PowerMarker: an integrated analysis environment for genetic marker analysis. - Kejun Liu; Spencer V. Muse (Bioinform., 2005)

HyPhy: hypothesis testing using phylogenies. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Spencer V. Muse (Bioinform., 2005)

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. - Wayne Delport; Konrad Scheffler; Gordon Botha; Mike B. Gravenor; Spencer V. Muse; Sergei L. Kosakovsky Pond (PLoS Comput. Biol., 2010)

Training the Next Generation of Quantitative Biologists in the Era of Big Data. - Kristine A. Pattin; Anna C. Greene; Russ B. Altman; Kevin Bretonnel Cohen; Elizabeth Wethington; Carsten Görg; Lawrence E. Hunter; Spencer V. Muse; Predrag Radivojac; Jason H. Moore (Pacific Symposium on Biocomputing, 2015)