J. Gregory Caporaso - Curriculum vitae

greg.caporaso@nau.edu

www.caporasolab.us

1350 S. Knoles Drive, Building 56, Room 225, Flagstaff, AZ 86011, USA

(928) 523-5845 (office)

(928) 523-4015 (shared fax; address to c/o Gregory Caporaso)

This document is available online at: http://bit.ly/jgcaporaso-cv

Table of contents

Education        2

Current Positions        2

Former Positions        2

Grant funding        3

Grant funding (completed)        4

Editorial boards        7

Conference organization roles        7

Select open-source software projects        7

Patents        7

Manuscripts in review        7

Publications        8

QIIME and QIIME 2 Workshops        16

Conference and Other Presentations        19

Teaching        26

Students and postdocs mentored        27

Awards and Honors        28


Education

Postdoctoral research scientist

2009-2011

Mentor: Rob Knight, Ph.D.

Department of Chemistry and Biochemistry

University of Colorado at Boulder, Boulder, CO, USA.

Ph.D., May 2009

Dissertation title: Extracting signal from noise in biological data: Evaluations and applications of text mining and sequence coevolution.

Mentor: Lawrence Hunter, Ph.D.

Program in Biophysics and Structural Biology

Department of Biochemistry and Molecular Genetics

University of Colorado Denver, Aurora, CO, USA. (Formerly U of C Health Sciences Center.)

 

Bachelor of Arts in Biochemistry, Minor in Chemistry, August 2004

University of Colorado at Boulder, College of Arts and Sciences, Boulder, CO, USA.

 

Bachelor of Science in Computer Science, May 2001

University of Colorado at Boulder, College of Engineering and Applied Science, Boulder, CO, USA.

Current Positions

Director, 2016 – Present

Center for Applied Microbiome Science (formerly PMI Microbiome Center)

Pathogen and Microbiome Institute

Northern Arizona University, Flagstaff, AZ USA.

Associate Professor, 2016 – Present

Assistant Professor, 2011 – 2016

Department of Biological Sciences

Department of Computer Science

Northern Arizona University, Flagstaff, AZ, USA.

Assistant Director, 2013 – 2016

Research Affiliate, 2012 – 2013

Pathogen and Microbiome Institute (formerly Center for Microbial Genetics and Genomics)

Northern Arizona University, Flagstaff, AZ, USA.

Former Positions

Visiting Scientist (while on sabbatical from NAU), September 2017 - June 2018

Division of Cancer Epidemiology and Genetics

National Cancer Institute, National Institutes of Health, Rockville, MD, USA.

Assistant Professor (summer appointment), 2012 – 2013

Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA.

Grant funding

Role: PI

Funding agency: National Cancer Institute / National Institutes of Health

July 2020 - June 2025

Advancing our Understanding of Cancer and the Human Microbiome with QIIME 2

Role: PI

Funding agency: Chan Zuckerberg Initiative / Silicon Valley Community Foundation

December 2019 - November 2020

Advancing microbiome research through QIIME 2 user and developer community development

Role: Investigator

Funding agency: Alfred P. Sloan Foundation / Australian National University

December 2019 - October 2022

Document Creation and Publishing Tools for Next-Generation Scientific Textbooks

Lead investigator: John Stachurski, Australian National University

Co-investigator: Chris Holdgraf, University of California, Berkeley

Role: MPI on Pilot Project #1

Funding agency: NIH/NCI

September 2019 - August 2024

The Partnership for Native American Cancer Prevention

Co-lead investigators: Melissa Herbst-Kralovetz, University of Arizona; Naomi Lee, Northern Arizona University

Role: MPI

Funding agency: NIH/NIAID

July 2019 - June 2022

Determining the Role of the Upper and Lower Airway Microbiota as Drivers of Concomitant Inflammatory Responses in patients with Chronic Rhinosinusitis and Asthma

Co-lead investigator: Emily Cope, Northern Arizona University

Role: MPI

Funding agency: Arizona Alzheimer’s Research Center, Inc

July 2018 - December 2020

Longitudinal analysis of the gut microbiome-brain axis in Alzheimer’s Disease

Co-lead investigator: Emily Cope, Northern Arizona University

Role: Investigator

Funding agency: University of Arizona / Arizona Biomedical Research Commission

April 2018 - March 2021

Role of the Small Intestine in the Prebiotic Treatment/or Obesity

Lead investigator: Frank Duca, University of Arizona

Role: Investigator on Research Project #1

Funding agency: NIH/National Institute on Minority Health and Health Disparities

July 2017 - June 2022

Southwest Health Equity Research Collaborative (SHERC)

Lead investigator: Talima Pearson, Northern Arizona University

Role: Co-PI

Funding agency: National Institute of Food and Agriculture

April 2017 - March 2022

Optimizing Plant-soil Feedbacks for High Intensity Crop Production Systems

Lead investigator: Ian Kaplan, Purdue University

Grant funding (completed)

Role: Subcontract

Funding agency: University of Arizona Multidisciplinary Program Feasibility Award (UAHS-MPFA)

July 2016 - June 2017

Binational Asthma Birth Cohort Pilot Project

PI: Anne Wright (UA)

Role: PI

Funding agency: National Science Foundation

May 2016 - April 2020

Extensible, reproducible and documentation-driven microbiome data science.

Co-PI: Rob Knight

For project details see: qiime2.org.

Role: PI (sole grantee)

Funding agency: Alfred P. Sloan Foundation

April 2015 - August 2018

An Introduction to Applied Bioinformatics: an open source, interactive bioinformatics text.

For project details, see readIAB.org.

Role: Co-PI

Funding Agency: National Health and Medical Research Council, Australian Government

January 2015 - January 2020

Project Grant APP1085372

Robust bioinformatics for predicting bacterial pathogens from microbiome sequencing

Lead investigator: Gavin Huttley

This was the first time the NHMRC has funded a purely computational project, and the first time they’ve funded a postdoctoral position outside of Australia.

Role: Co-PI

Funding agency: Alfred P. Sloan Foundation

January 2015 - August 2018

Moisture, wetting, and fungal growth measurement on common indoor surfaces.

Co-PIs: Jeffrey Siegel (University of Toronto)

Role: Subcontract

Funding agency: Flinn Foundation

January 2015 - December 2016

Investigating the causative role of Bile, obesity and the microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma

PI: Landon Inge (St. Joseph’s Hospital and Medical Center)

Role: Co-Leader (with Talima Pearson, NAU; and Peter Lance, Univ of AZ Cancer Center)

Funding agency: NIH/The Partnership for National American Cancer Prevention (U54 to NAU and Univ of AZ)

September 2014 - August 2018

Microbes, bile acids and colorectal cancer

Role: Co-PI

Funding agency: Northern Arizona University Technology and Research Initiative Fund Preliminary Studies Grant

PI: Bridget Barker

May, 2014 - April, 2015

 

Role: Subcontract

Funding agency: National Institutes of Health

January 2014 - December 2014 (subcontract period)

Development of Intestinal Ion Transport

PI: Pawel Kiela (University of Arizona)

Role: Co-PI

Funding agency: Northern Arizona University Technology and Research Initiative Fund Pilot Grants Program

PI: W. Linn Montgomery  (Northern Arizona University); Co-PI: Maribeth Watwood (Northern Arizona University)

October, 2013 - September, 2014

Community Analysis of a Model Gut Microbiome: Associates of the Largest Bacteria

Role: PI

Funding agency: Arizona Board of Regents

October 2013 - June 2015

Co-PIs: Rosa Krajmalnik-Brown (Arizona State University), Matthew Sullivan (University of Arizona)

The human gut microbiota and its viruses: Keys to treating autism?

Role: Co-PI

Funding agency: National Institutes of Health/NIAID R15

July 2013 - June 2015

Environmental sampling of Leptospira species in link to human leptospirosis cases

PI: Talima Pearson (Northern Arizona University); Co-PI: Jeffrey Foster  (Northern Arizona University), Gabriel Trueba (Universidad San Francisco De Quito, Ecuador)

 

Co-PI: Northern Arizona University Technology and Research Investment Fund Research Equipment Acquisition Program, August 2013

Environmental Genetics and Genomics Facility: Acquisition of an Illumina MiSeq for Massively Parallel DNA Sequencing

PI: Gery Allen (Northern Arizona University); Co-PIs: Tina Ayers (Northern Arizona University), Jeffrey Foster (Northern Arizona University), Catherine Gehring (Northern Arizona University), Catherine Propper (Northern Arizona University), Egbert Schwartz (Northern Arizona University), Tom Whitham (Northern Arizona University), Jason Wilder (Northern Arizona University)

Role: PI

Funding agency: Northern Arizona University Technology and Research Initiative Fund Preliminary Studies Grant

March, 2013 - May, 2014

Role: Co-PI

Funding agency: NSF Dimensions of Biodiversity

January 2013-December 2017

The taxonomic, genomic, and functional diversity of soil carbon dynamics

PI: Bruce Hungate (Northern Arizona University); Co-PIs: Jane Marks (Northern Arizona University), Egbert Schwartz (Northern Arizona University), Paul Dijkstra (Northern Arizona University), Lance Price (George Washington University)

Role: PI

Funding agency: Alfred P. Sloan Foundation

October 2012 – June 2015

Microbial succession on common office surfaces across three climates

Co-PIs: Rob Knight (University of Colorado), Jeffrey Siegel (University of Toronto), Scott Kelley (San Diego State University)

PI: Amazon Web Services Education Grant; July 2011; August 2012; December 2012.

Approximately $7000 in credit over multiple awards to support course work on the Amazon Web Services Elastic Compute Cloud.

PI: Lewis and Clark Fund for Exploration and Field Research in Astrobiology; Funding period: May, 2011

Microbial Community Characterization of the Atacama Desert Soils

PI: Amazon Web Services Research Grant; Funding period: January 2011, June 2011

Deploying Bioinformatics Software on the Amazon Elastic Compute Cloud

Co-PI: Rob Knight (University of Colorado)

 

Travel award for Argonne Soils Workshop

Provided registration and travel costs to attend the 2010 Argonne National Labs Soils Workshop, Sept. 2010.

 

NSF Travel Fellowship, Dec. 2008

Provided registration and travel costs to attend the 2008 Rocky Mountain Bioinformatics Conference.

National Library of Medicine Informatics Pre-Doctoral Training Fellowship

Funding period: July 2007 - July 2009; Grant number:  T15LM009451.        

Provided full funding, including tuition and stipend, for the final two years of my doctoral training.

Role: Co-PI

Funding agency: Northern Arizona University Technology and Research Investment Fund

PI: Talima Pearson  (Northern Arizona University; Dr. Pearson and I will co-mentor this post-doctoral scholar)

Two years salary and benefits support for post-doctoral scholar.

Role: Co-PI

Funding agency: Northern Arizona University Technology and Research Investment Fund

PI: David Wagner (Northern Arizona University; Dr. Wagner and I will co-mentor this post-doctoral scholar)

Two years salary and benefits support for post-doctoral scholar.

Editorial boards

  1. Editor, mSystems, July, 2015 - Present.
  2. Editorial Board Member, PeerJ, July, 2015 - Present.
  3. Editorial Board Member, International Society for Microbial Ecology Journal (Impact Factor: 9.302), July, 2015 - May, 2020.

Conference organization roles

  1. Computational Biology Track Chair, SciPy 2015 Conference, July, 2015.
  2. Organizing Committee Member, American Society for Microbiology 2015 Regional Meeting, May, 2015.
  3. Human Microbiome Session Chair, International Society for Microbial Ecology 15, Seoul, South Korea, August, 2014.
  4. International Society for Microbial Ecology 15 QIIME Workshop Director. I planned and organized this one-day, international bioinformatics workshop (see http://bit.ly/qiime-isme15). Seoul National University, August 2014, Seoul, South Korea.
  5. International Society for Microbial Ecology 14 Bioinformatics Workshop Director.  I planned and organized this one-day, international bioinformatics workshop (see http://bit.ly/isme14-bioinformatics). Copenhagen University, August, 2012, Copenhagen, Denmark.

Select open-source software projects

(For a comprehensive list see my GitHub activity at http://github.com/gregcaporaso)

QIIME 2 (https://qiime2.org); project lead

QIIME (Quantitative Insights Into Microbial Ecology) (http://www.qiime.org); lead developer

An Introduction to Applied Bioinformatics (http://readIAB.org); lead author/developer

Patents

  1. Microbiome Based Systems, Apparatus and Methods For The Exploration And Production of Hydrocarbons. Knight, R, Kshatrlya, A, Ely, J, Henshaw, P, Caporaso, JG, Knights, D, Gill, R. Patent number: US 9,771,795 B2; Issued 26 Sept 2017.

Manuscripts in review

  1. Bycura, Dierdra, Anthony Santos, Arron Shiffer, Shari Kyman, Kyle Winfree, Jay Sutliffe, Talima Pearson, Derek Sonderegger, Emily Cope, J Gregory Caporaso. “Impact of Different Exercise Modalities on the Human Gut Microbiome.” (In review).
  2. Bolyen, Evan, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, Jason W. Sahl, Andrew Sanchez, Chris Holdgraf, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew McKay, David M. Engelthaler, Michael Worobey, Paul Keim, J Gregory Caporaso. “Reproducibly Sampling SARS-CoV-2 Genomes Across Time, Geography, and Viral Diversity.” (In review at F1000 Research; pre-review version).
  3. Cocking, Jill Hager, Sgt. Ryan Turley, Viacheslav Y. Fofanov, Kimberly Samuels-Crow, Bruce Hungate, Rebecca L. Mau, Paul S. Keim, J. Gregory Caporaso, Crystal Hepp. “Forensic analysis of Soil Microbiomes: Linking Evidence to a Geographic Location.” (In review, bioarxiv pre-print).
  4. Bokulich, Nicholas A,* Łaniewski,Paweł,* Chase, Dana M., Caporaso, JG, Herbst-Kralovetz, Melissa M., “Integration of multi-omics data improves prediction of cervicovaginal microenvironment in cervical cancer.” *Equal contributions. (In review at Cancer Research, medarxiv pre-print).

Publications

  1. Ladner, Jason*, Larsen, Brendan*, Bowers, Jolene*, Hepp, Crystal*, Boylen, Evan, Folkerts, Megan, Sheridan, Krystal, Pfeiffer,  Ashlyn, Yaglom, Hayley, Lemmer, Darrin, Sahl, Jason, Kaelin, Emily, Maqsood, Rabia, Bokulich, Nicholas, Quirk, Grace, Watts, Thomas, Komatsu, Kenneth, Waddell, Victor, Lim, Efrem, Caporaso, J Gregory, Engelthaler, David, Worobey, Michael, and Keim, Paul. 2020 An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. mBio doi:10.1128/mBio.02107-20 *Equal contribution.
  2. Bassiouni, Ahmed , Sathish Paramasivan, Arron Shiffer, Matthew R Dillon, Emily Cope, Clare Cooksley, Mohammad Javed Ali, Benjamin Bleier, Claudio Callejas, Marjolein E Cornet, Richard G Douglas, Daniel Dutra, Christos Georgalas, Richard J Harvey, Peter H Hwang, Amber U Luong, Rodney J Schlosser, Pongsakorn Tantilipikorn, Marc A Tewfik, Sarah Vreugde, Peter-John Wormald, J Gregory Caporaso, Alkis J Psaltis. 2020. “Microbiotyping the sinonasal microbiome.” Frontiers in Cellular and Infection Microbiology. doi:10.3389/fcimb.2020.00137.
  3. Estaki, Mehrbod*, Lingjing Jiang*, Nicholas Bokulich, Daniel McDonald, Antonio González, Tomasz Kosciolek, Cameron Martino, Qiyun Zhu, Amanda Birmingham, Yoshiki Vázquez-Baeza, J Gregory Caporaso, and Rob Knight. 2020. “QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data.” Current Protocols 70 (1). doi: 10.1002/cpbi.100. *Equal contribution. Protocols in Bioinformatics.
  4. Kaplan, I*, Bokulich, NA*, Caporaso, JG, Enders, L, Ghanem, W, and Ingerslew, K. *Equal contribution. Evolutionary Applications. 2020. “Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?” Wiley Online Library. doi: 10.1111/eva.12956.
  5. Paramasivan, Sathish, Ahmed Bassiouni, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin Bleier, Claudio Callejas, Marjolein E. Cornet, Richard G. Douglas, Daniel Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter-John Wormald, J. Gregory Caporaso, and Alkis J. Psaltis. 2020. “The International Sinonasal Microbiome Study: A Multicentre, Multinational Characterization of Sinonasal Bacterial Ecology.” Allergy, March. doi:10.1111/all.14276.
  6. Vogtmann, Emily, Yongli Han, J. Gregory Caporaso, Nicholas Bokulich, Ashraf Mohamadkhani, Alireza Moayyedkazemi, Xing Hua, Farin Kamangar, Yunhu Wan, Shalabh Suman, Bin Zhu, Amy Hutchinson, Casey Dagnall, Kristine Jones, Belynda Hicks, Jianxin Shi, Reza Malekzadeh, Christian C. Abnet, and Akram Pourshams. 2020. “Oral Microbial Community Composition Is Associated with Pancreatic Cancer: A Case-Control Study in Iran.” Cancer Medicine 9 (2): 797–806. doi:10.1002/cam4.2660.
  7. Xavier, Joao B., Vincent B. Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T. Pearson, Paul Macklin, Amir Mitchell, Ilya Shmulevich, Lei Xie, J. Gregory Caporaso, Keith A. Crandall, Nicole L. Simone, Filipa Godoy-Vitorino, Timothy J. Griffin, Katrine L. Whiteson, Heather H. Gustafson, Daniel J. Slade, Thomas M. Schmidt, Marina R. S. Walther-Antonio, Tal Korem, Bobbie-Jo M. Webb-Robertson, Mark P. Styczynski, W. Evan Johnson, Christian Jobin, Jason M. Ridlon, Andrew Y. Koh, Michael Yu, Libusha Kelly, and Jennifer A. Wargo. 2020. “The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.” Trends in Cancer Research 6 (3): 192–204. doi:10.1016/j.trecan.2020.01.004.
  8. Bokulich, Nicholas A., Juan Maldonado, Dae-Wook Kang, Rosa Krajmalnik-Brown, and J. Gregory Caporaso. 2019. “Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles.” mSphere 4 (2). doi:10.1128/mSphere.00208-19.
  9. Bolyen, Evan, 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. 2019. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology 37 (8): 852–57. doi:10.1038/s41587-019-0209-9.
  10. Kaehler, Benjamin D., Nicholas A. Bokulich, Daniel McDonald, Rob Knight, J. Gregory Caporaso, and Gavin A. Huttley. 2019. “Species Abundance Information Improves Sequence Taxonomy Classification Accuracy.” Nature Communications 10 (1): 4643. doi:10.1038/s41467-019-12669-6.
  11. Kang, Dae-Wook, James B. Adams, Devon M. Coleman, Elena L. Pollard, Juan Maldonado, Sharon McDonough-Means, J. Gregory Caporaso, and Rosa Krajmalnik-Brown. 2019. “Long-Term Benefit of Microbiota Transfer Therapy on Autism Symptoms and Gut Microbiota.” Scientific Reports 9 (1): 5821. doi:10.1038/s41598-019-42183-0.
  12. Pearson, Talima, J. Gregory Caporaso, Monica Yellowhair, Nicholas A. Bokulich, Megha Padi, Denise J. Roe, Betsy C. Wertheim, Mark Linhart, Jessica A. Martinez, Cherae Bilagody, Heidie Hornstra, David S. Alberts, Peter Lance, and Patricia A. Thompson. 2019. “Effects of Ursodeoxycholic Acid on the Gut Microbiome and Colorectal Adenoma Development.” Cancer Medicine 8 (2): 617–28. doi:10.1002/cam4.1965.
  13. Stone, Nathan E., Amalee E. Nunnally, Victor Jimenez Jr, Emily K. Cope, Jason W. Sahl, Krystal Sheridan, Heidie M. Hornstra, Jacob Vinocur, Erik W. Settles, Kyle C. Headley, Charles H. D. Williamson, Jai Ram Rideout, Evan Bolyen, J. Gregory Caporaso, Joel Terriquez, Fernando P. Monroy, Joseph D. Busch, Paul Keim, and David M. Wagner. 2019. “Domestic Canines Do Not Display Evidence of Gut Microbial Dysbiosis in the Presence of Clostridioides (Clostridium) Difficile, despite Cellular Susceptibility to Its Toxins.” Anaerobe 58 (August): 53–72. doi:10.1016/j.anaerobe.2019.03.017.
  14. Bokulich, Nicholas A., Matthew R. Dillon, Evan Bolyen, Benjamin D. Kaehler, Gavin A. Huttley, and J. Gregory Caporaso. 2018. “q2-Sample-Classifier: Machine-Learning Tools for Microbiome Classification and Regression.” Journal of Open Research Software 3 (30). doi:10.21105/joss.00934.
  15. Bokulich, Nicholas A., Matthew R. Dillon, Yilong Zhang, Jai Ram Rideout, Evan Bolyen, Huilin Li, Paul S. Albert, and J. Gregory Caporaso. 2018. “q2-Longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data.” mSystems 3 (6). doi:10.1128/mSystems.00219-18.
  16. Bolyen, Evan, Jai Ram Rideout, John Chase, T. Anders Pitman, Arron Shiffer, Willow Mercurio, Matthew R. Dillon, and J. Gregory Caporaso. 2018. “An Introduction to Applied Bioinformatics: A Free, Open, and Interactive Text.” The Journal of Open Source Education 1 (5). doi:10.21105/jose.00027.
  17. Franzosa, Eric A., Lauren J. McIver, Gholamali Rahnavard, Luke R. Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, J. Gregory Caporaso, Nicola Segata, and Curtis Huttenhower. 2018. “Species-Level Functional Profiling of Metagenomes and Metatranscriptomes.” Nature Methods 15 (11): 962–68. doi:10.1038/s41592-018-0176-y.
  18. Gilbert, Jack A., Martin J. Blaser, J. Gregory Caporaso, Janet K. Jansson, Susan V. Lynch, and Rob Knight. 2018. “Current Understanding of the Human Microbiome.” Nature Medicine 24 (4): 392–400. doi:10.1038/nm.4517.
  19. Gonzalez, Antonio, Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus, Stefan Janssen, Austin D. Swafford, Stephanie B. Orchanian, Jon G. Sanders, Joshua Shorenstein, Hannes Holste, Semar Petrus, Adam Robbins-Pianka, Colin J. Brislawn, Mingxun Wang, Jai Ram Rideout, Evan Bolyen, Matthew Dillon, J. Gregory Caporaso, Pieter C. Dorrestein, and Rob Knight. 2018. “Qiita: Rapid, Web-Enabled Microbiome Meta-Analysis.” Nature Methods 15 (10): 796–98. doi:10.1038/s41592-018-0141-9.
  20. Knight, Rob, 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, and Pieter C. Dorrestein. 2018. “Best Practices for Analysing Microbiomes.” Nature Reviews. Microbiology 16 (7): 410–22. doi:10.1038/s41579-018-0029-9.
  21. Meisel, Jacquelyn S., Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, J. Gregory Caporaso, Sean Conlan, Jocelyne DiRuggiero, Samuel P. Forry, Nur A. Hasan, Jason Kralj, Paul M. Luethy, Donald K. Milton, Brian D. Ondov, Sarah Preheim, Shashikala Ratnayake, Stephanie M. Rogers, M. J. Rosovitz, Eric G. Sakowski, Nils Oliver Schliebs, Daniel D. Sommer, Krista L. Ternus, Gherman Uritskiy, Sean X. Zhang, Mihai Pop, and Todd J. Treangen. 2018. “Current Progress and Future Opportunities in Applications of Bioinformatics for Biodefense and Pathogen Detection: Report from the Winter Mid-Atlantic Microbiome Meet-Up, College Park, MD, January 10, 2018.” Microbiome 6 (1): 197. doi:10.1186/s40168-018-0582-5.
  22. Sinha, Rashmi, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso, Joseph Russell Carmical, Andrew T. Chan, Anthony Fodor, Mitchell H. Gail, Curtis C. Harris, Kathy Helzlsouer, Curtis Huttenhower, Rob Knight, Heidi H. Kong, Gabriel Y. Lai, Diane Leigh Smith Hutchinson, Loic Le Marchand, Hongzhe Li, Michael J. Orlich, Jianxin Shi, Ann Truelove, Mukesh Verma, Emily Vogtmann, Owen White, Walter Willett, Wei Zheng, Somdat Mahabir, and Christian Abnet. 2018. “Next Steps in Studying the Human Microbiome and Health in Prospective Studies, Bethesda, MD, May 16-17, 2017.” Microbiome 6 (1): 210. doi:10.1186/s40168-018-0596-z.
  23. Califf, Katy J., Karen Schwarzberg-Lipson, Neha Garg, Sean M. Gibbons, J. Gregory Caporaso, Jørgen Slots, Chloe Cohen, Pieter C. Dorrestein, and Scott T. Kelley. 2017. “Multi-Omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.” mSystems 2 (3). doi:10.1128/mSystems.00016-17.
  24. Kang, Dae-Wook, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. Sullivan, J. Gregory Caporaso, and Rosa Krajmalnik-Brown. 2017. “Microbiota Transfer Therapy Alters Gut Ecosystem and Improves Gastrointestinal and Autism Symptoms: An Open-Label Study.” Microbiome 5 (1): 10. doi:10.1186/s40168-016-0225-7.
  25. Neilson, Julia W., Katy Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L. Josephson, Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, and Raina M. Maier. 2017. “Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.” mSystems 2 (3). doi:10.1128/mSystems.00195-16.
  26. Bokulich, Nicholas A., Jai Ram Rideout, William G. Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F. Maurice, Rachel J. Dutton, Peter J. Turnbaugh, Rob Knight, and J. Gregory Caporaso. 2016. “Mockrobiota: A Public Resource for Microbiome Bioinformatics Benchmarking.” mSystems 1 (5). doi:10.1128/mSystems.00062-16.
  27. Chase, John, Jennifer Fouquier, Mahnaz Zare, Derek L. Sonderegger, Rob Knight, Scott T. Kelley, Jeffrey Siegel, and J. Gregory Caporaso. 2016. “Geography and Location Are the Primary Drivers of Office Microbiome Composition.” mSystems 1 (2). doi:10.1128/mSystems.00022-16.
  28. Chase, John H., Evan Bolyen, Jai Ram Rideout, and J. Gregory Caporaso. 2016. “Cual-Id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.” mSystems 1 (1). doi:10.1128/mSystems.00010-15.
  29. Fouquier, Jennifer, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J. Gregory Caporaso, and Scott T. Kelley. 2016. “Ghost-Tree: Creating Hybrid-Gene Phylogenetic Trees for Diversity Analyses.” Microbiome 4 (February): 11. doi:10.1186/s40168-016-0153-6.
  30. Fuentes, Sebastián, Bárbara Barra, J. Gregory Caporaso, and Michael Seeger. 2016. “From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.” Applied and Environmental Microbiology 82 (3): 888–96. doi:10.1128/AEM.02625-15.
  31. Kopylova, Evguenia, Jose A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J. Gregory Caporaso, and Rob Knight. 2016. “Open-Source Sequence Clustering Methods Improve the State Of the Art.” mSystems 1 (1). doi:10.1128/mSystems.00003-15.
  32. Laubitz, Daniel, Christy A. Harrison, Monica T. Midura-Kiela, Rajalakshmy Ramalingam, Claire B. Larmonier, John H. Chase, J. Gregory Caporaso, David G. Besselsen, Fayez K. Ghishan, and Pawel R. Kiela. 2016. “Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis.” PloS One 11 (4): e0152044. doi:10.1371/journal.pone.0152044.
  33. Morrissey, Ember M., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, Cindy M. Liu, Michaela Hayer, Theresa A. McHugh, Jane C. Marks, Lance B. Price, and Bruce A. Hungate. 2016. “Phylogenetic Organization of Bacterial Activity.” The ISME Journal 10 (9): 2336–40. doi:10.1038/ismej.2016.28.
  34. Rideout, Jai Ram, John H. Chase, Evan Bolyen, Gail Ackermann, Antonio González, Rob Knight, and J. Gregory Caporaso. 2016. “Keemei: Cloud-Based Validation of Tabular Bioinformatics File Formats in Google Sheets.” GigaScience 5 (June): 27. doi:10.1186/s13742-016-0133-6.
  35. Taylor, D. Lee, William A. Walters, Niall J. Lennon, James Bochicchio, Andrew Krohn, J. Gregory Caporaso, and Taina Pennanen. 2016. “Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.” Applied and Environmental Microbiology 82 (24): 7217–26. doi:10.1128/AEM.02576-16.
  36. Walters, William, Embriette R. Hyde, Donna Berg-Lyons, Gail Ackermann, Greg Humphrey, Alma Parada, Jack A. Gilbert, Janet K. Jansson, J. Gregory Caporaso, Jed A. Fuhrman, Amy Apprill, and Rob Knight. 2016. “Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.” mSystems 1 (1). doi:10.1128/mSystems.00009-15.
  37. He, Yan, J. Gregory Caporaso, Xiao-Tao Jiang, Hua-Fang Sheng, Susan M. Huse, Jai Ram Rideout, Robert C. Edgar, Evguenia Kopylova, William A. Walters, Rob Knight, and Hong-Wei Zhou. 2015. “Stability of Operational Taxonomic Units: An Important but Neglected Property for Analyzing Microbial Diversity.” Microbiome 3 (May): 20. doi:10.1186/s40168-015-0081-x.
  38. Holscher, Hannah D., J. Gregory Caporaso, Seema Hooda, Jennifer M. Brulc, George C. Fahey Jr, and Kelly S. Swanson. 2015. “Fiber Supplementation Influences Phylogenetic Structure and Functional Capacity of the Human Intestinal Microbiome: Follow-up of a Randomized Controlled Trial.” The American Journal of Clinical Nutrition 101 (1): 55–64. doi:10.3945/ajcn.114.092064.
  39. Hungate, Bruce A., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, Cindy M. Liu, Theresa A. McHugh, Jane C. Marks, Ember M. Morrissey, and Lance B. Price. 2015. “Quantitative Microbial Ecology through Stable Isotope Probing.” Applied and Environmental Microbiology 81 (21): 7570–81. doi:10.1128/AEM.02280-15.
  40. Kang, Dae-Wook, John K. DiBaise, Zehra Esra Ilhan, Michael D. Crowell, Jai Ram Rideout, J. Gregory Caporaso, Bruce E. Rittmann, and Rosa Krajmalnik-Brown. 2015. “Gut Microbial and Short-Chain Fatty Acid Profiles in Adults with Chronic Constipation before and after Treatment with Lubiprostone.” Anaerobe 33 (June): 33–41. doi:10.1016/j.anaerobe.2015.01.005.
  41. Marzinelli, Ezequiel M., Alexandra H. Campbell, Enrique Zozaya Valdes, Adriana Vergés, Shaun Nielsen, Thomas Wernberg, Thibaut de Bettignies, Scott Bennett, J. Gregory Caporaso, Torsten Thomas, and Peter D. Steinberg. 2015. “Continental-Scale Variation in Seaweed Host-Associated Bacterial Communities Is a Function of Host Condition, Not Geography.” Environmental Microbiology 17 (10): 4078–88. doi:10.1111/1462-2920.12972.
  42. McFadden, Rita-Marie T., Claire B. Larmonier, Kareem W. Shehab, Monica Midura-Kiela, Rajalakshmy Ramalingam, Christy A. Harrison, David G. Besselsen, John H. Chase, J. Gregory Caporaso, Christian Jobin, Fayez K. Ghishan, and Pawel R. Kiela. 2015. “The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.” Inflammatory Bowel Diseases 21 (11): 2483–94. doi:10.1097/MIB.0000000000000522.
  43. Bolnick, Daniel I., Lisa K. Snowberg, J. Gregory Caporaso, Chris Lauber, Rob Knight, and William E. Stutz. 2014. “Major Histocompatibility Complex Class IIb Polymorphism Influences Gut Microbiota Composition and Diversity.” Molecular Ecology 23 (19): 4831–45. doi:10.1111/mec.12846.
  44. Bolnick, Daniel I., Lisa K. Snowberg, Philipp E. Hirsch, Christian L. Lauber, Rob Knight, J. Gregory Caporaso, and Richard Svanbäck. 2014. “Individuals’ Diet Diversity Influences Gut Microbial Diversity in Two Freshwater Fish (threespine Stickleback and Eurasian Perch).” Ecology Letters 17 (8): 979–87. doi:10.1111/ele.12301.
  45. Bolnick, Daniel I., Lisa K. Snowberg, Philipp E. Hirsch, Christian L. Lauber, Elin Org, Brian Parks, Aldons J. Lusis, Rob Knight, J. Gregory Caporaso, and Richard Svanbäck. 2014. “Individual Diet Has Sex-Dependent Effects on Vertebrate Gut Microbiota.” Nature Communications 5 (July): 4500. doi:10.1038/ncomms5500.
  46. Flores, Gilberto E., J. Gregory Caporaso, Jessica B. Henley, Jai Ram Rideout, Daniel Domogala, John Chase, Jonathan W. Leff, Yoshiki Vázquez-Baeza, Antonio Gonzalez, Rob Knight, Robert R. Dunn, and Noah Fierer. 2014. “Temporal Variability Is a Personalized Feature of the Human Microbiome.” Genome Biology 15 (12): 531. doi:10.1186/s13059-014-0531-y.
  47. Goodrich, Julia K., Sara C. Di Rienzi, Angela C. Poole, Omry Koren, William A. Walters, J. Gregory Caporaso, Rob Knight, and Ruth E. Ley. 2014. “Conducting a Microbiome Study.” Cell 158 (2): 250–62. doi:10.1016/j.cell.2014.06.037.
  48. Huttenhower, Curtis, Rob Knight, C. Titus Brown, J. Gregory Caporaso, Jose C. Clemente, Dirk Gevers, Eric A. Franzosa, Scott T. Kelley, Dan Knights, Ruth E. Ley, Anup Mahurkar, Jacques Ravel, Scientists for Advancement of Microbiome Research, and Owen White. 2014. “Advancing the Microbiome Research Community.” Cell 159 (2): 227–30. doi:10.1016/j.cell.2014.09.022.
  49. Kopylova, Evguenia, Jose A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J. Gregory Caporaso, and Rob Knight. 2016. “Open-Source Sequence Clustering Methods Improve the State Of the Art.” mSystems 1 (1). doi:10.1128/mSystems.00003-15.
  50. Rideout, Jai Ram, Yan He, Jose A. Navas-Molina, William A. Walters, Luke K. Ursell, Sean M. Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C. Clemente, Jack A. Gilbert, Susan M. Huse, Hong-Wei Zhou, Rob Knight, and J. Gregory Caporaso. 2014. “Subsampled Open-Reference Clustering Creates Consistent, Comprehensive OTU Definitions and Scales to Billions of Sequences.” PeerJ 2 (August): e545. doi:10.7717/peerj.545.
  51. Rothrock, Michael J., Jr, Kelli L. Hiett, John Gamble, Andrew C. Caudill, Kellie M. Cicconi-Hogan, and J. Gregory Caporaso. 2014. “A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples.” Journal of Visualized Experiments: JoVE, no. 94 (December). doi:10.3791/52161.
  52. Sahl, Jason W., J. Gregory Caporaso, David A. Rasko, and Paul Keim. 2014. “The Large-Scale Blast Score Ratio (LS-BSR) Pipeline: A Method to Rapidly Compare Genetic Content between Bacterial Genomes.” PeerJ 2 (April): e332. doi:10.7717/peerj.332.
  53. Schwarzberg, Karen, Rosalin Le, Balambal Bharti, Suzanne Lindsay, Giorgio Casaburi, Francesco Salvatore, Mohamed H. Saber, Faisal Alonaizan, Jørgen Slots, Roberta A. Gottlieb, J. Gregory Caporaso, and Scott T. Kelley. 2014. “The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease.” PloS One 9 (1): e86708. doi:10.1371/journal.pone.0086708.
  54. Shade, Ashley, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer, and Jack A. Gilbert. 2014. “Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity.” mBio 5 (4): e01371–14. doi:10.1128/mBio.01371-14.
  55. Bates, Scott T., Steven Ahrendt, Holly M. Bik, Thomas D. Bruns, J. Gregory Caporaso, James Cole, Michael Dwan, Noah Fierer, Dai Gu, Shawn Houston, Rob Knight, Jon Leff, Christopher Lewis, Juan P. Maestre, Daniel McDonald, R. Henrik Nilsson, Andrea Porras-Alfaro, Vincent Robert, Conrad Schoch, James Scott, D. Lee Taylor, Laura Wegener Parfrey, and Jason E. Stajich. 2013. “Meeting Report: Fungal Its Workshop (october 2012).” Standards in Genomic Sciences 8 (1): 118–23. doi:10.4056/sigs.3737409.
  56. Bokulich, Nicholas A., Sathish Subramanian, Jeremiah J. Faith, Dirk Gevers, Jeffrey I. Gordon, Rob Knight, David A. Mills, and J. Gregory Caporaso. 2013. “Quality-Filtering Vastly Improves Diversity Estimates from Illumina Amplicon Sequencing.” Nature Methods 10 (1): 57–59. doi:10.1038/nmeth.2276.
  57. Flores, Gilberto E., Scott T. Bates, J. Gregory Caporaso, Christian L. Lauber, Jonathan W. Leff, Rob Knight, and Noah Fierer. 2013. “Diversity, Distribution and Sources of Bacteria in Residential Kitchens.” Environmental Microbiology 15 (2): 588–96. doi:10.1111/1462-2920.12036.
  58. Gibbons, Sean M., J. Gregory Caporaso, Meg Pirrung, Dawn Field, Rob Knight, and Jack A. Gilbert. 2013. “Evidence for a Persistent Microbial Seed Bank throughout the Global Ocean.” Proceedings of the National Academy of Sciences of the United States of America 110 (12): 4651–55. doi:10.1073/pnas.1217767110.
  59. Harris, J. Kirk, J. Gregory Caporaso, Jeffrey J. Walker, John R. Spear, Nicholas J. Gold, Charles E. Robertson, Philip Hugenholtz, Julia Goodrich, Daniel McDonald, Dan Knights, Paul Marshall, Henry Tufo, Rob Knight, and Norman R. Pace. 2013. “Phylogenetic Stratigraphy in the Guerrero Negro Hypersaline Microbial Mat.” The ISME Journal 7 (1): 50–60. doi:10.1038/ismej.2012.79.
  60. Hewitt, Krissi M., Frank L. Mannino, Antonio Gonzalez, John H. Chase, J. Gregory Caporaso, Rob Knight, and Scott T. Kelley. 2013. “Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs).” PloS One 8 (1): e54703. doi:10.1371/journal.pone.0054703.
  61. Langille, Morgan G. I., Jesse Zaneveld, J. Gregory Caporaso, Daniel McDonald, Dan Knights, Joshua A. Reyes, Jose C. Clemente, Deron E. Burkepile, Rebecca L. Vega Thurber, Rob Knight, Robert G. Beiko, and Curtis Huttenhower. 2013. “Predictive Functional Profiling of Microbial Communities Using 16S rRNA Marker Gene Sequences.” Nature Biotechnology 31 (9): 814–21. doi:10.1038/nbt.2676.
  62. McDonald, Daniel, Yoshiki Vázquez-Baeza, William A. Walters, J. Gregory Caporaso, and Rob Knight. 2013. “From Molecules to Dynamic Biological Communities.” Biology & Philosophy 28 (2): 241–59. doi:10.1007/s10539-013-9364-4.
  63. Michelou, Vanessa K., J. Gregory Caporaso, Rob Knight, and Stephen R. Palumbi. 2013. “The Ecology of Microbial Communities Associated with Macrocystis Pyrifera.” PloS One 8 (6): e67480. doi:10.1371/journal.pone.0067480.
  64. Navas-Molina, José A., Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, and Rob Knight. 2013. “Advancing Our Understanding of the Human Microbiome Using QIIME.” Methods in Enzymology 531: 371–444. doi:10.1016/B978-0-12-407863-5.00019-8.
  65. Ragan-Kelley, Benjamin, William Anton Walters, Daniel McDonald, Justin Riley, Brian E. Granger, Antonio Gonzalez, Rob Knight, Fernando Perez, and J. Gregory Caporaso. 2013. “Collaborative Cloud-Enabled Tools Allow Rapid, Reproducible Biological Insights.” The ISME Journal 7 (3): 461–64. doi:10.1038/ismej.2012.123.
  66. Shade, Ashley, J. Gregory Caporaso, Jo Handelsman, Rob Knight, and Noah Fierer. 2013. “A Meta-Analysis of Changes in Bacterial and Archaeal Communities with Time.” The ISME Journal 7 (8): 1493–1506. doi:10.1038/ismej.2013.54.
  67. Song, Se Jin, Christian Lauber, Elizabeth K. Costello, Catherine A. Lozupone, Gregory Humphrey, Donna Berg-Lyons, J. Gregory Caporaso, Dan Knights, Jose C. Clemente, Sara Nakielny, Jeffrey I. Gordon, Noah Fierer, and Rob Knight. 2013. “Cohabiting Family Members Share Microbiota with One Another and with Their Dogs.” eLife 2 (April): e00458. doi:10.7554/eLife.00458.
  68. Bik, Holly M., Dorota L. Porazinska, Simon Creer, J. Gregory Caporaso, Rob Knight, and W. Kelley Thomas. 2012. “Sequencing Our Way towards Understanding Global Eukaryotic Biodiversity.” Trends in Ecology & Evolution 27 (4): 233–43. doi:10.1016/j.tree.2011.11.010.
  69. Caporaso, J. Gregory, Christian L. Lauber, William A. Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M. Owens, Jason Betley, Louise Fraser, Markus Bauer, Niall Gormley, Jack A. Gilbert, Geoff Smith, and Rob Knight. 2012. “Ultra-High-Throughput Microbial Community Analysis on the Illumina HiSeq and MiSeq Platforms.” The ISME Journal 6 (8): 1621–24. doi:10.1038/ismej.2012.8.
  70. Caporaso, J. Gregory, Konrad Paszkiewicz, Dawn Field, Rob Knight, and Jack A. Gilbert. 2012. “The Western English Channel Contains a Persistent Microbial Seed Bank.” The ISME Journal 6 (6): 1089–93. doi:10.1038/ismej.2011.162.
  71. Fierer, Noah, Jonathan W. Leff, Byron J. Adams, Uffe N. Nielsen, Scott Thomas Bates, Christian L. Lauber, Sarah Owens, Jack A. Gilbert, Diana H. Wall, and J. Gregory Caporaso. 2012. “Cross-Biome Metagenomic Analyses of Soil Microbial Communities and Their Functional Attributes.” Proceedings of the National Academy of Sciences of the United States of America 109 (52): 21390–95. doi:10.1073/pnas.1215210110.
  72. Gilbert, Jack A., Joshua A. Steele, J. Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Alice C. McHardy, Rob Knight, Ian Joint, Paul Somerfield, Jed A. Fuhrman, and Dawn Field. 2012. “Defining Seasonal Marine Microbial Community Dynamics.” The ISME Journal 6 (2): 298–308. doi:10.1038/ismej.2011.107.
  73. Kuczynski, Justin, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, and Rob Knight. 2012. “Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities.” Current Protocols in Microbiology Chapter 1 (November): Unit 1E.5. doi:10.1002/9780471729259.mc01e05s27.
  74. McDonald, Daniel, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso. 2012. “The Biological Observation Matrix (BIOM) Format or: How I Learned to Stop Worrying and Love the Ome-Ome.” GigaScience 1 (1): 7. doi:10.1186/2047-217X-1-7.
  75. Ursell, Luke K., Jose C. Clemente, Jai Ram Rideout, Dirk Gevers, J. Gregory Caporaso, and Rob Knight. 2012. “The Interpersonal and Intrapersonal Diversity of Human-Associated Microbiota in Key Body Sites.” The Journal of Allergy and Clinical Immunology 129 (5): 1204–8. doi:10.1016/j.jaci.2012.03.010.
  76. Werner, Jeffrey J., Omry Koren, Philip Hugenholtz, Todd Z. DeSantis, William A. Walters, J. Gregory Caporaso, Largus T. Angenent, Rob Knight, and Ruth E. Ley. 2012. “Impact of Training Sets on Classification of High-Throughput Bacterial 16s rRNA Gene Surveys.” The ISME Journal 6 (1): 94–103. doi:10.1038/ismej.2011.82.
  77. Werner, Jeffrey J., Dennis Zhou, J. Gregory Caporaso, Rob Knight, and Largus T. Angenent. 2012. “Comparison of Illumina Paired-End and Single-Direction Sequencing for Microbial 16S rRNA Gene Amplicon Surveys.” The ISME Journal 6 (7): 1273–76. doi:10.1038/ismej.2011.186.
  78. Yatsunenko, Tanya, Federico E. Rey, Mark J. Manary, Indi Trehan, Maria Gloria Dominguez-Bello, Monica Contreras, Magda Magris, Glida Hidalgo, Robert N. Baldassano, Andrey P. Anokhin, Andrew C. Heath, Barbara Warner, Jens Reeder, Justin Kuczynski, J. Gregory Caporaso, Catherine A. Lozupone, Christian Lauber, Jose Carlos Clemente, Dan Knights, Rob Knight, and Jeffrey I. Gordon. 2012. “Human Gut Microbiome Viewed across Age and Geography.” Nature 486 (7402): 222–27. doi:10.1038/nature11053.
  79. Bates, Scott T., Donna Berg-Lyons, J. Gregory Caporaso, William A. Walters, Rob Knight, and Noah Fierer. 2011. “Examining the Global Distribution of Dominant Archaeal Populations in Soil.” The ISME Journal 5 (5): 908–17. doi:10.1038/ismej.2010.171.
  80. Bates, Scott T., Garrett W. G. Cropsey, J. Gregory Caporaso, Rob Knight, and Noah Fierer. 2011. “Bacterial Communities Associated with the Lichen Symbiosis.” Applied and Environmental Microbiology 77 (4): 1309–14. doi:10.1128/AEM.02257-10.
  81. Bergmann, Gaddy T., Scott T. Bates, Kathryn G. Eilers, Christian L. Lauber, J. Gregory Caporaso, William A. Walters, Rob Knight, and Noah Fierer. 2011. “The under-Recognized Dominance of Verrucomicrobia in Soil Bacterial Communities.” Soil Biology & Biochemistry 43 (7): 1450–55. doi:10.1016/j.soilbio.2011.03.012.
  82. Caporaso, J. Gregory, and Rob Knight. 2011. “New Insight into the Diversity of Life’s Building Blocks: Evenness, Not Variance.” Astrobiology. doi:10.1089/ast.2011.2280.
  83. Caporaso, J. Gregory, Rob Knight, and Scott T. Kelley. 2011. “Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition.” PloS One 6 (2): e16900. doi:10.1371/journal.pone.0016900.
  84. Caporaso, J. Gregory, Christian L. Lauber, Elizabeth K. Costello, Donna Berg-Lyons, Antonio Gonzalez, Jesse Stombaugh, Dan Knights, Pawel Gajer, Jacques Ravel, Noah Fierer, Jeffrey I. Gordon, and Rob Knight. 2011. “Moving Pictures of the Human Microbiome.” Genome Biology 12 (5): R50. doi:10.1186/gb-2011-12-5-r50.
  85. Caporaso, J. Gregory, Christian L. Lauber, William A. Walters, Donna Berg-Lyons, Catherine A. Lozupone, Peter J. Turnbaugh, Noah Fierer, and Rob Knight. 2011. “Global Patterns of 16S rRNA Diversity at a Depth of Millions of Sequences per Sample.” Proceedings of the National Academy of Sciences of the United States of America 108 Suppl 1 (March): 4516–22. doi:10.1073/pnas.1000080107.
  86. Kuczynski, Justin, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, and Rob Knight. 2011. “Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities.” Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis... [et Al.] Chapter 10 (December): Unit 10.7. doi:10.1002/0471250953.bi1007s36.
  87. Pirrung, Meg, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, and Rob Knight. 2011. “TopiaryExplorer: Visualizing Large Phylogenetic Trees with Environmental Metadata.” Bioinformatics 27 (21): 3067–69. doi:10.1093/bioinformatics/btr517.
  88. Walters, William A., J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, and Rob Knight. 2011. “PrimerProspector: De Novo Design and Taxonomic Analysis of Barcoded Polymerase Chain Reaction Primers.” Bioinformatics 27 (8): 1159–61. doi:10.1093/bioinformatics/btr087.
  89. Caporaso, J. Gregory, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. 2010. “PyNAST: A Flexible Tool for Aligning Sequences to a Template Alignment.” Bioinformatics 26 (2): 266–67. doi:10.1093/bioinformatics/btp636.
  90. Caporaso, J. Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K. Goodrich, Jeffrey I. Gordon, Gavin A. Huttley, Scott T. Kelley, Dan Knights, Jeremy E. Koenig, Ruth E. Ley, Catherine A. Lozupone, Daniel McDonald, Brian D. Muegge, Meg Pirrung, Jens Reeder, Joel R. Sevinsky, Peter J. Turnbaugh, William A. Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld, and Rob Knight. 2010. “QIIME Allows Analysis of High-Throughput Community Sequencing Data.” Nature Methods 7 (5): 335–36. doi:10.1038/nmeth.f.303.
  91. Chu, Haiyan, Noah Fierer, Christian L. Lauber, J. G. Caporaso, Rob Knight, and Paul Grogan. 2010. “Soil Bacterial Diversity in the Arctic Is Not Fundamentally Different from That Found in Other Biomes.” Environmental Microbiology 12 (11): 2998–3006. doi:10.1111/j.1462-2920.2010.02277.x.
  92. Rousk, Johannes, Erland Bååth, Philip C. Brookes, Christian L. Lauber, Catherine Lozupone, J. Gregory Caporaso, Rob Knight, and Noah Fierer. 2010. “Soil Bacterial and Fungal Communities across a pH Gradient in an Arable Soil.” The ISME Journal 4 (10): 1340–51. doi:10.1038/ismej.2010.58.
  93. Baumgartner, William A., Jr, Zhiyong Lu, Helen L. Johnson, J. Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K. White, Olga Medvedeva, K. Bretonnel Cohen, and Lawrence Hunter. 2008. “Concept Recognition for Extracting Protein Interaction Relations from Biomedical Text.” Genome Biology 9 Suppl 2 (September): S9. doi:10.1186/gb-2008-9-s2-s9.
  94. Caporaso, J. Gregory, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, and Lawrence Hunter. 2008. “Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 640–51. https://www.ncbi.nlm.nih.gov/pubmed/18229722.
  95. Caporaso, J. Gregory, Sandra Smit, Brett C. Easton, Lawrence Hunter, Gavin A. Huttley, and Rob Knight. 2008. “Detecting Coevolution without Phylogenetic Trees? Tree-Ignorant Metrics of Coevolution Perform as Well as Tree-Aware Metrics.” BMC Evolutionary Biology 8 (December): 327. doi:10.1186/1471-2148-8-327.
  96. Caporaso, J. Gregory, William A. Baumgartner Jr, David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter. 2007a. “MutationFinder: A High-Performance System for Extracting Point Mutation Mentions from Text.” Bioinformatics 23 (14): 1862–65. doi:10.1093/bioinformatics/btm235.
  97. Caporaso, J. Gregory, William A. Baumgartner, David A. Randolph, K. Bretonnel Cohen, and Lawrence Hunter. 2007b. “Rapid Pattern Development for Concept Recognition Systems: Application to Point Mutations.” Journal of Bioinformatics and Computational Biology 5 (6): 1233–59. doi:10.1142/s0219720007003144.
  98. Knight, Rob, Peter Maxwell, Amanda Birmingham, Jason Carnes, J. Gregory Caporaso, Brett C. Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J. Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, and Gavin A. Huttley. 2007. “PyCogent: A Toolkit for Making Sense from Sequence.” Genome Biology 8 (8): R171. doi:10.1186/gb-2007-8-8-r171.
  99. Caporaso, J. Gregory, Michael Yarus, and Rob Knight. 2005. “Error Minimization and Coding Triplet/binding Site Associations Are Independent Features of the Canonical Genetic Code.” Journal of Molecular Evolution 61 (5): 597–607. doi:10.1007/s00239-004-0314-2.
  100. Yarus, Michael, J. Gregory Caporaso, and Rob Knight. 2005. “Origins of the Genetic Code: The Escaped Triplet Theory.” Annual Review of Biochemistry 74: 179–98. doi:10.1146/annurev.biochem.74.082803.133119.

QIIME and QIIME 2 Workshops

Beginning in 2010, I  developed a workshop series teaching students around the world how to use the QIIME and QIIME 2 microbiome bioinformatics software platforms. Our team of instructors has expanded and I am no longer involved with teaching all of the workshops. The workshops listed here are ones that I have been personally involved with teaching. Information on other QIIME 2 workshops can be found at https://workshops.qiime2.org. We no longer maintain a list of QIIME 1 workshops, as that platform was succeeded by QIIME 2.

CZI/CABANA: Microbiome Bioinformatics with QIIME 2 Online Workshop

I led the planning, development, and teaching of this five-day workshop for 75 paying attendees (from at least 19 countries) and hundreds of viewers on YouTube. This was the first online QIIME 2 workshop.

Co-taught with 20 instructors from around the world, including undergraduate and graduate students at NAU.

October 2020.

Online.

Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this three-day workshop for 79 paying attendees.

Co-taught with Aeriel Belk, Evan Bolyen, Heather Deel, Matthew Dillon, Mehrbod Estaki, Nidhi Shah, and Emily Vogtmann.

January 2020

National Institutes of Health, Bethesda, MD, USA.

QIIME 2 mini-workshop.

Co-taught with Jose Clemente.

October 2019

World of Microbiome, Milan, Italy.

Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this two-day workshop for 40 students.

Co-taught with Evan Bolyen and Matthew Dillon.

December 2018

Universidad de Costa Rica, San Jose, Costa Rica.

Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this three-day workshop for 79 paying attendees.

Co-taught with Evan Bolyen, Nick Bokulich, Emily Cope, Matthew Dillon, Joslynn Lee, and Emily Vogtmann.

December 2018

National Institutes of Health, Bethesda, MD, USA.

Hacking microbiomes: using computers and genomes to improve our world.

September 2018

Flagstaff Festival of Science, Lowell Observatory, Flagstaff, AZ.

Teaching and Developing QIIME 2.

I led the planning, development, and teaching of this three-day conference, workshop, and hackathon for 50 attendees.

Co-taught with  Nick Bokulich, Evan Bolyen, Matthew Dillon, Antonio Gonzalez, and Rob Knight.

May 2018

University of California San Diego, La Jolla, CA, USA.

QIIME 2 2018.2 Workshop: Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this two-day workshop for 76 paying attendees.

Co-taught with Evan Bolyen, Matthew Dillon, and Nick Bokulich.

March 2018

National Institutes of Health, Bethesda, MD, USA.

QIIME 2 2017.6 Workshop: Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this three-day workshop for 55 paying attendees. This included a poster session and reception where attendees presented their own microbiome work.

Co-taught with Evan Bolyen, Matthew Dillon, Max von Hippel (undergraduate student), Arron Shiffer (graduate student), and Jamie Morton (graduate student).

June 2017

Las Vegas, Nevada, USA.

QIIME 2 2017.6 Workshop: Microbiome Bioinformatics with QIIME 2.

I led the planning, development, and teaching of this two-day workshop for 15 paying attendees.

Co-taught with Antonio Gonzalez.

June 2017

Columbia Medical School, New York, New York, USA.

An Introduction to using QIIME 2 in the cloud.

Human Microbiome Project Cloud Pilot User Group Meeting.

June 2017

University of Maryland, Maryland, USA.

QIIME 2 Workshop

Co-taught with Evan Bolyen and Matthew Dillon.

February 2017

University of New Hampshire, Durham, New Hampshire, USA.

QIIME 2 2016.11 Workshop

I led the planning, development, and teaching of this two-day workshop for 75 paying attendees.

Co-taught with Jai Rideout, Evan Bolyen, Matthew Dillon, Yoshiki Vazquez-Baeza (graduate student), and Antonio Gonzalez-Pena.

November 2016

Phoenix, Arizona, USA.

QIIME 2 Workshop

Co-taught with Jai Rideout.

October 2016

Matis, Rejkavik, Iceland.

QIIME Workshop: From the swab to the cloud, advances toward understanding our microbial world.

October 2015

The Fifth International Meeting on Microbial Electrochemistry and Technologies, Tempe, AZ, USA.

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

Co-taught with Jai Rideout.

October 2014

NSF Porphyra RCN, Acadia National Park, USA (Two-day course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

January 2014

Northern Arizona University, Flagstaff, AZ, USA. (Four-hour course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

October 2013

Argonne Soil Metagenomics Meeting, Chicago, IL, USA. (Three-hour course)

Computational Solutions for Biological Questions

Co-taught with Antonio Gonzalez-Pena

October 2013

Universidad Iberoamericana Ciudad de México, Santa Fe, Mexico City, Mexico. (Five-hour course)

Co-designed and taught a workshop for undergraduate Biomedical and Computer Engineering students on Bioinformatics.

Metagenomics in the cloud using QIIME (Metagenomic Approaches workshop)

May 2013

American Society for Microbiology, Denver, CO, USA.

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

February 2013

Swiss Microbial Ecology Satellite Symposium, Neuchâtel, Switzerland (Four-hour course)

Using QIIME for the Analysis of Viral Communities

February 2013

Taught three-hour course on using QIIME for viral metagenomics analysis.

Environmental Virology Workshop, Tucson, AZ, USA.

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

October 2012

Argonne Soil Metagenomics Meeting, Chicago, IL, USA. (Three-hour course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

October 2012

Microbiology of the Built Environment Meeting, Boulder, CO (Two-hour course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

July 2012

International Geobiology Course, Catalina Island, CA, USA. (Seven-day course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

May 2012

University of Arizona, Tucson, AZ, USA. (Eight-hour course.)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

January 2012

Northern Arizona University, Flagstaff, AZ, USA. (Five-hour course)

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

July 2011

International Geobiology Course, Catalina Island, CA, USA. (Seven-day course)

Workshop on Comparative Genomics.

July 2011

Co-taught for two days on the PyCogent and QIIME software packages.

Colorado State University, Fort Collins, CO, USA.

 

Extracting Ecological Signal From Noise.

September 2010

Co-taught a three-day course on computational tools for microbial ecology.

Molecular and Computational Biology Research School, Bergen, Norway.

Conference and Other Presentations

QIIME 2 

Chan-Zuckerberg Initiative Essential Open Source Software for Science inaugural meeting

Berkeley, CA, USA, February, 2020.

Developing and applying the next generation of microbiome bioinformatics tools to advance cancer research

December 2019

Arizona Conference on Developing Therapeutics for Cancer and Immunology, Phoenix, AZ.

Enabling the next generation of microbiome science with QIIME 2.

December 2019

Rocky Mountain Bioinformatics Conference, Snowmass, CO.

Studying the microbiome in the first thousand days of life.

October 2019

World of Microbiome, Milan, Italy.

Developing and applying the next generation of microbiome bioinformatics

September 2019

TGen/City of Hope Microbiome Retreat, Flagstaff, AZ.

Fecal microbiota transplant alters the gut ecosystem and improves gastrointestinal and autism symptoms.

Keynote presentation

December 2018

Investigación en Microbiomas y Bioinformática, Universidad de Costa Rica,.

Microbiome studies: Methods and Concepts

May 2018

Pancreatic and Gastric Cancer Consortia Meeting, Rockville, MD.

Developing and Applying the Next Generation of Microbiome Bioinformatics

April 2018

Food and Drug Administration.

Developing and Applying the Next Generation of Microbiome Bioinformatics

April 2018

United States Department of Agriculture.

Developing and Applying the Next Generation of Microbiome Bioinformatics

February 2018

National Institutes of Standards and Technology, Gaithersburg, MD, USA.

Developing and Applying the Next Generation of Microbiome Bioinformatics

December 2017

National Cancer Institute, Cancer Genomics Research Laboratory, Rockville, MD, USA.

Developing and Applying the Next Generation of Microbiome Bioinformatics

November 2017

Food and Drug Administration, Center for Food Safety and Applied Nutrition.

Developing and Applying the Next Generation of Microbiome Bioinformatics

October 2017

National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA.

Developing and Applying the Next Generation of Microbiome Bioinformatics

September 2017

National Cancer Institute, Division of Cancer Epidemiology and Genomics, Rockville, MD, USA.

QIIME 2: Decentralized, Extensible, and Reproducible Microbiome Analysis

May 2017

Next Steps in Studying the Human Microbiome and Health in Prospective Studies, Rockville, MD, USA.

QIIME 2: Decentralized, Extensible, and Reproducible Microbiome Analysis

Invited presentation, co-presented by Evan Bolyen and Matthew Dillion (software engineers in Caporaso Lab)

February 2017

Statistical and Algorithmic Challenges in Microbiome Data Analysis, Cambridge, MA, USA.

Fecal microbiota transplant alters gut ecosystem and improves gastrointestinal and autism symptoms.

January 2017

City of Hope, Burbank, CA, USA.

Fecal microbiota transplant alters gut ecosystem and improves gastrointestinal and autism symptoms.

July 2017

Keynote presentation

Arizona Biosafety Alliance, Flagstaff, AZ.

Fecal microbiota transplant alters gut ecosystem and improves gastrointestinal and autism symptoms.

April 2017

Keynote presentation

Arizona Academy of Nutrition and Dietetics, Flagstaff, AZ.

Fecal microbiota transplant alters gut ecosystem and improves gastrointestinal and autism symptoms.

February 2017

Feeding Your Genome, Tucson, AZ.

QIIME 2: Self-documenting, Extensible, and Reproducible Microbiome Analysis in Python 3.

July 2016

SciPy 2016, Austin, TX, USA. YouTube video

Gut microbiota changes in response to treatment with ursodeoxycholic acid.

Late-breaking poster presentation.

April 2016

American Association for Cancer Research, New Orleans, LA, USA.

Investigating the causative role of Bile, obesity and the microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma

Poster presentation; co-presented with Landon Inge.

February 2016

Arizona Biomedical Research Council and Flinn Foundation Awardee Research Conference, Phoenix, AZ, USA.

Toward self-documenting, customizable microbiome analysis and meta-analysis with scikit-bio, QIIME 2, and Qiita.

Co-presented with Rob Knight.

July 2015

Microbiology of the Built Environment, Boulder, CO, USA.

From the swab to the cloud: advances toward understanding our microbial world.

May 2015

University of Arizona, Tucson, Arizona, USA

From the swab to the cloud: advances toward understanding our microbial world.

September 2014

Flagstaff Festival of Science, Flagstaff, AZ, USA.

Gut microbiome and bile acid associations with ursodeoxycholic acid (UDCA) treatment for colorectal cancer.

August 2014

International Society for Microbial Ecology 15, Seoul, South Korea.

The Disadvantages of Bigger Data

August 2014

International Society for Microbial Ecology 15, Seoul, South Korea.

scikit-bio: core bioinformatics data structures and algorithms in Python.

July 2014

SciPy 2014, Austin, TX, USA.

Composition and dynamics of microbial communities on common office surfaces.

June 2014

Microbiology of the Built Environment, Boulder, CO, USA,.

From the swab to the cloud: advances toward understanding our microbial world.

April 2014

University of Arizona, Tucson, Arizona, USA.

Temporal Dynamics of the Human Microbiome: Advances Toward Understanding Our Microbial Selves.

May 2013

American Society for Microbiology, Denver, CO, USA.

Built Environment Surface Succession

May 2013

The Second Annual Conference on the Microbiology of the Built Environment, Boulder, CO, USA.

From the swab to the cloud: advances toward understanding our microbial world.

April 2013

Johns Hopkins University, Baltimore, Maryland, USA.

From the swab to the cloud: advances toward understanding our microbial world.

February 2013

Science on Tap, Flagstaff, AZ, USA.

From the swab to the cloud: advances toward understanding our microbial world.

February 2013

University of Naples, Naples, Italy.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

Keynote presentation

February 2013

Swiss Microbial Ecology Meeting, Neuchâtel, Switzerland.

From the swab to the cloud: advances toward understanding our microbial world.

January 2013

National Cancer Institute, Bethesda, Maryland, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

April 2012

American Society for Microbiology (Arizona regional meeting), Tempe, AZ, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

March 2012

Genomics Standards Consortium 13, Shenzhen, China.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

April 2011.

American Society for Microbiology (Colorado regional meeting), Boulder, CO, USA.

 

QIIME and the art of fungal community analysis.

Sloan Foundation Fungal Workshop, October 2012, Boulder, CO, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

June 2012

Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

April 2012

Arizona State University, Tempe, Arizona, USA.

Procrustes Analysis to Compare Biological Conclusions in Studies of the Human Microbiome

April 2012

Cloud Computing for the Microbiome, Boulder, CO, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

November 2012

Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

February 2012

University of Arizona, Tucson, Arizona, USA.

Earth Microbiome Project Data Analysis Update.

November 2011

Earth Microbiome Project/National Ecological Observatory Joint Meeting, Boulder, CO.

 

Argonne Soil Metagenomics Meeting Wrap-up Talk.

October 2011

3rd Argonne Soil Metagenomics Meeting, Chicago, IL, USA.

Recovery of biological soil crust-like microbial communities in previously submerged soils of Glen Canyon.

September 2011

11th Biennial Conference of Research on the Colorado Plateau, Flagstaff, AZ, USA.

Moving Pictures of the Human Microbiome.

June 2011

Infectious Disease Research Network: Microbial Community Profiling Workshop, London, UK.

 

Quantitative Insights Into Microbial Ecology.

June 2011

Infectious Disease Research Network: Microbial Community Profiling Workshop, London, UK.

Ultra-high-throughput microbial ecology: software, sequencing and practice for studying tens of thousands of environments.

April 2011

University of Montana, Bozeman, Montana, USA.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

September 2010

Los Alamos National Laboratories, Los Alamos, NM, USA.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

May 2010

Genomics Automation Congress, Boston, MA, USA.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Poster presentation

August 2010

13th International Symposium on Microbial Ecology (poster presentation), Seattle, WA, USA.

Detecting Coevolution by Disregarding Evolution? Tree-Ignorant Metrics of Coevolution Perform As Well As Tree-Aware Metrics.

November 2009

Genome Biology Seminars, Australian National University, Canberra, Australia.

Intermolecular Coevolution Suggests Interactions Between Type VI Secretion System Proteins.

April 2009

Bioinformatics Supergroup, University of Colorado at Boulder, Boulder, CO, USA.

Intermolecular Coevolution Suggests Interactions Between Type VI Secretion System Proteins

Oral and poster presentation

December 2008

Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA.

Detecting Coevolution by Disregarding Evolution? Tree-Ignorant Metrics of Coevolution Perform As Well As Tree-Aware Metrics.

April 2008

Bioinformatics Supergroup, University of Colorado at Boulder.

Rapid Pattern Development for Concept Recognition Systems.

April 2008

DMAP meeting, Aurora, CO, USA.

 

Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.

January 2008

Pacific Symposium on Biocomputing, Hawaii, USA.

 

A Comparison of Coevolution Detection Methods on Protein Alpha Helices.

Poster presentation

January 2008

Pacific Symposium on Biocomputing, Hawaii, USA.

A Comparison of Coevolution Detection Methods on Protein Alpha Helices.

Oral and poster presentation

December 2007

Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA.

 

Recognizing Point Mutations in Text: Techniques and Applications in Biomedical Text Mining.

Poster presentation.

January 2007

Pacific Symposium on Biocomputing, Hawaii, USA.

 

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question Answering.

December 2006

Rocky Mountain Bioinformatics Conference (oral and poster presentation) Snowmass, CO, USA.

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question Answering.

Poster presentation

November 2006

Text REtrieval Conference (TREC) 2006 (poster presentation), Gaithersburg, Maryland, USA.

 

A Sentence Recognizer for Mutant Protein Structure Studies: Toward Intelligent Systems for the Management of Structural Biology Data.

Oral and poster presentation

December 2005

Rocky Mountain Bioinformatics Conference, Snowmass, CO, USA.

Concept Recognition and the TREC Genomics Tasks.

Poster presentation

November 2005

Text REtrieval Conference (TREC) 2005, Gaithersburg, MD, USA.

 

Stereochemical and Adaptive Factors in Genetic Code Evolution.

Poster presentation

July 2004

Evolution 2004, Fort Collins, CO, USA.

Teaching

(All course materials available at http://caporasolab.us/teaching.)

BIO 485: Microbial Succession in Soil and Compost Development

Fall 2020

Led an undergraduate independent study for two students.

CS 685: Learning the Rust Programming Language

Fall 2020

Led an undergraduate independent study for three students and two NAU staff members.

BIO 450, BIO 599: Fundamentals of Bioinformatics, Northern Arizona University.

Spring 2020

Designed and taught an undergraduate bioinformatics course for computer science and biology students

BIO 450: Fundamentals of Bioinformatics, Northern Arizona University.

Spring 2019

Designed and taught an undergraduate bioinformatics course for computer science and biology students.

BIO 698: Microbiome Bioinformatics with QIIME 2, Northern Arizona University

Spring 2017

Designed and taught a one-credit graduate seminar focused on using QIIME 2 for studying microbiomes.

BIO 450: Fundamentals of Bioinformatics, Northern Arizona University.

Spring 2017 (lectures primarily given by my graduate student, Arron Shiffer).

Designed and taught an undergraduate bioinformatics course for computer science and biology students.

BIO 499/599, CS 499/599 (formerly BIO290/CS290): Applied Bioinformatics, Northern Arizona University.

Spring 2016.

Designed and taught a undergraduate/graduate bioinformatics course for computer science and biology students.

BIO290/CS290 (formerly CS299/BIO299): Introduction to Bioinformatics, Northern Arizona University.

Fall 2011, Spring 2013, Spring 2014, Spring 2015.

Designed and taught an undergraduate bioinformatics course for computer science and biology majors.

BIO599: Computational Biology, Northern Arizona University.

Fall 2012, Spring 2014, Spring 2015.

Designed and taught a graduate bioinformatics course for biology masters and doctoral students.

BIO698: Applied Bioinformatics/Bioinformatics Code Review

Fall 2013, Fall 2014.

Designed and taught a graduate seminar on practical considerations in bioinformatics.

CS486: Computer Science Senior Capstone, Northern Arizona University.

Spring 2012; Fall 2012; Spring 2013.

Mentored teams of Computer Science seniors as they design, implement, and deliver software tools to outside project sponsors.

CS399/BIO399: Introduction to Bioinformatics, Northern Arizona University.

Spring 2012.

Designed and taught an undergraduate bioinformatics course for computer science and biology majors.

 

Guest Lecturer, Fall semester, 2010; Fall semester 2009; Spring 2007.

Bioinformatics 7711/2, University of Colorado Denver, Aurora, CO.

 

Guest Lecturer, Spring semester, 2009.

CHEM/MCDB 4621/5621; CSCI 4317/5317, University of Colorado at Boulder, Boulder, CO.

 

High School Mathematics Tutor (IMP Program), December 2008 - June 2009.

Boulder, CO.

 

Curriculum Development: Mathematics assignments for undergraduate Biology students, 2003 - 2004.

Department of Human Resources, University of Colorado at Boulder, Boulder, CO.

Students and postdocs mentored

Postdoctoral scholars

  1. Nicholas Bokulich, February 2016 - May 2019. Now tenure-track faculty at ETH Zurich.
  2. Karen Schwarzberg, February 2014 - Spring 2016.
  3. Katy Califf, June 2013 - December 2015.
  4. Crystal Hepp, June 2013 - July 2015. Now tenure-track faculty at Northern Arizona University.  

Ph.D. students

  1. Chloe Herman, Informatics, Fall 2020 - Present
  2. Evan Bolyen, Informatics, Fall 2019 - Present
  3. Giorgio Casaburi, Biological Sciences, Università di Napoli (visiting NAU), Fall 2012 – Summer 2014.
  4. Sebastián Fuentes Alburquenque, Universidad Tecnica Federico Santa Maria (visiting NAU), Spring - Summer 2013.

Master’s students

  1. Chris Keefe, Informatics, Fall 2020 - Present.
  2. John Chase, Biological Sciences, Fall 2013 - Spring 2014.
  3. Huanhua Huang, Computer Science, Fall 2012 - Summer 2014. 

Undergraduate and post-baccalaureate students

  1. Anthony Simard, Computer Science, Spring 2019-Present
  2. David Rodriguez, Computer Science, Spring 2019-Spring 2020.
  3. Chris Keefe, Computer Science, Spring 2018-Spring 2020.
  4. Turan Naimey, Computer Science, Fall 2017-Spring 2019
  5. Max von Hippel, Computer Science, Summer 2017.
  6. Kestrel Gorlick, Computer Science, Summer 2017.
  7. Jorden Kreps, Computer Science, Spring 2016 - Summer 2017.
  8. William Mercurio, Biological Sciences, Fall 2014 - Summer 2016.
  9. Evan Bolyen, Computer Science, Spring 2013 - Spring 2016.
  10. John Chase, Biological Sciences, Northern Arizona University, Fall 2012 – Summer 2013.
  11. Jai Rideout, Computer Science, Northern Arizona University, Fall 2011-Spring 2012. Recipient of the Most Promising Undergraduate Researcher award at NAU in Spring of 2012. This was the first time this was awarded to a Computer Science student at NAU. 

High school students

  1. Kestrel Gorlick, BASIS Flagstaff, Fall 2014 - Summer 2016. (Primarily mentored in my lab by Jai Rideout, now an undergraduate at University of Arizona Department of Computer Science.)
  2. Isaiah Williams, Homeschooled, Fall 2013 - Spring 2014 (Primarily mentored in my lab by John Chase.)

Awards and Honors

Web of Science Highly Cited Researcher, November, 2020.

Web of Science Highly Cited Researcher, November, 2019.

Web of Science Highly Cited Researcher, November, 2018.

Web of Science Highly Cited Researcher, November, 2017.

Most Significant Research Award, Northern Arizona University, 2017.

For work on Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms.

Outstanding Dissertation Award Finalist, University of Colorado Denver, May 2009.

 

Outstanding Research Award, 23nd Annual Student Research Forum, University of Colorado Denver

Sequence co-occurrence and covariation suggest a model of the Type VI Secretion System, Jan. 2009.

 

Outstanding Research Award, 22nd Annual Student Research Forum, University of Colorado Denver

A Comparison of Coevolution Detection Methods on Protein Alpha Helices, Jan. 2008.

 

Best Presentation, Rocky Mountain Bioinformatics Conference

A Sentence Recognizer for Mutant Protein Structure Studies: Toward Intelligent Systems for the Management of Structural Biology Data, Dec. 2005.