Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences. - Jonathan A. Eisen; Maria-Ines Benito; Virginia Walbot (Nucleic Acids Res., 1994)

TIGRFAMs: a protein family resource for the functional identification of proteins. - Daniel H. Haft; Brendan J. Loftus; Delwood L. Richardson; Fan Yang; Jonathan A. Eisen; Ian T. Paulsen; Owen White (Nucleic Acids Res., 2001)

Evolution. - Nicholas H. Barton; Derek E. G. Briggs; Jonathan A. Eisen; David B. Goldstein; Nipam H. Patel (Cold Spring Harbor Laboratory Press, 2007)

CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. - Sourav Chatterji; Ichitaro Yamazaki; Zhaojun Bai; Jonathan A. Eisen (RECOMB, 2008)

WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences. - Amber L. Hartman; Sean Riddle; Timothy M. McPhillips; Bertram Ludäscher; Jonathan A. Eisen (BMC Bioinform., 2010)

Mauve Assembly Metrics. - Aaron E. Darling; Andrew J. Tritt; Jonathan A. Eisen; Marc T. Facciotti (Bioinform., 2011)

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. - Thomas J. Sharpton; Samantha J. Riesenfeld; Steven W. Kembel; Joshua Ladau; James P. O'Dwyer; Jessica L. Green; Jonathan A. Eisen; Katherine S. Pollard (PLoS Comput. Biol., 2011)

MicrobeDB: a locally maintainable database of microbial genomic sequences. - Morgan G. I. Langille; Matthew R. Laird; William W. L. Hsiao; Terry A. Chiu; Jonathan A. Eisen; Fiona S. L. Brinkman (Bioinform., 2012)

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. - Thomas J. Sharpton; Guillaume Jospin; Dongying Wu; Morgan G. I. Langille; Katherine S. Pollard; Jonathan A. Eisen (BMC Bioinform., 2012)

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. - Steven W. Kembel; Martin Wu; Jonathan A. Eisen; Jessica L. Green (PLoS Comput. Biol., 2012)

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. - Stephen Nayfach; Patrick H. Bradley; Stacia K. Wyman; Timothy J. Laurent; Alexander G. Williams; Jonathan A. Eisen; Katherine S. Pollard; Thomas J. Sharpton (PLoS Comput. Biol., 2015)