- Shen, Y., Schidlowski, M., 2000. New C isotope stratigraphy from southwest China: implications for the placement of the Precambrian-Cambrian boundary on the Yangtze Platform and global correlations. Geology 28: 623-626..
- Shen, Y., Buick, R., Canfield, D.E., 2001. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410: 77-81. (+ Shen and Buick, 2004. Earth-Sci Rev 64: 243-272, and Shen et al., 2009. EPSL 279: 383-391)..
- Shen, Y., Knoll, A.H., Walter, M.R., 2003. Evidence for low sulphate and anoxia in a mid-Proterozoic marine basin. Nature 423: 632-635..
- Nielsen, J.K., Shen, Y., 2004. Evidence for sulfidic deep water during the Late Permian in the East Greenland Basin. Geology 32: 1037-1040..
- Scott, C.,Lyons, T.W., Bekker, A., Shen, Y., Poulton, S.W.,Chu, X., Anbar, A.D., 2008. Tracing stepwise oxygenation of the Proterozoic ocean. Nature 452: 456-459..
- Shen, Y., Zhang, T., Hoffman, P.F., 2008. On the coevolution of Ediacaran oceans and animals. PNAS 105: 7376-7381..
- Nagy, R.M., Porter, S.M., Dehler, C.M., Shen, Y., 2009. Biotic turnover driven by eutrophication before the Sturtian low-latitude glaciation. Nature Geoscience 2: 415-418..
- Zhang, T., Shen, Y., Zhan, R., Shen, S., Chen, X., 2009. Large perturbations of the carbon and sulfur cycle associated with the Late Ordovician mass extinction in South China. Geology 37: 299-302..
- Shen, S.Z., Crowley, J.L., Wang, Y., Bowring, S.A., Erwin, D.H., Sadler, P.M., Cao, C.Q., Rothman, D.H., Henderson, C.M., Ramezani, J., Zhang, H., Shen, Y., Wang, X.D., Wang, W., Mu, L., Li, W.Z., Tang, Y.G., Liu, X.L., Liu, L.J., Zeng, Y., Jiang, Y.F., Jin, Y.G., 2011. Calibrating the end-Permian mass extinction. Science 334: 1367-1372..
- Zhang, T., Trela, W., Jiang, S-Y., Nielsen, J.K., Shen, Y., 2011. Major oceanic redox condition change correlated with the rebound of marine animal diversity during the Late Ordovician. Geology 39: 675-678..