Koretsky CM, Meile C, Van Cappellen P.  2002.  Quantifying bioirrigation using ecological parameters: a stochastic approach. Geochem. Trans. 3:17–30.
Bowles M.W., Samarkin V.A., Joye SB.  2001.  Improved measurement of microbial activity in deep-sea sediments at in situ pressure and methane concentration. Limnology and Oceanography: Methods. 9:499-506.
Meile C, Koretsky CM, Van Cappellen P.  2001.  Quantifying bioirrigation in aquatic sediments: an inverse modeling approach. Limnology and Oceanography. 46:164–177.
Ward B.B., Martino D., Diaz C., Joye SB.  2000.  Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California on the basis of 16S rRNA sequences. Applied and Environmental Microbiology. 66(7):2873-2881.
Fisher C.R., MacDonald I.R., Sassen R., Young C.M., Macko S.A., Hourdez S., Carney R.S., Joye SB, McMullin E..  2000.  Methane ice worms: Hesiocaeca methanicola colonizing fossil fuel reserves. Naturwissenschaften. 87(4):184-187.
Sassen R., Joye SB, Sweet S.T., DeFrietas D.A., Milkov A.V., MacDonald I.R..  1999.  Thermogenic gas hydrates and hydrocarbon gases in complex chemosynthetic communities, Gulf of Mexico, Continental Slope. Organic Geochemistry. 30:485-497.
Joye SB, Connell T.M., Miller L.G., Oremland R.S..  1999.  Oxidation of ammonia and methane in an alkaline, saline lake. Limnology & Oceanography. 44(1):178-188.
Sassen R., MacDonald I.R., Guinasso N.L., Joye SB, Requejo A.G., Sweet S.T., Alcala-Herrera J., DeFrietas D.A., Schink D.R..  1998.  Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments. Geology. 26:851-854.
Mayer L.M., Keil R.G., Macko S.A., Joye SB, Ruttenberg K.C., Aller R.C.  1998.  The importance of suspended particulates in riverine delivery of bioavailable nitrogen to coastal zones. Global Biogeochemical Cycles. 12:573-580.