Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 von Asnicar, Francesco, Thomas, Andrew Maltez, Beghini, Francesco, Mengoni, Claudia, Manara, Serena, Manghi, Paolo, Zhu, Qiyun, Bolzan, Mattia, Cumbo, Fabio, May, Uyen, Sanders, Jon G., Zolfo, Moreno, Kopylova, Evguenia, Pasolli, Edoardo, Knight, Rob, Mirarab, Siavash, Huttenhower, Curtis, Segata, Nicola

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Evaluating the Information Content of Shallow Shotgun Metagenomics von Hillmann, Benjamin, Al-Ghalith, Gabriel A, Shields-Cutler, Robin R, Zhu, Qiyun, Gohl, Daryl M, Beckman, Kenneth B, Knight, Rob, Knights, Dan

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USP18 recruits USP20 to promote innate antiviral response through deubiquitinating STING/MITA von Zhang, Man, Zhang, Meng-Xin, Zhang, Qiang, Zhu, Gao-Feng, Yuan, Lei, Zhang, Dong-Er, Zhu, Qiyun, Yao, Jing, Shu, Hong-Bing, Zhong, Bo

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High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing von Karst, Søren M., Ziels, Ryan M., Kirkegaard, Rasmus H., Sørensen, Emil A., McDonald, Daniel, Zhu, Qiyun, Knight, Rob, Albertsen, Mads

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HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers von Zhu, Qiyun, Kosoy, Michael, Dittmar, Katharina

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Challenges in benchmarking metagenomic profilers von Sun, Zheng, Huang, Shi, Zhang, Meng, Zhu, Qiyun, Haiminen, Niina, Carrieri, Anna Paola, Vázquez-Baeza, Yoshiki, Parida, Laxmi, Kim, Ho-Cheol, Knight, Rob, Liu, Yang-Yu

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MicroRNA-200c-targeted contactin 1 facilitates the replication of influenza A virus by accelerating the degradation of MAVS von Xu, Shuai, Han, Lu, Wei, Yanli, Zhang, Bo, Wang, Qian, Liu, Junwen, Liu, Minxuan, Chen, Zhaoshan, Wang, Zhengxiang, Chen, Hualan, Zhu, Qiyun

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Induction of OTUD4 by viral infection promotes antiviral responses through deubiquitinating and stabilizing MAVS von Liuyu, Tianzi, Yu, Keying, Ye, Liya, Zhang, Zhidong, Zhang, Man, Ren, Yujie, Cai, Zeng, Zhu, Qiyun, Lin, Dandan, Zhong, Bo

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The PB1 protein of influenza A virus inhibits the innate immune response by targeting MAVS for NBR1-mediated selective autophagic degradation von Zeng, Yan, Xu, Shuai, Wei, Yanli, Zhang, Xuegang, Wang, Qian, Jia, Yane, Wang, Wanbing, Han, Lu, Chen, Zhaoshan, Wang, Zhengxiang, Zhang, Bo, Chen, Hualan, Lei, Cao-Qi, Zhu, Qiyun

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

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Greengenes2 unifies microbial data in a single reference tree von McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, Knight, Rob

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Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria von Jiao, Jian-Yu, Fu, Li, Hua, Zheng-Shuang, Liu, Lan, Salam, Nimaichand, Liu, Peng-Fei, Lv, Ai-Ping, Wu, Geng, Xian, Wen-Dong, Zhu, Qiyun, Zhou, En-Min, Fang, Bao-Zhu, Oren, Aharon, Hedlund, Brian P., Jiang, Hong-Chen, Knight, Rob, Cheng, Lei, Li, Wen-Jun

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Origin of microbial biomineralization and magnetotaxis during the Archean von Lin, Wei, Paterson, Greig A., Zhu, Qiyun, Wang, Yinzhao, Kopylova, Evguenia, Li, Ying, Knight, Rob, Bazylinski, Dennis A., Zhu, Rixiang, Kirschvink, Joseph L., Pan, Yongxin

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Microbiome and metabolome profiles of high screen time in a cohort of healthy college students von Jasbi, Paniz, Mohr, Alex E., Shi, Xiaojian, Mahmood, Tara, Zhu, Qiyun, Bruening, Meg, Gu, Haiwei, Whisner, Corrie

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Chemically informed analyses of metabolomics mass spectrometry data with Qemistree von Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Gauglitz, Julia M., Wang, Mingxun, Dührkop, Kai, Nothias-Esposito, Mélissa, Acharya, Deepa D., Ernst, Madeleine, van der Hooft, Justin J. J., Zhu, Qiyun, McDonald, Daniel, Brejnrod, Asker D., Gonzalez, Antonio, Handelsman, Jo, Fleischauer, Markus, Ludwig, Marcus, Böcker, Sebastian, Nothias, Louis-Félix, Knight, Rob, Dorrestein, Pieter C.

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Exosome-mediated microRNA transfer plays a role in radiation-induced bystander effect von Xu, Shuai, Wang, Jufang, Ding, Nan, Hu, Wentao, Zhang, Xurui, Wang, Bing, Hua, Junrui, Wei, Wenjun, Zhu, Qiyun

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Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis von He, Ying, Kosciolek, Tomasz, Tang, Jinsong, Zhou, Yao, Li, Zongchang, Ma, Xiaoqian, Zhu, Qiyun, Yuan, Ning, Yuan, Liu, Li, Chunwang, Jin, Ke, Knight, Rob, Tsuang, Ming T., Chen, Xiaogang

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Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers von Zhu, Qiyun, Hou, Qiangchuan, Huang, Shi, Ou, Qianying, Huo, Dongxue, Vázquez-Baeza, Yoshiki, Cen, Chaoping, Cantu, Victor, Estaki, Mehrbod, Chang, Haibo, Belda-Ferre, Pedro, Kim, Ho-Cheol, Chen, Kaining, Knight, Rob, Zhang, Jiachao

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KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples von Minich, Jeremiah J, Zhu, Qiyun, Janssen, Stefan, Hendrickson, Ryan, Amir, Amnon, Vetter, Russ, Hyde, John, Doty, Megan M, Stillwell, Kristina, Benardini, James, Kim, Jae H, Allen, Eric E, Venkateswaran, Kasthuri, Knight, Rob

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An evolutionary optimum amid moderate heritability in prokaryotic cell size von Secaira-Morocho, Henry, Chede, Abhinav, Gonzalez-de-Salceda, Luis, Garcia-Pichel, Ferran, Zhu, Qiyun

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