Qiyun Zhu

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 26

Top Venues

Nature microbiology

Nature biotechnology

Nature

Proceedings of the National Academy of Sciences of the United States of America

University of California San Diego Health Sciences

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California San Diego Health Sciences Aug 15 2016

United States

Postdoctoral Scholar :: Pediatrics

J Craig Venter Institute - West Coast Campus Oct 27 2014 - Aug 14 2016

United States

Postdoctoral Fellow :: Genomic Medicine

Publications

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 Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Gregory D Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Rob Knight
Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature (2024)
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 Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
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 Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Gregory D Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Rob Knight
Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature (2024)
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 Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
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 Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology (2024)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Author Correction: Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
Metin Balaban, Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab
Author Correction: Generation of accurate, expandable phylogenomic trees with uDance. Nature biotechnology (2023)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
Metin Balaban, Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab
Generation of accurate, expandable phylogenomic trees with uDance. Nature biotechnology (2023)
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford, Promi Das, Justin P Shaffer, Franck Lejzerowicz, Pedro Belda Ferre, Aki Samuli Havulinna, Guillaume Méric, Teemu J Niiranen, Leo Lahti, Veikko V Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A Gilbert, Rob Knight
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems 7 (2) (2022)
Justin P Shaffer, Louis-Felix Nothias, Luke R Thompson, Jon G Sanders, Rodolfo A Salido, Sneha P Couvillion, Asker D Brejnrod, Franck Lejzerowicz, Niina Haiminen, Shi Huang, Holly L Lutz, Qiyun Zhu, Cameron Martino, James T Morton, Smruthi Karthikeyan, Mélissa Nothias-Esposito, Kai Dührkop, Sebastian Böcker, Hyun Woo Kim, Alexander A Aksenov, Wout Bittremieux, Jeremiah J Minich, Clarisse Marotz, MacKenzie M Bryant, Karenina Sanders, Tara Schwartz, Greg Humphrey, Yoshiki Vásquez-Baeza, Anupriya Tripathi, Laxmi Parida, Anna Paola Carrieri, Kristen L Beck, Promi Das, Antonio González, Daniel McDonald, Joshua Ladau, Søren M Karst, Mads Albertsen, Gail Ackermann, Jeff DeReus, Torsten Thomas, Daniel Petras, Ashley Shade, James Stegen, Se Jin Song, Thomas O Metz, Austin D Swafford, Pieter C Dorrestein, Janet K Jansson, Jack A Gilbert, Rob Knight, null null
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nature microbiology 7 (12) (2022)
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 A 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
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems 6 (2) (2021)
Søren Michael Karst, Ryan M Ziels, Rasmus Hansen Kirkegaard, Emil Aarre Sørensen, Daniel McDonald, Qiyun Zhu, Rob Knight, Mads Albertsen
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nature methods 18 (2) (2021)
Metin Balaban, Yueyu Jiang, Daniel Roush, Qiyun Zhu, Siavash Mirarab
Fast and accurate distance-based phylogenetic placement using divide and conquer. Molecular ecology resources (2021)
George Armstrong, Kalen Cantrell, Shi Huang, Daniel McDonald, Niina Haiminen, Anna Paola Carrieri, Qiyun Zhu, Antonio Gonzalez, Imran McGrath, Kristen L Beck, Daniel Hakim, Aki Samuli Havulinna, Guillaume Méric, Teemu J Niiranen, Leo Lahti, Veikko V Salomaa, Mohit Jain, Michael Inouye, Austin D Swafford, Ho-Cheol Kim, Laxmi Parida, Yoshiki Vázquez-Baeza, Rob Knight
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. Genome research 31 (11) (2021)
Gregory D Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Rob Knight
Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 579 (7800) (2020)
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 Z Xu, Jesse R Zaneveld, Qiyun Zhu, J Gregory Caporaso, Pieter C Dorrestein
Best practices for analysing microbiomes. Nature reviews. Microbiology 16 (7) (2019)
Laura-Isobel McCall, Chris Callewaert, Qiyun Zhu, Se Jin Song, Amina Bouslimani, Jeremiah J Minich, Madeleine Ernst, Jean F Ruiz-Calderon, Humberto Cavallin, Henrique S Pereira, Atila Novoselac, Jean Hernandez, Rafael Rios, OraLee H Branch, Martin J Blaser, Luciana C Paulino, Pieter C Dorrestein, Rob Knight, Maria G Dominguez-Bello
Home chemical and microbial transitions across urbanization. Nature microbiology 5 (1) (2019)
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
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature communications 10 (1) (2019)
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric John Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodriguez, 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 P 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 A Lozupone, Massoud Maher, Clarisse A 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 R Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam R Rivers, Michael Scott 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 Johan Jozias 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
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37 (8) (2019)
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
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nature communications 9 (1) (2018)
Lea Weinisch, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
Origin of microbial biomineralization and magnetotaxis during the Archean. Proceedings of the National Academy of Sciences of the United States of America 114 (9) (2017)
Lea Weinisch, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
Reply to Wang and Chen: An ancient origin of magnetotactic bacteria. Proceedings of the National Academy of Sciences of the United States of America 114 (26) (2017)
Yunzhou Yang, Qiyun Zhu, Shuqin Liu, Chunjiang Zhao, Changxin Wu
The origin of Chinese domestic horses revealed with novel mtDNA variants. Animal science journal = Nihon chikusan Gakkaiho 88 (1) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Qiyun Zhu