Xiaoyan Jing#, Yanhai Gong#, Zhidian Diao#, Yan Ma#, Yu Meng, Jie Chen, Yishang Ren, Yuting Liang, Yinchao Li, Weihan Sun, Jia Zhang, Yuetong Ji, Zhiqi Cong, Shengying Li, Bo Ma, Zhisong Cui*, Li Ma*, Jian Xu*. Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-Seq. The Innovation, 2025, 6(3):100759. https://doi.org/10.1016/j.xinn.2024.100759

Luyang Sun# *, Xiaolu Liu#, Li Zhou#, Hao Wang, Chao Lian, Zhaoshan, Zhong, Minxiao Wang, Hao Chen, Chaolun Li*. Shallow-water mussels adapt to deep-sea environment through transcriptomic and metagenomic insights. Communications Biology, 2025, 8(1):46. https://doi.org/10.1038/s42003-024-07382-0

Fengyi Liu, Anle Ge, Xixian Wang, Fei Wu, Jian Xu, Bo Ma*. A contracted channel droplet reinjection chip-based simple integrated ddpcr System for SARS-CoV-2 and H1N1 detection. Analytical Chemistry, 97(4):2195-2203. https://doi.org/10.1021/acs.analchem.4c05201

Xiaoshan Zheng#, Rui Li#, Ting Wang#, Xunrong Li, Xiao Han, Yajie Dai, Jiquan Liu*, Jian Xu*. Unraveling antibacterial mechanisms of surfactants against Staphylococcus aureus via single-cell Raman spectroscopy. Analytical Chemistry, 2025, 97(17):9202-9211. https://doi.org/10.1021/acs.analchem.4c06380

Jia Zhang#*, Jianmei Wang#, Pengfei Zhu#, Zhidian Diao#, Shuhua Tian, Ziyuan Ding, Yongming Duan, Teng Xu, Xuan Zhou, Xixian Wang, Xia Ma, Ting Sun, Xiaoyan Jing, Weilian Hung, Bo Ma, Shi Huang*, Xiaowei Zheng*, Jian Xu*. Raman flow cytometry based single-cell species classification, viable-cell counting and vitality test for probiotic products. iMetaOmics, 2025, 2(3):e70024. https://doi.org/10.1002/imo2.70024

Xixian Wang#, Sen Wang#, Zhidian Diao#, Xibao Hou#, Yanhai Gong, Qing Sun, Jiaping Zhang, Lihui Ren, Yuandong Li, Yuetong Ji, Wei Shen, Yifeng Yin, Shi Huang, Xiaojin Song, Qiu Cui, Yingang Feng*, Jian Xu*, Bo Ma*. Label-free high-throughput live-cell sorting of genome-wide random mutagenesis libraries for metabolic traits by Raman flow cytometry. Proceedings of the National Academy of Sciences of the United States of America, 2025, 122(22):e2503641122. https://doi.org/10.1073/pnas.2503641122

Jianmei Wang, Lei Zhang, Xuechao Zhao, Jia Zhang, Rongze Chen, Yuetong Ji, Bo Ma, Fang Yang*, Jian Xu*. Rapid profiling of between-species metabolic interactions in cocultures by D2O‑probed single-cell Raman microspectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2025, 343:126513. https://doi.org/10.1016/j.saa.2025.126513

Zhidian Diao#, Anle Ge#, Hao Zhou, Xuan Zhou, Lingyan Kan, Wei Gao, Wei Shen, Yuetong Ji, Hongwei Wang, Jian Xu*, Xixian Wang*, Bo Ma*. Rapid quantitative detection, identification and antimicrobial susceptibility testing of pathogens in blood using the static droplet array (SDA) chip-based method. Sensors and Actuators B: Chemical, 2025, 442: 138183. https://doi.org/10.1016/j.snb.2025.138183

Xiaotong Ji#, Xixian Wang#, Wenjun Zhou*, Lin Chen, Tianzhong Liu, Jian Xu, Bo Ma*. Label-free isolation of lipid-rich Saccharomyces cerevisiae mutant by high-throughput flow-mode Raman-activated cell sorting and multi-omics analysis for uncovering the mechanism of enhanced lipid accumulation. Biotechnology for Biofuels and Bioproducts, 2025, 18(1):75. https://doi.org/10.1186/s13068-025-02677-8

Yanhai Gong#, Qintao Wang#, Li Wei, Lianhong Wang, Nana Lv, Xuefeng Du, Chen Shen, Yi Xin, Luyang Sun*, Jian Xu*. Multi-dimensional epigenomic dynamics converge on H3K4 regulation of low CO₂ adaptation in Nannochloropsis oceanica. Plant Communications, 2025, 6(12):101534. https://doi.org/10.1016/j.xplc.2025.101534

Zhidian Diao#, Qiqun Peng#, Sijun Luo, Lingyan Kan, Anle Ge, Wei Gao, Runxia Li, Weiwei Bao, Xixian Wang, Yuetong Ji, Jian Xu*, Shihui Yang*, Bo Ma*. AI-powered high-throughput digital colony picker platform for sorting microbial strains by multi-modal phenotypes. Nature Communications, 2025, 16: 8769. https://doi.org/10.1038/s41467-025-63929-7

Li Liu, Bing Feng, Yang Song, Taijie Zhan, Dongxin Liu, Jia Ding, Xiaohui Song, Jian Xu#, Duochun Wang#, Qiang Wei#. Detecting and classifying metabolic activity of Staphylococcus aureus by D₂O-probed single-cell Raman spectroscopy and machine learning. Biosafety and Health, 2025, 7(2):94-102. https://doi.org/10.1016/j.bsheal.2025.03.004 （第五单位）

Xinxin Kang#, Weixing Liu#, Xixian Wang, Muhammad Aslam, Guanglei Liu*, Zhe Chi*. Iron-derepressed robust production of fusarinine C siderophore by Aureobasidium melanogenum. ACS Synthetic Biology, 2025, 14(5):1625-1637. https://doi.org/10.1021/acssynbio.4c00897（第三单位）

Fang Yang#, Fei Teng#*, Yufeng Zhang#, Yanfei Sun, Jian Xu*, Shi Huang*. Single-tooth resolved, whole-mouth prediction of early childhood caries via spatiotemporal variations of plaque microbiota. Cell Host & Microbe, 2025, 33(6):1019-1032.e6. https://doi.org/10.1016/j.chom.2025.05.006 （第五单位）

Xiaoyan Jing, Yanhai Gong, Yishang Ren, Liyan Wang, Runzhi Mu, Pengcheng Sun, Zhidian Diao, Yu Meng, Liming Huang, Xixian Wang, Jia Zhang, Jiaxuan Luan, Yuetong Ji, Bo Ma, Huihui Pan*, Yushu Jing*, Jian Xu*. Mining robust in situ phosphorus-accumulating organisms via single-cell RACS-Culture for rational ecosystem engineering. Water Research, 2025, 284:124025. https://doi.org/10.1016/j.watres.2025.124025（第二单位）

刘佳, 任义尚, 荆晓艳*, 许拉*. 基于拉曼光谱“先筛后养”策略在功能微生物资源挖掘中的应用与展望. 生物技术通报, 2025, 42(5):1-13. https://doi.org/10.13560/j.cnki.biotech.bull.1985.2025-0480（第二单位）

Yang He#, Yuehui He#, Yuanyuan Zhou, Xunrong Li, Xinran Zhang, Yuetong Ji, Junhong Yu*, Jian Xu*. Tracking production and interconversion of extra- and intra-cellular metabolites during beer fermentation by ramanomics. Bioresource Technology, 2025, 443:133788. https://doi.org/10.1016/j.biortech.2025.133788 （第二单位）

Huaizhi Zhang, Xiaoyan Jing, Yanhai Gong, Pengfei Zheng, Yishang Ren, Rongze Chen, YuMei Wu, Shuziyi Liu, Lijie Zhang*, Jian Xu*, Yan Xu*. Single-cell phenotyping and sequencing uncover metabolically active low-abundance yeasts in thermophilic fermentation. Bioresource Technology, 2025. https://doi.org/10.1016/j.biortech.2025.133803（第二单位）

刘双江, 戴磊, 等. 合成微生物组工程[M]. 北京: 山东科学技术出版社和科学出版社, 2025:39-48.