Concept Recognition and the TREC Genomics Tasks. - J. Gregory Caporaso; William A. Baumgartner Jr.; K. Bretonnel Cohen; Helen L. Johnson 001; Jesse Paquette; Lawrence Hunter (TREC, 2005)

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 001; Olga Medvedeva; Anna Lindemann; Lynne M. Fox; Elizabeth K. White; K. Bretonnel Cohen; Lawrence Hunter (TREC, 2006)

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)

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)

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 (Pacific Symposium on Biocomputing, 2008)

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 001 (Bioinform., 2010)

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. - Meg Pirrung; Ryan Kennedy; J. Gregory Caporaso; Jesse Stombaugh; Doug Wendel; Rob Knight 001 (Bioinform., 2011)

PrimerProspector: de novo 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 001 (Bioinform., 2011)

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)

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; et al. (PLoS Comput. Biol., 2021)

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)

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; et al. (CoRR, 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., 2023)