Publications

Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities
Huan Du, Meng Li, Yang Liu
Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage
Yang Tong, Xinying Wu, Yang Liu, Huiyu Chen, Yan Zhou, Li Jiang, Meng Li, Suwen Zhao, Yan Zhang
The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea
Yang Liu, Meng Li
The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis
Zhichao Zhou, Yang Liu, Karthik Anantharaman, Meng Li
Microbial active functional modules derived from network analysis and metabolic interactions decipher the complex microbiome assembly in mangrove sediments
Huan Du, Jie Pan, Dayu Zou, Yuhan Huang, Yang Liu, Meng Li
Subgroup level differences of physiological activities in marine Lokiarchaeota
Xiuran Yin, Mingwei Cai, Yang Liu, Guowei Zhou, Tim Richter-Heitmann, David A. Aromokeye, Ajinkya C. Kulkarni, Rolf Nimzyk, Henrik Cullhed, Zhichao Zhou, Jie Pan, Yuchun Yang, Ji-Dong Gu, Marcus Elvert, Meng Li, Michael W. Friedrich
Rotifers stimulate the specific uptake rate in lotic phototrophic biofilms
Yang Liu, Michèle Tackx, Alain Dauta, Frédéric Julien, Evelyne Buffan‐Dubau
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway
Jia-Wei Zhang, Hong-Po Dong, Li-Jun Hou, Yang Liu, Ya-Fei Ou, Yan-Ling Zheng, Ping Han, Xia Liang, Guo-Yu Yin, Dian-Ming Wu, Min Liu, Meng Li
Expanded diversity of Asgard archaea and their relationships with eukaryotes
Yang Liu, Kira S. Makarova, Wen-Cong Huang, Yuri I. Wolf, Anastasia N. Nikolskaya, Xinxu Zhang, Mingwei Cai, Cui-Jing Zhang, Wei Xu, Zhuhua Luo, Lei Cheng, Eugene V. Koonin, Meng Li
Ecological features and global distribution of Asgard archaea
Mingwei Cai, Tim Richter-Heitmann, Xiuran Yin, Wen-Cong Huang, Yuchun Yang, Cuijing Zhang, Changhai Duan, Jie Pan, Yang Liu, Yue Liu, Michael W. Friedrich, Meng Li
Diversity of cellulolytic microorganisms and microbial cellulases
Lirui Liu, Wen-Cong Huang, Yang Liu, Meng Li
Desulfovibrio feeding Methanobacterium with electrons in conductive methanogenic aggregates from coastal zones
Shiling Zheng, Meng Li, Yang Liu, Fanghua Liu
Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota
Wen-Cong Huang, Yang Liu, Xinxu Zhang, Cui-Jing Zhang, Dayu Zou, Shiling Zheng, Wei Xu, Zhuhua Luo, Fanghua Liu, Meng Li
Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea
Kira S. Makarova, Yuri I. Wolf, Sergey A. Shmakov, Yang Liu, Meng Li, Eugene V. Koonin
The aquatic microbial community: a bibliometric analysis of global research trends (1991– 2018)
Wanlin Du, Yang Liu, Jinhui Sun, Naicheng Wu, Yongzhan Mai, Chao Wang
Perspectives on Cultivation Strategies of Archaea
Yihua Sun, Yang Liu, Jie Pan, Fengping Wang, Meng Li
Modelling fungal growth with fractional transport models
Huan Du, Patrick Perré, Ian Turner
Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary
Dayu Zou, Ru Wan, Lili Han, Min Nina Xu, Yang Liu, Hongbin Liu, Shuh-Ji Kao, Meng Li
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments
Cui-Jing Zhang, Jie Pan, Yang Liu, Chang-Hai Duan, Meng Li
Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota
Jie Pan, Zhichao Zhou, Oded Béjà, Mingwei Cai, Yuchun Yang, Yang Liu, Ji-Dong Gu, Meng Li
Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment
Zhichao Zhou, Yang Liu, Wei Xu, Jie Pan, Zhu-Hua Luo, Meng Li
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes
Zhichao Zhou, Yang Liu, Jie Pan, Brandi R. Cron, Brandy M. Toner, Karthik Anantharaman, John A. Breier, Gregory J. Dick, Meng Li
Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation
Mingwei Cai, Yang Liu, Xiuran Yin, Zhichao Zhou, Michael W. Friedrich, Tim Richter-Heitmann, Rolf Nimzyk, Ajinkya Kulkarni, Xiaowen Wang, Wenjin Li, Jie Pan, Yuchun Yang, Ji-Dong Gu, Meng Li
Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems
Yuchun Yang, Jie Pan, Zhichao Zhou, Jiapeng Wu, Yang Liu, Jih-Gaw Lin, Yiguo Hong, Xiaoyan Li, Meng Li, Ji-Dong Gu
Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea
Zhongyi Lu, Ting Fu, Tianyi Li, Yang Liu, Siyu Zhang, Jinquan Li, Junbiao Dai, Eugene V. Koonin, Guohui Li, Huiying Chu, Meng Li
Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems
Yuchun Yang, Holger Daims, Yang Liu, Craig W. Herbold, Petra Pjevac, Jih-Gaw Lin, Meng Li, Ji-Dong Gu
A novel lattice-based model for investigating three-dimensional fungal growth on solid media
Huan Du, Patrick Perré
Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench
Jiwen Liu, Yanfen Zheng, Heyu Lin, Xuchen Wang, Meng Li, Yang Liu, Meng Yu, Meixun Zhao, Nikolai Pedentchouk, David J. Lea-Smith, Jonathan D. Todd, Clayton R. Magill, Wei-Jia Zhang, Shun Zhou, Delei Song, Haohui Zhong, Yu Xin, Min Yu, Jiwei Tian, Xiao-Hua Zhang
Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes
Cui-Jing Zhang, Jie Pan, Chang-Hai Duan, Yong-Ming Wang, Yang Liu, Jian Sun, Hai-Chao Zhou, Xin Song, Meng Li
Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge
Zongbao Liu, Uli Klümper, Yang Liu, Yuchun Yang, Qiaoyan Wei, Jih-Gaw Lin, Ji-Dong Gu, Meng Li
Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)
Zhichao Zhou, Yang Liu, Karen G. Lloyd, Jie Pan, Yuchun Yang, Ji-Dong Gu, Meng Li
Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons
Baozhan Wang, Wei Qin, Yi Ren, Xue Zhou, Man-Young Jung, Ping Han, Emiley A. Eloe-Fadrosh, Meng Li, Yue Zheng, Lu Lu, Xin Yan, Junbin Ji, Yang Liu, Linmeng Liu, Cheryl Heiner, Richard Hall, Willm Martens-Habbena, Craig W. Herbold, Sung-keun Rhee, Douglas H. Bartlett, Li Huang, Anitra E. Ingalls, Michael Wagner, David A. Stahl, Zhongjun Jia
A 3-variable PDE model for predicting fungal growth derived from microscopic mechanisms
Huan Du, Thi-Bich-Thuy Tran, Patrick Perré
Two or three domains: a new view of tree of life in the genomics era
Zhichao Zhou, Yang Liu, Meng Li, Ji-Dong Gu
Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench
Xinxu Zhang, Wei Xu, Yang Liu, Mingwei Cai, Zhuhua Luo, Meng Li
Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages
Xiaobo Liu, Meng Li, Cindy J. Castelle, Alexander J. Probst, Zhichao Zhou, Jie Pan, Yang Liu, Jillian F. Banfield, Ji-Dong Gu
Global trends in phytoplankton research of river ecosystems during 1991–2016: A bibliometric analysis
Chao Wang, Yang Liu, Qin Zhan, Wanling Yang, Naicheng Wu
Diversity and distribution of Archaea in global estuarine ecosystems
Xiaobo Liu, Jie Pan, Yang Liu, Meng Li, Ji-Dong Gu
Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota
Yang Liu, Zhichao Zhou, Jie Pan, Brett J. Baker, Ji-Dong Gu, Meng Li
A lattice-based system for modeling fungal mycelial growth in complex environments
Huan Du, Mehdi Ayouz, Pin Lv, Patrick Perré
A global analysis on the distribution pattern of the bacteria coupling simultaneous methane oxidation to nitrite reduction
Xiaowei Zhang, Yang Liu, Ji-Dong Gu
Using river microalgae as indicators for freshwater biomonitoring: Review of published research and future directions
Naicheng Wu, Xuhui Dong, Yang Liu, Chao Wang, Annette Baattrup-Pedersen, Tenna Riis
Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing
Zhichao Zhou, Han Meng, Yang Liu, Ji-Dong Gu, Meng Li
Role of biodiversity in the biogeochemical processes at the water-sediment interface of macroporous river bed: An experimental approach
Yang Liu, Karine Dedieu, Jose-Miguel Sánchez-Pérez, Bernard Montuelle, Evelyne Buffan-Dubau, Frédéric Julien, Frédéric Azémar, Sabine Sauvage, Pierre Marmonier, Jingmei Yao, Philippe Vervier, Magali Gerino
Morphological Characterization and Quantification of the Mycelial Growth of the Brown-Rot Fungus Postia placenta for Modeling Purposes
Huan Du, Pin Lv, Mehdi Ayouz, Arnaud Besserer, Patrick Perré
Short-term effects of nutrient enrichment on river biofilm: N–NO3− uptake rate and response of meiofauna
Yang Liu, Nabil Majdi, Michèle Tackx, Alain Dauta, Magali Gerino, Frédéric Julien, Evelyne Buffan-Dubau