XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data. - Daniel N. Frank (BMC Bioinform., 2008)

BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. - Daniel N. Frank (BMC Bioinform., 2009)

Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases. - Tianyi Zhang 005; Robert A. DeSimone; Hongyan Chen; Christina M. Hamm; Jeffrey Yuan; Qing Qing Gong; Steven R. Hunt; Themistocles Dassopoulos; Rodney D. Newberry; Daniel N. Frank; Charles E. Robertson; Norman R. Pace; et al. (ICCABS, 2011)

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. - Charles E. Robertson; J. Kirk Harris; Brandie D. Wagner; David Granger; Kathy Browne; Beth Tatem; Leah M. Feazel; Kristin Park; Norman R. Pace; Daniel N. Frank (Bioinform., 2013)

Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. - Xiao Wu; Kathryn Berkow; Daniel N. Frank; Ellen Li; Ajay S. Gulati; Wei Zhu 008 (BMC Bioinform., 2013)

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R. - Charlie M. Carpenter; Daniel N. Frank; Kayla Williamson; Jaron Arbet; Brandie D. Wagner; Katerina J. Kechris; Miranda Kroehl (BMC Bioinform., 2021)