Publications

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LD Lab publications @ SIAT

*co-first author, #co-corresponding author, LD Lab members

To be published

• Spatial profiling of microbial communities by sequential FISH with error-robust encoding
  Zhaohui Cao*, Wenlong Zuo*, Lanxiang Wang, Junyu Chen, Zepeng Qu, Fan Jin, Lei Dai. Nature Communications, in revision

2022

• StrainPanDA: linked reconstruction of strain composition and gene contents from metagenomic data Han Hu*, Yuxiang Tan*, Chenhao Li*, Junyu Chen, Yan Kou, Zhenjiang Zech Xu, Yang-Yu Liu, Yan Tan#, Lei Dai#. iMeta (2022)
• Profiling of d-alanine production by the microbial isolates of rat gut microbiota Cindy J. Lee*, Tian A. Qi*, Zhilai Hong*, Zhenkun Zhang, Yuhao Min, ,Linzixuan Zhang, Lei Dai, Huimin Zhao, Tong Si#, Jonathan V. Sweedler#. FASEB Journal (2022)
• Ecological dynamics of the gut microbiome in response to dietary fiber
  Hongbin Liu*, Chen Liao*, Lu Wu, Jinhui Tang, Junyu Chen, Chaobi Lei, Linggang Zheng, Chenhong Zhang, Yang-Yu Liu, Joao Xavier, Lei Dai. ISME Journal (2022)
• Biosynthesis of Gut-Microbiota-Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal
  Yingying Zhang*, Zhilai Hong*, Liang Zhou*, Zhenkun Zhang, Ting Tang, Erpeng Guo, Jie Zheng, Ciji Wang, Lei Dai, Tong Si#, Huan Wang#, Angewandte Chemie (2022)
• CRISPR/Cas-based genome editing for human gut commensal Bacteroides species
  Linggang Zheng*, Yang Tan*, Yucan Hu, Juntao Shen, Zepeng Qu, Xianbo Chen, Chun Loong Ho, Elaine Lai-Han Leung, Wei Zhao, Lei Dai. ACS Synthetic Biology (2022)
• Establishment and resilience of transplanted gut microbiota in aged mice Ying Wang*, Jinhui Tang*, Qingqing Lv, Yuxiang Tan, Xiaoxiao Dong, Hongbin Liu, Nannan Zhao, Zhen He, Yan Kou, Yan Tan, Xin-an Liu, Liping Wang, Yang-Yu Liu, Lei Dai. iScience (2022)

2021

• Microbiota in mesenteric adipose tissue from Crohn’s disease promote colitis in mice
  Zhen He, Jinjie Wu, Junli Gong, Jia Ke, Tao Ding, Wenjing Zhao, Wai Ming Cheng, Zhanhao Luo, Qilang He, Wanyi Zeng, Jing Yu, Na Jiao, Yanmin Liu, Bin Zheng, Lei Dai, Min Zhi, Xiaojian Wu, Christian Jobin, Ping Lan. Microbiome (2021)
• Living fabrication of functional semi-interpenetrating polymeric materials
  Zhuojun Dai, Xiaoyu Yang, Feilun Wu, Lihua Wang, Kun Xiang, Pengcheng Li, Qingqing Lv, Jinhui Tang, Anders Dohlman, Lei Dai, Xiling Shen, Lingchong You. Nature Communications (2021)
• Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants
  Yu Deng, Yue Huang, You Che, Yu Yang, Xiaole Yin, Aixin Yan, Lei Dai, Yang-Yu Liu, Martin Polz, Tong Zhang. ISME Journal (2021)
• Evaluation of the Anti-Inflammatory and Anti-Oxidative Effects of Therapeutic Human Lactoferrin Fragments
  Yu Pan, Zhao Liu, Yijie Wang, Linshen Zhang, Niying Chua, Lei Dai, Jun Chen, Chun Loong Ho. Frontiers in Bioengineering and Biotechnology (2021)
• Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath
  Tie‐Yuan Liu, Nenghui Ye, Xinyu Wang, Debatosh Das, Yuxiang Tan, Xiangkai You, Mingxiu Long, Tianming Hu, Lei Dai, Jianhua Zhang, Mo‐Xian Chen. Journal of Integrative Plant Biology (2021)
• Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data
  Yan Kou, Xiaomin Xu, Zhengnong Zhu, Lei Dai#, Yan Tan#. Scientific Reports (2020)

Reviews

• Accelerating strain engineering in biofuel research via build and test automation of synthetic biology
  Jianzhi Zhang, Yongcan Chen, Lihao Fu, Erpeng Guo, Bo Wang, Lei Dai, Tong Si. Current Opinion in Biotechnology (2021)
• Engineered Live Biotherapeutics: Progress and Challenges
  Yang Tan, Juntao Shen, Tong Si, Chun Loong Ho, Yinqing Li, Lei Dai. Biotechnology Journal (2020)
• Advances in Bacterial Biofilm Management for Maintaining Microbiome Homeostasis
  Zhao Liu, Can‐Jian Hong, Yongshuai Yang, Lei Dai, Chun Loong Ho. Biotechnology Journal (2020)
• Research progress and applications of strain analysis based on metagenomic data
  (in Chinese) 基于宏基因组数据的菌株分析方法及其应用
  Yuxiang Tan*, Han Hu*, Chenhao Li, Xiaozhou Luo, Yan Tan, Lei Dai. Chinese Journal of Biotechnology 生物工程学报(2020)
• Research advances in synthetic microbial communities.
  (in Chinese) 合成微生物群落研究进展
  Zepeng Qu, Moxian Chen, Zhaohui Cao, Wenlong Zuo, Ye Chen, Lei Dai. Synthetic Biology Journal 合成生物学 (2020)
• Design and application of synthetic microbial communities
  (in Chinese) 合成微生物群落的构建与应用
  Moxian Chen, Zhong Wei, Liang Tian, Yang Tan, Jiandong Huang, Lei Dai. Chinese Science Bulletin 科学通报 (2020)

Selected previous works

Evolution: fitness landscapes

• Quantifying the evolutionary constraints and potential of Hepatitis C Virus NS5A protein
  Dai, L.*, Du, Y.*, … Lloyd-Smith, J.O., Sun, R. mSystems (2021)
• Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease
  Zhang, T.*,Dai, L.*# , Barton JP , … Lloyd-Smith, J.O., Sun, R#. PLoS Genetics (2020)
• Evolving generalists in switching rugged landscapes
  Wang, S., Dai, L. PLoS Computational Biology (2019) 
• Adaptation in protein fitness landscapes is facilitated by indirect paths
  Wu, N.C.*, Dai, L.*, Olson, C.A., Lloyd-Smith, J.O., Sun, R.  eLife (2016)

Ecology: population dynamics

• Relation between stability and resilience determines the performance of early warning signals under different environmental drivers 
  Dai, L.#, Korolev, K.S., Gore, J. PNAS (2015)
• Dynamics of a producer-freeloader ecosystem on the brink of collapse
  Chen, A., Sanchez, A., Dai, L., Gore, J. Nature Communications (2014)
• Slower recovery in space before collapse of connected populations
  Dai, L.#, Korolev, K.S., Gore, J#. Nature (2013)
• Generic indicators for loss of resilience before a tipping point leading to population collapse
  Dai, L.*, Vorselen, D.*, Korolev, K.S., Gore, J. Science (2012)