J. Gregory Caporaso

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)

gregcaporaso@gmail.com

www.caporasolab.us

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

Associate Professor, 2016 – Present

Assistant Professor, 2011 – 2016

Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.

Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA.

Associate Director, 2016 – Present

Assistant Director, 2013 – 2016

Research Affiliate, 2012 – 2013

Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff, AZ, USA.

Principal Data Scientist, 2013 – Present

Biota Technology, Inc.

Former Positions

Assistant Professor (summer appointment), 2012 – 2013

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

Grant and contract funding (extramural)

Role: PI

Funding agency: National Science Foundation

May 2016 - April 2019

Extensible, reproducible and documentation-driven microbiome data science.

$525,795

Commitment: 1.0 summer months

For project details see: qiime.org.

Role: PI (sole grantee)

Funding agency: Alfred P. Sloan Foundation

April 2015 - March 2017

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

$239,775

Commitment: 2.0 summer months.

For project details, see readIAB.org.

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 2016

Microbes, bile acids and colorectal cancer

$375,000 (Total direct costs to NAU)

Commitment: 0.1 summer months.

Role: Co-PI

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

March 2015 - February 2018

Project Grant APP1085372

Robust bioinformatics for predicting bacterial pathogens from microbiome sequencing

Co-PIs: Gavin Huttley; Von Bing Yap; Rob Knight

$530,000 ($617,000 AUD; NAU subaward $208,618 USD)

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.

Commitment: 0.1 summer months.

Role: Co-PI

Funding agency: Alfred P. Sloan Foundation

January 2015 - December 2016

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

Co-PIs: Jeffrey Siegel (University of Toronto)

$250,000 (NAU subaward: $104,160)

Commitment: 0.1 summer months.

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)

$39,931 (subcontract to NAU)

Commitment: 0.1 summer months.

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)

$1,487,750

Commitment: 0.1 summer months.

Role: Subcontract

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

July 2016 - June 2017

Binational Asthma Birth Cohort Pilot Project

PI:

$11,500 (subcontract to NAU)

Commitment: 0.1 summer months

Grant funding (intramural)

Role: Co-PI

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

PI: Bridget Barker

May, 2014 - April, 2015

$90,000

 

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.

Grant funding (completed)

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)

$299,982

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?

$281,950

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)

$249,876

Role: PI

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

March, 2013 - May, 2014

$95,522

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

$24,844

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)

$18,500 (subcontract to NAU)

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)

$62,500 in credit (total for initial grant and two renewals)

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)

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

Microbial Community Characterization of the Atacama Desert Soils

$5000

 

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.

 

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.

 

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.

Editorial boards

  1. Editor, mSystems (a new journal of the American Society for Microbiology), July, 2015 - Present.
  2. Editorial Board Member, International Society for Microbial Ecology Journal (Impact Factor: 9.302), July, 2015 - June, 2018.
  3. Editorial Board Member, PeerJ, July, 2015 - Present.

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

scikit-bio (http://scikit-bio.org); project lead

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

Manuscripts (preprints, submitted or under review)

  1. Empowering the Brazilian microbiome research community: How to better explore the invisible biodiversity. Under review, Nature Biotechnology.
  2. Metagenomics Reveals Dysbiosis and a Potentially Pathogenic N. flavescens Strain in duodenum of Adult Celiac Patients. D’Argenio, V, Casaburi, G, Precone, V, Pagliuca, C, Colicchio, R, Sarnataro, D, Discepolo, V, Kim, SM, Russo, I, Del Vecchio Blanco, G, Horner, DS, Chiara, M, Pesole, G, Salvatore, P, Monteleone, G, Ciacci, C, Caporaso, JG, Jabrì, B, Salvatore, F, Sacchetti, L. Under review at American Journal of Gastroenterology.

Publications

  1. Microbiota transfer alters gut ecosystem and improves gastrointestinal and autism symptoms. Kang, D, Adams, JB, Gregory, A, Borody, T, Chittick, L, Fasano, A, Khoruts, A, Geis, E, Maldonado, J, McDonough-Means, S, Pollard, EL, Roux, S, Sadowsky, MJ, Lipson, KS, Sullivan, MB, Caporaso, JG, and Krajmalnik-Brown, R. Microbiome (2017).
  2. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. Bokulich, NA, Rideout, JR, Mercurio, WG, Wolfe, B, Maurice, CF, Dutton, RJ, Turnbaugh, PJ, Knight, R, Caporaso​, JG. mSystems (2016).
  3. Geography and location are the primary drivers of office microbiome composition. Chase, JH, Fourquier, J, Zare, M, Sonderegger, DL, Knight, R, Kelley, S, Siegel, JA, Caporaso, JG. mSystems (2016).
  4. ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Fouquier, J, Rideout, JR, Bolyen, E, Chase, JH, Shiffer, A, McDonald, D, Knight, R, Caporaso, JG, Kelley, ST​. Microbiome (2016).
  5. The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention. McFadden, RT, Larmonier, CB, Shehab, KW, Midura-Kiela, M, Ramalingam, R, Harrison, CA, Besselsen, DG, Chase, JH, Caporaso, JG, Jobin, C, Ghishan,FK, and Kiela, PR. Inflammatory Bowel Diseases (2015).
  6. cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative -omics studies. Chase JH, Bolyen ET, Rideout JR, Caporaso JG. mSystems (2015).
  7. From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation. Fuentes, S, Barra, B, Caporaso, JG, Seeger, M. Applied and Environmental Microbiology (2015).
  8. Quantitative Microbial Ecology Through Stable Isotope Probing. Hungate, B, Mau, R, Schwartz, E, Caporaso, JG, Dijkstra, P, van Gestel, N, Koch, B, Liu, C, McHugh, T, Marks, J, Morrissey, E, and Price, L. Applied and Environmental Microbiology (2015).
  9. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography. Marzinelli EM, Campbell AH, Zozaya Valdes E, Vergés A, Nielsen S, Wernberg T, de Bettignies T, Bennett S, Caporaso JG, Thomas T, Steinberg PD. Environmental Microbiology (2015).
  10. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. He, Y, Caporaso, JG, Jiang, X, Sheng, H, Huse, S, Rideout, J, Edgar, RC, Kopylova, E, Walters, WA, Knight, R, and Zhou, H. Microbiome, 2015.
  11. Using QIIME to evaluate the microbial communities within hydrocarbon environments. Ursell, LK, Robbins-Pianka, A, Scott, N, Gonzalez, A, Knights, D, Rideout, J, Kshatriya, A, Caporaso, JG, Knight, R. Hydrocarbon and Lipid Microbiology Protocols (2015).
  12. Temporal variability is a personalized feature of the human microbiome. Flores, GE*, Caporaso, JG*,  Henley, JB, Rideout, JR, Domogala, D, Chase, J, Leff, J, Vazquez Baeza, Y, Gonzalez, A, Knight, R, Dunn, RR, Fierer, N (*contributed equally). Genome Biology, December, 2014.
  13. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. Rideout, JR, He, Y, Navas-Molina, JA, Walters, WA, Ursell, LK, Gibbons, SM, Chase, JH, McDonald, D, Gonzalez, A, Robbins-Pianka, A, Clemente, JC, Gilbert, J, Huse, SM, Zhou, H, Knight, R, Caporaso​, JG. Peer J, August, 2014.
  14. The Human Microbiome: Getting Personal. Califf, K, Gonzalez, A, Knight, R and Caporaso, JG. Microbe. Volume 9(10) November, 2014. Includes a biological profile of Dr. Caporaso.
  15. Advancing the microbiome research community. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O. Cell. September, 2014
  16. Fiber supplementation influences phylogenetic structure and functional capacity of the  human intestinal microbiome: follow-up of a randomized controlled trial. Holscher, HC, Caporaso, JG, Hooda, S, Brulc, JM, Fahey, Jr., GC, Swanson, KS. The American Journal of Clinical Nutrition, November, 2014.
  17. Individual diet has sex-dependent effects on vertebrate gut microbiota. Bolnick, DI, Snowberg, LK,  Hirsch, PE, Lauber, CL, Org, E, Parks, B, Lusis, AJ, Knight, R, Caporaso, JG, Svanbäck, R. Nature Communications, July, 2014.
  18. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. MBio. July, 2014
  19. Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R. Ecol Lett. 2014 May 2014.
  20. Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. D Bolnick, L Snowberg, W Stutz, JG Caporaso, C Lauber, R Knight. Molecular Ecology, July 2014.
  21. Conducting a Microbiome Study. Goodrich, J, Poole, A, Koren, O, Cullender, T, Di Rienzi, S, Walters, WA, Caporaso, JG, Knight, R, and Ley, RE. Cell, 2014.
  22. The personal human oral microbiome obscures the effects of treatment on periodontal disease. Schwarzberg, K, Le, R, Bharti, B, Lindsay, S, Casaburi, G, Salvatore, F, Saber, MH, Alonaizan, F, Slots, J, Gottlieb, RA, Caporaso, JG, Kelley, ST. PLoS One, 2014.
  23. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. Sahl JW, Caporaso JG, Rasko DA, Keim P. PeerJ. 2014 Apr 1.
  24. Advancing our understanding of the human microbiome using QIIME. Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R. Methods in Enzymology, 2013.
  25. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.  Langille, MGI, Zaneveld, J, Caporaso, JG, McDonald, D, Knights, D, Reyes, JA, Clemente, JC, Burkepile, DE, Vega-Thurber, RL, Knight, R, Beiko, RG, Huttenhower, C.  Nature Biotechnology, 2013.
  26. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. Nature Methods, 2013.
  27. Evidence for a persistent microbial seed bank throughout the global ocean. Gibbons, SM,  Caporaso, JG, Pirrung, M, Field, D, Knight, R and Gilbert, JA.  Proceedings of the National Academy of Science, 2013.
  28. Meeting report: Fungal ITS Workshop (October, 2012). Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE. Standards in Genomic Science, 2013.
  29. The Ecology of Microbial Communities Associated with Macrocystis pyrifera. Michelou VK, Caporaso JG, Knight R, Palumbi SR. PLoS One, 2013.
  30. Cohabiting family members share microbiota with one another and with their dogs. Song, S, Lauber, C, Costello, EK, Lozupone, CA, Humphrey, G, Berg-Lyons, D, Caporaso, JG, Knights, D,  Clemente, JC, Nakielny, S, Gordon, JI, Fierer, F, Knight, R. eLife, 2013.
  31. A meta-analysis of changes in bacterial and archaeal communities with time. Shade, A, Caporaso, JG, Handelsman, J, Knight, R, Fierer, N. ISME Journal, 2013.
  32. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. Harris JK*, Caporaso JG*, Walker JJ, Spear, JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR (*contributed equally). International Society for Microbial Ecology Journal, 2013.
  33. Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Roy, AS, Gibbons, SM, Schunck, H, Owens, S, Caporaso, JG, Sperling, M, Nissimov, JI, Romac, S, Bittner, L, Mühling, M, Riebesell, U, LaRoche, J, Gilbert, JA. Biogeosciences, 2013.
  34. From molecules to dynamic biological communities. McDonald, D, Vazquez-Baeza, Y, Walters, WA, Caporaso, JG, Knight, R. Biology and Philosophy, 2013.
  35. Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs). Hewitt, KM, Mannino, FL, Gonzalez, A, Chase, JH, Caporaso, JG, Knight, R, and Kelley, ST. PLoS One, 2013.
  36. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG. Proceedings of the National Academy of Science, 2012.
  37. Human gut microbiome viewed across age and geography. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Nature, 2012.
  38. Collaborative cloud-enabled tools allow rapid, reproducible biological insights. Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG. International Society for Microbial Ecology Journal, 2012
  39. The Biological Observation Matrix (BIOM) Format or: How I Learned To Stop Worrying and Love the Ome-ome. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG. GigaScience, 2012.
  40. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Caporaso JG, Lauber C, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Betley J, Fraser L, Bauer M, Gormley N, Smith G and Knight R. International Society for Microbial Ecology Journal, 2012. *ISME Journal Top Ten download articles list from April 2012-July 2013. Selected for review by Faculty of 1000.
  41. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. Journal of Allergy and Clinical Immunology, 2012.
  42. Diversity, distribution and sources of bacteria in residential kitchens. Flores GE, Bates ST, Caporaso JG, Lauber CL, Leff JW, Knight R, Fierer N. Environmental Microbiology, 2012.
  43. Sequencing our way towards understanding global eukaryotic biodiversity. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. Trends in Ecology and Evolution, 2012.
  44. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. Soil Biology and Biochemistry, 2011.
  45. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R. Current Protocols in Bioinformatics, 2012.
  46. The Western English Channel contains a persistent microbial seed bank. Caporaso JG, Paszkiewicz K, Field D, Knight R, Gilbert JA. International Society for Microbial Ecology Journal, 2012.
  47. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. International Society for Microbial Ecology Journal, 2011.
  48. TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R. Bioinformatics, 2011
  49. Defining seasonal marine microbial community dynamics. Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D. International Society for Microbial Ecology Journal, 2011.
  50. Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. Werner JJ, Koren O, Hugenholtz P, Desantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE. International Society for Microbial Ecology Journal, 2011.
  51. Moving Pictures of the Human Microbiome. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. Genome Biol. 2011 May 30;12(5):R50. * Selected for review by Faculty of 1000.
  52. New insight into the diversity of life's building blocks: evenness, not variance. Caporaso JG, Knight R. Astrobiology. 2011 Apr;11(3):197-8.
  53. PrimerProspector: de novo design and taxonomic analysis of barcoded PCR primers. Walters WA*, Caporaso JG*, Lauber CL, Berg-Lyons D, Fierer N Knight R (*contributed equally). Bioinformatics. 2011 Apr 15;27(8):1159-61.
  54. Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition. Caporaso JG, Knight R, Kelley ST. PLoS One. 2011 Feb 24;6(2):e16900.
  55. Bacterial communities associated with the lichen symbiosis. Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. Appl Environ Microbiol. 2011 Feb;77(4):1309-14.
  56. Examining the global distribution of dominant archaeal populations in soil. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. International Society for Microbial Ecology Journal 2010
  57. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. Environmental Microbiology, 2010 Nov;12(11):2998-3006.
  58. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Proceedings of the National Academy of Science, 2010.
  59. Soil bacterial and fungal communities across a pH gradient in an arable soil. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. International Society for Microbial Ecology Journal, 2010.
  60. QIIME allows analysis of high-throughput community sequencing data. Caporaso JG*, Kuczynski J*, Stombaugh J*, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (*contributed equally). Nature Methods, 2010.
  61. PyNAST: a flexible tool for aligning sequences to a template alignment. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. Bioinformatics 2010, 26(2):266-7.
  62. Detecting Coevolution by Disregarding Evolution? Tree-Ignorant Metrics of Coevolution Perform As Well As Tree-Aware Metrics. Caporaso JG, Smit S, Easton BC, Hunter,L, Huttley GA, Knight R. BMC Evolutionary Biology 2008, 8:327.
  63. An Integrated Approach to Concept Recognition in Biomedical Text. Baumgartner WA Jr., Lu Z, Johnson HL, Caporaso JG, Paquette J, Lindemann A, White EK, Medvedeva O, Cohen KB, Hunter L. Genome Biology, 2008, Suppl 2:S9.
  64. Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Caporaso JG, Deshpande N, Fink JL, Bourne PE, Cohen KB, Hunter L. Pacific Symposium on Biocomputing 13:640-651(2008).
  65. Rapid Pattern Development for Concept Recognition Systems: Application to Point Mutations. Caporaso JG, Baumgartner WA Jr., Randolph DA, Cohen KB, Hunter L. Journal of Bioinformatics and Computational Biology, 2007 Dec;5(6):1233-59.
  66. PyCogent: A Toolkit for Making Sense from Sequence. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. Genome Biology 2007, 8:R171.
  67. MutationFinder: A High-Performance System for Extracting Point Mutation Mentions from Text. Caporaso JG, Baumgartner WA Jr, Randolph DA, Cohen KB, Hunter L. Bioinformatics, 2007 23(14):1862-1865.
  68. Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question Answering. Caporaso JG, Baumgartner WA Jr., Kim H, Lu Z, Johnson HL, Medvedeva O, Lindemann A, Fox LM, White EK, Cohen KB, and Hunter L. TREC 2006 Conference Proceedings, January, 2007.
  69. Concept recognition and the TREC Genomics tasks. Caporaso JG, Baumgartner WA Jr, Cohen KB, Johnson HL, Paquette J, Hunter L. TREC 2005 Conference Proceedings, January, 2006.
  70. Error Minimization and Coding Triplet/Binding Site Associations are Independent Features of the Canonical Genetic Code. Caporaso JG, Yarus M, and Knight R. Journal of Molecular Evolution, 2005.
  71. Origins of the Genetic Code: The Escaped Triplet Theory. Yarus,M, Caporaso JG, and Knight R. Annual Review of Biochemistry, 2005.

Conference Presentations

QIIME 2: Decentralized, Extensible, and Reproducible Microbiome Analysis

Next Steps in Studying the Human Microbiome and Health in Prospective Studies, Rockville, MD, March 2017.

QIIME 2: Decentralized, Extensible, and Reproducible Microbiome Analysis

Co-presented by Evan Bolyen and Matthew Dillion (research software engineers in Caporaso Lab)

Statistical and Algorithmic Challenges in Microbiome Data Analysis, Cambridge, MA, February 2017.

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

Feeding Your Genome, Tucson, AZ, February 2017.

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

SciPy, 2016, Austin, TX, USA, July, 2016. Oral presentation. YouTube video

Gut microbiota changes in response to treatment with ursodeoxycholic acid.

American Association for Cancer Research, New Orleans, LA, USA, April 2016. Late-breaking poster presentation.

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

Co-presented with Landon Inge.

Arizona Biomedical Research Council and Flinn Foundation Awardee Research Conference, Phoenix, AZ, USA, February 2016. Poster presentation.

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

Invited Presentation: The Fifth International Meeting on Microbial Electrochemistry and Technologies, Tempe, AZ, USA, October 2015.

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

Co-presented with Rob Knight.

Microbiology of the Built Environment, Boulder, CO, USA, July 2015.

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

International Society for Microbial Ecology 15, Seoul, South Korea, August 2014.

The Disadvantages of Bigger Data

International Society for Microbial Ecology 15, Seoul, South Korea, August 2014.

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

SciPy 2014, Austin, TX, USA, July 2014.

Composition and dynamics of microbial communities on common office surfaces.

Microbiology of the Built Environment, Boulder, CO, USA, June 2014.

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

American Society for Microbiology, Denver, CO, USA, May 2013.

Built Environment Surface Succession

The Second Annual Conference on the Microbiology of the Built Environment, Boulder, CO, USA, May 2013.

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

Keynote presentation: Swiss Microbial Ecology Meeting, February 2013, Neuchâtel, Switzerland.

American Society for Microbiology (Arizona regional meeting), Tempe, AZ, USA, April, 2012.

Genomics Standards Consortium 13, March 2012, Shenzhen, China.

American Society for Microbiology (Colorado regional meeting), Boulder, CO, USA, April, 2011.

 

QIIME and the art of fungal community analysis

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

 

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

Cloud Computing for the Microbiome, April 2012, Boulder, CO, USA.

 

Earth Microbiome Project Data Analysis Update

Earth Microbiome Project/National Ecological Observatory Joint Meeting, November 2011, Boulder, CO.

 

Argonne Soil Metagenomics Meeting Wrap-up Talk

3rd Argonne Soil Metagenomics Meeting, October 2011, Chicago, IL, USA.

 

Moving Pictures of the Human Microbiome

Infectious Disease Research Network: Microbial Community Profiling Workshop, June 2011, London, UK.

 

Quantitative Insights Into Microbial Ecology

Infectious Disease Research Network: Microbial Community Profiling Workshop, June 2011, London, UK.

 

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

Genomics Automation Congress, May 2010, Boston, MA, USA.

13th International Symposium on Microbial Ecology (poster presentation), Seattle, WA, USA, August, 2010.

 

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

11th Biennial Conference of Research on the Colorado Plateau, Flagstaff, AZ, USA, September, 2011.

 

Intermolecular Coevolution Suggests Interactions Between Type VI Secretion System Proteins

Rocky Mountain Bioinformatics Conference (oral and poster presentation), December, 2008.

 

Rapid Pattern Development for Concept Recognition Systems.

DMAP meeting, April, 2008, Aurora, CO.

 

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

Pacific Symposium on Biocomputing (oral presentation), January, 2008.

 

A Comparison of Coevolution Detection Methods on Protein Alpha Helices

Pacific Symposium on Biocomputing (poster presentation), January, 2008.

Rocky Mountain Bioinformatics Conference (oral and poster presentation), December, 2007.

 

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

Pacific Symposium on Biocomputing (poster presentation), January, 2007.

 

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

Rocky Mountain Bioinformatics Conference (oral and poster presentation), December, 2006.

Text REtrieval Conference (TREC) 2006 (poster presentation), November, 2006.

 

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

Rocky Mountain Bioinformatics Conference (oral and poster presentation), December, 2005.

 

Concept Recognition and the TREC Genomics Tasks

Text REtrieval Conference (TREC) 2005 (poster presentation), November, 2005.

 

Stereochemical and Adaptive Factors in Genetic Code Evolution

Evolution 2004 (poster presentation), July, 2004.

Invited (non-conference) Presentations

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

Invited seminar, City of Hope, Burbank, CA, January 2017.

QIIME 2 Workshop

Co-presented with Jai Rideout.

Matis, Rejkavik, Iceland, October, 2016.

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

University of Arizona, May 2015, Tucson, Arizona, USA.

University of Arizona, April 2014, Tucson, Arizona, USA.

Flagstaff Festival of Science, September 2014, Flagstaff, AZ, USA.

Johns Hopkins University, April 2013, Baltimore, Maryland, USA.

Science on Tap, February 2013, Flagstaff, AZ, USA.

University of Naples, February 2013, Naples, Italy.

National Cancer Institute, January 2013, Bethesda, Maryland, USA.

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

Fred Hutchinson Cancer Research Center, November 2012, Seattle, Washington, USA.

Lawrence Berkeley National Laboratory, June 2012, Berkeley, CA, USA.

Arizona State University, April 2012, Tempe, Arizona, USA.

University of Arizona, February 2012, Tucson, Arizona, USA.

University of Montana, April 2011, Bozeman, Montana, USA.

 

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

Los Alamos National Laboratories, September 2010, Los Alamos, NM, USA.

 

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

Genome Biology Seminars, Australian National University, November 2009, Canberra, Australia.

Bioinformatics Supergroup, University of Colorado at Boulder, April, 2008.

Intermolecular Coevolution Suggests Interactions Between Type VI Secretion System Proteins.

Bioinformatics Supergroup, University of Colorado at Boulder, April, 2009.

Teaching

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

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.

Quantitative Insights Into Microbial Ecology (QIIME) Workshop

NSF Porphyra RCN, October 2014, Acadia National Park, USA (Two-day course)

Northern Arizona University, January 2014, Flagstaff, AZ, USA. (Four-hour course)

Argonne Soil Metagenomics Meeting, October 2013, Chicago, IL, USA. (Three-hour course)

Swiss Microbial Ecology Satellite Symposium, February 2013, Neuchâtel, Switzerland (Four-hour course)

Argonne Soil Metagenomics Meeting, October 2012, Chicago, IL, USA. (Three-hour course)

Microbiology of the Built Environment Meeting, October 2012, Boulder, CO (Two-hour course)

International Geobiology Course, July 2012, Catalina Island, CA, USA. (Seven-day course)

University of Arizona, May 2012, Tucson, AZ, USA. (Eight-hour course.)

Northern Arizona University, January 2012, Flagstaff, AZ, USA. (Five-hour course)

International Geobiology Course, July 2011, Catalina Island, CA, USA. (Seven-day course)

Computational Solutions for Biological Questions

Universidad Iberoamericana Ciudad de México, Santa Fe, Mexico City, Mexico, October, 2013. (Five-hour course)

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

 

Metagenomics in the cloud using QIIME (Metagenomic Approaches workshop)

American Society for Microbiology, Denver, CO, USA, May 2013.

Using QIIME for the Analysis of Viral Communities

Environmental Virology Workshop, February 2013, Tucson, AZ, USA. (Three-hour course)

 

Workshop on Comparative Genomics, July 2011.

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

 

Extracting ecological signal from noise workshop. September 2010.

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

Molecular and Computational Biology Research School, Bergen, Norway.

 

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 - Present.
  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. Arron Shiffer, Biological Sciences, Fall 2014 - Present. Winner of Best Poster Award at regional ASM Meeting, 2015.
  2. Giorgio Casaburi, Biological Sciences, Università di Napoli (visiting NAU), Fall 2012 – Summer 2014.
  3. Sebastián Fuentes Alburquenque, Universidad Tecnica Federico Santa Maria (visiting NAU), Spring - Summer 2013.

Master’s students

  1. John Chase, Biological Sciences, Northern Arizona University, Fall 2013 - Spring 2014. (Now a data scientist at Biota Technology)
  2. Huanhua Huang, Computer Science, Fall 2012 - Summer 2014. 

Undergraduate and post-baccalaureate students

  1. Jorden Kreps, Computer Science, Spring 2016 - Present.
  2. William Mercurio, Biological Sciences, Fall 2014 - Summer 2016. (Now a PhD student at University of Colorado at Boulder)
  3. Evan Bolyen, Computer Science, Spring 2013 - Spring 2016.  (Now a Research Software Engineer in my lab.)
  4. John Chase, Biological Sciences, Northern Arizona University, Fall 2012 – Summer 2013. (Now a Data Scientist at Biota Technology.)
  5. 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. (Now a Research Software Engineer in my lab.)

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

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.

Previous Positions

Research assistant, January 2003 - August 2004.

Michael Yarus and Rob Knight Laboratories, Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO.

 

Contract Web Developer,  1999 - 2002.

American Business English Internet School, Boulder, CO.

 

Software Engineer, 2001 - 2002.

Freshwater Software (acquired by Mercury Interactive), Boulder, CO.

 

Student Intern,  2000 - 2001.

Freshwater Software, Boulder, CO.

 

Web Developer, System Administrator,  1998 - 2000.

Web Communications, University of Colorado at Boulder, Boulder, CO.

Professional Society Memberships

International Society for Microbial Ecology, since 2010.

American Society for Microbiology, since 2011.

International Society for Computational Biology, 2005-2009.

American Association for the Advancement of Science, 2006-2009.

 

References available upon request