Project Histories: Managing Data Provenance Across Collection-Oriented Scientific Workflow Runs. - Shawn Bowers; Timothy M. McPhillips; Martin Wu; Bertram Ludäscher (DILS, 2007)

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. - Martin Wu; Alexandra J. Scott (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)