et al. Association between psychophysical characteristics and genome-wide gene expression changes during human adaptation to the extreme Antarctic environment. Molecular Psychiatry. 2015;20:536–544. https://doi: 10.1038/mp.2014.72

Additional selected publications:

Wang L, Watters JW, Ju X, Lu G, Liu S. Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. Molecular Cell. 2023;83:1153–1164. https://doi: 10.1016/j.molcel.2023.02.017.

Zhao Y, Huang F, Zou Z, Bi Y, Yang Y, Zhang C, Liu Q, Shang D, Yan Y, Ju X, et al. Avian influenza viruses suppress innate immunity by inducing trans-transcriptional readthrough via SSU72. Cellular & Molecular Immunology. 2022;19:702–714. https://doi: 10.1038/s41423-022-00843-8

Zou Z, Yan Y, Shu Y, Gao R, Sun Y, Li X, Ju X, et al. Angiotensin-converting enzyme 2 protects from lethal avian influenza A H5N1 infections. Nature Communications. 2014;5:3594. https://doi.org/10.1038/ncomms4594

morefold