Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
Amir, Amnon, McDonald, Daniel, Navas-Molina, Jose A, Kopylova, Evguenia, Morton, James T, Zech Xu, Zhenjiang, Kightley, Eric P, Thompson, Luke R, Hyde, Embriette R, Gonzalez, Antonio, Knight, Rob
Published in mSystems (01.03.2017)
Published in mSystems (01.03.2017)
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Journal Article
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota
Teng, Fei, Yang, Fang, Huang, Shi, Bo, Cunpei, Xu, Zhenjiang Zech, Amir, Amnon, Knight, Rob, Ling, Junqi, Xu, Jian
Published in Cell host & microbe (09.09.2015)
Published in Cell host & microbe (09.09.2015)
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Journal Article
Vitamin D metabolites and the gut microbiome in older men
Thomas, Robert L., Jiang, Lingjing, Adams, John S., Xu, Zhenjiang Zech, Shen, Jian, Janssen, Stefan, Ackermann, Gail, Vanderschueren, Dirk, Pauwels, Steven, Knight, Rob, Orwoll, Eric S., Kado, Deborah M.
Published in Nature communications (26.11.2020)
Published in Nature communications (26.11.2020)
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Journal Article
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, Alexandra J., Tito, Raul Y., Metcalf, Jessica, Sankaranarayanan, Krithivasan, Clemente, Jose C., Ursell, Luke K., Zech Xu, Zhenjiang, Van Treuren, Will, Knight, Rob, Gaffney, Patrick M., Spicer, Paul, Lawson, Paul, Marin-Reyes, Luis, Trujillo-Villarroel, Omar, Foster, Morris, Guija-Poma, Emilio, Troncoso-Corzo, Luzmila, Warinner, Christina, Ozga, Andrew T., Lewis, Cecil M.
Published in Nature communications (25.03.2015)
Published in Nature communications (25.03.2015)
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Journal Article
Cancer type classification using plasma cell-free RNAs derived from human and microbes
Chen, Shanwen, Jin, Yunfan, Wang, Siqi, Xing, Shaozhen, Wu, Yingchao, Tao, Yuhuan, Ma, Yongchen, Zuo, Shuai, Liu, Xiaofan, Hu, Yichen, Chen, Hongyan, Luo, Yuandeng, Xia, Feng, Xie, Chuanming, Yin, Jianhua, Wang, Xin, Liu, Zhihua, Zhang, Ning, Zech Xu, Zhenjiang, Lu, Zhi John, Wang, Pengyuan
Published in eLife (11.07.2022)
Published in eLife (11.07.2022)
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Journal Article
Exposure to toxic metals triggers unique responses from the rat gut microbiota
Richardson, Joshua B., Dancy, Blair C. R., Horton, Cassandra L., Lee, Young S., Madejczyk, Michael S., Xu, Zhenjiang Zech, Ackermann, Gail, Humphrey, Gregory, Palacios, Gustavo, Knight, Rob, Lewis, John A.
Published in Scientific reports (26.04.2018)
Published in Scientific reports (26.04.2018)
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Journal Article
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Janssen, Stefan, McDonald, Daniel, Gonzalez, Antonio, Navas-Molina, Jose A, Jiang, Lingjing, Xu, Zhenjiang Zech, Winker, Kevin, Kado, Deborah M, Orwoll, Eric, Manary, Mark, Mirarab, Siavash, Knight, Rob
Published in mSystems (01.05.2018)
Published in mSystems (01.05.2018)
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Journal Article
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
Song, Se Jin, Amir, Amnon, Metcalf, Jessica L, Amato, Katherine R, Xu, Zhenjiang Zech, Humphrey, Greg, Knight, Rob
Published in mSystems (01.05.2016)
Published in mSystems (01.05.2016)
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Journal Article
Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction
Zhou, Youlian, Xu, Zhenjiang Zech, He, Yan, Yang, Yunsheng, Liu, Le, Lin, Qianyun, Nie, Yuqiang, Li, Mingsong, Zhi, Fachao, Liu, Side, Amir, Amnon, González, Antonio, Tripathi, Anupriya, Chen, Minhu, Wu, Gary D, Knight, Rob, Zhou, Hongwei, Chen, Ye
Published in mSystems (01.01.2018)
Published in mSystems (01.01.2018)
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Journal Article
Human Skin, Oral, and Gut Microbiomes Predict Chronological Age
Huang, Shi, Haiminen, Niina, Carrieri, Anna-Paola, Hu, Rebecca, Jiang, Lingjing, Parida, Laxmi, Russell, Baylee, Allaband, Celeste, Zarrinpar, Amir, Vázquez-Baeza, Yoshiki, Belda-Ferre, Pedro, Zhou, Hongwei, Kim, Ho-Cheol, Swafford, Austin D, Knight, Rob, Xu, Zhenjiang Zech
Published in mSystems (11.02.2020)
Published in mSystems (11.02.2020)
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Journal Article
PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community
Liu, Zhi, Mi, Kai, Xu, Zhenjiang Zech, Zhang, Qiankun, Liu, Xingyin
Published in Genomics, proteomics & bioinformatics (01.02.2021)
Published in Genomics, proteomics & bioinformatics (01.02.2021)
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Journal Article
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis
Wu, Zhenhua, Huang, Shimeng, Li, Tiantian, Li, Na, Han, Dandan, Zhang, Bing, Xu, Zhenjiang Zech, Zhang, Shiyi, Pang, Jiaman, Wang, Shilan, Zhang, Guolong, Zhao, Jiangchao, Wang, Junjun
Published in Microbiome (07.09.2021)
Published in Microbiome (07.09.2021)
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Journal Article
Tiny microbes, enormous impacts: what matters in gut microbiome studies?
Debelius, Justine, Song, Se Jin, Vazquez-Baeza, Yoshiki, Xu, Zhenjiang Zech, Gonzalez, Antonio, Knight, Rob
Published in Genome Biology (19.10.2016)
Published in Genome Biology (19.10.2016)
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Journal Article
Open-Source Sequence Clustering Methods Improve the State Of the Art
Kopylova, Evguenia, Navas-Molina, Jose A, Mercier, Céline, Xu, Zhenjiang Zech, Mahé, Frédéric, He, Yan, Zhou, Hong-Wei, Rognes, Torbjørn, Caporaso, J Gregory, Knight, Rob
Published in mSystems (01.01.2016)
Published in mSystems (01.01.2016)
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Journal Article
Normalization and microbial differential abundance strategies depend upon data characteristics
Weiss, Sophie, Xu, Zhenjiang Zech, Peddada, Shyamal, Amir, Amnon, Bittinger, Kyle, Gonzalez, Antonio, Lozupone, Catherine, Zaneveld, Jesse R, Vázquez-Baeza, Yoshiki, Birmingham, Amanda, Hyde, Embriette R, Knight, Rob
Published in Microbiome (03.03.2017)
Published in Microbiome (03.03.2017)
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Journal Article
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
Weiss, Sophie, Van Treuren, Will, Lozupone, Catherine, Faust, Karoline, Friedman, Jonathan, Deng, Ye, Xia, Li Charlie, Xu, Zhenjiang Zech, Ursell, Luke, Alm, Eric J, Birmingham, Amanda, Cram, Jacob A, Fuhrman, Jed A, Raes, Jeroen, Sun, Fengzhu, Zhou, Jizhong, Knight, Rob
Published in The ISME Journal (01.07.2016)
Published in The ISME Journal (01.07.2016)
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Journal Article
Partial order relation–based gene ontology embedding improves protein function prediction
Li, Wenjing, Wang, Bin, Dai, Jin, Kou, Yan, Chen, Xiaojun, Pan, Yi, Hu, Shuangwei, Xu, Zhenjiang Zech
Published in Briefings in bioinformatics (22.01.2024)
Published in Briefings in bioinformatics (22.01.2024)
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Journal Article
Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria
Liu, Feng, Lu, Hui, Dong, Biao, Huang, Xiaochang, Cheng, Hongyu, Qu, Ru, Hu, Yichen, Zhong, Luyun, Guo, Zhenni, You, Yuehua, Xu, Zhenjiang Zech
Published in mSystems (27.04.2023)
Published in mSystems (27.04.2023)
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Journal Article
Microbial community assembly and metabolic function during mammalian corpse decomposition
Metcalf, Jessica L., Xu, Zhenjiang Zech, Weiss, Sophie, Lax, Simon, Van Treuren, Will, Hyde, Embriette R., Song, Se Jin, Amir, Amnon, Larsen, Peter, Sangwan, Naseer, Haarmann, Daniel, Humphrey, Greg C., Ackermann, Gail, Thompson, Luke R., Lauber, Christian, Bibat, Alexander, Nicholas, Catherine, Gebert, Matthew J., Petrosino, Joseph F., Reed, Sasha C., Gilbert, Jack A., Lynne, Aaron M., Bucheli, Sibyl R., Carter, David O., Knight, Rob
Published in Science (American Association for the Advancement of Science) (08.01.2016)
Published in Science (American Association for the Advancement of Science) (08.01.2016)
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Journal Article