Rosales, S.M, Huebner, L.K., Evans, J.S., Apprill, A., Baker, A.C., Bellantuono, A.J., Brandt, M.E., Clark, A.S., del Campo, J., Dennison, C.E., Huntly, N.E., Kellog, C.A., Medina, M., Meyer, J.L., Muller, E.M., Rodriguez-Lanetty, M., Salerno, J.L., Schill, W.B., Shilling, E.N., Stewart, J., Voss, J.D. (in review). A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in lesions and unaffected tissue of diseased colonies. ISME J.

Pavlopoulos, G.A, Baltoumas, F.A., Liu, S., Selvitopi, O., Nayfach, S., Azad, A., Call, L., Camargo, A.P., Ivanova, N.N., Chen, I.M., Paez-Espino, D., Karatzas, E, Novel Metagenome Protein Families Consortium (including Medina), Iliopoulos, I., Konstantinidis, K., Tiedje, J.M., Visel, A., Baker, D., Ouzounis, C.A., Ovchinnikov, S., Buluc, A., Kyrpides, N. (in review). Discovery, diversity and distribution of functional dark matter through global metagenomics.

Simpson, S., Bettauer, V., Ramachandran, A., Kramer, S., Mahon, S. Medina, M., Valles, Y., Dumeaux, V., Valles, H., Walsh, D., Hallet, M.T. (in review). A metagenomic-based study of two sites from the Barbadian reef system. Coral Reefs BioRxiv. doi: 1101/2021.01.02.425083

Tandon, K., Ricci, F., Costa, J., Medina, M., Kuhl, M., Blackall, L., Verbruggen, H. (in review). Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera. doi: 21203/rs.3.rs-1890655/v1

Shantz, A.A., Lopez, T., Gomez-Campo, K., Iglesias-Prieto, R., Lopez-Victoria, M., Medina, M. (in review). The declining role of herbivory in structuring a heavily impacted urban coral reef. doi: 21203/rs.3.rs-901931/v1

Ohdera, A., Attarwala, K., Rubain H., Laird, H., Fitt, W., Medina, M.  (in review). Comparative genomic insights into bacterial induction of larval settlement and metamorphosis in the upside-down jellyfish BioRxiv doi: 10.1101/2022.06.24.497576

Neri, U., Wolf, Y.I., Roux, S., Camargo, A., Lee, B., Kazlauskas, D., Chen, I.M., Ivanova, N.N., Zigler, L., Paez-Espino, D., Bryant, D.A., Bhaya, D., RNA Virus Discovery Consortium (including Medina), Krupovic, M., Dolja, V.V., Kyrpides, N.C., Koonin, E.V., Gophna, U. (in review). A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages. BioRxiv doi: 10.1101/2022.02.15.480533

López-Londoño, T. Gómez-Campo, K., Galindo-Martínez, C.T., González-Guerrero, L.A., Roitman, S., Pollock, J.F., López-Victoria, M., Medina, M., Iglesias-Prieto, R. (in press). Sobrevivencia y ajustes fisiológicos de corales expuestos a elevada turbidez en el arrecife Varadero, Caribe colombiano. Investigaciones Marinas y Costeras

Puntin, G., Sweet, M., Fraune, S., Medina, M., Sharp, K., Weis, V.M., Ziegler, M. (in press). Harnessing the power of model organisms to unravel microbial functions in the coral holobiont. MMBR

Traylor-Knowles, N., Baker, A.C., Beavers, K.M., Garg. N., Guyon, J.R., Hawthorn, A., MacKnight, N.J., Medina, M., Myrdlaz, L., Peters, E.C., Stewart, J.M., Studivan, M.S., Voss, J.D. (2022). Advances in Immunity ‘Omics in response to coral disease outbreaks’. Mar. Sci. 9:952199. doi: 10.3389/fmars.2022.952199

Diaz-Almeyda, E.M., Ryba, T., Ohdera, A.H., Collins, S.M., Shafer, N., Link, C., Prado-Zapta, M., Ruhnke, C., Moore, M., Gonzalez-Angel, A.M., Pollock, F.J., Medina, M. (2022). Thermal stress has minimal effects on bacterial communities of thermotolerant Symbiodinium Frontiers in Ecology and Evolution 20: 764086. doi: 10.3389/fevo.2022.764086

Prada, C., López-Londoño, T., Pollock, J.P., Roitman, S., Ritchie, K., Woodley, C., Levitan, D., Knowlton, N., Iglesias-Prieto, R., Medina, M. (2022). Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals. Proceedings of the Royal Society Series B. 9: 211591. doi: 1098/rsos.211591

Galindo-Martinez, C.T., Weber, M., Avila-Magaña, V., Enriquez, S., Kitano, H., Medina, M., Iglesias-Prieto, R. (2022). The role of the endolithic alga Ostreobium during coral bleaching recovery. Scientific Reports 12:2977. doi: 10.1038/s41598-022-07017-6

Medina M, Baker DM, Baltrus DA, Bennett GM, Cardini U, Correa AMS, Degnan SM, Christa G, Kim E, Li J, Nash DR, Marzinelli E, Nishiguchi M, Prada C, Roth MS, Saha M, Smith CI, Theis KR and Zaneveld J (2022) Grand Challenges in Coevolution. Front. Ecol. Evol.  PDF


Ohdera, A.H., Avila-Magaña, V., Sharp, V., Watson, K., Darymple, J., Steinworth, B., Diaz-Almeyda, E.M., Kitchen, S.A., Poole, A.Z., Bellantuono, A., Haridas, S., Grigoriev, I., Goentoro, L., Vallen, E., Baker, D.M., LaJeunesse, T.C., Martindale, M.Q., DeGennaro, M., Fitt, W.K., Medina, M. (in review). Symbiosis drives development in the upside-down jellyfish Cassiopea xamachana. PDF

Avila-Magaña, V., Kamel, B., DeSalvo, M., Gómez-Campo, K., Enríquez, S. Kitano, H., Rohlfs, R., Iglesias-Prieto, R., Medina, M. (in press). Elucidating the adaptive potential of coral holobionts under thermal stress. Nature Communications. PDF

Lopez, T., Galindo-Martinez, C.T., Gomez-Campo, K., Gonzalez-Guerrero, L.A., Roitman, S., Pollock, F.J., Pizarro, V., Lopez-Victoria, M., Medina, M., Iglesias-Prieto, R. (2021). Degradation of the underwater light environment: physiological and ecological consequences for reef corals. Coral Reefs. Doi: 10.1007/s00338-021-02133-7

Sweet, M., Villela, H., Keller-Costa, T., Costa, R., Romano, S., Bourne, D., Cardenas, A., Huggett, M., Kerwin, A.,  Kuek, F., Medina, M., Meyer, J., Müller, M., Pollock, J., Rappe, M., Séré, M., Sharp, K., Voolstra, C., Zaccardi, N., Ziegler, M., Peixoto, R. (2021) Insights into the cultured bacterial fraction of corals. mSystems doi: 10.1128/mSystems.01249-20.PDF

Dittami, S.M., Arboleda, E., Auguet, J.C., Bigalke, A., Briand, E., Cardenas, P., Cardini, U., Decelle, J., Engelen, A.H., Eveillard, D., Gachon, C.M.M., Griffiths, S.M., Harder, T., Kayal, El, Kazamia, E., Lallier, F.H., Medina, M., Marzinelli, E.M., Morganti, T., NuNez Pons, L., Prado, S., Pintado Valverde, J., Saha, M., Selosse, M.A., Skillings, D., Stock, W., Sunagawa, S., Toulza, E., Vorobev, A., Leblanc, C., Not, F. (2021). A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJPDF

Iha, C., Varela, J.A., Avila, V., Jackson, C.J., Bogaert, K.A., Chen, Y., Judd, L.M., Wick, R., Holt, K.E., Pasella, M.M., Ricci, F., Repetti, S.I., Medina, M., Marcelino, V.R., Chan, C.X., Verbruggen, H. (2021). Genomic adaptations to an endolithic lifestyle in the coral-associated alga OstreobiumCurrent Biology 31(1-10).PDF

Book chapter:

Medina, M., Ohdera, A., Bellantuono, A., Dalrymple, J., Gamero-Mora, E., Sharp, V., Steinworth, B., Hogmann, D.K., Martindale, M.Q., Morandini, A.C., DeGennaro, M., Fitt, W.K. (in press). The Upside-down Jellyfish Cassiopea xamachana as an emerging model system to study cnidarian-algal symbiosis. In Established and Emerging Organisms in Experimental Biology. Boutet A. And Shierwater B. CRC Press.PDF

Rouzé, H. GalandP.E., Medina, M., Raina, J.B., Bongaerts, P., Pichon, M., Perez-Rosales, G., Torda, G., Moya, A., UTP III Team, Hédouin, L. (2021). Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth). ISMEJ doi: Dio:


Nayfach, S., Roux, S. Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I-M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T.B.K., Nielsen, T., Kirton, E., Faria, J.P., Edirisinghe, J.N., Henry, C.s., Jungblkuth, S. P., Chician, D., Dehal, P., Wood-Charlson, E.M., Arkin, A.P., Tringe, S., Visel, A., IMG/M Data Consortium*, Woyke, T., Mouncey, N.J., Ivanova, N.N., Kyrpides, N.C., Eloe-Fadrosh, W.A. (2020). A genomic catalog of Earth’s microbiomes. Nature Biotechnology. *including Medina, M. and Avila-Magaña V. doi: 10.1038/s41587-020-0718-6

Cerullo, A., Lai, T.Y, Allam, B., Baer, A., Barnes, W.J.P., Barrientos, Z., Deheyen, D.D., Fudge, D.S., Gould, J., Harrington, M.J., Holford, M., Hung, C.S., Jain, G., Mayer, G., Medina, M., Monge-Nájera, J., Napolitano, T., Espinosa, E.P., Schmind, S., Thomposon, E.M., Braunschweig, A.B., (2020). Comparative animal mucomics: Inspiration for functional materials from ubiquitous and understudied biopolymers. ACS Biomaterials Science & Engineering 6(10):5377-5398. doi:10.1021/acsbiomaterials.0c00713

Roitman, S., López-Londono, T., Pollock, F.J., Ritchie, K.B., Galindo-Martinez, C.T., Gómez-Campo, K., Gonzalez-Guerrero, L.A., Pizarro, V., López-Victoria, M., Iglesias-Prieto, R., Medina, M. (2020). Surviving marginalized reefs: assessing the implications of the microbiome on coral physiology and survivorship. Coral Reefs 39: 795–807 doi: Dio:

vanOppen, M.J.H., Medina, M. (2020). Coral evolutionary responses to microbial symbiosis. Philosophical Transactions Series B. 375:20190591. PDF

Simpson, A.G.B., and Medina, M. (2020). Opisthokonta T. Cavalier-Smith 1987. Converted clade name. in Phylonyms: A Companion to the PhyloCode (K. de Queiroz, P. D. Cantino, and J. A. Gauthier, eds.). CRC Press, Boca Raton, FL.

Silva Lima, A.W., Froes, A.M., Garcia, G.D., Tonon, L.A.C., Swings, J., Cosenza, C.A.N., Medina, M., Penn, K., Thompson, J.R., Thompson, C.C., Thompson, F.L., (2020). Mussismilia braziliensis White Plague Disease is characterized by an affected coral immune system and dysbiosis. Microbial Ecology. Doi: PDF

Silva Lima, A.W., Salomon, P.S., Thompson, J., Medina, M., Thompson, F. (2020). Redox regulation, iron homeostasis and calcium signalling mediates Symbiodinium transcriptomic response to heat stress. Symbiosis 80(2): 183-193. doi:10.1007/s13199-020-00664-1


Ricci, F., Marcelino, V.R., Blackall, L.L., Medina, M., Verbruggen, H. (2019). Beneath the surface: community assembly and functions of the coral skeleton microbiome. Microbiome 7:159. PDF

Ohdera, A., Ames, C.L., Dikow, R.B., Kayal, E., Chiodin, M., Busby, B., La, S., Pirro, S., Collins, A.G., Medina, M., Ryan, J.F. (2019). Box, stalked and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). Giga Science. PDF

Hartmann, A.C., Marhaver. K.L., Klueter, A., Lovci, M., Closek, C.J., Diaz-Almeyda, Chamberland, E.V.F., Archer, F.I., Deheyn, D.D., Vermeij, M.J.A., Medina, M. (2019). Temporally coupled symbiont acquisition and metamorphosis in corals: the right-time right-place hypothesis. Molecular Ecology 28:141–155.

Hartmann, A.C, Marhaver, K.L., Klueter, A., Lovci, M.T., Closek, C.J., Diaz, E., Chamberland, V.F., Archer, F.I., Deheyn, D.D., Vermeij, M.J.A., Medina, M. (2019). Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host. Molecular Ecology 28:141–155. PDF

Lopez, J.V., Kamel, B., Medina, M., Collins, T., Baums, I.B. (2019). Multiple Facets of Marine Invertebrate Conservation Genomics. Annual Review of Animal Biosciences, vol. 7.PDF


Pollock, F.J., McMinds, R., Smith, S., Bourne, D.G., Willis, B.L., Medina, M., Vega Thurber, R., Zaneveld, J. (2018). Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nature Communications 9, Article number: 492. PDF

González, A.M., Prada, C.P., Ávila, V., Medina, M. (2018). Ecological Speciation in corals. In: . Population Genomics. Springer, ChamPDF

Roitman, S., Pollock, F.J., Medina, M. (2018) Coral microbiomes as bioindicators of reef health. In: . Population Genomics. Springer, Cham.PDF

Ohdera, A.H., Abrams, M.J., Ames, C.L., Baker, D.M., Suescún-Bolívar, L.P., Collins, A.G.,  Freeman, C.J., Gamero-Mora, E., Goulet, T.L., Hofmann, D.K., Jaimes-Becerra, A.J., Long, P.F., Marques, A.C., Miller, L.A., Mydlarz, L.D., Morandini, A.C., Newkirk, C.R., Putri, S.P., Samson, J.E., Stampar, SN., Steinworth, B., Templeman, M., Thomé, P.E., Vlok, M., Woodley, C.M., Wong, J.C.Y., Martindale, M.Q., Fitt., W.K., Medina, M. (2018). Upside-Down but Headed in the Right Direction: Review of the Highly Versatile Cassiopea xamachana System.PDF

Guillemette, R., Kaneko, R., Blanton, J., Tan, J., Witt, M., Hamilton, S., Allen, E.E., Medina, M., Hamasaki, K., Koch, B.P., Azam, F. (2018) Bacterioplankton drawdown of coral mass-spawned organic matter. The ISME Journal. PDF


Pizarro, V., Rodríguez, S.C., López-Victoria, M., Zapata, F.A., Zea, S., Galindo-Martínez., C.T., Iglesias-Prieto, R., Pollock, J., Medina, M. (2017)  Unraveling the structure and composition of Varadero Reef, an improbable and imperiled coral reef in the Colombian Caribbean. PeerJ. PDF

Díaz-Almeyda, E.M., Prada, C., Ohdera, A.H.Moran, H., Civitello, D.J., Iglesias-Prieto, R., Carlo, T.A.,  LaJeunesse, T.C., Medina, M. (2017) Intraspecific and interspecific variation in thermotolerance and photoacclimation in Symbiodinium dinoflagellates. Proceedings of the Royal Society Biological Sciences. PDF


Prada, C., Hanna, B., Budd, A. F.., Woodley, C., Schmutz, J., Grimwood, J.,  Iglesias-Prieto, R., Pandolfi, J. M., Levitan, D., Knowlton, N., Kitano, H.,  DeGiorgio, M., Medina, M. (2016) Empty niches after extinctions increase population sizes of modern corals. Current Biology. PDF

Moya, A., Howes, E.L., Lacoue-Labarthe, T., Foret, S., Hanna, B., Medina, M., Munday, P.L., Ong, J.S., Teyssie, J.L., Torda, G., Watson, S.A., Miller, D.J., Bijma, J., Gattuso, J.P. (2016). Near-future pH conditions severely impact calcification, metabolism and the nervous system in the pteropod Heliconoides inflatus. Global Change Biology. PDF

Bhattacharya, D., Agrawal, S., Aranda, M., Baumgarten, S., Belcaid, M., Drake, J.L., Erwin, D., Foret, S., Gates, R.D., Gruber, D.F., Kamel, B., Lesser, M.P., Levy, O., Liew, Y.J., MacManes, M., Mass, T., Medina, M., Mehr, S., Meye, E., Price, D.C., Putnam, H.M., Qiu, H., Shinzato, C., Shogushi, E., Stokes, A.J., Tambutté, S., Tchernov, D., Voolstra, C.R., Wagner, N., Walker, C.W., Weber, A.P.M., Weis, V., Zelzion, E., Zoccola, D, Falkowski, P.G. (2016). Comparative genomics explains the evolutionary success of reef-forming corals. eLIFE. PDF


Baker, E.C., Layden, M.J., van Rossum, D.B., Kamel, B., Medina, M., Simpson, E., Jegla, T. (2015). Functional Characterization of Cnidarian HCN Channels Points to an Early Evolution of Ih. PDF

Pinzón, J.H., Kamel, B., Burge, C.A., Harvell, C.D., Medina, M., Weil, E., Mydlarz, L. (2015). Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral. The Royal Society. PDF

Li, X., Liu, H., Luo, J.C., Rhodes, S.A., Trigg, L.M., van Rossum, D.B., Anishkin, A., Diatta, F.H., Sassic, J.K., Simmons, D.K., Kamel, B., Medina, M., Martindale, M.Q., Jegla, T. (2015). Major diversification of voltage-gated K+ channels occurred in ancestral parahoxozoans. PNAS. PDF

Marhaver, K.L., Vermeij, M.J.A.., Medina, M. (2015). Reproductive natural history and successful juvenile propagation of the threatened Caribbean Pillar Coral Dendrogyra cylindrus. BMC Ecology. PDF

Thompson, J.R., Rivera, H.E., Closek, C.J., Medina, M. (2015). Microbes in the coral holobiont: partners through evolution, development, and ecological interactions. Frontiers in Cellular and Infection Microbiology. PDF


Vue, Z., Kamel, B.S., Capo, T.R., Bardales, A.T., Medina, M. (2014). Comparative analysis of early ontogeny in Bursatella leachii and Aplysia californica. PeerJ. PDF

Green, E., Davies, S., Matz, M., Medina, M. (2014). Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ. PDF

Closek C.J., Sunagawa, S., DeSalvo, M.K., Piceno, Y.M., DeSantis, T.Z., Brodie, E.L., Weber, M., Voolstra, C.R., Andersen, G.L., Medina, M. (2014). Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. ISME Journal. PDF

Sorek, M., Diaz-Almeyda, E., Medina, M., Levy, O. (2014). Circadian clocks in symbiotic corals: the duet between Symbiodinium algae and their coral-host. Marine Genomics.  PDF

GIGA consortium. (2014). Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrate genomes. Journal of Heredity. PDF


Shoguchi, E., Shinzato, C., Kawashima, T., Gyoja, F., Mungpakdee, S., Koyanagi, R., Takeuchi, T., Hisata, K., Tanaka, M., Fujiwara, M., Hamada, M., Seidi, A., Fujie, M., Usami, T., Goto, H., Yamasaki, S., Arakaki, N., Suzuki, Y., Sugano, S., Toyoda, A., Kuroki, Y., Fujiyama, A., Medina, M., Coffroth, M.A., Bhattacharya, D., Satoh, N. (2013). Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Current Biology. PDF

Davies, S.W., Rahman, M., Meyer, E., Green, E.A., Buschiazzo, E., Medina, M., Matz, M.V. (2013). Novel polymorphic microsatellite markers for population genetics of the endangered Caribbean star coral, Montastraea faveolata. Marine Biodiversity. PDF

Vollmer, S.V., Baker, A.C., Coffroth, M.A., Harvell, C.D., and Medina, M. (2013). Understanding the coral holobiont through science and scuba. In: Research and Discoveries: The Revolution of Science through Scuba. Lang, M., Taylor, P., Roberts, S., Marinelli, R. (eds). Smithsonian Institution Press. Pp. 173-186. PDF


Weber, M., and Medina, M. (2012). The role of microalgal symbionts (Symbiodinium) in holobiont physiology. Ed. Piganeau, G. Genomic insights into the biology of algae. Elsevier. Pp. 119-140. PDF

Morandini, A., and Medina, M. (2012). Eumetazoos In:  El árbol de la vida: sistemática y evolución de los seres vivos, Eds. Vargas, P. and Zardoya, R. Reverté, Barcelona. Pp. 178-187. PDF

Ezenwa, V.O., Gerardo, N.M., Inouye, D.W., Medina, M., Xavier, J.B. (2012). Animal behavior and the microbiome. Science. PDF

Aranda, M., DeSalvo, M.K., Bayer, T., Medina, M., Voolstra, C.R. (2012). Evolutionary insights into scleractinian corals using comparative genomic hybridizations. BMC Genomics. PDF

Bayer*, T., Aranda*, M., Sunagawa, S., Yum, L.K., DeSalvo, M., Lindquist, E., Coffroth, M.A., Voolstra, C.R., Medina, M. (2012). Symbiodinium transcriptomes: Genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One. *equal contributors PDF


Medina, M. (2011). Analyzing coral reefs and their microbial assemblages. Microbe. PDF

Leggat, W., Yellowlees, D., Medina, M. (2011). Recent progress in Symbiodinium transcriptomics. Journal of Experimental Marine Biology and Ecology. PDF

Aranda, M., Banaszak, A.T., Bayer, T., Luyten, J.R., Medina, M., Voolstra, C.R. (2011). Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of competence. Molecular Ecology. PDF

DeSalvo, M.K., Estrada, A., Sunagawa, S., Medina, M. (2011). Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. Coral Reefs. PDF

Voolstra*, C.R., Sunagawa*, S., Matz, M.V., Bayer, T., Aranda, M., Buschiazzo, E., DeSalvo, M.K., Lindquist, E., Szmant, A.M., Coffroth, M.A., Medina, M. (2011) Rapid evolution of coral proteins responsible for interaction with the environment. PLoS One *equally contributing PDF

Medina, M., Lal, S., Vallès, Y., Takaoka, T.L., Dayrat, B.A., Boore, J.L., Gosliner, T. (2011). Crawling through time: transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomics. Marine Genomics. PDF

Heyland, A., Vue, Z., Voolstra, C.R., Medina, M., Moroz, L. (2011). Developmental transcriptome of Aplysia californica. Journal of Experimental Zoology. PDF


Robinson, G., Banks, J., Padilla, D., Burggren, W., Cohen, C., Delwiche, C., Funk, V., Hoekstra, H., Jarvis, E., Johnson, L. Martindale, M., Martinez del Rio, C., Medina, M., Salt, D., Sinha, S., Specht, C., Spradling, A., Strange, K., Strassmann, J., Swalla, B., and Tomanek, L. (2010). Empowering 21st century biology. BioScience. PDF

Polato, N.R, Voolstra, C.R., Schnetzer, J., DeSalvo, M.K., Randall, C.J., Szmant, A.M., Medina, M., Baums, I.B. (2010). Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata. PLoS ONE. PDF

Portune, K.J., Voolstra, C.R., Medina, M., Szmant, A. (2010). Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata. Marine Genomics. PDF

DeSalvo, M.K., Sunagawa, S., Voolstra, C.R., Medina, M. (2010). Transcriptomic responses to heat stress and bleaching in the Elkhorn coral Acropora palmata. Marine Ecology Progress Series. PDF

Sunagawa, S., Woodley, C.M., Medina, M. (2010). Threatened corals provide underexplored microbial habitats. PLoS ONE. PDF

Medina, M., Sachs, J.L. (2010). Symbiont genomics, our new tangled bank. Genomics. PDF

DeSalvo, M.K.*, Sunagawa, S.*, Fisher, P.L., Voolstra, C.R., Iglesias-Prieto, R., Medina, M. (2010). Coral host transcriptomic states are correlated with Symbiodinium genotypes. Molecular Ecology *equally contributing PDF


Voolstra, C.R., Schnetzer,  J., Peshkin, L., Randall, C.J., Szmant, A.M., Medina, M. Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. BMC Genomics. PDF

Reyes-Bermudez, A.*, DeSalvo, M.K.*, Voolstra, C.R., Sunagawa, S., Szmant, A.M., Iglesias-Prieto, R., Medina, M. (2009). Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata. Marine Genomics *equally contributing PDF

Sunagawa. S., Wilson. E.C., Thaler, M., Smith, M.L., Caruso, C., Pringle, J.R., Weis, V.M., Medina, M., Schwarz, J.A. (2009). Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. BMC Genomics. PDF

Medina, M. (2009). Functional genomics opens doors to understanding metamorphosis in nonmodel invertebrate organisms. Molecular Ecology. PDF

Voolstra, C.R., Schwarz, J.A., Schnetzer, J., Sunagawa, S., DeSalvo, M.K., Szmant, A.M., Coffroth, M.A., Medina, M. (2009). The host transcriptome remains unaltered during the establishment of coral-algal symbioses. Molecular Ecology. PDF

Sunagawa, S., DeSalvo, M.K., Voolstra, C.R., Reyes-Bermudez, A., Medina, M. (2009). Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals. PLoS ONE. PDF

Sunagawa, S., DeSantis, T.Z., Piceno, Y.M., Brodie, E.L., DeSalvo, M.K., Voolstra, C.R., Weil, E.,  Andersen, G.L., Medina, M. (2009). Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J. PDF

Voolstra, C.R., Sunagawa, S., Schwarz, J.A., Coffroth, M.A., Yellowlees, D., Leggat, W., Medina, M. (2009). Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comp Biochem Physiol, Part D. PDF


Barlow, M., Reik, R.A.,  Jacobs, S.D., Medina, M., Meyer, M.P., McGowan Jr,  J.E., Tenover, F.C. (2008). High rate of mobilization for blaCTX-Ms. Emerg Infect Dis. PDF

Sunagawa, S., Choi, J., Forman, H.J., Medina, M. (2008). Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida. Comp Biochem Physiol B PDF

DeSalvo, M.K., Voolstra, C.R., Sunagawa, S., Schwarz, J.A., Stillman, J.H., Coffroth, M.A., Szmant, A.M., Medina, M. (2008). Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. Mol Ecol. PDF

Schwarz, J.A., Brokstein, P.B., Voolstra, C., Terry, A.Y., Szmant, A., Coffroth, M.A., Miller, D.J., and Medina, M. (2008). Coral Life History and Symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics. PDF


Concepcion, G.T., Medina, M., and Toonen, R.J. (2006). Noncoding mitochondrial loci for corals. Mol Ecol Notes. PDF

Medina, M., Collins, A.G., Takaoka, T.L., Kuehl, J.V. and Boore, J.L. (2006). Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci. PDF

Tyler, B.M., S. Tripathy, X. Zhang, P. Dehal, R. H. Jiang, A. Aerts, F. D. Arredondo, L. Baxter, D. Bensasson, J. L. Beynon, J. Chapman, C. M. Damasceno, A. E. Dorrance, D. Dou, A. W. Dickerman, I. L. Dubchak, M. Garbelotto, M. Gijzen, S. G. Gordon, F. Govers, N. J. Grunwald, W. Huang, K. L. Ivors, R. W. Jones, S. Kamoun, K. Krampis, K. H. Lamour, M. K. Lee, W. H. McDonald, M. Medina, H. J. Meijer, E. K. Nordberg, D. J. Maclean, M. D. Ospina-Giraldo, P. F. Morris, V. Phuntumart, N. H. Putnam, S. Rash, J. K. Rose, Y. Sakihama, A. A. Salamov, A. Savidor, C. F. Scheuring, B. M. Smith, B. W. Sobral, A. Terry, T. A. Torto-Alalibo, J. Win, Z. Xu, H. Zhang, I. V. Grigoriev, D. S. Rokhsar and J. L. Boore. (2006). Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. PDF

Collins, A.G., Schuchert, P., Marques, A.C., Jankowski, T., Medina, M. and Schierwater, B. (2006). Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models. Syst Biol. PDF

Pola, M., Valles, Y., Cervera, J.L., Medina, M. and Gosliner, T.M. (2006). Taxonomic status of Tambja abdere and Tambja fusca based on morphological and molecular evidence, with comments on the phylogeny of the subfamily Nembrothinae (Nudibranchia, Polyceridae). Ann Zool Fenn. PDF

Schwarz, J.A., Brokstein, P., Manohar, C., Coffroth, M.A., Szmant, A.M., and Medina, M. (2006). Coral Reef Genomics: Developing tools for functional genomics of coral symbiosis. 10th International Coral Reef Symposium, Okinawa, Japan. Okinawa, Japan: 274-281. PDF


Medina, M., Collins, T., and Walsh, P.J. (2005). Phylogeny of sea hares in the Aplysia clade based on mitochondrial DNA sequence data. Bull Mar Sci. PDF

Medina, M. (2005). Genomes, phylogeny, and evolutionary systems biology. Proc Natl Acad Sci PDF


Armbrust, E. V., J. A. Berges, C. Bowler, B. R. Green, D. Martinez, N. H. Putnam, S. Zhou, A. E. Allen, K. E. Apt, M. Bechner, M. A. Brzezinski, B. K. Chaal, A. Chiovitti, A. K. Davis, M. S. Demarest, J. C. Detter, T. Glavina, D. Goodstein, M. Z. Hadi, U. Hellsten, M. Hildebrand, B. D. Jenkins, J. Jurka, V. V. Kapitonov, N. Kroger, W. W. Lau, T. W. Lane, F. W. Larimer, J. C. Lippmeier, S. Lucas, M. Medina, A. Montsant, M. Obornik, M. S. Parker, B. Palenik, G. J. Pazour, P. M. Richardson, T. A. Rynearson, M. A. Saito, D. C. Schwartz, K. Thamatrakoln, K. Valentin, A. Vardi, F. P. Wilkerson and D. S. Rokhsar (2004). The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. (Selected by Faculty of 1000). PDF

Boore, J.L., Medina, M. and Rosenberg, L.A. (2004). Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol. PDF


Walsh, P.J., Mayer, G.D., Medina, M., Bernstein, M.L., Barimo, J.F., and Mommsen, T.P. (2003). A second glutamine synthetase gene with expression in the gills of the gulf toadfish (Opsanus beta). J Exp Biol. PDF

Medina, M., Collins, A.G., Taylor, J.W., Valentine, J.W., Lipps, J.H., Amaral-Zettler, L., and Sogin, M.L. (2003). Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa. International Journal of Astrobiology. PDF


Dehal, P., Y. Satou, R. K. Campbell, J. Chapman, B. Degnan, A. De Tomaso, B. Davidson, A. Di Gregorio, M. Gelpke, D. M. Goodstein, N. Harafuji, K. E. Hastings, I. Ho, K. Hotta, W. Huang, T. Kawashima, P. Lemaire, D. Martinez, I. A. Meinertzhagen, S. Necula, M. Nonaka, N. Putnam, S. Rash, H. Saiga, M. Satake, A. Terry, L. Yamada, H. G. Wang, S. Awazu, K. Azumi, J. Boore, M. Branno, S. Chin-Bow, R. DeSantis, S. Doyle, P. Francino, D. N. Keys, S. Haga, H. Hayashi, K. Hino, K. S. Imai, K. Inaba, S. Kano, K. Kobayashi, M. Kobayashi, B. I. Lee, K. W. Makabe, C. Manohar, G. Matassi, M. Medina, Y. Mochizuki, S. Mount, T. Morishita, S. Miura, A. Nakayama, S. Nishizaka, H. Nomoto, F. Ohta, K. Oishi, I. Rigoutsos, M. Sano, A. Sasaki, Y. Sasakura, E. Shoguchi, T. Shin-i, A. Spagnuolo, D. Stainier, M. M. Suzuki, O. Tassy, N. Takatori, M. Tokuoka, K. Yagi, F. Yoshizaki, S. Wada, C. Zhang, P. D. Hyatt, F. Larimer, C. Detter, N. Doggett, T. Glavina, T. Hawkins, P. Richardson, S. Lucas, Y. Kohara, M. Levine, N. Satoh and D. S. Rokhsar. (2002). The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (Selected by Faculty of 1000). PDF


Medina, M., Collins, T., and Walsh, P.J. (2001). mtDNA ribosomal gene phylogeny of sea hares in the genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): Implications for comparative neurobiology. Syst Biol. PDF

Medina, M., Collins, A.G., Silberman, J.D., and Sogin, M.L. (2001). Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc Natl Acad Sci (Selected by Faculty of 1000). PDF


Medina, M. and P. J. Walsh (2000). Comparison of four mendelian loci of the California sea hare (Aplysia californica) from populations of the coast of California and the Sea of Cortez. Mar Biotechnol. PDF

Walsh, P. J., Heitz, M.J., Campbell, C.E., Cooper, G.J., Medina, M., Wang, Y.S., Goss, G.G., Vincek, V., Wood, C.M., and Smith, C.P. (2000). Molecular characterization of a urea transporter in the gill of the gulf toadfish (Opsanus beta). J Exp Biol. PDF

Medina, M. and Walsh, P.J. (2000). Molecular systematics of the order Anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI). Mol Phylogenet Evol. PDF


Medina, M., Weil, E. and Szmant, A.M. (1999). Examination of the Montastraea annularis species complex (Cnidaria: Scleractinia) using ITS and COI sequences. Mar Biotechnol. PDF


Brawn, J.D., Collins, T., Medina, M., and Bermingham, E. (1996). Association between physical isolation and geographical variation within three species of Neotropical birds. Mol Ecol. PDF