Publications

Yunfan Jin, Jiyun Cui, Rulong Liu, Hongli Ma, Xiaomin Xu, Shufang Wu, Fei Gan, Zhi John Lu, Zhenjiang Zech Xu (2026). Conserved 3′ stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes. Microbiome.

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Biao Dong, Bin Wang, Jiongjin Chen, Xiaomin Xu, Zhenjiang Zech Xu (2026). Adaptive graph learning of microbial phylogeny enables accurate and interpretable microbiome-based host phenotype prediction. Applied and Environmental Microbiology.

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Qiwen Xie, Huan Xu, Xiaoming Yang, Ying Chen, Zhenjiang Zech Xu (2026). Natural carrier-free self-assembled binary polyphenol nanoparticles remodel the gut microenvironment for inflammatory bowel disease prevention. Materials Today Bio.

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Matthew Aton, Daniel McDonald, Jorge Cañardo Alastuey, Raeed Azom, Paarth Batra, Valentyn Bezshapkin, Evan Bolyen, Alexander Cagle, J. Gregory Caporaso, Justine W. Debelius, Kestrel Gorlick, Nirmitha Hamsanipally, Lars Hunger, Aryan Keluskar, Disen Liao, Yang Young Lu, Jose A. Navas-Molina, Anders Pitman, Jai Ram Rideout, Anton Sazonov, Bharath Sathappan, Karen Schwarzberg Lipson, Igor Sfiligoi, Chris Tapo, Yoshiki Vázquez-Baeza, Zijun Wu, Zhenjiang Zech Xu, Mingsong Sam Ye, Jianshu Zhao, Rob Knight, James T. Morton, Qiyun Zhu (2026). Scikit-bio: a fundamental Python library for biological omic data analysis. Nature Methods.

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Liting Liu, Yong Huang, Huan Xu, Yifan Sun, Zhenjiang Zech Xu, Xiaochang Huang (2026). Dietary Nisin Exacerbates Diabetic Vascular Complications through Gut Microbiota Modulation and NF-κB Signaling. Ecotoxicology and Environmental Safety.

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Yuesong Jiang, Jiang Liu, Yufeng Zhang, Lisha Zhou, Enoch Kao, Shuwen Hou, Qianya Niu, Yongxin Liu, Zhenjiang Zech Xu, Tao Ding, Yu-Xiong Su, Yu Liu, Gao Zhang, Xiuping Wang, Fei Teng, Shi Huang (2025). High-Resolution Microbiome Analysis of Host-Rich Samples Using 2bRAD-M without Host Depletion. npj Biofilms and Microbiomes.

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Zhiqin Sang, Yufeng Zhang, Enoch Kao, Tingting Zhu, Jiazhen Yang, Zhenjiang Zech Xu, Shi Huang, Fei Teng, Wanchun Wang (2025). Decoding Oral Leukoplakia: Microbiome Dysbiosis and Inflammatory Dynamics Unveiled in a Rat Model. Frontiers in Microbiology.

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Feng Liu, Biao Dong, Zhongsun Wang, Dan Lin, Huan Xu, Baisheng Ke, Wanying Kang, Yang Jin, Xiuting Huang, Hui Lu, Liqing Zhao, Yun Qian, Liangling Cai, Long Xu, Zhenjiang Zech Xu (2025). Survival and Safety Evaluation of Bifidobacterium Longum Subsp. Longum ZS-8 in Healthy Adults, Determined Using PMAxx-qPCR and Amplicon Sequencing. Microbiology Spectrum.

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Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu, Zhi John Lu (2025). RNA–ligand interaction scoring via data perturbation and augmentation modeling. Nature Computational Science.

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Stephany Flores Ramos, Nicole Siguenza, Wuling Zhong, Ipsita Mohanty, Amulya Lingaraju, R. Alexander Richter, Smruthi Karthikeyan, April L. Lukowski, Qiyun Zhu, Wilhan D. G. Nunes, Jasmine Zemlin, Zhenjiang Zech Xu, Jeff Hasty, Pieter C. Dorrestein, Satchidananda Panda, Rob Knight, Amir Zarrinpar (2025). Metatranscriptomics Uncovers Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects. Cell Host & Microbe.

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Zewen Han, Yichen Hu, Xin Lin, Hongyu Cheng, Biao Dong, Xuan Liu, Buling Wu, Zhenjiang Zech Xu (2025). Systematic Analyses Uncover Robust Salivary Microbial Signatures and Host-Microbiome Perturbations in Oral Squamous Cell Carcinoma. mSystems.

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Ping Li, Ru Qu, Ming Li, Ping Sheng, Liang Jin, Xiaochang Huang, Zhenjiang Zech Xu (2024). Impacts of food additives on gut microbiota and host health. Food Research International.

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Ming Li, Ru Qu, Ping Li, Xuan Mo, Juan Liu, Biao Dong, Liting Liu, Zhenjiang Zech Xu (2024). Epimedium polysaccharides mitigates textitPorphyromonas gingivalis-exacerbated intestinal inflammation by suppressing the Th17 pathway and modulating the gut microbiota. International Journal of Biological Macromolecules.

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Huiyu Zhang, Qiwen Zhang, Yan Li, Zhenjiang Zech Xu, Xiaochang Huang (2024). Screening of Lactic Acid Bacteria from Freshwater Fish Intestines and Their Effects on Growth, Immunity, and Disease Resistance in Zebrafish. Aquaculture International.

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Wenjing Li, Bin Wang, Jin Dai, Yan Kou, Xiaojun Chen, Yi Pan, Shuangwei Hu, Zhenjiang Zech Xu (2024). Partial order relation–based gene ontology embedding improves protein function prediction. Briefings in Bioinformatics.

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Zachary M. Burcham, Aeriel D. Belk, Bridget B. McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R. Zhang, Pixu Shi, Alexandra Emmons, Heather L. Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C. Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C. Reed, Greg C. Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M. S. Watson, Giovanna Vidoli, Dawnie Steadman, Aaron M. Lynne, Sibyl Bucheli, Pieter C. Dorrestein, Kelly C. Wrighton, David O. Carter, Rob Knight, Jessica L. Metcalf (2024). A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature Microbiology.

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Bin Wang, Yulong Shen, Jingyan Fang, Xiaoquan Su, Zhenjiang Zech Xu (2024). DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis. Advanced Science.

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Yan Li, Yichen Hu, Xiang Zhan, Ying Song, Meng Xu, Shijie Wang, Xiaochang Huang, Zhenjiang Zech Xu (2023). Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression. Gut Microbes.

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Ting Fu, Tao Huan, Gibraan Rahman, Hui Zhi, Zhenjiang Zech Xu, Tae Gyu Oh, Jian Guo, Sally Coulter, Anupriya Tripathi, Cameron Martino, Justin L. McCarville, Qiyun Zhu, Fritz Cayabyab, Brian Low, Mingxiao He, Shipei Xing, Fernando Vargas, Ruth T. Yu, Annette Atkins, Christopher Liddle, Janelle Ayres, Manuela Raffatellu, Pieter C. Dorrestein, Michael Downes, Rob Knight, Ronald M. Evans (2023). Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression. Cell Reports.

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Lepeng Zhou, Wen Qiu, Jie Wang, Aihua Zhao, Chuhui Zhou, Tao Sun, Ziyu Xiong, Peihua Cao, Wei Shen, Jingfen Chen, Xiaolu Lai, Liu-Hong Zhao, Yue Wu, Meng Li, Feng Qiu, Yanhong Yu, Zhenjiang Zech Xu, Hongwei Zhou, Wei Jia, Yan Liao, Ravi Retnakaran, Daniel Krewski, Shi Wu Wen, Jose C. Clemente, Tianlu Chen, Ri-Hua Xie, Yan He (2023). Effects of Vaginal Microbiota Transfer on the Neurodevelopment and Microbiome of Cesarean-Born Infants: A Blinded Randomized Controlled Trial. Cell Host & Microbe.

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Feng Liu, Hui Lu, Biao Dong, Xiaochang Huang, Hongyu Cheng, Ru Qu, Yichen Hu, Luyun Zhong, Zhenni Guo, Yuehua You, Zhenjiang Zech Xu (2023). Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria. mSystems.

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Zhiyuan Pan, Yichen Hu, Zongyu Huang, Ni Han, Yan Li, Xiaomei Zhuang, Jiye Yin, Hui Peng, Quansheng Gao, Wenpeng Zhang, Yong Huang, Yujun Cui, Yujing Bi, Zhenjiang Zech Xu, Ruifu Yang (2022). Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge. Science China Life Sciences.

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Ping Li, Ming Li, Tao Wu, Ying Song, Yan Li, Xiaochang Huang, Hui Lu, Zhenjiang Zech Xu (2022). Systematic evaluation of antimicrobial food preservatives on glucose metabolism and gut microbiota in healthy mice. npj Science of Food.

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Shanwen Chen, Yunfan Jin, Siqi Wang, Shaozhen Xing, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu, Zhi John Lu, Pengyuan Wang (2022). Cancer type classification using plasma cell-free RNAs derived from human and microbes. eLife.

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Yichen Hu, Amnon Amir, Xiaochang Huang, Yan Li, Shi Huang, Elaine Wolfe, Sophie Weiss, Rob Knight, Zhenjiang Zech Xu (2022). Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling. Genome Research.

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Ya-Shuai Kong, Hong-Yu Ren, Rui Liu, Ricardo R. Da Silva, Alexander A. Aksenov, Alexey v. Melnik, Ming Zhao, Miao-Miao Le, Zhi-Wei Ren, Feng-Qing Xu, Xiao-Wei Yan, Li-Jun Yu, Yu Zhou, Zhong-Wen Xie, Da-Xiang Li, Xiao-Chun Wan, Yan-Hua Long, Zhenjiang Zech Xu, Tie-Jun Ling (2022). Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation. Journal of Agricultural and Food Chemistry.

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Yichen Hu, Zhiyuan Pan, Zongyu Huang, Yan Li, Ni Han, Xiaomei Zhuang, Hui Peng, Quansheng Gao, Qing Wang, B. J. Yang Lee, Heping Zhang, Ruifu Yang, Yujing Bi, Zhenjiang Zech Xu (2022). Gut Microbiome-Targeted Modulations Regulate Metabolic Profiles and Alleviate Altitude-Related Cardiac Hypertrophy in Rats. Microbiology Spectrum.

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Han Hu, Yuxiang Tan, Chenhao Li, Junyu Chen, Yan Kou, Zhenjiang Zech Xu, Yang-Yu Liu, Yan Tan, Lei Dai (2022). StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data. iMeta.

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Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Zech Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao, Junjun Wang (2021). Gut Microbiota from Green Tea Polyphenol-Dosed Mice Improves Intestinal Epithelial Homeostasis and Ameliorates Experimental Colitis. Microbiome.

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Hui Lu, Ping Li, Xiaochang Huang, Charles Hantsing Wang, Ming Li, Zhenjiang Zech Xu (2021). Zebrafish model for human gut microbiome-related studies: advantages and limitations. Medicine in Microecology.

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Ping Li, Shengliang Deng, Zhenjiang Zech Xu (2021). Toxicant substitutes in immunological assays for mycotoxins detection: A mini review. Food Chemistry.

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Heather Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David O. Carter, Aaron Lynne, Rob Knight, Zhenjiang Zech Xu, Sibyl Bucheli, Jessica L. Metcalf (2021). A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere.

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Robert L. Thomas, Lingjing Jiang, John S. Adams, Zhenjiang Zech Xu, Jian Shen, Stefan Janssen, Gail Ackermann, Dirk Vanderschueren, Steven Pauwels, Rob Knight, Eric S. Orwoll, Deborah M. Kado (2020). Vitamin D metabolites and the gut microbiome in older men. Nature Communications.

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Mengchen Guo, Huixia Wang, Sixie Xu, Yaoyao Zhuang, Jingang An, Chuan Su, Yankai Xia, Jingyun Chen, Zhenjiang Zech Xu, Qisha Liu, Jianwei Wang, Zhou Dan, Kun Chen, Xiaoting Luan, Zhi Liu, Kangjian Liu, Faming Zhang, Yumin Xia, Xingyin Liu (2020). Alteration in gut microbiota is associated with dysregulation of cytokines and glucocorticoid therapy in systemic lupus erythematosus. Gut Microbes.

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Xiaoquan Su, Gongchao Jing, Zheng Sun, Lu Liu, Zhenjiang Zech Xu, Daniel McDonald, Zengbin Wang, Honglei Wang, Antonio Gonzalez, Yufeng Zhang, Shi Huang, Gavin Huttley, Rob Knight, Jian Xu (2020). Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. mSystems.

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Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu (2020). Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. mSystems.

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Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B. Yin, Shi Huang, Nimaichand Salam, Jian-Yu Jiao, Zijun Wu, Zhenjiang Zech Xu, Kalen Cantrell, Yimeng Yang, Erfan Sayyari, Maryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight (2019). Phylogenomics of 10,575 Genomes Reveals Evolutionary Proximity between Domains Bacteria and Archaea. Nature Communications.

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Yanwen Xue, Fang Huang, Rongxue Tang, Qingsheng Fan, Bing Zhang, Zhenjiang Zech Xu, Xiaoming Sun, Zheng Ruan (2019). Chlorogenic Acid Attenuates Cadmium-Induced Intestinal Injury in Sprague--Dawley Rats. Food and Chemical Toxicology.

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Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Zech Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Marlon Liyanage, Jason W. Dang, Vanessa v. Phelan, Robert A. Quinn, Anton Bankevich, John T. Chang, Tariq M. Rana, Douglas J. Conrad, William J. Sandborn, Larry Smarr, Pieter C. Dorrestein, Pavel A. Pevzner, Rob Knight (2019). Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biology.

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Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andr\\\́s Mauricio \Caraballo-Rodr\í\guez\, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey v. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. Van Der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max Von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J. Gregory Caporaso (2019). Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nature Biotechnology.

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Whitney A. Kodama, Zhenjiang Zech Xu, Jessica L. Metcalf, Se Jin Song, Nicholas Harrison, Rob Knight, David O. Carter, Christopher B. Happy (2019). Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. Journal of Forensic Sciences.

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Anupriya Tripathi, Zhenjiang Zech Xu, Jin Xue, Orit Poulsen, Antonio Gonzalez, Gregory Humphrey, Michael J. Meehan, Alexey v. Melnik, Gail Ackermann, Dan Zhou, Atul Malhotra, Gabriel G. Haddad, Pieter C. Dorrestein, Rob Knight (2019). Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. mSystems.

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Cyrielle Caussy, Anupriya Tripathi, Greg Humphrey, Shirin Bassirian, Seema Singh, Claire Faulkner, Ricki Bettencourt, Emily Rizo, Lisa Richards, Zhenjiang Zech Xu, Michael R. Downes, Ronald M. Evans, David A. Brenner, Claude B. Sirlin, Rob Knight, Rohit Loomba (2019). A Gut Microbiome Signature for Cirrhosis Due to Nonalcoholic Fatty Liver Disease. Nature Communications.

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Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight (2019). Calour: an Interactive, Microbe-Centric Analysis Tool. mSystems.

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Yuqing Feng, Yunfeng Duan, Zhenjiang Zech Xu, Na Lyu, Fei Liu, Shihao Liang, Baoli Zhu (2019). An examination of data from the American Gut Project reveals that the dominance of the genus Bifidobacterium is associated with the diversity and robustness of the gut microbiota. MicrobiologyOpen.

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Johannes Braun, Sandra Fischer, Zhenjiang Zech Xu, Hongying Sun, Dalia H. Ghoneim, Anna T. Gimbel, Uwe Plessmann, Henning Urlaub, David H. Mathews, Julia E. Weigand (2018). Identification of New High Affinity Targets for Roquin Based on Structural Conservation. Nucleic Acids Research.

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Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight (2018). Striped UniFrac: Enabling Microbiome Analysis at Unprecedented Scale. Nature Methods.

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Rob Knight, Alison Vrbanac, Bryn C. Taylor, Alexander Aksenov, Chris Callewaert, Justine Debelius, Antonio Gonzalez, Tomasz Kosciolek, Laura-Isobel McCall, Daniel McDonald, Alexey v. Melnik, James T. Morton, Jose Navas, Robert A. Quinn, Jon G. Sanders, Austin D. Swafford, Luke R. Thompson, Anupriya Tripathi, Zhenjiang Zech Xu, Jesse R. Zaneveld, Qiyun Zhu, J. Gregory Caporaso, Pieter C. Dorrestein (2018). Best Practices for Analysing Microbiomes. Nature Reviews Microbiology.

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Amir Zarrinpar, Amandine Chaix, Zhenjiang Zech Xu, Max W. Chang, Clarisse A. Marotz, Alan Saghatelian, Rob Knight, Satchidananda Panda (2018). Antibiotic-Induced Microbiome Depletion Alters Metabolic Homeostasis by Affecting Gut Signaling and Colonic Metabolism. Nature Communications.

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Stefan Janssen, Daniel McDonald, Antonio Gonzalez, Jose A. Navas-Molina, Lingjing Jiang, Zhenjiang Zech Xu, Kevin Winker, Deborah M. Kado, Eric Orwoll, Mark Manary, Siavash Mirarab, Rob Knight (2018). Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems.

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Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip v. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey v. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems.

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Jennifer M. Michaud, Luke R. Thompson, Drishti Kaul, Josh L. Espinoza, R. Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M. Pham, Charlotte M. Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D. Burkart, Christopher L. Dupont, Kimberly A. Prather (2018). Taxon-Specific Aerosolization of Bacteria and Viruses in an Experimental Ocean-Atmosphere Mesocosm. Nature Communications.

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Joshua B. Richardson, Blair C. R. Dancy, Cassandra L. Horton, Young S. Lee, Michael S. Madejczyk, Zhenjiang Zech Xu, Gail Ackermann, Gregory Humphrey, Gustavo Palacios, Rob Knight, John A. Lewis (2018). Exposure to toxic metals triggers unique responses from the rat gut microbiota. Scientific Reports.

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Aeriel Belk, Zhenjiang Zech Xu, David O. Carter, Aaron Lynne, Sibyl Bucheli, Rob Knight, Jessica L. Metcalf (2018). Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. Genes.

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Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, Amnon Amir, Antonio Gonz\á\lez, Anupriya Tripathi, Minhu Chen, Gary D. Wu, Rob Knight, Hongwei Zhou, Ye Chen (2018). Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. mSystems.

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Jeremiah J. Minich, Qiyun Zhu, Zhenjiang Zech Xu, Amnon Amir, Maxon Ngochera, Moses Simwaka, Eric E. Allen, Hastings Zidana, Rob Knight (2018). Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen.

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Yoshiki Vázquez-Baeza, Antonio Gonzalez, Zhenjiang Zech Xu, Alex Washburne, Hans H. Herfarth, R. Balfour Sartor, Rob Knight (2018). Guiding longitudinal sampling in IBD cohorts. Gut.

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Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Stefan Janssen, Evguenia Kopylova, Yoshiki \V\á\zquez-Baeza\, Antonio Gonz\\\́lez, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Lingjing Jiang, Mohamed F. Haroon, Jad Kanbar, Qiyun Zhu, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Gregory Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie, Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight, The Earth Microbiome Project Consortium, Jose L. Agosto Rivera, Lisa Al-Moosawi, John Alverdy, Katherine R. Amato, Jason Andras, Largus T. Angenent, Dionysios A. Antonopoulos, Amy Apprill, David Armitage, Kate Ballantine, Jir\\textasciicaron\\\'iánd Baum, Julia K. B\\'ŕta, Allison Berry, Ashish Bhatnagar, Monica Bhatnagar, Jennifer F. Biddle, Lucie Bittner, Bazartseren Boldgiv, Eric Bottos, Donal M. Boyer, Josephine Braun, William Brazelton, Francis Q. Brearley, Alexandra H. Campbell, J. Gregory Caporaso, Cesar Cardona, JoLynn Carroll, S. Craig Cary, Brenda B. Casper, Trevor C. Charles, Haiyan Chu, Danielle C. Claar, Robert G. Clark, Jonathan B. Clayton, Jose C. Clemente, Alyssa Cochran, Maureen L. Coleman, Gavin Collins, Rita R. Colwell, M\\'ó̧a Contreras, Benjamin B. Crary, Simon Creer, Daniel A. Cristol, Byron C. Crump, Duoying Cui, Sarah E. Daly, Liliana Davalos, Russell D. Dawson, Jennifer Defazio, Fr\\'e\d'́e\riánd Dionisi, Hebe M. Delsuc, Maria Gloria Dominguez-Bello, Robin Dowell, Eric A. Dubinsky, Peter O. Dunn, Danilo Ercolini, Robert E. Espinoza, Vanessa Ezenwa, Nathalie Fenner, Helen S. Findlay, Irma D. Fleming, Vincenzo Fogliano, Anna Forsman, Chris Freeman, Elliot S. Friedman, Giancarlo Galindo, Liza Garcia, Maria Alexandra Garcia-Amado, David Garshelis, Robin B. Gasser, Gunnar Gerdts, Molly K. Gibson, Isaac Gifford, Ryan T. Gill, Tugrul Giray, Antje Gittel, Peter Golyshin, Donglai Gong, Hans-Peter Grossart, Kristina Guyton, Sarah-Jane Haig, Vanessa Hale, Ross Stephen Hall, Steven J. Hallam, Kim M. Handley, Nur A. Hasan, Shane R. Haydon, Jonathan E. Hickman, Glida Hidalgo, Kirsten S. Hofmockel, Jeff Hooker, Stefan Hulth, Jenni Hultman, Embriette Hyde, \Ib\\'a\\\~éz-\\'A\lamo ́Juan Diego, Julie D. Jastrow, Aaron R. Jex, L. Scott Johnson, Eric R. Johnston, Stephen Joseph, Stephanie D. Jurburg, Diogo Jurelevicius, Anders Karlsson, Roger Karlsson, Seth Kauppinen, Colleen T. E. Kellogg, Suzanne J. Kennedy, Lee J. Kerkhof, Gary M. King, George W. Kling, Anson v. Koehler, Monika Krezalek, Jordan Kueneman, Regina Lamendella, Emily M. Landon, Kelly Lane-DeGraaf, Julie LaRoche, Peter Larsen, Bonnie Laverock, Simon Lax, Miguel Lentino, Iris I. Levin, Pierre Liancourt, Wenju Liang, Alexandra M. Linz, David A. Lipson, Yongqin Liu, Manuel E. Lladser, Mariana Lozada, Catherine M. Spirito, Walter P. MacCormack, Aurora MacRae-Crerar, Magda Magris, Antonio M. \Mart\\'i\n-Plaŕo\, Manuel \Mart\\'i\n-Vivaí\, L.árgarita Mart\\'i\nez, ́ Manuel \Mart\\'i\nez-Buen, Ezequiel M. Marzinelli, Olivia U. Mason, Gregory D. Mayer, Jamie M. McDevitt-Irwin, James E. McDonald, Krista L. McGuire, Katherine D. McMahon, Ryan McMinds, M\\'o\nica Medina, Joseph R. Ńdelson, Jessica L. Metcalf, Folker Meyer, Fabian Michelangeli, Kim Miller, David A. Mills, Jeremiah Minich, Stefano Mocali, Lucas Moitinho-Silva, Anni Moore, Rachael M. Morgan-Kiss, Paul Munroe, David Myrold, Josh D. Neufeld, Yingying Ni, Graeme W. Nicol, Shaun Nielsen, Jozef I. Nissimov, Kefeng Niu, Matthew J. Nolan, Karen Noyce, Sarah L. O'Brien, Noriko Okamoto, Ludovic Orlando, Yadira Ortiz Castellano, Olayinka Osuolale, Wyatt Oswald, Jacob Parnell, Ju ́M. \Peralta-S\\'a\nchez\, Peter Petraitis, Catherine Pfister, Elizabeth Pilon-Smits, Paola Piombino, Stephen B. Pointing, F. Joseph Pollock, Caitlin Potter, Bharath Prithiviraj, Christopher Quince, Asha Rani, Ravi Ranjan, Subramanya Rao, Andrew P. Rees, Miles Richardson, Ulf Riebesell, Carol Robinson, Karl J. Rockne, Selena Marie Rodriguezl, Forest Rohwer, Wayne Roundstone, Rebecca J. Safran, Naseer Sangwan, Virginia Sanz, Matthew Schrenk, Mark D. Schrenzel, Nicole M. Scott, Rita L. Seger, Andaine Seguin-Orlando, Lucy Seldin, Lauren M. Seyler, Baddr Shakhsheer, Gabriela M. Sheets, Congcong Shen, Yu Shi, Hakdong Shin, Benjamin D. Shogan, Dave Shutler, Jeffrey Siegel, Steve Simmons, Sara Sj\\"o\ling, Daniel P. Smith, Juan J. Soler, Martin Sperling, Peter D. Steinberg, Brent Stephens, Melita A. Stevens, Safiyh Taghavi, Vera Tai, Karen Tait, Chia L. Tan, ̧ Neslihan Tas\\, D. Lee Taylor, Torsten Thomas, Ina Timling, Benjamin L. Turner, Tim Urich, Luke K. Ursell, Daniel Van Der Lelie, William Van Treuren, Lukas Van Zwieten, Daniela Vargas-Robles, Rebecca Vega Thurber, Paola Vitaglione, Donald A. Walker, William A. Walters, Shi Wang, Tao Wang, Tom Weaver, Nicole S. Webster, Beck Wehrle, Pamela Weisenhorn, Sophie Weiss, Jeffrey J. Werner, Kristin West, Andrew Whitehead, Susan R. Whitehead, Linda A. Whittingham, Eske Willerslev, Allison E. Williams, Stephen A. Wood, Douglas C. Woodhams, Yeqin Yang, Jesse Zaneveld, Iratxe Zarraonaindia, Qikun Zhang, Hongxia Zhao (2017). A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity. Nature.

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Jessica L. Metcalf, Zhenjiang Zech Xu, Amina Bouslimani, Pieter Dorrestein, David O. Carter, Rob Knight (2017). Microbiome Tools for Forensic Science. Trends in Biotechnology.

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Scott D. Wankel, Wiebke Ziebis, Carolyn Buchwald, Chawalit Charoenpong, Dirk De Beer, Jane Dentinger, Zhenjiang Zech Xu, Karsten Zengler (2017). Evidence for Fungal and Chemodenitrification Based N₂O Flux from Nitrogen Impacted Coastal Sediments. Nature Communications.

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Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight (2017). Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems.

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Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight (2017). Normalization and Microbial Differential Abundance Strategies Depend upon Data Characteristics. Microbiome.

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Amina Bouslimani, Alexey v. Melnik, Zhenjiang Zech Xu, Amnon Amir, Ricardo R. Da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein (2016). Lifestyle chemistries from phones for individual profiling. Proceedings of the National Academy of Sciences.

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Jack A. Gilbert, Robert A. Quinn, Justine Debelius, Zhenjiang Zech Xu, James Morton, Neha Garg, Janet K. Jansson, Pieter C. Dorrestein, Rob Knight (2016). Microbiome-wide association studies link dynamic microbial consortia to disease. Nature.

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Sophie Weiss, Will Van Treuren, Catherine Lozupone, Karoline Faust, Jonathan Friedman, Ye Deng, Li Charlie Xia, Zhenjiang Zech Xu, Luke Ursell, Eric J. Alm, Amanda Birmingham, Jacob A. Cram, Jed A. Fuhrman, Jeroen Raes, Fengzhu Sun, Jizhong Zhou, Rob Knight (2016). Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The ISME Journal.

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Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight (2016). Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems.

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Evguenia Kopylova, Jose A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight (2016). Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems.

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Justine Debelius, Se Jin Song, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight (2016). Tiny microbes, enormous impacts: what matters in gut microbiome studies?. Genome Biology.

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Zhenjiang Zech Xu, David H. Mathews (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. RNA Structure Determination.

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Zhenjiang Zech Xu, David H. Mathews (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. RNA Structure Determination.

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Jessica L. Metcalf, Zhenjiang Zech Xu, Sophie Weiss, Simon Lax, Will Van Treuren, Embriette R. Hyde, Se Jin Song, Amnon Amir, Peter Larsen, Naseer Sangwan, Daniel Haarmann, Greg C. Humphrey, Gail Ackermann, Luke R. Thompson, Christian Lauber, Alexander Bibat, Catherine Nicholas, Matthew J. Gebert, Joseph F. Petrosino, Sasha C. Reed, Jack A. Gilbert, Aaron M. Lynne, Sibyl R. Bucheli, David O. Carter, Rob Knight (2016). Microbial community assembly and metabolic function during mammalian corpse decomposition. Science.

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Zhenjiang Zech Xu, David H. Mathews (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. RNA Structure Determination.

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Justine W. Debelius, Yoshiki Vázquez-Baeza, Daniel McDonald, Zhenjiang Zech Xu, Elaine Wolfe, Rob Knight (2015). Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project. Journal of Microbiology & Biology Education.

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Fei Teng, Fang Yang, Shi Huang, Cunpei Bo, Zhenjiang Zech Xu, Amnon Amir, Rob Knight, Junqi Ling, Jian Xu (2015). Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota. Cell Host & Microbe.

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Yinghan Fu, Zhenjiang Zech Xu, Zhi J. Lu, Shan Zhao, David H. Mathews (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS ONE.

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Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis (2015). Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications.

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Gang Yang, Zhenjiang Zech Xu, Xiangli Tian, Shuanglin Dong, Mo Peng (2015). Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation. Biochemical and Biophysical Research Communications.

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Daniel McDonald, Zhenjiang Zech Xu, Embriette R. Hyde, Rob Knight (2015). Ribosomal RNA, the Lens into Life. RNA.

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Zhenjiang Zech Xu, Rob Knight (2015). Dietary effects on human gut microbiome diversity. British Journal of Nutrition.

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Zhenjiang Zech Xu, Daniel Malmer, Morgan G. I. Langille, Samuel F. Way, Rob Knight (2014). Which Is More Important for Classifying Microbial Communities: Who's There or What They Can Do?. The ISME Journal.

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William A. Walters, Zhenjiang Zech Xu, Rob Knight (2014). Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Letters.

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Jeremiah J. Trausch, Zhenjiang Zech Xu, Andrea L. Edwards, Francis E. Reyes, Phillip E. Ross, Rob Knight, Robert T. Batey (2014). Structural basis for diversity in the SAM clan of riboswitches. Proceedings of the National Academy of Sciences.

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José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, Rob Knight (2013). Advancing Our Understanding of the Human Microbiome Using QIIME. Methods in Enzymology.

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Karyn Schmidt, Zhenjiang Zech Xu, David H. Mathews, J. Scott Butler (2012). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA.

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Zhenjiang Zech Xu, Anthony Almudevar, David H. Mathews (2012). Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research.

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Michael-Paul Vockenhuber, Cynthia M. Sharma, Michaela G. Statt, Denis Schmidt, Zhenjiang Zech Xu, Sascha Dietrich, Heiko Liesegang, David H. Mathews, Beatrix Suess (2011). Deep Sequencing-Based Identification of Small Non-Coding RNAs in Streptomyces Coelicolor. RNA Biology.

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Zhenjiang Zech Xu, David H. Mathews (2011). Multilign: An Algorithm to Predict Secondary Structures Conserved in Multiple RNA Sequences. Bioinformatics.

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