List of works cited#

[AMR+21]

George Armstrong, Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Gal Mishne, and Rob Knight. Uniform manifold approximation and projection (UMAP) reveals composite patterns and resolves visualization artifacts in microbiome data. mSystems, 6(5):e0069121, October 2021.

[BDZ+18]

Nicholas A Bokulich, Matthew R Dillon, Yilong Zhang, Jai Ram Rideout, Evan Bolyen, Huilin Li, Paul S Albert, and J Gregory Caporaso. Q2-longitudinal: longitudinal and Paired-Sample analyses of microbiome data. mSystems, November 2018.

[BRD+19]

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, 2nd, 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, and J Gregory Caporaso. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol., July 2019.

[CMR+16]

Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, and Susan P Holmes. DADA2: high-resolution sample inference from illumina amplicon data. Nat. Methods, May 2016.

[DBA+21]

Matthew R Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R Keefe, Jamie T Morton, Renato R M Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vázquez-Baeza, Michal Ziemski, Hazuki E Miwa, Terry A Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D Kaehler, Emily K Cope, Jessica L Metcalf, Michael S Robeson, Ii, Nicholas A Bokulich, and J Gregory Caporaso. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol., 17(6):e1009056, June 2021.

[KBM+19]

Benjamin D Kaehler, Nicholas A Bokulich, Daniel McDonald, Rob Knight, J Gregory Caporaso, and Gavin A Huttley. Species abundance information improves sequence taxonomy classification accuracy. Nat. Commun., 10(1):4643, October 2019.

[LTC+21]

Chen Liao, Bradford P Taylor, Camilla Ceccarani, Emily Fontana, Luigi A Amoretti, Roberta J Wright, Antonio L C Gomes, Jonathan U Peled, Miguel-Angel Perales, Marcel R M van den Brink, Eric Littmann, Eric G Pamer, Jonas Schluter, and Joao B Xavier. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Sci Data, 8(1):71, March 2021.

[OBP11]

Brian D Ondov, Nicholas H Bergman, and Adam M Phillippy. Interactive metagenomic visualization in a web browser. BMC Bioinformatics, 12:385, September 2011.

[RORourkeK+21]

Michael S Robeson, 2nd, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, and Nicholas A Bokulich. RESCRIPt: reproducible sequence taxonomy reference database management. PLoS Comput. Biol., 17(11):e1009581, November 2021.

[TCS+18]

Ying Taur, Katharine Coyte, Jonas Schluter, Elizabeth Robilotti, Cesar Figueroa, Mergim Gjonbalaj, Eric R Littmann, Lilan Ling, Liza Miller, Yangtsho Gyaltshen, Emily Fontana, Sejal Morjaria, Boglarka Gyurkocza, Miguel-Angel Perales, Hugo Castro-Malaspina, Roni Tamari, Doris Ponce, Guenther Koehne, Juliet Barker, Ann Jakubowski, Esperanza Papadopoulos, Parastoo Dahi, Craig Sauter, Brian Shaffer, James W Young, Jonathan Peled, Richard C Meagher, Robert R Jenq, Marcel R M van den Brink, Sergio A Giralt, Eric G Pamer, and Joao B Xavier. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med., September 2018.