J. Gregory Caporaso

According to our database, J. Gregory Caporaso authored at least 16 papers between 2005 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt.

Chloe Herman, Evan Bolyen, Anthony Simard, Elizabeth Gehret, J. Gregory Caporaso

PLoS Comput. Biol., 2025

Jupyter Book 2 and the MyST Document Stack.

Project Jupyter, Evan Bolyen, J. Gregory Caporaso, Rowan Cockett, Danny Garside, Chris Holdgraf, Angus Hollands, Julia Kent, Franklin Koch, Jim Madge, Matthew McKay, Mike Morrison, Fernando Pérez, Steve Purves, Min Ragan-Kelley, Brian E. J. Rose, Malvika Sharan, Brigitta M. Sipocz, Stefan Johann van der Walt, Kirstie Jane Whitaker

Proceedings of the 24th Python in Science Conference, 2025

2024

Best practices to evaluate the impact of biomedical research software - metric collection beyond citations.

Awan Afiaz, Andrey Ivanov, John Chamberlin, David Hanauer, Candace Savonen, Mary J. Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright

Bioinform., 2024

2023

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.

Christopher R. Keefe, Matthew R. Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V. Wood, Evan Bolyen, J. Gregory Caporaso

PLoS Comput. Biol., November, 2023

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?

Awan Afiaz, Andrey Ivanov, John Chamberlin, David Hanauer, Candace Savonen, Mary J. Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright

CoRR, 2023

2022

Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment.

Nicholas A. Bokulich, Pawel Laniewski, Anja Adamov, Dana M. Chase, J. Gregory Caporaso, Melissa M. Herbst-Kralovetz

PLoS Comput. Biol., 2022

2021

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Matthew R. Dillon, Evan Bolyen, Anja Adamov, Aeriel Belk, Emily Borsom, Zachary Burcham, Justine W. Debelius, Heather Deel, Alex Emmons, Mehrbod Estaki, Chloe Herman, Christopher R. Keefe, Jamie T. Morton, Renato R. M. Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vazquez-Baeza, Michal Ziemski, Hazuki E. Miwa, Terry A. Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D. Kaehler, Emily K. Cope, Jessica L. Metcalf, Michael S. Robeson II, Nicholas A. Bokulich, J. Gregory Caporaso

PLoS Comput. Biol., 2021

2018

q2-sample-classifier: machine-learning tools for microbiome classification and regression.

Nicholas A. Bokulich, Matthew R. Dillon, Evan Bolyen, Benjamin D. Kaehler, Gavin A. Huttley, J. Gregory Caporaso

J. Open Source Softw., 2018

2011

PrimerProspector: <i>de novo</i> design and taxonomic analysis of barcoded polymerase chain reaction primers.

William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight

Bioinform., 2011

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight

Bioinform., 2011

2010

PyNAST: a flexible tool for aligning sequences to a template alignment.

J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight

Bioinform., 2010

2008

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

J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter

Proceedings of the Biocomputing 2008, 2008

2007

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter

J. Bioinform. Comput. Biol., 2007

MutationFinder: a high-performance system for extracting point mutation mentions from text.

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter

Bioinform., 2007

2006

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

J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter

Proceedings of the Fifteenth Text REtrieval Conference, 2006

2005

Concept Recognition and the TREC Genomics Tasks.

J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter

Proceedings of the Fourteenth Text REtrieval Conference, 2005