At the MBL

Xia, Li Charlie, J.A. Steele, J. Cram, Z.G. Cardon, S.L. Simmons , J.J. Vallino , J.A. Fuhrman, F. Sun (2011). Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. In press at BMC Systems Biology.

Postdoctoral work on acid mine drainage microbes

Simmons, S.L.*, G. DiBartolo*, V.J. Denef, D.S.A. Goltsman, M.P. Thelen, J.F. Banfield (2008), Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biology 6(7): e177. (* co-first authors). PubMed

Wilmes, P., S.L. Simmons, V.J. Denef, J.F. Banfield (2009), The dynamic genetic repertoire of microbial communities. FEMS Microbiology Reviews 33(1): 109-132. PubMed

Dick, G.J., A.F. Andersson, B. Baker, S.L. Simmons, B.C. Thomas, J.F. Banfield (2009), Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85. PubMed

Yelton, Alexis P., Brian C. Thomas, Sheri L. Simmons, Paul Wilmes, Adam Zemla, Michael P. Thelen, Nicholas Justice, and Jillian F. Banfield. 2011. “A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes.” PLoS Computational Biology 7 (10) (October 20): e1002230. doi:10.1371/journal.pcbi.1002230. PLoS Comp Biol

Graduate work on marine magnetotactic bacteria

Simmons, S.L., D.A. Bazylinski, and K.J. Edwards (2007), Population dynamics of marine magnetotactic bacteria in a meromictic coastal pond measured with qPCR. Environmental Microbiology 9(9): 2162-2174. PubMed

Simmons, S.L. and K.J. Edwards (2007), Unexpected diversity in populations of the many-celled magnetotactic prokaryote. Environmental Microbiology 9(1): 206-215. PubMed

Simmons, S.L. and K.J. Edwards (2007), Geobiology of magnetotactic bacteria. In Magnetoreception and Magnetosomes in Bacteria (D. Schüler, ed). Berlin: Springer-Verlag, pp. 77-102. Link

Simmons, S. L., D. A. Bazylinski, and K. J. Edwards (2006), South-seeking magnetotactic bacteria in the Northern Hemisphere. Science 311:371-374. PubMed

Simmons, S.L., S.M. Sievert, R.B. Frankel, D.A. Bazylinski, K.J. Edwards (2004), Spatio-temporal distribution of marine magnetotactic bacteria in a coastal salt pond. Applied and Environmental Microbiology 70(10): 6230-6239. PubMed

My graduate thesis (via dspace.mit.edu)