• Epstein, S.S. (2009) Microbial awakenings. Nature 457: 1083. | PubMed 19242455
• Epstein, S.S., (2009) Uncultivated Microorganisms.  Series: Microbiology Monographs, Vol. 10; Springer Berlin / Heidelberg, 208. ISBN:978-3-540-85464-7 | SpringerLink | Preface.
• Epstein, S.S. (2009) General Model of Microbial Uncultivability, in Uncultivated Microorganisms, (Ed. S.S. Epstein): . Series: Microbiology Monographs (Series Ed. Alexander Steinbuchel), Vol. 10; Springer Berlin / Heidelberg, 131-150. ISBN:978-3-540-85464-7 | SpringerLink | Preface.
• Stoeck, T., and S. S. Epstein (2009) Crystal Ball-2009: Protists and the rare biosphere. Environmental Microbiology Reports, 1:20-22. | Wiley InterScience
• Hong, S.-H, Bunge, J., Leslin, C., Jeon, S-O., and S. S. Epstein (2009). Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME Journal. | PubMed 19693101
• Edgcomb, V., Orsi, W., Chesley Leslin, C., Epstein S. S., Bunge, J. Jeon, S.-O., Yakimov, M. M., Behnke, A., and T. Stoeck (2009). Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea. Extremophiles 13:151–167. | PubMed 19057844 | Springer Link
  

• Gavrish, E., Bollmann, A., Epstein, S. S., and Lewis, K. (2008) A trap for in situ cultivation of filamentous actinobacteria. J. Microbiol. Methods 72: 257–262. Full Text
• Lewis, K., Epstein, S. S., Godoy, V. G., and S.-H. Hong (2008). Intact DNA in ancient permafrost. Trends in Microbiol. 16: 92-94. | PubMed 18291656
• Jeon, S., Bunge, J., Leslin, C., Stoeck, T., Hong, S.-H., and S. S. Epstein (2008) Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiol. 8: 222-234. | Full Text
• Nichols D., Lewis, K., Orjala, J., Mo, S., Ortenberg, R., O'Connor, P., Zhao, C., Vouros, P., Kaeberlein, T., and S. S. Epstein (2008) Short peptide induces an "uncultivable" microorganism to grow in vitro. Appl. Environ. Microbiol., 74: 4889-4897. Full Text

• Bollmann, A., K.Lewis, and S. S. Epstein (2007). Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered Isolates. Applied and Environmental Microbiology 73: 6386–6390. Full Text
• Giovannoni, S. J, R. Foster, M. S. Rappé, and S. S. Epstein (2007). New cultivation strategies bring more microbial plankton species into the laboratory. Journal of the Oceanography Society 20: 24-30. | The Oceanography Society PDF
  

• Bunge, J., S. S. Epstein, and D. G. Peterson (2006). Comment on “Computational improvements reveal great bacterial diversity and high metal toxicity in soil”. Science 313: 918c. | PubMed 16917045 | ScienceMag
• Hong, S-H., Bunge, J., Jeon, S-O., and S. S. Epstein (2006). Predicting microbial species richness. PNAS 103: 117-122. | Full Text
• Jeon S.-O., Bunge, J., Stoeck, T., Barger, K. J.-A., Hong, S.-H., and S. S. Epstein (2006). Synthetic statistical approach reveals high richness of microbial eukaryotes in anoxic water column. Appl. Environ. Microbiol. 72: 6578-6583. | Full Text
• Stoeck, T., Hayward, B., Taylor, G.T., Varela, R., and S. S. Epstein (2006). A Multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157: 31-43. | PubMed 16431157
  

• Hayward, B. H., R. Droste and S. S. Epstein (2003). Interstitial ciliates: benthic microaerophiles or planktonic anaerobes? Journal of Eukaryotic Microbiology, 50: 356-359. | PubMed 14563174
• Stoeck, T., G. Taylor, and S. S. Epstein (2003). Novel eukaryotes from a permanently anoxic Cariaco Basin (Caribbean Sea). Applied and Environmental Microbiology 69: 5656-5663. | Full Text
• Stoeck, T., and S. S. Epstein (2003). Novel eukaryotic lineages inferred from SSU rRNA analyses in oxygen-depleted marine environments. Applied and Environmental Microbiology 69: 2657-2663. | Full Text
• Stoeck, T., W. Fowle, and S. S. Epstein (2003). Methodology of protistan discovery: from rRNA detection to quality SEM images. Appl. Environ. Microbiol. 69: 6856 6863. | Full Text
• T.Kaeberlein, K. Lewis, and S. S. Epstein (2002). Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129 Abstract | Full Text.
• Epstein, S. S. (2001) Microbial interactions, version 1.0. In: Nature Encyclopedia of Life Sciences. London: Nature Publishing Group. | Full Text
• Bazylinski, D. A., D. A. Schlezinger, B.L. Howes, R. B. Frankel, and S. S. Epstein (2000). Occurrence and distribution of diverse populations of magnetic protists in a chemically stratified coastal salt pond. Chemical Geology 169: 319-328. | ScienceDirect
• Epstein, S. S., W. Fowle, and D. Bazylinski (1998). Epibiotic bacteria on several ciliates from marine sediments. Journal of Eukaryotic Microbiology. 45: 64-70. | InterScience
• Epstein, S. S. (1997a). Microbial food webs in marine sediments. I. Trophic interactions and grazing rates in two tidal flat communities. Microbial Ecology 34: 188-198. | SpringerLink
• Epstein, S. S. (1997b). Microbial food webs in marine sediments. II. Seasonal changes in trophic interactions in a sandy tidal flat community. Microbial Ecology 34: 199-209. | SpringerLink
• Epstein, S. S., D. Alexander, K. Cosman, A. Dompé, S. Gallagher, J. Jarsobski, E. Laning, R. Martinez, G. Panasik, C. Peluso, R. Runde, and E. Timmer (1997). Enumeration of sandy sediment bacteria: are the counts quantitative or relative? Marine Ecology Progress Series 151: 11-16. | InterScience
• Epstein, S. S. (1996). Microbial food webs in marine sediments: the role of proto- and micrometazoan grazing. Eos 76 Nº 3 (Suppl.) p. OS69.
• Epstein, S. S. (1995). Simultaneous enumeration of protozoa and micrometazoa from marine sandy sediments. Aquatic Microbial Ecology 9: 219-227. | InterScience
  
• Berninger, U.-G. and S. S. Epstein (1995). Vertical distribution of benthic ciliates in response to the oxygen concentration in an intertidal North Sea Sediment. Aquatic Microbial Ecology 9: 229-236. | InterScience
  
• Epstein, S. S., and J. Rossel (1995b). Methodology of in situ grazing experiments: evaluation of a new vital dye for preparation of fluorescently labeled bacteria. Marine Ecology Progress Series 128: 143-150. | InterScience
  
• Epstein, S. S., and J. Rossel (1995a). Enumeration of sandy sediment bacteria: search for optimal protocol. Marine Ecology Progress Series 117: 289-298. | InterScience
• Epstein, S. S. (1994). A new marine interstitial ciliate from Northwest Atlantic, Tracheloraphis primitarum sp. n. (Ciliophora, Karyorelictida, Trachelocercidae). Journal of Eukaryotic Microbiology, 41: 500-503. | InterScience
• Epstein, S. S., and M. P. Shiaris (1992a). Size-selective grazing of coastal bacterioplankton by natural assemblages of pigmented flagellates, colorless flagellates, and ciliates. Microbial Ecology 23: 211-225. | SpringerLink
  
• Epstein, S. S., and M. P. Shiaris (1992b). The rates of microbenthos- and meiobenthos bacterivory in a temperate muddy tidal-flat community. Applied and Environmental Microbiology 58: 2426-2431. | PubMed 16348746
  
• Epstein, S. S., I. V. Burkovsky, and M. P. Shiaris (1992). Ciliate grazing on bacteria, flagellates, and microalgae in a temperate sandy-flat: ingestion rates and food niche partitioning. Journal of Experimental Marine Biology and Ecology 165: 103-123. | ScienceDirect
• Epstein, S. S., and E. D. Gallagher (1992). Evidence for facilitation and inhibition of ciliate population growth by meiofauna on a temperate sandflat. Journal of Experimental Marine Biology and Ecology 155: 27-39. | ScienceDirect
• Epstein, S. S. (1984). Growth rates of benthic ciliates from White Sea sediments under experimental conditions. Oceanology 24: 116-118.
• Epstein, S. S. (1983). Experimental study of grazing rates of marine sediment ciliates. Oceanology 23: 767-772.
• Burkovsky, I.V., and S. S. Epstein (1982). Additional data on food specialization and trophic structure of a marine sediment ciliate community (the White Sea, Russia). Zoologicheski Zhournal 61: 129-132.
• Burkovsky, I.V., S. S. Epstein, and N. N. Moliboga (1980). Food specialization and trophic structure of a marine sediment ciliate community (the White Sea, Russia). Zoologicheski Zhournal 59: 325-334.