Rhona K. Stuart

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-452
Livermore, CA 94550

Building 361, Rm 1941
email: stuart25@llnl.gov
phone: 925 422 3493



University of California San Diego

Ecology, Behavior, Evolution

B.Sc. 2003

Scripps Institution of Oceanography, University of California, San Diego

Marine Biology

Ph.D., 2012


My research interests include microbial ecology, genetics, and metal biogeochemistry.  Currently, I am part of a project investigating photosynthetic microbial mats, specifically looking at the role of extracellular polymeric substances in carbon cycling.  I am interested in how microbes, cyanobacteria in particular, play a role in transforming their environment and responding to change, using genomic, proteomic, and metabolomics approaches as well as classic genetic approaches in culture. I am also interested in integrating data using ‘omics techniques (transcriptomics, proteomics, metabolomics), with stable isotope probing and novel imaging strategies  Poster - Characterization of Extracellular Polymeric Substances in Hypersaline Cyanobacterial Mats and Mat-forming Cyanobacterial Isolates.


Stuart, R.K, X.Mayali, J.Z. Lee, R.C. Everroad, M.Hwang, B.Bebout, P. Weber, J. Pett-Ridge, M.P. Thelen. 2015. Cyanobacterial reuse of extracellular organic carbon in microbial mats. ISME J., AOP 23 Oct. 2015 (doi: 10.1038/ismej.2015.180)

Stuart, R.K, B.Brahamsha, and B. Palenik. 2014.  A putative Deg-protease in marine Synechococcus is involved in stress response and outer membrane protein organization. Front. Mar. Sci., 29 June 2014 (doi: 10.3389/fmars.2014.00016) (link)

Stuart, R.K., B. Brahamsha, K. Busby and B. Palenik. 2013. Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress.  ISME J 7: 1139-1149 (link)

Stuart, R. K., C. L. Dupont, D. A. Johnson, I. T. Paulsen, and B. Palenik. 2009. Coastal Strains of Marine Synechococcus Species Exhibit Increased Tolerance to Copper Shock and a Distinctive Transcriptional Response Relative to Those of Open-Ocean Strains. Applied and Environmental Microbiology 75: 5047-5057. (link)

Shivlova, I.N., J.C. Robidart, H.J.Tripp, K.Turk-Kubo, B.Wawrik, A.Post, A.W.Thompson, B.Ward, J.T.Hollibaugh, A.Millard, M.Ostrowski, D.Scanlan, R.W.Paerl, R.K. Stuart, J.P.Zehr. 2014. A microarray for assessing transcription from pelagic microbial taxa. ISME J 8, 1476–1491.  (link)

Tetu, S.G, D.A. Johnson, D.R.Varkey, K.Phillippy, R.K. Stuart, C.L.Dupont, K.A.Hassan, B.P.Palenik and I.T.Paulsen. 2013. Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Front. Microbiol. 4. doi: 10.3389/fmicb.2013.00232 (link)

Mao, X.Z, V. Olman, R. K. Stuart, I. T. Paulsen, B. Palenik and Y. Xu. 2010. Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics 11: 291. (link)

Heintzman, N. D., G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark, L. F. Harp, Z. Ye, L. Lee, R. K. Stuart, C. Ching, K. A. Ching, J. E. Antosiewicz-Bourget, H. Liu, X. M. Zhang, R. D. Green, V. V. Lobanenkov, R. Stewart, J. A. Thomson, G.E. Crawford, M. Kellis, B. Ren. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112. (link)

Heintzman, N.D., R.K. Stuart, G. Hon, Y. T. Fu, C. W. Ching, R. D. Hawkins, L. O. Barrera, S. Van Calcar, X. C. Qu, K. A. Ching, W. Wang, Z. P. Weng, R. D. Green, G. E. Crawford, B. Ren. 2007.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics 39: 311-318. (link)

Maynard, N. D., J. Chen, R. K. Stuart, J. B. Fan, and B. Ren. 2008. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nature Methods 5: 307-309. (link)

Birney, E. …R. K. Stuart…and others. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816 (link)