Silveira C. B., F. H. Coutinho, G. Cavalcanti, A. C. Soares, G. G. Z. Silva, V. A. Cantu, M. Doane, B. Knowles, R. B. Francini-Filho, C. C. Thompson, E.A. Dinsdale, G. B. Gregoracci, F. Rohwer, F. Thompson. 2017 Bacteriophage genomic signatures and transfer of bacterial virulence genes in coral reefs. Frontiers in Microbiology 8:784

Silveira, C. B., G. S. Cavalcanti, J. Walter, A. W. Silva-Lima, E.A. Dinsdale, D. Bourne, C. C. Thompson, F. L. Thompson 2017 Microbial processes driving coral reef organic carbon flow. FEMS Microbiology Reviews doi: 10.1093/femsre/fux018

Andrade, A. C. A. Fróes, F. Álvares Cardoso Lopes, F. L Thompson, R. Henrique Krüger, E. Dinsdale, T. Bruce 2017 Diversity of microbial Carbohydrate-Active enZYmes (CAZYmes) associated with freshwater and soil samples from Caatinga BiomeMicrobial Ecology 1-17

Walsh, K, J.M. Haggerty, J. Spangler, M.B. Turner, C. Lee, G. Amado-Filho, R. Francini-Filho, C.B. Silveira, R. L. Moura, TT. Harkins, R. A. Edwards, F.L. Thompson, and E. A. Dinsdale 2017 Aura-biomes are present in the water layer above coral reef benthic macro-organisms. Peer J DOI 10.7717/peerj.3666

Doane, M.P. J. M. Haggerty, D. Kacev, B. Papudeshi, E. A. Dinsdale. 2017 The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and gene functional β-diversity. Environmental Microbiology Reports

Morris Megan M., Haggerty John M., Papudeshi Bhavya N., Vega Alejandro A., Edwards Matthew S., Dinsdale Elizabeth A 2016 Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera. Frontiers in Microbiology. doi: 10.3389/fmicb.2016.01800

Haggerty, J. M. and E. A. Dinsdale 2016 Distinct Biogeography and Evolution of Marine Microbial Taxonomy and Function. Journal of Global Ecology and Biogeography. DOI: 10.1111/geb.12528

Haas, A.F., M F. M. Fairoz, L W. Kelly, C E. Nelson, E. A. Dinsdale, R. A. Edwards, S. Giles, M. Hatay, N. Hisakawa, B. Knowles, Y. W. Lim, H. Maughan, O. Pantos, T. Roach, S. E. Sanchez, C. B. Silveira, S. Sandin, J. E. Smith, and F. Rohwer. 2016 Global microbialization of coral reefs. Nature Microbiology doi:10.1038/nmicrobiol.2016.42

Knowles B, Silveira CB, Bailey BA, Barott K, Cantu A, Cobián-Güemes AG, Coutinho FH,Dinsdale E, Felts B, Furby KA, George EE, Green KT, Gregoracci GB, Haas AF, Haggerty JM, Hester ER, Hisakawa NG, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, de Oliveira LS5, Quistad SD, Robinett NL, Sala E, Salamon P, Sanchez SE, Sandin S, Silva GGZ, Smith J, Sullivan C, Thompson C, Vermeij MJA, Youle M, Young C, Zgliczynski B, Brainard R, Edwards RA, Nulton J, Thompson F, Rohwer F. Lytic to Temperate Switching of Viral Communities. Nature. 531: 466-470

Haas, A.F., M. Guibert, A. Foerschner, T. Co, S. Calhoun, E. George, M. Hatay, E.A. Dinsdale, S. Sandin, J.E. Smith, M. Vermeij, B. Felts, P Dustan, P Salamon and F Rohwer 2015 Computational evaluation of coral reef aesthetics.Peer J DOI 10.7717/peerj.1390

Dinsdale, E.A., S.C.R. Elgin, N Grandgenett, W. Morgan, A. Rosenwald, W. Tapprich, E.W. Triplett and M.A. Pauley 2015 NIBLSE: A Network for Integrating Bioinformatics into Life Sciences Education. CBE–Life Sciences Education.December 1, 2015 14:le3; doi:10.1187/cbe.15-06-0123

Meirelles, PM, G.M. Amado-Filho, G.H. Pereira-Filho, H.T. Pinheiro, R.L. de Moura, J. C. Joyeux, E.F. Mazzei, A. C. Bastos, R.A. Edwards, E. Dinsdale, R. Paranhos, E. O. Santos, T. Iida, K. Gotoh, S. Nakamura, T. Sawabe, C. E. Rezende, L. M. R. Gadelha, R. B. Francini-Filho, C. Thompson, F. L. Thompson 2015 Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data. PLOS ONE 10.1371/journal.pone.0130084.

Busch, J.C., Rubem Magalhães, A., J. Ribeiro do Nascimento, E. A. Dinsdale 2015 Copper tolerance of microbes associated with Macrocystis pyrifera across three southern Californian locations. Ecotoxicology 1-10

Matthews, D.  R. Schmieder, G. G Silva B. Matlock,  D. Green, N. Cassman, J. Busch, B. Heffern, G. Olsen, L. Hanna, D. Schifferli S. Maloy, E. A. Dinsdale R.A. Edwards 2015 Genomic Comparison of the Closely-related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum PLoS ONE 10.1371/journal.pone.0126883.

Cuevas, D.A., D. Garza, S. E. Sanchez, J. Rostron, C. Henry, V. Vonstein, R. A. Overbeek, F. Rohwer, E.A. Dinsdale, R. A. Edwards 2014 Elucidating Genomic Gaps using Phenotypic Profiles.Foundation 1000

Lim YW, Cuevas DA, Silva GGZ, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez* SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJA, Rohwer F, Edwards RA. 2014 Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ 2:e520.

Dutilh, B.E., N. Cassman, K. McNair, L. Boling, S. Sanchez, M. Wellington-Oguri, J.J. Barr, R.K. Aziz, B. Felts, JL. Mokili, E.A. Dinsdale, RA. Edwards 2014. Ubiquitous phage genome and host identified by depth profiling across metagenomes. Nature Communications. 5: 4498. doi:10.1038/ncomms5498

Dutilh, B., Thompson, C., Vicente, A., Marin, M., Lee, C., Silva, G., Schmieder, R., Andrade, B., Chimetto, L., Cuevas, D., Garza, D., Okeke, I., Aboderin, O., Spangler, J., Ross, T., Dinsdale, E.A., Thompson, F., Harkins, T., and Edwards, R. 2014. Genomic landscape of Vibrio cholerae connects genotype and phenotype across time, space and habitat. BMC genomics 15 (1), 65.

Wegley Kelly, L., G.J. Williams, K.L. Barott, C.A. Carlson, E.A. Dinsdale,R.A. Edwards, A. F. Haas, M. Haynes, Y. W. Lim, T. McDole, C. E. Nelson, E. Sala, S. A. Sadin, J. E. Smith, M. J.A. Vermeij, M. Youlei, and F. Rohwer 2014Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy doi: 10.1073/pnas.1403319111

Mark Eppinger, Katelyn McNair, Xhavit Zogaj, Elizabeth Dinsdale, Robert Edwards, and Karl 2013 Whole Genome Draft Sequence of the fish pathogen Piscirickettsia salmonis” (genomeA00926-13). doi:10.1128/genomeA.00926-13

Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA 2013 Combining de novo and reference-guided assembly with scaffold_builderSource Code Biol Med , 8:23. doi: 10.1186/1751-0473-8-23

Edwards, R. A., J.M. Haggerty, N. Cassman, J. C. Busch, K. Aguinaldo$, S. Chinta, R. Morey, M. Houle Vaughn, T.T. Harkins, C. Teiling, K. Fredrikson, and E. A Dinsdale 2013 Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics 14:600.

Lipson, D. A., J.M. Haggerty, A. Srinivas, S. Sathe, T. K. Raab, E. A. Dinsdale. 2013 Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. Plos One 8(5): e64659. doi:10.1371/journal.pone.0064659

Dinsdale, E. A., R. A. Edwards, B. Bailey, I. Tuba, S. Akhter, K. McNair, R. Schmieder, N. Apkarian, M. Creek, E. Guan, M. Hernandez, K. Isaacs, C. Peterson, T. Regh, V. Ponomarenko. 2013 Multivariate analysis of functional metagenomes. Frontiers in Genetics 4:41. doi: 10.3389/fgene.2013.00041

Haggerty, J.M. M.N. Brett, R. B. Francini Filho, E. A. Dinsdale. 2012 Night surveys along  the Abrolhos Bank, Brazil, generate first observation of mucous cocoon production in Scarus trispinosus.  Bulletin of Marine Science, 88(4):883-88.

Cassman, N.,  Prieto-Davó, A. F. Angly, S. Akhter, K Barott, J. Busch, T. McDole, J. M. Haggerty, K. Walsh, G. G. Z. Silva, B, Dutilh, G. Alarcón, O. Ulloa, E. F. DeLong, F. Rohwer, E. A. Dinsdale. 2012 Oxygen minimum zones harbor novel but low diversity viral communities. Environ Microbiol. doi:10.1111/j.1462-2920.2012.02891.

Bruce T, P. M. Meirelles, G. Garcia, R. Paranhos, C. E. Rezende, R. L. de Moura, R. Francini Filho, A. Tereza Vasconcelos, G. Amado Filho, M. Hatay, R. Edwards, R. Schmieder, E.A Dinsdale and F. L. Thompson 2012 Abrolhos Reef Bank health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomassPLoS One.  2012; 7(6):e36687

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2012 Assembly rules of reef corals are flexible along a steep climate gradient. Current Biology 22:1-6 Citations – 11 DOI: 10.1016/j.cub.2012.02.068

Hanna, F.L.A, T.D. Matthews, EA Dinsdale, R, Hasty, RA Edwards, 2012  Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis strain LK5. Appl Environ Microbiol  12:1785-1793

Wegley Kelly, L., K. L. Barott, E. A. Dinsdale, B. Nosrat, D. Obura, S. Sandin, J. E. Smith, D. Willner, and F. Rohwer 2011 Black Reefs: Iron induced phase shifts on coral reefs. ISME J   6: 638–649 Citations – 7 DOI: 10.1038/ismej.2011.114

Jeffries, T.C., J. R. Seymour, E. A. Dinsdale, K. Newton, S. S.C. Leterme, B. Roudnew, R. J. Smith, J. A. Gilbert, L. Seuront, J. G. Mitchell 2011 Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS One  10.1371

Barott, K.L, J. E. Caselle, E. A. Dinsdale, A. M. Friedlander, J. E. Maragos, D. Obura, F. L. Rohwer, S. A. Sandin, J. E. Smith, and B. Zgliczynski 2010 The Lagoon at Caroline/Millennium Atoll, Republic of Kiribati: Natural history of a nearly pristine ecosystem. PLoS One 2010; 5(6): e10950.

Raina, J.B, E.A. Dinsdale, B. L. Willis and D. G. Bourne 2010 Do organic sulfur compounds DMSP and DMS drive coral microbial associations? Trends Microbiol 18: 101-108

Rodriguez-Brito, B., L.Li, L. Wegley, M. Furlan, F. Angly, M. Breitbart, J. Buchanan, C. Desnues, E. A. Dinsdale, R. Edwards, B. Felts, D. Willner, M. Haynes, H. Liu, D. Lipson, J Mahaffy, A-B. Martin-Cuadrado, A. Mira-Obrador, J. Nulton, L. Pasic, S. Rayhawk, J. Rodriguez-Mueller, F. Rodriguez-Valera, P. Salamon, S. Srinagesh, T. Frede Thingstad, R. Vega Thurber, T. Tran, F. Rohwer 2010 Kill-the-winner in four aquatic environments. ISME J   11 doi:10.1038/ismej.2010.

Dinsdale, E.A. 2009 Linking ecological and perceptual assessments for environmental management: a coral reef case study. Ecology and Society 14(2): 28. [online] URL:

Barott K, Smith J, Dinsdale E, Hatay M, Sandin S, et al. 2009 Hyperspectral and physiological analyses of coral-algal interactions. PLoS One  4(11):e8043. doi:10.1371/journal.pone.0008043

Angly, FE, D. Willner, A. Prieto-Davo, R. A. Edwards, R. Schmieder, R. Vega Thurber, D. A. Antonopoulos, K. Barott, M.T. Cottrell, C. Desnues, EA. Dinsdale  M Furlan, M. Haynes 1, M. R. Henn, Y. Hu, D L. Kirchman, T McDole, J. D. McPherson, F. Meyer, R. M. Miller, E. Mundt, R. K. Naviaux, B. Rodriguez-Brito, R Stevens, L. Wegley, L. Zhang and B. Zhu, F. Rohwer 2009 The GAAS Metagenomic Tool and its Estimations of Viral and Microbial Average Genome Size in Four Major BiomesPLoS Comput Biol  5: 12 Number: e1000593

Breitbart, M, A. Hoare, A. Nitti, J. Siefert, M. Haynes, E.A. Dinsdale, R.A. Edwards, V. Souza, F. Rohwer, D. Hollander 2009Microbial communities and stable isotopic analyses of modern microbialites in Cuatro Ciénegas, Mexico. Environ Microbiol  11:16- 34

Brulc J M., D.A. Antonopoulos, M.E. Berg, M.K. Wilson, A.C. Yannarell, E.A. Dinsdale, R.A. Edwards, E.D. Frank, J.B. Emerson, P. Wacklin, P.M. Coutinho, B. Henrissat, K.E. Nelson, and B.A. White 2009 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106:1948-1953

Vega Thurber R., D. Hall-Willner, B. Rodriguez-Brito, C. Desnues, R.A. Edwards, F. Angly, E.A. Dinsdale, L. Kelly, and F. Rohwer. 2009 Metagenomic Analysis of Stressed Coral Holobionts Environ Microbiol   11: 2148–2163

Dinsdale, E.A., R.A. Edwards, D. Hall, F. Angly, M. Breitbart, J.M. Brulc, M. Furlan, C. Desnues, M. Haynes; L. Li, L. McDaniel, M.A. Moran, K.E. Nelson, C. Nilsson, R. Olson, J. Paul, B. Rodriguez Brito, Y. Ruan, B.K. Swan, R. Stevens, D. L. Valentine, R. Vega Thurber, L. Wegley, B.A. White, and F. Rohwer 2008 Functional metagenomic profiling of nine biomes. Nature   452:629-632

Dinsdale, E.A. and F. Rohwer 2008 Dissecting microbial employment. Nat Biotechnol   26:997-998

Dinsdale, E.A., O. Pantos, S. Smriga, R.A. Edwards, L. Wegley, F. Angly, E. Brown$, M. Haynes, L. Krause, E. Sala, S. Sandin, R. Vega Thurber, B.L. Willis, N. Knowlton, F. Azam, and F. Rohwer. 2008. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One   3(2) e1584

Sandin, S., J.E. Smith, E. DeMartini, E.A. Dinsdale, A. Friedlander, J.B.C. Jackson, N. Knowlton, M. Malay, J. Maragos, D. Obura, G. Paulay, M. Richie, S. Walsh, E. Sala. 2008 Degradation and recovery of coral reefs across a gradient of human disturbance.PloS One 3(2) e1548

Qu, A, J.M Brulc, M.K. Wilson, B.F. Law, J.R. Theoret, L.A. Joens, M.E. Konkel, F. Angly, E.A. Dinsdale, R.A. Edwards, K.E. Nelson, and B.A. White 2008. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3(8): e2945

Edwards R.A. and Dinsdale E.A. 2007 Marine environmental genomics: unlocking the oceans secrets. Oceanography 20:56-61

Dinsdale E.A. and D.M. Fenton 2006 Assessing coral reef condition: eliciting community meanings. Society and Natural Resources 19: 239-295

Dinsdale E.A., and Harriott V.J. 2004 Assessing anchor damage on coral reefs: a case study in selection of environmental indicators. Environ Manage  33: 126-139

Hughes T.P, A.H. Baird, E.A. Dinsdale, V.J. Harriott, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2002 Latitudinal patterns in larval recruitment: Detecting regional variation using meta-analysis and large-scale sampling.Ecology 83:436-541[0436:DRVUMA]2.0.CO;2

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2000 Supply side ecology in reverse: The link between adults, fecundity and larval recruits. Ecology 81:2241-2249

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 1999 Patterns of recruitment and abundance of corals along the Great Barrier Reef. Nature 397:59-63

In Review
Walsh, K, J.M. Haggerty, J. Spangler, M.B. Turner, C. Lee, G. Amado-Filho, R. Francini-Filho, C.B. Silveira, R. L. Moura, TT. Harkins, R. A. Edwards, F.L. Thompson, and E. A. Dinsdale 2014 Macro-organism Influence on Coral Reef Microbial Communities. Molecular Ecology
Book Chapters 

Minich, J.J. and E. A. Dinsdale 2013 Experimental metagenomics: Experimental metagenomics: Influence of pulses of carbon dioxide on kelp forest microbial ecology. In Nelson, K. (ed) Encyclopedia of metagenomics. Springer

Dinsdale, E.A. and F. Rohwer 2010 Fish or Germs? A microbial perspective on changing trophic structure on coral reefs. Chapter 16, Coral Reef: an ecosystem in transition. In Press (ed) Z. Dubinski, Springer-verlag.

Dinsdale, E. A. 2011 Microbes. Pages 697-698 in D. Hopley (ed) Encyclopedia of Modern Coral Reefs: Structure, Form and Process. Springer-Verlag

Willis, B.L. C. Page, D. Bourne, L. Owens, S. Anthony, H. Boyett, E.A. Dinsdale, D. Harvell, D. Jacobson, C. Lonergan, S. Neale, C. Palmer, L. Raymundo, M. Sussman 2009 Coral disease on the Great Barrier Reef and in the Western Pacific. Pages 234-243 in Galloway, S.B., Bruckner,

A.W. and Woodley, C.M. (eds.), 2009. Coral Health and Disease in the Pacific: Vision for Action. NOAA Technical Memorandum NOS NCCOS97 and CRCP 7. National Oceanic and Atmospheric Administration, Silver Spring, MD

Willis B.L., C. Page and E.A. Dinsdale 2004 Coral disease in the Indo-Pacific. Pages 69-104. Loya Y. and R. Rosenberg (eds) Coral health and disease. Springer-verlag.