StrandSpecRNASeqEval by Levin et al. (Nature Methods, 2010)

Microsoft Word add-in for the GenePattern Reproducible Research Document (GRRD), by Mesirov (Science, 2010)

AuDIT by Abbatiello et al. (Clinical Chemistry, 2010)

FLAME by Pyne et al. (PNAS, 2009)

ESPPredictor by Fusaro et al. (Nature Biotechnology, 2009)