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PUBLICATIONS
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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, mSystmes (2023)
Yang, Lili; Mai, Guoqin; Hu, Zheng; Zhou, Haokui; Dai, Lei; Deng, Ziqing; Ma, Yingfei. 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 research international (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. Archives of Virology (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. Journal of Virology (2020).
Ling Chen#, Jiqiang Fan#, Tingwei Yan, Quan Liu, Shengjian Yuan, Haoran Zhang, Jinfang Yang, Deng Deng, Shuqiang Huang* and 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 Research International (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. Archives of Virology (2019).
Jinming Cui#, Guoqin Mai#, Zuowei Wang, Quan Liu, Yan Zhou,Yingfei Ma* and 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 and 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. Archives of virology (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. Archives of Virology (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. Scientific Reports (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. Journal of applied microbiology(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. Emerging Microbes & Infections (2016).
Liying Yang, Michael A Poles, Gene S Fisch, Yingfei Ma, Carlos Nossa, Joan A Phelan, Zhiheng Pei. Loss of colonization resistance in the proximal gut in HIV infection. AIDS (2016).
Wuze Ren, Yingfei Ma, Liying Yang, Agegnehu Gettie, January Salas, Kasi Russell, James Blanchard, Amy Davidow, Zhiheng Pei, Theresa L Chang, Cecilia Cheng-Mayer. Fast disease progression in SHIV infected female macaques is accompanied by a robust local inflammatory innate immune and microbial response. AIDS (2015).
Yingfei Ma, Lisa Zeigler Allen, Brian Palenik Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environ Microbiol Rep (2014).
Yingfei Ma, Ramana Madupu, Ulas Karaoz, Carlos W. Nossa, Liying Yang, Shibu Yooseph, Patrick S. Yachimski, Eoin L. Brodie, Karen E. Nelson, Zhiheng Pei.Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. J Virol (2014).
Yingfei Ma, Ian T Paulsen, Brian Palenik. Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environ Microbiol (2012).
Lei Liu, JianFeng Wu, YingFei Ma, ShengYue Wang, GuoPing Zhao, ShuangJiang Liu. A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with comamonas sp. Strain cnb-1. J Bacteriol (2007).
Chenli Liu, Yehui Wu, Li Li, Yingfei Ma, Zongze Shao. Thalassospira xiamenensis sp. Nov. And thalassospira profundimaris sp. Nov. Int J Syst Evol Microbiol (2007).
Yun Zhang1, YingFei Ma, SuWei Qi, Bo Meng, Muhammad Tausif Chaudhry, SiQi Liu, ShuangJiang Liu. Responses to arsenate stress by comamonas sp. Strain cnb-1 at genetic and proteomic levels. Microbiology (2007).
YingFei Ma, JianFeng Wu, ShengYue Wang, ChengYing Jiang, Yun Zhang, SuWei Qi, Lei Liu, GuoPing Zhao.Nucleotide sequence of plasmid pCNB1 from Comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. Appl Environ Microbiol (2007).
Jianfeng Wu, Chengying Jiang, Baojun Wang, Yingfei Ma, Zhipei Liu, Shuangjiang Liu. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in comamonas sp. Strain cnb-1. Appl Environ Microbiol (2006).
Yingfei Ma, Lin Wang, Zongze Shao. Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from antarctic soils and the role of large plasmids in horizontal gene transfer. Environ Microbiol (2006).
YingFei Ma, Yun Zhang, JiaYue Zhang, DongWei Chen, Yongqian Zhu, Huajun Zheng, ShengYue Wang, ChengYing Jiang, GuoPing Zhao, ShuangJiang Liu. The complete genome of comamonas testosteroni reveals its genetic adaptations to changing environments. Appl Environ Microbiol(2009).
