A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. - Omry Koren; Dan Knight; Antonio González; Levi Waldron; Nicola Segata; Rob Knight 001; Curtis Huttenhower; Ruth E. Ley (PLoS Comput. Biol., 2013)

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes. - Gabriel A. Al-Ghalith; Emmanuel Montassier; Henry N. Ward; Dan Knight (PLoS Comput. Biol., 2016)

SHOGUN: a modular, accurate and scalable framework for microbiome quantification. - Benjamin Hillmann; Gabriel A. Al-Ghalith; Robin R. Shields-Cutler; Qiyun Zhu; Rob Knight 001; Dan Knight (Bioinform., 2020)

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)