• Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R. 2019. Charting the complexity of the marine microbiome through single cell genomics. Cell 179:1623–1635.

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• Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam S Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358:1046–1051.

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• Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MJ, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, and Lubys A (2017) Improved genome recovery and integrated cell-size analyses of individual, uncultured microbial cells and viral particles. Nature Communications 8:84

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• Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom R, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. 2014. Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416-420

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• Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu W-T, Eisen JA, Hallam S, Kyrpides N, Stepanauskas R, Rubin E, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431-437

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• Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, Gonzalez JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson B, Poulton NJ, Schwientek P, Gonzalez-Acinas S, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. PNAS 110:11463-11468

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• Lloyd KG, Schreiber L, Petersen DG, Kjeldsen K, Lever MA, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jorgensen BB. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215-218

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• Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland D, Lluesma Gomez M, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296-1300

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• Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D. 2011 Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714-717

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• Stepanauskas R, Sieracki ME. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. PNAS 104:9052-9057