BayGO: Bayesian analysis of ontology term enrichment in microarray data. - Ricardo Z. N. Vêncio; Tie Koide; Suely L. Gomes; Carlos A. de B. Pereira (BMC Bioinform., 2006)

Integration and visualization of systems biology data in context of the genome. - J. Christopher Bare; Tie Koide; David J. Reiss; Dan Tenenbaum; Nitin S. Baliga (BMC Bioinform., 2010)

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. - Marc T. Facciotti; Wyming Lee Pang; Fang-Yin Lo; Kenia Whitehead; Tie Koide; Ken-ichi Masumura; Min Pan; Amardeep Kaur; David J. Larsen; David J. Reiss; Linh Hoang; Ewa Kalisiak; et al. (BMC Syst. Biol., 2010)