N. J. Ulrich, G. Shen, D. A. Bryant and S.R. Miller. 2024. Ecological diversification of a cyanobacterium through divergence of its novel chlorophyll d-based light-harvesting system. Curr. Biol., https://doi.org/10.1016/j.cub.2024.05.022.

H. E. Abresch, T. Bell and S.R. Miller. 2024. Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont. ISME J. 18, wrae064, https://doi.org/10.1093/ismejo/wrae064.

A. I. Garber, E. B. Sano, A. L. Gallagher and S.R. Miller. 2024. Duplicate gene expression and possible mechanisms of paralog retention during bacterial genome expansion. Genome Biol. Evol. 16, evae089, https://doi.org/10.1093/gbe/evae089.

S. R. Miller, H. E. Abresch, J. J. Baroch, C. K. Fishman Miller, A. I. Garber, A. R. Oman and N. J. Ulrich. 2022. Genomic and functional variation of the Chlorophyll d-producing cyanobacterium Acaryochloris marina. Microorganisms 10, 569.

N. J. Ulrich, H. Uchida, Y. Kanesaki, E. Hirose, A. Murakami and S.R. Miller. 2021. Reacquisition of light-harvesting genes in a marine cyanobacterium confers a broader solar niche. Curr. Biol. DOI:https://doi.org/10.1016/j.cub.2021.01.047

S. R. Miller, P. R. Hutchins, R. Longley and T. Bauersachs. 2020. Cellular innovation of the cyanobacterial heterocyst by the adaptive loss of plasticity. Curr. Biol. 30:344-350.

A. L. Gallagher and S. R. Miller. 2018. Expression of novel gene content drives adaptation to low iron in the cyanobacterium Acaryochloris. Genome Biol. Evol. 10:1484-1492.

E. B. Sano , C. A. Wall, P. R. Hutchins and S. R. Miller. 2018. Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nature Ecol. Evol. doi:10.1038/s41559-017-0435-9.

S. R. Miller 2017. An appraisal of the enzyme stability-activity trade-off. Evolution 71:1876-1887.

D. Pedersen and S. R. Miller. 2017. Photosynthetic temperature adaptation during niche diversification of the thermophilic cyanobacterium Synechococcus A/B clade. ISME J. 11:1053-1057.

P. R. Hutchins and S. R. Miller. 2017. Genomics of variation in nitrogen fixation activity in a population of the thermophilic cyanobacterium Mastigocladus laminosus. ISME J.11:78-86.

C. A. Wall, G. J. Koniges and S. R. Miller. 2014. Divergence with gene flow in a population of thermophilic bacteria: a potential role for spatially varying selection. Mol. Ecol. 23:3371-3383.

S. R. Miller, M. A. McGuirl and D. Carvey. 2013. The evolution of RuBisCO stability at the thermal limit of photoautotrophy. Mol. Biol. Evol. 30:752-60.

C. G. Klatt, W. P. Inskeep, M. Herrgard, Z.J. Jay, D.B. Rusch, S.G. Tringe, M.N. Parenteau, D.M. Ward, S.M. Boomer, D.A. Bryant and S.R. Miller. 2013. Community structure and function of high-temperature phototrophic microbial mats inhabiting diverse geothermal environments. Front. Microbiol. doi: 10.3389/fmicb.2013.00106.

W. P. Inskeep et al. 2013. The YNP metagenome project:  environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front. Microbiol. doi: 10.3389/fmicb.2013.00067.

D. M. Ward, R. W. Castenholz and S. R. Miller. 2012. Cyanobacteria in geothermal habitats. In: The Ecology of Cyanobacteria, 2nd ed.

S. R. Miller, A. M. Wood, R. E. Blankenship, M. Kim and S. Ferriera. 2011. Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: Implications for the ecological niche. Genome Biol. Evol. 3:601-613. 

S. R. Miller, A. L. Strong, K. L. Jones and M. C. Ungerer. 2009. Barcoded pyrosequencing reveals shared bacterial community properties along two alkaline hot spring temperature gradients in Yellowstone National Park. Appl. Environ. Microbiol. 75:4565-4572.

S. R. Miller, C. Williams, A. L. Strong and D. Carvey.  2009. Ecological specialization in a spatially structured population of the thermophilic cyanobacterum Mastigocladus laminosus. Appl. Environ. Microbiol. 75:729-734.

S. R. Miller, R. W. Castenholz and D. Pedersen. 2007. Phylogeography of the thermophilic cyanobacterium Mastigocladus laminosus.  Appl. Environ. Microbiol. 73:4751-4759.

S. R. Miller, M. D. Purugganan and S. E. Curtis. 2006.  Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Environ. Microbiol. 72:2793-2800.

R. E. Ley, J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. L. Sogin and N. R. Pace. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72:3685-3695.

S. R. Miller, S. Augustine, T. Le Olson, R. E. Blankenship, J. Selker, and A. M. Wood. 2005. Discovery of a free-living, chlorophyll-d producing cyanobacterium with a hybrid proteobacterial/cyanobacterial SSU rRNA gene. Proc. Natl. Acad. Sci. U.S.A. 102:850-855.

S. R. Miller and R. W. Castenholz. 2000.  The evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus.  Appl. Environ. Microbiol. 66:4222-4229.