@article{din2026longread,
  author = {Din, M. Omar and Brennan, Caitriona and Zhao, Jianshu and Oles, Renee and Patel, Lucas and Birmingham, Amanda and Sevilir, Dilara M. and Hansen, Lauren and Wright, Gillian M. and Ambre, Madison and Tomita, Meika and others},
  title = {Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics},
  journal = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.28.754546},
  note = {Preprint. Jianshu Zhao is a co-first author},
  keywords = {firstauthor, cofirstauthor, preprint}
}

@article{zhao2025gigascale,
  author = {Zhao, Jianshu and Both, Jean Pierre and Knight, Rob},
  title = {Ultra-fast and Efficient Network Embedding for Gigascale Biological Datasets},
  journal = {bioRxiv},
  year = {2025},
  month = jun,
  doi = {10.1101/2025.06.18.660497},
  note = {Preprint. Jianshu Zhao is first author},
  keywords = {firstauthor, preprint}
}

@article{zhao2024bindash,
  author = {Zhao, Jianshu and Zhao, Xiaofei and Pierre-Both, Jean and Konstantinidis, Konstantinos T.},
  title = {{BinDash} 2.0: New {MinHash} Scheme Allows Ultra-fast and Accurate Genome Search and Comparisons},
  journal = {bioRxiv},
  year = {2024},
  month = mar,
  doi = {10.1101/2024.03.13.584875},
  note = {Preprint. Jianshu Zhao is first author},
  keywords = {firstauthor, preprint}
}

@article{zhao2026dartunifrac,
  author = {Zhao, Jianshu and McDonald, Daniel and Sfiligoi, Igor and Lladser, Manuel E. and Patel, Lucas and Weng, Yuhan and Khatib, Lora and Degregori, Samuel and Gonzalez, Antonio and Lozupone, Catherine A. and Knight, Rob},
  title = {Megascale microbiome analysis with {DartUniFrac}},
  journal = {Nature Biotechnology},
  year = {2026},
  month = aug,
  doi = {10.1038/s41587-026-03260-8},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{khatib2026fivecountry,
  author = {Khatib, Lora and Oles, Renee and Hern{\'a}ndez, Alejandra R{\'i}os and Myers, Tyler and Zhao, Jianshu and Kumar, Megha and Laroya, Ana and Tolosa-Enguis, Veronica and Matsunami, Nobuko and Suzuki, Daisuke and Chiba, Nodoka and others},
  title = {Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation},
  journal = {Nature Communications},
  year = {2026},
  month = sep,
  doi = {10.1038/s41467-026-77928-9}
}

@article{aton2025scikitbio,
  author = {Aton, Matthew and McDonald, Daniel and Ca{\~n}ardo Alastuey, Jorge and Azom, Raeed and Batra, Paarth and Bezshapkin, Valentyn and Bolyen, Evan and Cagle, Alexander and Caporaso, J. Gregory and Debelius, Justine W. and Gorlick, Kestrel and Hamsanipally, Nirmitha and Hunger, Lars and Keluskar, Aryan and Liao, Disen and Lu, Yang Young and Navas-Molina, Jose A. and Pitman, Anders and Rideout, Jai Ram and Sazonov, Anton and Sathappan, Bharath and Schwarzberg Lipson, Karen and Sfiligoi, Igor and Tapo, Chris and V{\'a}zquez-Baeza, Yoshiki and Wu, Zijun and Xu, Zhenjiang Zech and Ye, Mingsong Sam and Zhao, Jianshu and Knight, Rob and Morton, James T. and Zhu, Qiyun},
  title = {Scikit-bio: a fundamental {Python} library for biological omic data analysis},
  journal = {Nature Methods},
  volume = {23},
  number = {2},
  pages = {274--276},
  year = {2026},
  month = feb,
  doi = {10.1038/s41592-025-02981-z}
}

@article{zhao2025rarebiosphere,
  author = {Zhao, Jianshu and Brandt, Genevieve and Gronniger, Jessica L. and Wang, Zhao and Li, Jiaqian and Hunt, Dana E. and Rodriguez-R, Luis M. and Hatt, Janet K. and Konstantinidis, Konstantinos T.},
  title = {Quantifying the contribution of the rare biosphere to natural disturbances},
  journal = {The ISME Journal},
  volume = {19},
  number = {1},
  pages = {wraf129},
  year = {2025},
  month = jan,
  doi = {10.1093/ismejo/wraf129},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{zhao2025sar11,
  author = {Zhao, Jianshu and Pachiadaki, Maria and Conrad, Roth E. and Hatt, Janet K. and Bristow, Laura A. and Rodriguez-R, Luis M. and Rossello-Mora, Ramon and Stewart, Frank J. and Konstantinidis, Konstantinos T.},
  title = {Promiscuous and genome-wide recombination underlies the sequence-discrete species of the {SAR11} lineage in the deep ocean},
  journal = {The ISME Journal},
  volume = {19},
  number = {1},
  pages = {wraf072},
  year = {2025},
  month = jan,
  doi = {10.1093/ismejo/wraf072},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{zhu2025arg,
  author = {Zhu, Congmin and Wu, Linwei and Ning, Daliang and Tian, Renmao and Gao, Shuhong and Zhang, Bing and Zhao, Jianshu and Zhang, Ya and Xiao, Naijia and Wang, Yajiao and others},
  title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems},
  journal = {Nature Communications},
  volume = {16},
  number = {1},
  pages = {4006},
  year = {2025},
  month = apr,
  doi = {10.1038/s41467-025-59019-3}
}

@article{zhao2024gsearch,
  author = {Zhao, Jianshu and Both, Jean Pierre and Rodriguez-R, Luis M. and Konstantinidis, Konstantinos T.},
  title = {{GSearch}: ultra-fast and scalable genome search by combining {K}-mer hashing with hierarchical navigable small world graphs},
  journal = {Nucleic Acids Research},
  volume = {52},
  number = {16},
  pages = {e74},
  year = {2024},
  month = jul,
  doi = {10.1093/nar/gkae609},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{zhao2024annembed,
  author = {Zhao, Jianshu and Both, Jean Pierre and Konstantinidis, Konstantinos T.},
  title = {Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data},
  journal = {NAR Genomics and Bioinformatics},
  volume = {6},
  number = {4},
  pages = {lqae172},
  year = {2024},
  month = sep,
  doi = {10.1093/nargab/lqae172},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{qi2024subsoil,
  author = {Qi, Qi and Ning, Shijie and Guo, Xue and Zhao, Jianshu and Tian, Renmao and Gui, Haoran and He, Jin-Sheng and Wang, Hao and Zhang, Zhenhua and Konstantinidis, Konstantinos T. and Gao, Qun and Wang, Yuxin and Li, Shunyi and Zhao, Weishu and Yang, Yunfeng and Zhou, Jizhong},
  title = {More sensitive microbial responses to the interactive effects of warming and altered precipitation in subsoil than topsoil of an alpine grassland ecosystem},
  journal = {Global Change Biology},
  volume = {30},
  number = {9},
  pages = {e17487},
  year = {2024},
  month = sep,
  doi = {10.1111/gcb.17487}
}

@article{menezes2022quinone,
  author = {Menezes, Osmar and Kocaman, Kumru and Wong, Stanley and Rios-Valenciana, Erika E. and Baker, Eliot J. and Hatt, Janet K. and Zhao, Jianshu and Madeira, Camila L. and Krzmarzick, Mark J. and Spain, Jim C. and Sierra-Alvarez, Reyes and Konstantinidis, Konstantinos T. and Field, Jim A.},
  title = {Quinone Moieties Link the Microbial Respiration of Natural Organic Matter to the Chemical Reduction of Diverse Nitroaromatic Compounds},
  journal = {Environmental Science \& Technology},
  volume = {56},
  number = {13},
  pages = {9387--9397},
  year = {2022},
  month = jun,
  doi = {10.1021/acs.est.2c01329}
}

@article{qi2022methane,
  author = {Qi, Qi and Zhao, Jianshu and Tian, Renmao and Zeng, Yufei and Xie, Changyi and Gao, Qun and Dai, Tianjiao and Wang, Hao and He, Jin-Sheng and Konstantinidis, Konstantinos T. and Yang, Yunfeng and Zhou, Jizhong and Guo, Xue},
  title = {Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a {Tibetan} alpine grassland},
  journal = {Global Change Biology},
  volume = {28},
  number = {23},
  pages = {6906--6920},
  year = {2022},
  month = oct,
  doi = {10.1111/gcb.16444}
}

@article{qi2021flux,
  author = {Qi, Qi and Haowei, Yue and Zhang, Zhenhua and Van Nostrand, Joy D. and Wu, Linwei and Guo, Xue and Feng, Jiajie and Wang, Mengmeng and Yang, Sihang and Zhao, Jianshu and Gao, Qun and Zhang, Qiuting and Zhao, Mengxin and Xie, Changyi and Ma, Zhiyuan and He, Jin-Sheng and Chu, Haiyan and Huang, Yi and Zhou, Jizhong and Yang, Yunfeng},
  title = {Microbial Functional Responses Explain Alpine Soil Carbon Fluxes under Future Climate Scenarios},
  journal = {mBio},
  volume = {12},
  number = {1},
  pages = {e00761-20},
  year = {2021},
  month = feb,
  doi = {10.1128/mbio.00761-20}
}

@article{wan2020paddy,
  author = {Wan, Xiaoling and Gao, Qun and Zhao, Jianshu and Feng, Jiajie and van Nostrand, Joy D. and Yang, Yunfeng and Zhou, Jizhong},
  title = {Biogeographic patterns of microbial association networks in paddy soil within {Eastern China}},
  journal = {Soil Biology and Biochemistry},
  volume = {142},
  pages = {107696},
  year = {2020},
  month = mar,
  doi = {10.1016/j.soilbio.2019.107696}
}

@article{zhao2019fungal,
  author = {Zhao, Jianshu and Gao, Qun and Zhou, Jizhong and Wang, Mengmeng and Liang, Yuting and Sun, Bo and Chu, Haiyan and Yang, Yunfeng},
  title = {The scale dependence of fungal community distribution in paddy soil driven by stochastic and deterministic processes},
  journal = {Fungal Ecology},
  volume = {42},
  pages = {100856},
  year = {2019},
  month = dec,
  doi = {10.1016/j.funeco.2019.07.010},
  note = {Jianshu Zhao is first author},
  keywords = {firstauthor}
}

@article{gao2019diazotrophic,
  author = {Gao, Qun and Yang, Yunfeng and Feng, Jiajie and Tian, Renmao and Guo, Xue and Ning, Daliang and Hale, Lauren and Wang, Mengmeng and Cheng, Jingmin and Wu, Linwei and Zhao, Mengxin and Zhao, Jianshu and others},
  title = {The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil},
  journal = {Global Ecology and Biogeography},
  volume = {28},
  number = {8},
  pages = {1093--1105},
  year = {2019},
  month = may,
  doi = {10.1111/geb.12917}
}

@article{huang2015pgpr,
  author = {Huang, Yan and Sun, Li and Zhao, Jianshu and Huang, Rong and Li, Rong and Shen, Qirong},
  title = {Utilization of different waste proteins to create a novel {PGPR}-containing bio-organic fertilizer},
  journal = {Scientific Reports},
  volume = {5},
  number = {1},
  pages = {7766},
  year = {2015},
  month = jan,
  doi = {10.1038/srep07766}
}

@article{shen2015ammonia,
  author = {Shen, Zongzhuan and Zhong, Shutang and Zhao, Jianshu and Zhang, Jian and Li, Rong and Ruan, Yunze and Shen, Qirong},
  title = {Effects of ammonia fumigation on soil microflora and banana production in an orchard with serious {Fusarium} wilt disease},
  journal = {Acta Ecologica Sinica},
  volume = {35},
  number = {9},
  pages = {2946--2953},
  year = {2015},
  doi = {10.5846/stxb201309082233}
}