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Ezenwa, V.O., Gerardo, N.M., Inouye, D.W., Medina, M., Xavier, J.B. (2012). Animal behavior and the microbiome. Science 338, 198-199. doi: 10.1126/science.1227412

Aranda, M., DeSalvo, M.K., Bayer, T., Medina, M., Voolstra, C.R. (2012). Evolutionary insights into scleractinian corals using comparative genomic hybridizations. BMC Genomics 13:501. doi 10.1186/1471-2164-13-501

Bayer*, T., Aranda*, M., Sunagawa, S., Yum, L.K., DeSalvo, M., Lindquist, E., Schwarz, J., Coffroth, M.A., Voolstra*, C.R., Medina*, M. (2012). The transcriptome of dinoflagellate symbionts from reef-building corals. PLoS One 7(4): e35269. doi:10.1371/journal.pone.0035269. *equal contributors

Leggat, W., Yellowlees, D., Medina, M. (2011). Recent progress in Symbiodinium transcriptomics. Journal of Experimental Marine Biology and Ecology 408:120-125. doi:10.1016/j.jembe.2011.07.032

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 duringthe onset of competence. Molecular Ecology 20, 2955–2972. doi: 10.1111/j.1365-294X.2011.05153.x

DeSalvo MK, Estrada A, Sunagawa S, Medina M (2011). Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. Coral Reefs. doi:10.1007/s00338-011-0833-4.

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. 6(5): e20392. doi:10.1371/journal.pone.0020392 *equally contributing.

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 4:51-59.

Heyland, A., Vue, Z., Voolstra, C.R., Medina, M., Moroz, L. (2011). A transcription atlas of Aplysia californica development and neurogenesis. Journal of Experimental Zoology 316B (2):113-134.

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 60(11):923-930.

Polato NR, Voolstra CR, Schnetzer J, DeSalvo MK, Randall CJ, Szmant AM, Medina M, Baums IB (2010). Location-Specific Responses to Thermal Stress in Larvae of the Reef-Building Coral Montastraea faveolata. PLoS ONE 5(6): e11221. doi:10.1371/journal.pone.0011221

Portune KJ, Voolstra CR, Medina M, Szmant A (2010). Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata. Marine Genomics 3: 51-62.

DeSalvo MK, Sunagawa S, Voolstra CR, Medina M (2010). Transcriptomic responses to heat stress and bleaching in the Elkhorn coral Acropora palmata. Marine Ecology Progress Series: 402, 97-113.

Sunagawa S, Woodley CM, Medina M (2010) Threatened Corals Provide Underexplored Microbial Habitats. PLoS ONE 5(3): e9554. doi:10.1371/journal.pone.0009554

Medina M, Sachs JL (2010). Symbiont genomics, our new tangled bank, Genomics 95(3): 129-137. doi:10.1016/j.ygeno.2009.12.004

DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M (2010). Coral host transcriptomic states are correlated with Symbiodinium genotypes. Mol Ecol 19(6): 1174-1186. doi:10.1111/j.1365-294X.2010.04534.x. *equally contributing.

C.R. Voolstra, J. Schnetzer, L. Peshkin, C.J. Randall, A.M. Szmant, and M. Medina, Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. BMC Genomics 10 (2009) 627. doi:10.1186/1471-2164-10-627.

Reyes-Bermudez A*, DeSalvo MK*, Voolstra CR, Sunagawa S, Szmant AM, Iglesias-Prieto R, Medina M (2009). Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata. Mar Genomics 2: 149-159. doi:10.1016/j.margen.2009.07.002. *equally contributing.

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. Sunagawa S, Wilson EC, Thaler M, Smith ML, Caruso C, Pringle JR, Weis VM, Medina M, Schwarz JA BMC Genomics: 10, 258, 2009. doi: 10.1186/1471-2164-10-258

M. Medina (2009). Functional genomics opens doors to understanding metamorphosis in nonmodel invertebrate organisms. Mol Ecol 18 (5): 763-764 doi:10.1111/j.1365-294X.2008.04079.x

Voolstra, C.R., J.A. Schwarz, J. Schnetzer, S. Sunagawa, M.K. DeSalvo, A.M. Szmant, M.A. Coffroth, M. Medina (2009). The host transcriptome remains unaltered during the establishment of coral-algal symbioses. Mol Ecol: 18(9), 1823-1833, 2009. doi:10.1111/j.1365-294X.2009.04167.x

Sunagawa, S., M.K. DeSalvo, C.R. Voolstra, A. Reyes-Bermudez, M. Medina (2009). Identification and Gene Expression Analysis of a Taxonomically Restricted Cysteine-Rich Protein Family in Reef-Building Corals. PLoS ONE 4(3): 4(3). doi:10.1371/journal.pone.0004865

Sunagawa, S., T.Z. DeSantis, Y.M. Piceno, E.L. Brodie, M.K. DeSalvo, C.R. Voolstra, E. Weil, G.L. Andersen, M. Medina (2009). Bacterial Diversity and White Plague Disease-Associated Community Changes in the Caribbean Coral Montastraea faveolata. ISME J: 3(5), 512-521. doi:10.1038/ismej.2008.131

Voolstra, C.R., S. Sunagawa, J. A. Schwarz, M.A. Coffroth, D. Yellowlees, W. Leggat, M. Medina (2009). Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comp Biochem Physiol D: 4, 67-74. doi:10.1016/j.cbd.2008.11.001

Barlow, M., R.A. Reik, S.D. Jacobs, M. Medina, M.P. Meyer, J.E. McGowan, Jr., F.C. Tenover (2008). High rate of mobilization for blaCTX-Ms. Emerg Infect Dis 14, 423-428. doi: 10.3201/eid1403.070405

Sunagawa, S., J. Choi, H.J. Forman, M. Medina (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 151: 133-138. doi:10.1016/j.cbpb.2008.06.007

DeSalvo, M.K., C.R. Voolstra, S. Sunagawa, J.A. Schwarz, J.H. Stillman, M.A. Coffroth, A.M. Szmant, M. Medina (2008). Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. Mol Ecol 17 (17): 3952-3971. doi:10.1111/j.1365-294X.2008.03879.x

Schwarz, J. A., P. B. Brokstein, C. Voolstra, A. Y. Terry, A. Szmant, M. A. Coffroth, D. J. Miller, and M. Medina (2008). Coral Life History and Symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics 9: 97. doi:10.1186/1471-2164-9-97

Concepcion, G. T., M. Medina and R. J. Toonen (2006). "Noncoding mitochondrial loci for corals." Mol Ecol Notes 6(4): 1208-1211. doi:10.1111/j.1471-8286.2006.01493.x

Medina, M., A. G. Collins, T. L. Takaoka, J. V. Kuehl and J. L. Boore (2006). "Naked corals: skeleton loss in Scleractinia." Proc Natl Acad Sci U S A 103(24): 9096-100. doi:10.1073/pnas.0602444103

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 313(5791): 1261-6. doi: 10.1126/science.1128796

Collins, A. G., P. Schuchert, A. C. Marques, T. Jankowski, M. Medina and B. Schierwater (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 55(1): 97-115. doi: 10.1080/10635150500433615

Pola, M., Y. Valles, J. L. Cervera, M. Medina and T. M. Gosliner (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 43(1): 52-64. link

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

Medina, M., T. Collins and P. J. Walsh (2005). "Phylogeny of sea hares in the Aplysia clade based on mitochondrial DNA sequence data." Bull Mar Sci 76 (3): 691-698. link

Medina, M. (2005). "Genomes, phylogeny, and evolutionary systems biology." Proc Natl Acad Sci U S A 102 Suppl 1: 6630-5. doi: 10.1073/pnas.0501984102

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 306(5693): 79-86. (Selected by Faculty of 1000). doi: 10.1126/science.1101156

Boore, J. L., M. Medina and L. A. Rosenberg (2004). "Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis." Mol Biol Evol 21(8): 1492-503. doi: 10.1093/molbev/msh090

Walsh, P. J., G. D. Mayer, M. Medina, M. L. Bernstein, J. F. Barimo and T. P. Mommsen (2003). "A second glutamine synthetase gene with expression in the gills of the gulf toadfish (Opsanus beta)." J Exp Biol 206(9): 1523-1533. doi: 10.1242/jeb.00251

Medina, M., A. G. Collins, J. W. Taylor, J. W. Valentine, J. H. Lipps, L. A. Amaral Zettler and M. L. Sogin (2003). "Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa." International Journal of Astrobiology 2(3): 203-211. doi:10.1017/S1473550403001551

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 298(5601): 2157-67. (Selected by Faculty of 1000). doi: 10.1126/science.10800

Medina, M., T. Collins and P. J. Walsh (2001). "mtDNA ribosomal gene phylogeny of sea hares in the genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): Implications for comparative neurobiology." Syst Biol 50(5): 676-688. doi:10.1080/106351501753328802

Medina, M., A. G. Collins, J. D. Silberman and M. L. Sogin (2001). "Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA." Proc Natl Acad Sci U S A 98(18): 9707-9712. (Selected by Faculty of 1000). doi:10.1073/pnas.171316998

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 2(5): 449-455. doi:10.1007/s101260000020

Walsh, P. J., M. J. Heitz, C. E. Campbell, G. J. Cooper, M. Medina, Y. X. S. Wang, G. G. Goss, V. Vincek, C. M. Wood and C. P. Smith (2000). "Molecular characterization of a urea transporter in the gill of the gulf toadfish (Opsanus beta)." J Exp Biol 203(15): 2357-2364.

Medina, M. and P. J. Walsh (2000). "Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI)." Mol Phylogenet Evol 15(1): 41-58. doi:10.1006/mpev.1999.0736
Medina, M., E. Weil and A. M. Szmant (1999). "Examination of the Montastraea annularis species complex (Cnidaria: Scleractinia) using ITS and COI sequences." Mar Biotechnol 1: 89-97. doi:10.1007/PL00011756

Brawn, J. D., T. Collins, M. Medina and E. Bermingham (1996). "Association between physical isolation and geographical variation within three species of Neotropical birds." Mol Ecol 5: 33-46. doi:10.1111/j.1365-294X.1996.tb00289.x

Book chapters

Morandini, A. and M. Medina (in press). Eumetazoos. In: El árbol de la vida: sistemática y evolución de los seres vivos. Eds. Vargas, P. and Zardoya, R. Reverté, Barcelona.

Wägele, H., A. Klussmann-Kolb, V. Vonnemann, and M. Medina (2008). Heterobranchia I. The Opisthobranchia. In: Phylogeny and Evolution of the Mollusca. D. Lindberg and W. Ponder (eds). 383-406. University of California Press. link

Boore, J. L., J. R. Macey, and M. Medina (2005).  Whole mitochondrial genome sequencing and gene order comparisons of animals. In: Methods in Enzymology: Producing the Biochemical Data II, E. A. Zimmer and E. Roalson  (eds). 395: 311-341. link

Medina, M. and A. Collins. (2003). The Role of Molecules in Understanding Molluscan Evolution. In: Molecular Systematics and Phylogeography of Mollusks. C. Lydeard and D. Lindberg (eds). Smithsonian Institution Press: 14-44