Strainer: software for analysis of population variation in community genomic datasets. - John M. Eppley; Gene W. Tyson; Wayne M. Getz; Jillian F. Banfield (BMC Bioinform., 2007)

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. - Chongle Pan; Byung-Hoon Park; William H. McDonald; Patricia A. Carey; Jillian F. Banfield; Nathan Verberkmoes; Robert L. Hettich; Nagiza F. Samatova (BMC Bioinform., 2010)

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes. - Alexis P. Yelton; Brian C. Thomas; Sheri L. Simmons; Paul Wilmes; Adam T. Zemla; Michael P. Thelen; Nicholas Justice; Jillian F. Banfield (PLoS Comput. Biol., 2011)

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems. - Matthew C. Schmidt; Andrea M. Rocha; Kanchana Padmanabhan; Yekaterina Shpanskaya; Jillian F. Banfield; Kathleen Scott; James R. Mihelcic; Nagiza F. Samatova (PLoS Comput. Biol., 2012)

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity. - Ariel D. Weinberger; Christine L. Sun; Mateusz M. Plucinski; Vincent J. Denef; Brian C. Thomas; Philippe Horvath; Rodolphe Barrangou; Michael S. Gilmore; Wayne M. Getz; Jillian F. Banfield (PLoS Comput. Biol., 2012)

New CRISPR-Cas systems from uncultivated microbes. - David Burstein; Lucas B. Harrington; Steven C. Strutt; Alexander J. Probst; Karthik Anantharaman; Brian C. Thomas; Jennifer A. Doudna; Jillian F. Banfield (Nat., 2017)