(1) Kelley, S.T. and B.D. Farrell. (1998) Is specialization a dead-end?: The phylogeny of host use in Dendroctonus bark beetles (Coleoptera: Scolytidae). Evolution 52: 1731-1743.
(2) Kelley, S.T. and J.B. Mitton. (1998) Strong differentiation in mitochondrial DNA of Dendroctonus brevicomis (Coleoptera: Scolytidae). Annals of the Entomological Society of America 92: 193-197.
  (3) Kelley, S.T. and R.G. Latta. (1998) Evidence for high rates of self-fertilization in the alpine herb Epilobium anagallidifolium (Onagraceae). Canadian Journal of Botany 76: 1978-1980.
(4) Kelley, S.T. and V.G. Thackray. (1999) Phylogenetic analyses reveal ancient duplication of estrogen receptor isoforms.  Journal of Molecular Evolution 49: 609-614.
(5) Akmaev, V.R., S.T. Kelley and G.D. Stormo. (1999) A phylogenetic approach to RNA structure prediction. Intelligent Systems for Molecular Biology 1999 Proceedings:10-7.
(6) Ramey, R.R., S. T. Kelley, W.M. Boyce and B.D. Farrell. (2000). Phylogeny and host specificity of Psoroptic mange mites (Acarina: Psoroptidae) as indicated by ITS sequence data. Journal of Medical Entomology 37:791-6.
(7) Kelley, S.T., B.D. Farrell and J.B. Mitton. (2000) Effects of specialization on genetic differentiation in sister species of bark beetles. Heredity 84: 218-227.
(8) Scott, V.L., S.T. Kelley and K. Strickler. (2000) Reproductive biology of two Coelioxys parasites in relation to their Megachile hosts (Hymenoptera: Megachilidae). Annals of the Entomological Society of America 93: 941-948.
(9) Akmaev, V.R., S.T. Kelley and G.D. Stormo. (2000) Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics 16: 501-512.
(10) Kelley, S.T., V.R. Akmaev and G.D. Stormo. (2000) Improved statistical methods reveal direct interactions between 16S and 23S ribosomal RNA. Nucleic Acids Research 28: 4938-4943.
(11) Kelley, S.T., J.K. Harris and N.R. Pace. (2001) Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities. RNA 7: 1310-1316.
(12) J.K. Harris, S.T. Kelley., G.B. Spiegelmam and N.R. Pace. (2003) The genetic core of the universal ancestor. Genome Research 13:407-412.
(13) Kelley, S.T., U. Theisen, L.T. Angenent, A. St Amand and N.R. Pace. (2004) Molecular analysis of shower curtain biofilm microbes. Applied and Environmental Microbiology 70:4187-92.
(14) Harris, J.K., S.T. Kelley and N.R. Pace. (2004) New perspective on uncultured bacterial phylogenetic division OP11. Applied and Environmental Microbiology 70:845-9.
(15) Breitbart, M., B. Felts, S.T. Kelley, J.M. Mahaffy, J. Nulton, P. Salamon and F. Rohwer. (2004) Diversity and population structure of a near-shore marine-sediment viral community. Proceedings of the Royal Society of London Series B Biological Science 271:565-74
(16) Angenent, L.T., S.T. Kelley, A. St. Amand, N.R. Pace and M.T. Hernandez. (2005) Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proceedings of the National Academy of Sciences USA 102: 4860-65.
(17) Marquez, S.M., J.K. Harris, S. T. Kelley, J.W. Brown, S.C. Dawson, E.C. Roberts, and N.R. Pace. (2005) Structural implications of novel diversity in eucaryal RNase P RNA. RNA 11:739-751.
(18) McManus, C.J. and S.T. Kelley. (2005) Molecular survey of aeroplane bacterial contamination. Journal of Applied Microbiology 99: 502-6.
(19) Jensen J.L., A.J. Bohonak and S.T. Kelley. (2005) Isolation by Distance, Web Service. BMC Genetics  6:13-6
(20) Ellis, D.G., R.W. Bizzoco, Y. Maezato, J.N. Baggett, J.N. and S. T. Kelley. (2005) Microscopic  Examination  of Acidic Hot Springs of  Waiotapu, North Island, New Zealand. New Zealand Journal of Marine and Freshwater Research 39:1001-11.
Abstract link:  http://www.rsnz.org/publish/nzjmfr/2005/082.php
(21) Kelley S.T., E.F. Cassirer, G.C. Weiser and S. Safaee. (2006) Phylogenetic Diversity of Pasteurellaceae and Horizontal Gene Transfer of Leukotoxin in Wild and Domestic Sheep. Infection, Genetics and Evolution 7:13-23.
(22) Nguyen, T.X., E.R. Alegre and S.T. Kelley. (2006) Analysis of General Bacterial Porins: A Phylogenomic Case Study. Journal of Molecular Microbiology and Biotechnology 11:291-301.
(23) Safaee, S., G.C. Weiser, E.F. Cassirer, R.R. Ramey and S.T. Kelley. (2006) Microbial diversity in bighorn sheep revealed by culture-independent methods. Journal of Wildlife Diseases 42:545-555.
(24) Angly, F.E…, S.T. Kelley (9th of 18),.. and F. Rohwer. (2006) Marine Viromes of Four Oceanic Regions. Public Library of Science (PLoS) Biology 11: 2121-2131.
(25) Lozupone, C.A., M. Hamady, S.T. Kelley and R. Knight. (2007) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Applied and Environmental Microbiolog, 73: 1576-1585.
(26) Mathur, J., R.W. Bizzoco, D.G. Ellis, D.A. Lipson, A. Poole, R. Levine and S.T. Kelley. (2007) Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs. Applied and Environmental Microbiology 73: 2612-2623.
(27) Lee, L., S. Tin and S.T. Kelley. (2007) Culture-independent analysis of bacterial diversity in a child-care facility. BMC Microbiology 7: 27.
(28) Thackray, L.B., C.E. Wobus, K.A. Chachu, B. Liu, E.R. Alegre, K.S. Henderson, S.T. Kelley andH.W. Virgin. (2007) Murine noroviruses comprising a single genogroup exhibit biological diversity despite limited sequence divergence. Journal of Virology 81: 10460-10473.
(29) Townsend T.M., E.R. Alegre, S.T. Kelley, J.J. Wiens, T.W. Reeder. (2008) Rapid Development of Multiple Nuclear Loci for Phylogenetic Analysis Using Genomic Resources. Molecular Phylogenetics and Evolution 47: 129-142.
(30) Ellis, D., R.W. Bizzoco, and S.T. Kelley. (2008) Halophilic Archaea identified in fumarole steam vapor from vents around the world. Environmental Microbiology 10: 1582-1590.
(31) Desnues, C.D., B. Rodriguez-Brito, S. Rayhawk, S.T. Kelley, T. Tran, Matthew Haynes, H. Liu, D. Hall, F.E. Angly, R.A. Edwards, R.V. Thurber, P. Reid, J. Siefert, V. Souza, M. Breitbart, and F. Rohwer. (2008) Endemism of phages in modern stromatolites and thrombolites. Nature 452: 340-343.
(32) Lutz, K., N. Diaz, R.A. Edwards, F. Rohwer, S.T. Kelley, and J. Stoye. (2008) Taxonomic classification of short environmental DNA fragments. Nucleic Acids Research 36: 2230-2239.
(33) Breitbart, M., M. Haynes, S.T. Kelley, F. Angly, R.A. Edwards, B. Felts, J.M. Mahaffy, J. Mueller, J. Nulton, S. Rayhawk, B. Rodriguez-Brito, P. Salamon, and F. Rohwer. (2008) Viral diversity and dynamics in an infant gut. Research in Microbiology 5: 367-373.
(34) Kelley, S.T., C. Alger, and D. Deutschman. (2008) Extreme Programming in a Bioinformatics Class. Bioscene 35: 58-65.
(35) Holzman, J.P., A.J. Bohonak, L.R. Kirkendall, and S.T. Kelley. (2009) Inbreeding variability and population structure in the haplodiploid palm-seed borer beetle (Coccotrypes dactyliperda). Journal of Evolutionary Biology, 22:1076-1087
(36) Turner, J. L., S.T. Kelley, J.S. Otto, F. Valafar, and A.J. Bohonak. (2009) Parallelization and optimization of genetic analyses in isolation by distance web service. BMC Genetics, 10:28.
(37) Gottlieb, D., J.P. Holzman, Y. Lubin, A. Bouskila, S.T. Kelley, and A.R. Harari. (2009) Mate availability contributes to maintain the mixed-mating system in a scolytid beetle. Journal of Evolutionary Biology, 22: 1526-1534.
(38) J. Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K. Goodrich, Jeffrey I. Gordon, Gavin A. Huttley, Scott T. Kelley, Dan Knights, Jeremy E. Koenig, Ruth E. Ley, Catherine A. Lozupone, Daniel McDonald, Brian D. Muegge, Meg Pirrung, Jens Reeder, Joel R. Sevinsky, Peter J. Turnbaugh, William A. Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7: 335–336.
Abstract (39) J. Kuczynski, E.K. Costello, D.R. Nemergut, J. Zaneveld, C.L. Lauber, D. Knights, O. Koren, N. Fierer, S.T. Kelley, R.E. Ley, J.I. Gordon, R. Knight. (2010) Direct sequencing of the human microbiome readily reveals community differences. Genome Biology, 11:210.
(40) Casas, V., J. Magbanua, G. Sobrepena, S.T. Kelley and S. Maloy. (2010) Reservoir of Bacterial Exotoxin Genes in the Environment. International Journal of Microbiology, DOI:10.1155/2010/754368.
(41) Kelley, S.T. and S. Dobler. (2011) Comparative analysis of gut microbial community diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae). Genetica, 139: 541-550.
(42) Knights D., J. Kuczynski, O. Koren, R.E. Ley, D. Field, R. Knight, T.Z. DeSantis, and S.T. Kelley. (2011) Supervised classification of microbiota mitigates mislabeling errors. The ISME Journal, 5: 570-573.
(43) Benson, C.A., R.W. Bizzoco, D.L. Lipson, and S.T. Kelley. (2011) Microbial diversity in Non-sulfur, Sulfur and Iron geothermal steam vents. FEMS Microbial Ecology, 76:74-88.
(44) Caporaso, J.G., R. Knight, and S.T. Kelley. (2011) Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition. PLoS ONE, 6:e16900.
(45) Tin, S., R.W. Bizzoco and S.T. Kelley. (2011) Role of the terrestrial subsurface in shaping geothermal spring microbial communities. Environmental Microbiology Reports, 3:491-499.
(46) Yilmaz, P., … S.T. Kelley (48th of 96) … and F.O. Glöckner. (2011) The “Minimum Information about a MARKer gene Sequence” (MIMARKS) specification. Nature Biotechnology, 29:415-420.
(47) Wehausen, J.D., S.T. Kelley, R.R. Ramey. (2011) Domestic sheep, bighorn sheep, and respiratory disease: a review of the experimental evidence. California Fish and Game, 97:7-24.
(48) Knights , D., J. Kuczynski , E.S. Charlson , J. Zaneveld , M.C. Mozer, R. Collman , F. Bushman , R. Knight and S.T. Kelley. (2011) Bayesian community-wide culture-independent microbial source tracking. Nature Methods, 8:761–763.
(49) Benson, C.A., R.W. Bizzoco, D.A. Lipson and S.T. Kelley. (2011) Microbial diversity in non-sulfur and iron geothermal steam vents. Yellowstone Science, 20: 5-6.
(50) Abubucker, S., N. Segata, J. Goll, A.M. Schubert, J. Izard, B.L. Cantarel, B. Rodriguez-Mueller, J. Zucker, M. Thiagarajan, B. Henrissat, O. White, S.T. Kelley, B. Methé, P. D Schloss, D. Gevers, M. Mitreva, C. Huttenhower. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Computational Biology, In Press.