Risking "trust" in a public key infrastructure: old techniques of managing risk applied to new technology. - Andrew D. Fernandes (Decis. Support Syst., 2001)

Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. - Andrew D. Fernandes; William R. Atchley (Bioinform., 2008)

Estimating the evidence of selection and the reliability of inference in unigenic evolution. - Andrew D. Fernandes; Benjamin P. Kleinstiver; David R. Edgell; Lindi M. Wahl; Gregory B. Gloor (Algorithms Mol. Biol., 2010)

Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself? - Andrew D. Fernandes; Gregory B. Gloor (Bioinform., 2010)