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Qiyun Zhu
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, CC Abnet, GA Al-Ghalith, ...
Nature biotechnology 37 (8), 852-857, 2019
139302019
A communal catalogue reveals Earth’s multiscale microbial diversity
LR Thompson, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, ...
Nature 551 (7681), 457-463, 2017
22342017
Best practices for analysing microbiomes
R Knight, A Vrbanac, BC Taylor, A Aksenov, C Callewaert, J Debelius, ...
Nature Reviews Microbiology 16 (7), 410-422, 2018
14812018
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
E Bolyen, JR Rideout, MR Dillon, NA Bokulich, C Abnet, GA Al-Ghalith, ...
PeerJ Preprints, 2018
9382018
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
GD Poore, E Kopylova, Q Zhu, C Carpenter, S Fraraccio, S Wandro, ...
Nature 579 (7800), 567-574, 2020
8332020
American gut: an open platform for citizen science microbiome research
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ...
Msystems 3 (3), 10.1128/msystems. 00031-18, 2018
6682018
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
F Asnicar, AM Thomas, F Beghini, C Mengoni, S Manara, P Manghi, ...
Nature communications 11 (1), 2500, 2020
4212020
FXR regulates intestinal cancer stem cell proliferation
T Fu, S Coulter, E Yoshihara, TG Oh, S Fang, F Cayabyab, Q Zhu, ...
Cell 176 (5), 1098-1112. e18, 2019
3512019
Evaluating the information content of shallow shotgun metagenomics
B Hillmann, GA Al-Ghalith, RR Shields-Cutler, Q Zhu, DM Gohl, ...
Msystems 3 (6), 10.1128/msystems. 00069-18, 2018
3002018
QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data
M Estaki, L Jiang, NA Bokulich, D McDonald, A González, T Kosciolek, ...
Current protocols in bioinformatics 70 (1), e100, 2020
2852020
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
SM Karst, RM Ziels, RH Kirkegaard, EA Sřrensen, D McDonald, Q Zhu, ...
Nature methods 18 (2), 165-169, 2021
2812021
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Q Zhu, U Mai, W Pfeiffer, S Janssen, F Asnicar, JG Sanders, ...
Nature communications 10 (1), 5477, 2019
2502019
A gut-derived metabolite alters brain activity and anxiety behaviour in mice
BD Needham, M Funabashi, MD Adame, Z Wang, JC Boktor, J Haney, ...
Nature 602 (7898), 647-653, 2022
2222022
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
Y Qin, AS Havulinna, Y Liu, P Jousilahti, SC Ritchie, A Tokolyi, ...
Nature Genetics 54 (2), 134-142, 2022
2112022
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions
L Narunsky-Haziza, GD Sepich-Poore, I Livyatan, O Asraf, C Martino, ...
Cell 185 (20), 3789-3806. e17, 2022
2052022
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
RH Mills, PS Dulai, Y Vázquez-Baeza, C Sauceda, N Daniel, RR Gerner, ...
Nature microbiology 7 (2), 262-276, 2022
1352022
HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers
Q Zhu, M Kosoy, K Dittmar
BMC genomics 15, 1-18, 2014
1262014
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
ZS Hua, YN Qu, Q Zhu, EM Zhou, YL Qi, YR Yin, YZ Rao, Y Tian, YX Li, ...
Nature communications 9 (1), 2832, 2018
1242018
Origin of microbial biomineralization and magnetotaxis during the Archean
W Lin, GA Paterson, Q Zhu, Y Wang, E Kopylova, Y Li, R Knight, ...
Proceedings of the National Academy of Sciences 114 (9), 2171-2176, 2017
1212017
Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis
Y He, T Kosciolek, J Tang, Y Zhou, Z Li, X Ma, Q Zhu, N Yuan, L Yuan, ...
European Psychiatry 53, 37-45, 2018
1122018
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Articles 1–20