A full and continuously updated publication list is available on Google Scholar. Selected representative papers from the PKU-EMBL Lab and related research program are listed below.
# Equal contribution. * Corresponding author.
BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis
Z Qiu#, L Yuan, C Lian, B Lin, J Chen, R Mu, X Qiao, L Zhang, Z Xu, Lu Fan, Yunzeng Zhang, Shanquan Wang, Junyi Li, Huiluo Cao, Bing Li, Baowei Chen, Chi Song, Yongxin Liu, Lili Shi, Yonghong Tian, Jinren Ni, Tong Zhang, Jizhong Zhou, Wei-Qin Zhuang, K Yu#*
Nature Communications, 2024, 15: 2179
Increased replication rates of dissimilatory nitrogen-reducing bacteria leads to decreased anammox reactor performance
R Keren#, J Lawrence#, W Zhuang, D Jenkins, J Banfield, L Alvarez-Cohen, L Zhou*, K Yu*
Microbiome, 2020, 8: 6
An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community
K Yu*#, S Yi#, B Li, F Guo, X Peng, Z Wang, Y Wu, L Alvarez-Cohen and T Zhang*
Microbiome, 2019, 7: 16
A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant
C Deng#, T Chen#, Z Qiu, H Zhou, B Li, Y Zhang, X Xu, CA Lian, X Qiao, K Yu*
Water Research, 2024, 253: 121310
Nitrite impairs bioreactor performance due to decreased replication of Candidatus Brocadia sapporoensis by unbalanced energy allocation
X Qiao#, L Zhang, Z Qiu, Y Wu, C Deng, Y Geng, Y Zhang, Y Yan, B Li, LJ Zhang, W Zhuang, K Yu*
Water Research, 2025, 283: 123806
Bidirectional enhancement of nitrogen removal by indigenous synergetic microalgal-bacterial consortia in harsh low-C/N wastewater
Y Geng#, Z Xiong, L Yang*, CA Lian, S Pavlostathis, Z Qiu, H Chen, Q Luo, Y Liu, Z Liu, P Shao, J Zou, H Jiang, S Luo, K Yu*, X Luo*
Environmental Science & Technology, 2024, 58(12): 5394-5404
Large scale exploration reveals rare taxa as key members shaping microbial assembly in alkaline lake sediments
Z Qiu#, S He#, C Lian, Q Zhang, X Qiao, C Yao, R Mu, L Wang, X Cao, Y Yan, K Yu*
npj Biofilms & Microbiomes, 2024, 10: 62
An integrated meta-omics approach reveals the different response mechanisms of two anammox bacteria towards fluoroquinolone antibiotics
X Qiao#, L Ding, F Fang, C Fu, R Wei, Y Chen, S Zheng, X Wang, Y Yan, K Yang, N Xu, H Tao, K Yu*, L Zhang*
Environment International, 2024, 185: 108505
Self-adaptation of tolerant microalgae-bacterial consortia in landfill leachate: Simultaneous achievement of efficient nitrogen removal and value-added utilization
Y Geng#, C Lian, L Yang, S Pavlostathis, Z Qiu, X Qiao, Z Xiong, N Dong, J Hu, X Luo, K Yu*
Chemical Engineering Journal, 2025, 504: 158912
Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes
Z Qiu#, Y Zhu, Q Zhang, X Qiao, R Mu, Z Xu, Y Yan, F Wang, T Zhang, K Yu*
Environmental Science and Ecotechnology, 2024, 20: 100359
