*co-first author, #co-corresponding author, Ma Lab member

Yan Huang, Teng Wang, Yingfei Ma. Gut microbiome: Temperate and latent phages are dominant in the human gut. Curr Biol (2025)

Shengjian Yuan^*, Yanchen Li^*, Chunhua Kou, Yichen Sun, Yingfei Ma. CRISPR/Cas12a-based genome editing for cyanophage of Anabeana sp. Synth Syst Biotechnol (2024) 

Xin Tan*, Kai Chen*, Zhihuan Jiang, Ziqiang Liu, Siyun Wang, Yong Ying, Jieqiong Zhang, Shengjian Yuan, Zhipeng Huang, Ruyue Gao, Min Zhao, Aoting Weng, Yongqing Yang, Huilong Luo, Daizhou Zhang, Yingfei Ma. Evaluation of the impact of repeated intravenous phage doses on mammalian host-phage interactions. J Virol (2024)

Siyun Wang, Xin Tan^#, Ziqiang Liu, Hui Ma, Tianbin Liu, Yongqing Yang, Yong Ying, Ruyue Gao, Daizhou Zhang, Yingfei Ma, Kai Chen^#, Lin Lin^#, Zhihuan Jiang^#, Jialin Yu^#. Pharmacokinetics and safety evaluation of intravenously administered Pseudomonas phage PA_LZ7 in a mouse model. Microbiol Spectr (2024).

Min Zhao, Xin Tan^#, Zi-qiang Liu, Lei Dou, Dong Liu, Yong-jun Pan, Ying-fei Ma^#, Jia-lin Yu^#. Engineered phage with cell-penetrating peptides for intracellular bacterial infections. mSystems (2023)

Lili Yang,  Guoqin Mai, Zheng Hu, Haokui Zhou, Lei Dai, Ziqing Deng, Yingfei Ma. Global transmission of broad-host-range plasmids derived from the human gut microbiome. Nucleic Acids Research (2023).

Weijie Liang^*，Yuqiong Yang^*, Shenhai Gong^*, Mingyuan Wei^*, Yingfei Ma^*, Ruipei Feng, Jingyuan Gao, Xiaomin Liu, Fuyi Tu, Wei Ma, Xinzhu Yi, Zhenyu Liang, Fengyan Wang, Lingwei Wang, Dandan Chen, Wensheng Shu, Bruce E Miller, Ruth Tal-Singer, Gavin C Donaldson, Jadwiga A Wedzicha, Dave Singh, Tom M A Wilkinson, Christopher E Brightling, Rongchang Chen, Nanshan Zhong, Zhang Wang.  Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease. Cell Host & Microbe (2023).

Juntao Shen, Jieqiong Zhang, Luofei Mo, Yanchen Li, Yake Li, Cun Li, Xiaoxian Kuang, Zining Tao, Zepeng Qu, Lu Wu, Junyu Chen, Shiying Liu, Linfang Zeng, Zexi He, Zuohong Chen, Yu Deng, Tong Zhang, Bing Li, Lei Dai^#, Yingfei Ma^#. Large-scale phage cultivation for commensal human gut bacteria. Cell Host & Microbe (2023).

Ran Li^*, Yongming Wang^*, Han Hu, Yan Tan, Yingfei Ma. Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut. Nat Commun (2022). 

Peifen Chen^*, Ziqiang Liu^*, Xin Tan^*, Haijiang Wang, Yiyang Liang, Yingjun Kong, Wenxue Sun, Liqin Sun, Yingfei Ma^#, Hongzhou Lu^#. Bacteriophage therapy for empyema caused by carbapenem-resistant Pseudomonas aeruginosa. Bioscience Trends (2022).

Shengjian Yuan, Juan Shi,Jianrong Jiang, Yingfei Ma. Genome-scale top-down reduction of phages to generate viable minimal phage genomes. Nucleic Acids Research (2022).

Shun Guo, Haoran Zhang, Yunmeng Chu, Qingshan Jiang^#, Yingfei Ma^#. A neural network-based framework to understand the Type 2 Diabetes (T2D)-related alteration of the human gut microbiome. iMeta (2022).

Yunmeng Chu^*, Shun Guo^*, Dachao Cui, Xiongfei Fu, Yingfei Ma. DeephageTP: A Convolutional Neural Network Framework for Identifying Phage-specific Proteins from metagenomic sequencing data. PeerJ (2022).

Xin Tan^*, Huaisheng Chen^*, Min Zhang, Ying Zhao, Yichun Jiang, Xueyan Liu, Wei Huang^#, Yingfei Ma^#. Clinical experience of personalized phage therapy against carbapenem-resistant Acinetobacter baumannii lung infection in a patient with chronic obstructive pulmonary disease. Front Cell Infect Microbiol (2021).

Yijing Chen, Lihua Fang, Shuo Chen, Haokui Zhou, Yingying Fan, Li Lin, Jing Li, Jinying Xu, Yuewen Chen, Yingfei Ma^#, Yu Chen^#. Gut microbiome alterations precede cerebral amyloidosis and microglial pathology in a mouse model of Alzheimer's disease. BioMed Res int (2020).

Lingling Wen^*, Ling Chen^*, Shengjian Yuan, Linyu Tian, Tingwei Yan, Haoran Zhang, Yang Tan, Yue Yu, Hui Wen, Yingfei Ma, Ting Wei^#, Shuqiang Huang^#. Complete genome analysis of PaGz-1 and PaZq-1, two novel phages belonging to the genus Pakpunavirus. Arch Virol (2020).

Ling Chen, Quan Liu, Jiqiang Fan, Tingwei Yan, Haoran Zhang, Jinfang Yang, Deng Deng, Chaolan Liu, Ting Wei^#, and Yingfei Ma^#. Characterization and genomic analysis of ValSw3-3, a new Siphoviridae bacteriophage infecting Vibrio alginolyticus. J Virol (2020).

Ling Chen^*, Jiqiang Fan^*, Tingwei Yan, Quan Liu, Shengjian Yuan, Haoran Zhang, Jinfang Yang, Deng Deng, Shuqiang Huang^#, Yingfei Ma^#. Isolation and characterization of specific phages to prepare a cocktail preventing Vibrio sp. Va-F3 infections in shrimp (Litopenaeus vannamei). Front Microbiol (2019).

Guoqin Mai, Limei Chen, Ran Li, Quan Liu, Haoran Zhang, and Yingfei Ma. Common Core Bacterial Biomarkers of Bladder Cancer Based on Multiple Datasets. BioMed Res Int (2019).

Ling Chen^*, Guoye Guan^*, Quan Liu, Shengjian Yuan, Tingwei Yan, Linyu Tian, Yan Zhou, Yixuan Zhao, Yingfei Ma, Ting Wei^#, Xiongfei Fu^#.  Characterization and complete genomic analysis of two Salmonella phages, SenALZ1 and SenASZ3, new members of the genus Cba120virus.  Arch Virol (2019). 

Jinming Cui^*, Guoqin Mai^*, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma^#, Chenli Liu^#. Metagenomic insights into a cellulose-rich niche reveal microbial cooperation in cellulose degradation. Front Microbiol (2019). 

Ling Chen, Shengjian Yuan, Quan Liu, Guoqing Mai, Jinfang Yang, Deng Deng, Bingzhao Zhang, Chenli Liu, Yingfei Ma. In vitro design and evaluation of phage cocktails against Aeromonas salmonicida. Front Microbiol (2018).

Shengjian Yuan, Ling Chen, Quan Liu, Yan Zhou, Jingfang Yang, Deng Deng, Hongping Li, Yingfei Ma. Characterization and genomic analyses of Aeromonas hydrophila phages AhSzq-1 and AhSzw-1, isolates representing new species within the T5virus genus. Arch Virol (2018).

Yingfei Ma^#, Xiaoyan You, Guoqin Mai, Taku Tokuyasu, Chenli Liu^#. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome (2018).

Minzhi Jiang, Zhijun Qiu, Guangwu Zhang, Shiyin Gao, Xiaoyan You^#, Ying-fei Ma^#. Mucilaginibacter xinganensis sp. nov., a phenanthrene-degrading bacterium isolated from wetland soil. Antonie Van Leeuwenhoek (2018).

Zhenlong Yang^*, Shengjian Yuan^*, Ling Chen, Quan Liu, Haoran Zhang, Yingfei Ma, Ting Wei^#, Shuqiang Huang^#. Complete genome analysis of bacteriophage AsXd-1, a new member of the genus Hk97virus, family Siphoviridae. Arch Virol (2018).

Jiqiang Fan^*, Limei Chen^*, Guoqin Mai, Haoran Zhang, Jinfang Yang, Deng Deng, Yingfei Ma. Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight. Sci Rep (2018).

Jinming Cui^*, Minfeng Xiao^*, Mingzhu Liu, Zuowei Wang, Furong Liu, Hailin Meng, Honggang Zhang, Jinfang Yang, Deng Deng, Huang, Shuqiang Huang, Yingfei Ma^#, Chenli Liu^#. Coupling metagenomics with cultivation to select host-specific probiotic micro-organisms for subtropical aquaculture. J Appl Microbiol (2017).

Yang Sun^*, Yingfei Ma^*, Ping Lin^*, Yiwei Tang, Liying Yang, Yinzhong Shen, Renfan Zhang, Li Liu, Jun Cheng, Jiashen Shao, Tangkai Qi, Yan Tang, Rentian Cai, Liqian Guan, Bin Luo, Meiyan Sun, Ben Li^#, Zhiheng Pei, Hongzhou Lu^#. Fecal bacterial microbiome diversity in chronic HIV-infected patients in China. Emerg Microbes Infect (2016).