Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ. 2014. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile.  Frontiers in Microbiology. In press.

Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. 2014. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression of anammox and denitrification in the oxygen minimum zone off northern Chile.  mBio. In press.

Dmytrenko O, Russel SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve Solemya velum: A blueprint for thriving in and out of symbiosis.  BMC Genomics. In press.

Sarode N, Parris DJ, Ganesh S, Seston SL, Stewart FJ. 2014. Generation and analysis of microbial metatranscriptomes. Manual of Environmental Microbiology, Fourth Edition.  In press.

Lee FJ, Rusch D, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental Microbiology. In press.  DOI: 10.1111/1462-2920.12526

Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. 2014. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Research. 42: 7473-7485.

Stewart FJ, Ulloa O. 2014. Microbial metagenomics of oxygen minimum zones. Marco D (ed.) Metagenomics of the Microbial Nitrogen Cycle: Current innovations and future trends. Horizon Scientific Press. http://www.horizonpress.com/n2

Ganesh S, Parris DJ, DeLong EF, Stewart FJ. 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J. 8: 187-211. pdf copy

Stewart FJ. 2013. Where the genes flow. Nature Geoscience. 6: 688-690. link to Open Access copy

Stewart FJ. 2013. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Methods in Enzymology: Microbial Community Metagenomics, Metatranscriptomics, and Metaproteomics. 531:187-218.

Cavanaugh, CM, McKiness ZP, Newton ILG, Stewart FJ.  2013.  Marine chemosynthetic symbioses. In: Rosenberg et al. (eds). The Prokaryotes, Prokaryotic Biology and Symbiotic Associations. 1: 579-607.  Springer-Verlag, New York. Online: http://link.springer.com/book/10.1007/978-3-642-30194-0

Sanders JG, Beinart RA, Stewart FJ, DeLong EF, Girguis PR. 2013. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. ISME J. 7: 1556-1567. link to Open Access copy

Dimond JL, Kerwin AH, Rotjan R, Sharp K, Stewart FJ, Thornhill DJ. 2013. A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata. Coral Reefs. 32:401-409. link to article

Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ. 2012. Perspective: Microbial oceanography of anoxic oxygen minimum zones. P. Natl. Acad. Sci. USA. 109: 15996-16003. link to Open Access copy

Stewart FJ, Dalsgaard T, Thamdrup B, Revsbech NP, Ulloa O, Canfield DE, and DeLong EF. Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton. PLoS ONE. 7: e37118. link to Open Access copy

Bryant JA, Stewart FJ, Eppley JM, and DeLong EF. 2012. Microbial community phylogenetic and trait diversity decline steeply with depth in a marine oxygen minimum zone. Ecology. 93: 1659-1673. link to article

Stewart FJ, Ulloa O, DeLong EF. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ. Microbiol. 14:23-40. pdf copy

Stewart FJ, 2011. Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective. Biochem. Soc. Trans. 39: 1859-63. pdf copy

Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM. 2011. Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Front. Microbiol. 2:134. pdf copy

Stewart FJ, Cavanaugh CM. Pyrosequencing analysis of endosymbiont diversity.  2011. In: de Bruijn FJ (ed.). Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats.  Wiley-Blackwell.

Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF. 2011. Community transcriptomics reveals universal patterns of protein sequence conservation in microbial communities. Genome Biol. 12:R26. link to Open Access copy

Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, DeLong EF, Revsbech NP, Ulloa O. 2010. A cryptic sulfur cycle in oxygen-minimum zone waters off the Chilean Coast. Science. 330: 1375-1378. link to copy, pdf of Perspectives Article (A. Teske)

Stewart FJ, Ottesen EA, DeLong EF. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J. 4: 896-907. pdf copy, protocol

Roeselers G, Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson P, Barry K, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2010. Complete genome sequence of Candidatus Ruthia magnifica. Stan. Genomic Sci. 3: 163-173.

Stewart FJ, Baik AHY, Cavanaugh CM. 2009. Genetic subdivision of chemosynthetic endosymbionts of Solemya velum along the southern New England coast. Appl. Environ. Microbiol. 75:6005-6007. pdf copy

Stewart FJ, Cavanaugh CM. 2009. Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam. Environ. Microbiol. 11:2136-2147. pdf copy

Stewart FJ, Young CR, Cavanaugh CM. 2009. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol. Biol. Evol. 26: 1391-1404. pdf copy

Fritsen CH, Memmott JC, Stewart FJ.  2008. Inter-annual sea ice dynamics and micro-algal biomass in winter pack ice: Marguerite Bay, Antarctica.  Deep-Sea Res. Pt II. 55:2059-2067. pdf copy

Stewart FJ, Young CR, Cavanaugh CM. 2008. Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Mol. Biol. Evol. 25:673-687. pdf copy

Stewart FJ, Cavanaugh CM. 2007. Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in Bacteria. J. Mol. Evol. 65:44-67. pdf copy

Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 315:998-1000. pdf copy

Stewart FJ, Cavanaugh CM. 2006. Bacterial endosymbioses in Solemya (Mollusca, Bivalvia): model systems for studies of symbiont-host adaptation. Anton. Leeuw. Int. J. G. 90:343-360. pdf copy

Cavanaugh CM, McKiness ZP, Newton ILG, Stewart FJ. 2006. Marine chemosynthetic symbioses.  In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds.). The Prokaryotes. Third Edition. A Handbook on the Biology of Bacteria:Symbiotic Associations, Biotechnology, Applied Microbiology. Springer, New York. pdf copy

Mix LJ, Armstrong JC, Mandell AM, Mosier AC, Raymond J, Raymond SN, Stewart FJ, von Braun K, Zhaxybayeva O (eds.). 2006. The Astrobiology Primer: An outline of general knowledge.  Astrobiology. 6(5):735-813. pdf copy

Stewart FJ, Cavanaugh CM. 2005. Symbiosis of thioautotrophic bacteria with Riftia pachyptila. In: Overmann, J. (ed.). Molecular Basis of Symbiosis. Springer-Verlag, Berlin. p.197-225. pdf copy

Stewart FJ, Newton ILG, Cavanaugh CM. 2005. Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces. Trends Microbiol. 13(9): 439-448. pdf copy

Stewart FJ, Fritsen CH, Garrison DL. 2005. Bacteria-algae associations in the sea ice and upper water column of the Ross Sea in late austral summer.  Antarct. J. US. 33: 38-41. pdf copy

Stewart FJ, Fritsen CH. 2004. Bacteria-algae relationships in Antarctica sea ice. Antarct. Sci. 16(2): 143-156. pdf copy

Stewart FJ. 2000. Bacteria and bacteria-phototroph associations in ice habitats of the Ross Sea and the McMurdo Dry Valleys, Antarctica. undergraduate thesis. Middlebury College.