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.
PKU EMBL Comprehensive List of Publications & Citation Metrics
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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, L Fan, Y Zhang, S Wang, J Li, H Cao, B Li, B Chen, C Song, Y Liu, L Shi, Y Tian, J Ni, T Zhang, J Zhou, W Zhuang, K Yu#*
Nature Communications, 2024
Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments
Zhiguang Qiu#, Shuhang He#, Chun-Ang Lian, Xuejiao Qiao, Qing Zhang, Ciqin Yao, Rong Mu, Li Wang, Xiao-Ai Cao, Yan Yan & Ke Yu*
npj Biofilms and Microbiomes, 2024
Rethinking Text-based Protein Understanding: Retrieval or LLM?
Juntong Wu, Zijing Liu, He Cao, Li Hao, Bin Feng, Zishan Shu, Ke Yu, Li Yuan, Yu Li*
EMNLP Oral, 2025
Increased replication of dissimilatory nitrogen-reducing bacteria leads to decreased anammox reactor performance
R Keren#, J E.Lawrence#, W Zhuang, D Jenkins, J F.Banfield, L Alvarez-Cohen, L Zhou, K Yu
Microbiome, 2020
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, T Zhang
Microbiome, 2019
Unlocking microbial synergy in mcroalgae-bcteria gnules: RSM-driven optimization and lifecycle microbial metagenomics for high-ammonia wastewater treatment
Yanni Geng, Chun-Ang Lian, Liming Yang, Spyros G Pavlostathis, Xuejiao Qiao, Zhiguang Qiu, Yu Wang, Nan Dong, Anjie Li, Xubiao Luo, Ke Yu*
Water Research, 2025
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, C Lian, X Qiao, K Yu*
Water Research, 2024
Bidirectional enhancement of nitrogen removal by indigenous synergetic microalgal− bacterial consortia in harsh low-C/N Wastewater
Y Geng#, Z Xiong, Li Yang, C Lian, S G.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
Prenatal transfer of polybrominated diphenyl ethers (PBDEs) results in developmental neurotoxicity in zebrafish larvae
L Chen#, K Yu#, C Huang, L Yu, B Zhu, PK Lam, JCW Lam, B Zhou*
Environmental Science & Technology, 2012
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
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, W Zhuang, K Yu*
Environmental Science and Ecotechnology, 2024