Publications

Yanwen Xue, Fang Huang, Rongxue Tang, Qingsheng Fan, Bing Zhang, Zhenjiang Zech Xu, Xiaoming Sun, Zheng Ruan (2019). Chlorogenic acid attenuates cadmium-induced intestinal injury in Sprague–Dawley rats. Food and Chemical Toxicology.

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. 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-Rodríguez, 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 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 Lozupone, Massoud Maher, Clarisse 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 Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. 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 J. J. 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 (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology.

Whitney A. Kodama, Zhenjiang Zech Xu, Jessica L. Metcalf, Se Jin Song, Nicholas Harrison, Rob Knight, David O. Carter, Christopher B. Happy (2019). Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. Journal of Forensic Sciences.

Anupriya Tripathi, Zhenjiang Zech Xu, Jin Xue, Orit Poulsen, Antonio Gonzalez, Gregory Humphrey, Michael J. Meehan, Alexey V. Melnik, Gail Ackermann, Dan Zhou, Atul Malhotra, Gabriel G. Haddad, Pieter C. Dorrestein, Rob Knight (2019). Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. mSystems.

Cyrielle Caussy, Anupriya Tripathi, Greg Humphrey, Shirin Bassirian, Seema Singh, Claire Faulkner, Ricki Bettencourt, Emily Rizo, Lisa Richards, Zhenjiang Zech Xu, Michael R. Downes, Ronald M. Evans, David A. Brenner, Claude B. Sirlin, Rob Knight, Rohit Loomba (2019). A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Nature Communications.

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 (2019). Calour: an Interactive, Microbe-Centric Analysis Tool. mSystems.

Johannes Braun, Sandra Fischer, Zhenjiang Zech Xu, Hongying Sun, Dalia H. Ghoneim, Anna T. Gimbel, Uwe Plessmann, Henning Urlaub, David H. Mathews, Julia E. Weigand (2018). Identification of new high affinity targets for Roquin based on structural conservation. Nucleic Acids Research.

Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight (2018). Striped UniFrac: enabling microbiome analysis at unprecedented scale. Nature Methods.

Amir Zarrinpar, Amandine Chaix, Zhenjiang Zech Xu, Max W. Chang, Clarisse A. Marotz, Alan Saghatelian, Rob Knight, Satchidananda Panda (2018). Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nature Communications.

Stefan Janssen, Daniel McDonald, Antonio Gonzalez, Jose A. Navas-Molina, Lingjing Jiang, Zhenjiang Zech Xu, Kevin Winker, Deborah M. Kado, Eric Orwoll, Mark Manary, Siavash Mirarab, Rob Knight (2018). Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems.

Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems.

Jennifer M. Michaud, Luke R. Thompson, Drishti Kaul, Josh L. Espinoza, R. Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M. Pham, Charlotte M. Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D. Burkart, Christopher L. Dupont, Kimberly A. Prather (2018). Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nature Communications.

Joshua B. Richardson, Blair C. R. Dancy, Cassandra L. Horton, Young S. Lee, Michael S. Madejczyk, Zhenjiang Zech Xu, Gail Ackermann, Gregory Humphrey, Gustavo Palacios, Rob Knight, John A. Lewis (2018). Exposure to toxic metals triggers unique responses from the rat gut microbiota. Scientific Reports.

Aeriel Belk, Zhenjiang Zech Xu, David O. Carter, Aaron Lynne, Sibyl Bucheli, Rob Knight, Jessica L. Metcalf (2018). Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. Genes.

Jeremiah J. Minich, Qiyun Zhu, Zhenjiang Zech Xu, Amnon Amir, Maxon Ngochera, Moses Simwaka, Eric E. Allen, Hastings Zidana, Rob Knight (2018). Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen.

Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Stefan Janssen, Evguenia Kopylova, Yoshiki Vázquez-Baeza, Antonio González, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Lingjing Jiang, Mohamed F. Haroon, Jad Kanbar, Qiyun Zhu, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Gregory Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie, Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight, The Earth Microbiome Project Consortium, Jose L. Agosto Rivera, Lisa Al-Moosawi, John Alverdy, Katherine R. Amato, Jason Andras, Largus T. Angenent, Dionysios A. Antonopoulos, Amy Apprill, David Armitage, Kate Ballantine, Jirˇí Bárta, Julia K. Baum, Allison Berry, Ashish Bhatnagar, Monica Bhatnagar, Jennifer F. Biddle, Lucie Bittner, Bazartseren Boldgiv, Eric Bottos, Donal M. Boyer, Josephine Braun, William Brazelton, Francis Q. Brearley, Alexandra H. Campbell, J. Gregory Caporaso, Cesar Cardona, JoLynn Carroll, S. Craig Cary, Brenda B. Casper, Trevor C. Charles, Haiyan Chu, Danielle C. Claar, Robert G. Clark, Jonathan B. Clayton, Jose C. Clemente, Alyssa Cochran, Maureen L. Coleman, Gavin Collins, Rita R. Colwell, Mónica Contreras, Benjamin B. Crary, Simon Creer, Daniel A. Cristol, Byron C. Crump, Duoying Cui, Sarah E. Daly, Liliana Davalos, Russell D. Dawson, Jennifer Defazio, Frédéric Delsuc, Hebe M. Dionisi, Maria Gloria Dominguez-Bello, Robin Dowell, Eric A. Dubinsky, Peter O. Dunn, Danilo Ercolini, Robert E. Espinoza, Vanessa Ezenwa, Nathalie Fenner, Helen S. Findlay, Irma D. Fleming, Vincenzo Fogliano, Anna Forsman, Chris Freeman, Elliot S. Friedman, Giancarlo Galindo, Liza Garcia, Maria Alexandra Garcia-Amado, David Garshelis, Robin B. Gasser, Gunnar Gerdts, Molly K. Gibson, Isaac Gifford, Ryan T. Gill, Tugrul Giray, Antje Gittel, Peter Golyshin, Donglai Gong, Hans-Peter Grossart, Kristina Guyton, Sarah-Jane Haig, Vanessa Hale, Ross Stephen Hall, Steven J. Hallam, Kim M. Handley, Nur A. Hasan, Shane R. Haydon, Jonathan E. Hickman, Glida Hidalgo, Kirsten S. Hofmockel, Jeff Hooker, Stefan Hulth, Jenni Hultman, Embriette Hyde, Juan Diego Ibáñez-Álamo, Julie D. Jastrow, Aaron R. Jex, L. Scott Johnson, Eric R. Johnston, Stephen Joseph, Stephanie D. Jurburg, Diogo Jurelevicius, Anders Karlsson, Roger Karlsson, Seth Kauppinen, Colleen T. E. Kellogg, Suzanne J. Kennedy, Lee J. Kerkhof, Gary M. King, George W. Kling, Anson V. Koehler, Monika Krezalek, Jordan Kueneman, Regina Lamendella, Emily M. Landon, Kelly Lane-deGraaf, Julie LaRoche, Peter Larsen, Bonnie Laverock, Simon Lax, Miguel Lentino, Iris I. Levin, Pierre Liancourt, Wenju Liang, Alexandra M. Linz, David A. Lipson, Yongqin Liu, Manuel E. Lladser, Mariana Lozada, Catherine M. Spirito, Walter P. MacCormack, Aurora MacRae-Crerar, Magda Magris, Antonio M. Martín-Platero, Manuel Martín-Vivaldi, L. Margarita Martínez, Manuel Martínez-Bueno, Ezequiel M. Marzinelli, Olivia U. Mason, Gregory D. Mayer, Jamie M. McDevitt-Irwin, James E. McDonald, Krista L. McGuire, Katherine D. McMahon, Ryan McMinds, Mónica Medina, Joseph R. Mendelson, Jessica L. Metcalf, Folker Meyer, Fabian Michelangeli, Kim Miller, David A. Mills, Jeremiah Minich, Stefano Mocali, Lucas Moitinho-Silva, Anni Moore, Rachael M. Morgan-Kiss, Paul Munroe, David Myrold, Josh D. Neufeld, Yingying Ni, Graeme W. Nicol, Shaun Nielsen, Jozef I. Nissimov, Kefeng Niu, Matthew J. Nolan, Karen Noyce, Sarah L. O’Brien, Noriko Okamoto, Ludovic Orlando, Yadira Ortiz Castellano, Olayinka Osuolale, Wyatt Oswald, Jacob Parnell, Juan M. Peralta-Sánchez, Peter Petraitis, Catherine Pfister, Elizabeth Pilon-Smits, Paola Piombino, Stephen B. Pointing, F. Joseph Pollock, Caitlin Potter, Bharath Prithiviraj, Christopher Quince, Asha Rani, Ravi Ranjan, Subramanya Rao, Andrew P. Rees, Miles Richardson, Ulf Riebesell, Carol Robinson, Karl J. Rockne, Selena Marie Rodriguezl, Forest Rohwer, Wayne Roundstone, Rebecca J. Safran, Naseer Sangwan, Virginia Sanz, Matthew Schrenk, Mark D. Schrenzel, Nicole M. Scott, Rita L. Seger, Andaine Seguin-Orlando, Lucy Seldin, Lauren M. Seyler, Baddr Shakhsheer, Gabriela M. Sheets, Congcong Shen, Yu Shi, Hakdong Shin, Benjamin D. Shogan, Dave Shutler, Jeffrey Siegel, Steve Simmons, Sara Sjöling, Daniel P. Smith, Juan J. Soler, Martin Sperling, Peter D. Steinberg, Brent Stephens, Melita A. Stevens, Safiyh Taghavi, Vera Tai, Karen Tait, Chia L. Tan, Neslihan Tas¸, D. Lee Taylor, Torsten Thomas, Ina Timling, Benjamin L. Turner, Tim Urich, Luke K. Ursell, Daniel van der Lelie, William Van Treuren, Lukas van Zwieten, Daniela Vargas-Robles, Rebecca Vega Thurber, Paola Vitaglione, Donald A. Walker, William A. Walters, Shi Wang, Tao Wang, Tom Weaver, Nicole S. Webster, Beck Wehrle, Pamela Weisenhorn, Sophie Weiss, Jeffrey J. Werner, Kristin West, Andrew Whitehead, Susan R. Whitehead, Linda A. Whittingham, Eske Willerslev, Allison E. Williams, Stephen A. Wood, Douglas C. Woodhams, Yeqin Yang, Jesse Zaneveld, Iratxe Zarraonaindia, Qikun Zhang, Hongxia Zhao (2017). A communal catalogue reveals Earth's multiscale microbial diversity. Nature.

Yoshiki Vázquez-Baeza, Antonio Gonzalez, Zhenjiang Zech Xu, Alex Washburne, Hans H. Herfarth, R. Balfour Sartor, Rob Knight (2017). Guiding longitudinal sampling in IBD cohorts. Gut.

Jessica L. Metcalf, Zhenjiang Zech Xu, Amina Bouslimani, Pieter Dorrestein, David O. Carter, Rob Knight (2017). Microbiome Tools for Forensic Science. Trends in Biotechnology.

Scott D. Wankel, Wiebke Ziebis, Carolyn Buchwald, Chawalit Charoenpong, Dirk de Beer, Jane Dentinger, Zhenjiang Zech Xu, Karsten Zengler (2017). Evidence for fungal and chemodenitrification based N$_textrm2$O flux from nitrogen impacted coastal sediments. Nature Communications.

Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight (2017). Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems.

Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight (2017). Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome.

Amina Bouslimani, Alexey V. Melnik, Zhenjiang Zech Xu, Amnon Amir, Ricardo R. da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein (2016). Lifestyle chemistries from phones for individual profiling. Proceedings of the National Academy of Sciences.

Jack A. Gilbert, Robert A. Quinn, Justine Debelius, Zhenjiang Zech Xu, James Morton, Neha Garg, Janet K. Jansson, Pieter C. Dorrestein, Rob Knight (2016). Microbiome-wide association studies link dynamic microbial consortia to disease. Nature.

Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight (2016). Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems.

Evguenia Kopylova, Jose A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight (2016). Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems.

Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight (2016). Tiny microbes, enormous impacts: what matters in gut microbiome studies?. Genome Biology.

Zhenjiang Zech Xu, David H. Mathews (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. RNA Structure Determination.

Zhenjiang Zech Xu, David H. Mathews (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. RNA Structure Determination.

Zhenjiang Zech Xu, David H. Mathews (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. RNA Structure Determination.

Justine W. Debelius, Yoshiki Vázquez-Baeza, Daniel McDonald, Zhenjiang Zech Xu, Elaine Wolfe, Rob Knight (2015). Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project. Journal of Microbiology & Biology Education.

Fei Teng, Fang Yang, Shi Huang, Cunpei Bo, Zhenjiang Zech Xu, Amnon Amir, Rob Knight, Junqi Ling, Jian Xu (2015). Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota. Cell Host & Microbe.

Yinghan Fu, Zhenjiang Zech Xu, Zhi J. Lu, Shan Zhao, David H. Mathews (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS ONE.

Daniel McDonald, Zhenjiang Zech Xu, Embriette R. Hyde, Rob Knight (2015). Ribosomal RNA, the lens into life. RNA.

Gang Yang, Zhenjiang Zech Xu, Xiangli Tian, Shuanglin Dong, Mo Peng (2015). Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation. Biochemical and Biophysical Research Communications.

Zhenjiang Zech Xu, Rob Knight (2015). Dietary effects on human gut microbiome diversity. British Journal of Nutrition.

Zhenjiang Zech Xu, Daniel Malmer, Morgan G. I. Langille, Samuel F. Way, Rob Knight (2014). Which is more important for classifying microbial communities: who's there or what they can do?. The ISME Journal.

William A. Walters, Zhenjiang Zech Xu, Rob Knight (2014). Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Letters.

Jeremiah J. Trausch, Zhenjiang Zech Xu, Andrea L. Edwards, Francis E. Reyes, Phillip E. Ross, Rob Knight, Robert T. Batey (2014). Structural basis for diversity in the SAM clan of riboswitches. Proceedings of the National Academy of Sciences.

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, Rob Knight (2013). Advancing Our Understanding of the Human Microbiome Using QIIME. Methods in Enzymology.

Karyn Schmidt, Zhenjiang Zech Xu, David H. Mathews, J. Scott Butler (2012). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA.

Zhenjiang Zech Xu, Anthony Almudevar, David H. Mathews (2012). Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research.

Michael-Paul Vockenhuber, Cynthia M. Sharma, Michaela G. Statt, Denis Schmidt, Zhenjiang Zech Xu, Sascha Dietrich, Heiko Liesegang, David H. Mathews, Beatrix Suess (2011). Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biology.

Zhenjiang Zech Xu, David H. Mathews (2011). Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics.