Denoising PCR-amplified metagenome data. - Michael J. Rosen; Benjamin J. Callahan; Daniel S. Fisher; Susan P. Holmes (BMC Bioinform., 2012)

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data. - Benjamin J. Callahan; Diana Proctor; David A. Relman; Julia Fukuyama; Susan P. Holmes (PSB, 2016)

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. - Mohammad Sajjad Ghaemi; Daniel B. DiGiulio; Kévin Contrepois; Benjamin J. Callahan; Thuy T. M. Ngo; Brittany Lee-McMullen; Benoit Lehallier; Anna Robaczewska; David Mcilwain; Yael Rosenberg-Hasson; Ronald J. Wong; Cecele Quaintance; et al. (Bioinform., 2019)