The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. - Robert Hoehndorf; Colin R. Batchelor; Thomas Bittner; Michel Dumontier; Karen Eilbeck; Rob Knight 001; Chris Mungall; Jane S. Richardson; Jesse Stombaugh; Eric Westhof; Craig L. Zirbel; Neocles Leontis (Appl. Ontology, 2011)

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. - Meg Pirrung; Ryan Kennedy; J. Gregory Caporaso; Jesse Stombaugh; Doug Wendel; Rob Knight 001 (Bioinform., 2011)

Boulder ALignment Editor (ALE): a web-based RNA alignment tool. - Jesse Stombaugh; Jeremy Widmann; Daniel McDonald; Rob Knight 001 (Bioinform., 2011)

SitePainter: a tool for exploring biogeographical patterns. - Antonio González; Jesse Stombaugh; Christian L. Lauber; Noah Fierer; Rob Knight 001 (Bioinform., 2012)