RNA: An Expanding View of Function and Evolution

by Xinwei Han, Yuan Chen, Liuyang Wang, Wenwen Fang, Ning Zhang, Qiyun Zhu
Published 2015-01-01

Introductory Editorial: RNA: An Expanding View of Function and Evolution

by Xinwei Han, Yuan Chen, Liuyang Wang, Wenwen Fang, Ning Zhang, Qiyun Zhu
Published 2016-01-01

Comparative Pathogenicity and Transmissibility of Pandemic H1N1, Avian H5N1, and Human H7N9 Influenza Viruses in Tree Shrews

by Shuai Xu, Xuyong Li, Jiayun Yang, Zhengxiang Wang, Yane Jia, Lu Han, Liang Wang, Qiyun Zhu
Published 2019-12-01

Expanding magnetic organelle biogenesis in the domain Bacteria

by Wei Lin, Wensi Zhang, Greig A. Paterson, Qiyun Zhu, Xiang Zhao, Rob Knight, Dennis A. Bazylinski, Andrew P. Roberts, Yongxin Pan
Published 2020-10-01

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea

by Qiyun Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin M. Pham, Zhi-Dong Jiang, Herbert L. DuPont, Sarah K. Highlander
Published 2018-11-01

Bartonella spp. in fruit bats and blood-feeding Ectoparasites in Madagascar.

by Cara E Brook, Ying Bai, Andrew P Dobson, Lynn M Osikowicz, Hafaliana C Ranaivoson, Qiyun Zhu, Michael Y Kosoy, Katharina Dittmar
Published 2015-02-01

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

by Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
Published 2019-02-01

Evaluating the Information Content of Shallow Shotgun Metagenomics

by Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl M. Gohl, Kenneth B. Beckman, Rob Knight, Dan Knights
Published 2018-11-01

USP49 negatively regulates cellular antiviral responses via deconjugating K63-linked ubiquitination of MITA.

by Liya Ye, Qiang Zhang, Tianzi Liuyu, Zhigao Xu, Meng-Xin Zhang, Min-Hua Luo, Wen-Bo Zeng, Qiyun Zhu, Dandan Lin, Bo Zhong
Published 2019-04-01

Calour: an Interactive, Microbe-Centric Analysis Tool

by 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
Published 2019-01-01

The PB1 protein of influenza A virus inhibits the innate immune response by targeting MAVS for NBR1-mediated selective autophagic degradation.

by Yan Zeng, Shuai Xu, Yanli Wei, Xuegang Zhang, Qian Wang, Yane Jia, Wanbing Wang, Lu Han, Zhaoshan Chen, Zhengxiang Wang, Bo Zhang, Hualan Chen, Cao-Qi Lei, Qiyun Zhu
Published 2021-02-01

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

by Jeremiah J. Minich, Qiyun Zhu, Stefan Janssen, Ryan Hendrickson, Amnon Amir, Russ Vetter, John Hyde, Megan M. Doty, Kristina Stillwell, James Benardini, Jae H. Kim, Eric E. Allen, Kasthuri Venkateswaran, Rob Knight
Published 2018-03-01

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiom...

by Shi Huang, Shuaiming Jiang, Dongxue Huo, Celeste Allaband, Mehrbod Estaki, Victor Cantu, Pedro Belda-Ferre, Yoshiki Vázquez-Baeza, Qiyun Zhu, Chenchen Ma, Congfa Li, Amir Zarrinpar, Yang-Yu Liu, Rob Knight, Jiachao Zhang
Published 2021-06-01

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

by Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, Nicola Segata
Published 2020-05-01

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

by Zheng-Shuang Hua, Yan-Ni Qu, Qiyun Zhu, En-Min Zhou, Yan-Ling Qi, Yi-Rui Yin, Yang-Zhi Rao, Ye Tian, Yu-Xian Li, Lan Liu, Cindy J. Castelle, Brian P. Hedlund, Wen-Sheng Shu, Rob Knight, Wen-Jun Li
Published 2018-07-01

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

by Tiago Leão, Mingxun Wang, Nathan Moss, Ricardo da Silva, Jon Sanders, Sergey Nurk, Alexey Gurevich, Gregory Humphrey, Raphael Reher, Qiyun Zhu, Pedro Belda-Ferre, Evgenia Glukhov, Syrena Whitner, Kelsey L. Alexander, Robert Rex, Pavel Pevzner, Pieter C. Dorrestein, Rob Knight, Nuno Bandeira, William H. Gerwick, Lena Gerwick
Published 2021-01-01

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

by Xin Fang, Jonathan M. Monk, Sergey Nurk, Margarita Akseshina, Qiyun Zhu, Christopher Gemmell, Connor Gianetto-Hill, Nelly Leung, Richard Szubin, Jon Sanders, Paul L. Beck, Weizhong Li, Weizhong Li, William J. Sandborn, William J. Sandborn, Scott D. Gray-Owen, Rob Knight, Rob Knight, Rob Knight, Emma Allen-Vercoe, Bernhard O. Palsson, Bernhard O. Palsson, Bernhard O. Palsson, Bernhard O. Palsson, Larry Smarr, Larry Smarr, Larry Smarr
Published 2018-10-01

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

by 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 Z. 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
Published 2019-12-01

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

by Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. 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
Published 2019-10-01

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

by Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
Published 2021-04-01