Symbiosis@UM

The University of Miami includes an interactive community of ten symbiosis | microbiome research groups. Our research represents a diverse set of systems and a wide range of approaches. We share ideas, equipment, resources, lab meetings, and sometimes food!

Cards

Afkhami Lab

Afkhami Lab

We study mutualisms, microbiomes, and plant-microbial interactions at scales ranging from genes to ecosystems.

Lariviere

Lariviere Lab

We study animal-microbe symbiosis at the molecular level.

Silveira Lab

Silveira Lab

We study the interactions between viruses and bacteria in coral reefs.

Wilson Lab

Wilson Lab

We work to elucidate the mechanisms of host/endosymbiont integration in insect models.

Dallman Lab

Dallman Lab

We study how microbes in the gut influence behavior in zebrafish models of autism spectrum disorder.

Luque Lab

Luque Lab

We study the evolution of viral capsids and their relationship with cellular metabolic compartments.

Quimbayo Lab

Quimbayo Lab

We explore marine interactions to uncover the ecological rules that shape community assembly in ocean habitats.

Rieger Lab

Rieger Lab

We study how nerves and skin cells interact with microbial communities to promote appendage regeneration.

Rosser Lab

Rosser Lab

We study butterfly–plant interactions to understand how ecology shapes evolution and biodiversity.

Taylor Knowles Lab

Traylor-Knowles Lab

We study the interaction between the cnidarian immune system and microbes.

Publications

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  • 2025

    • Li, V., J. Fowler, A.S. David, S.Y. Strauss, C.A. Searcy, & M.E. Afkhami (2025) Climate variability disrupts mutualism-driven increases in population persistence. Nature Ecology and Evolution. (Accepted)
    • Afkhami, M.E., A.T. Classen, C. Dice, D.J. Hernandez, V. Li, A.H. Rawstern, J.A. Rudgers, J.R. Stinchcombe, and K. Crawford (2025) Unravelling complexity in climate change effects on beneficial plant–microbe interactions: Mechanisms, resilience, & future directions. Invited “Tansley Review” for New Phytologist. doi.org/10.1111/nph.70644.
    • Hernandez, D.J., G.B. Pohlmann, and M.E. Afkhami. (2025) Gene Family Expansions Provide Molecular Flexibility Required for Context-Dependent Species Interactions. Ecology Letters. e70213. doi: 10.1111/ele.70213
    • Zhang, B., Y. Yuan, M. Zu, K.M. Pajerowska-Mukhtar, M.E. Afkhami, A. Hastings, J. Qiu, and J. Zhang. (2025) Microbial effects on invasive grass’ response to water and nutrient stress. Elementa: Science of the Anthropocene. (Accepted) doi: 10.21203/rs.3.rs-117418/v1
    • Revillini, D., C.A Searcy, and M.E. Afkhami. (2025) 50-year fire legacy regulates soil microbial carbon and nutrient cycling responses to new fire. Soil Biology and Biochemistry. 208: 109868. doi:10.1016/j.soilbio.2025.109868
    • Rawstern, A.H., L.J. Carbajal, T.J. Slade, and M.E. Afkhami. (2025) Non-additive interactions between multiple mutualists and host plant genotype simultaneously promote increased plant growth and pathogen defence. Plant, Cell, and Environment. 1-18. doi:10.1111/pce.15631
    • Li VW and Afkhami ME (2025) How Past Stress Helps Microbes Benefit Plants. Front. Young Minds. 13:1481801. doi: 10.3389/frym.2025.1481801
    • Rawstern, A.H., Hernandez, D.J., and M.E. Afkhami. (2025) Central Taxa Are Keystone Microbes During Early Succession. Ecology Letters. 28 (1) e70031. doi:10.1111/ele.70031
    • Kiesewetter, K.N., A.H. Rawstern, E. Cline, G.R. Ortiz, F. Santamaria, C. Coronado, F.H. Sklar, and M.E. Afkhami. (2025) Microbes in Reconstructive Restoration: Divergence in Constructed and Natural Tree Island Soil Fungi Affects Tree Growth. Ecological Applications. 35(1): e70007. doi:10.1002/eap.70007
    • Hay, E.E., M.E. Afkhami, C.A. Searcy. (2025) What drives birdsong evolution? The joint roles of habitat and morphology. Frontiers for Young Minds. 13: 1461108: 1-8. doi:10.3389/frym.2025.1461108
    • Kline, J., Kholiavchenko, M., Stevens, S., van Tiel, N., Zhong, A., Banerji, N., Sheets, A., Balasubramaniam, S., Duporge, I., Thompson, M., Campolongo, E., Miliko, J., Rosser, N., Berger-Wolf, T., Stewart, C.V. and Rubenstein, D.I., 2025. kabr-tools: Automated Framework for Multi-Species Behavioral Monitoring. arXiv preprint arXiv:2510.02030.
    • Feng, Z., Wang, Z., Gu, J., Ibaven Bueno, S., Frelek, T., Ramesh, A., Bai, J., Wang, L., Huang, Z., Yoo, J., Pan, T-Y., Chowdhury, A., Ramirez, M., Campolongo, E.G., Thompson, M.J., Lawrence, C.G., Record, S., Rosser, N., Karpatne, A., Rubenstein, D., Lapp, H., Stewart, C.V., Berger-Wolf, T., Su, Y. and Chao, W-L., 2025. Static Segmentation by Tracking: A Label-Efficient Approach for Fine-Grained Specimen Image Segmentation. arXiv preprint arXiv:2501.06749.
    • Ben Chehida, Y., van der Heijden, E.S., Page, E.J., Salazar C, P.A., Rosser, N., Gabriela Gavilanes Córdova, K., Sánchez-Prado, M., Sánchez-Carvajal, M.J., Chandi, F., Arias-Cruz, A.P. and Radford, M., 2025. Genetic parallelism underpins convergent mimicry coloration across Lepidoptera. bioRxiv, pp.2025-06.
    • Pérochon, E., Rosser, N., Kozak, K., McMillan, W.O., Huertas, B., Mallet, J., Ready, J., Willmott, K., Elias, M. and Doré, M., 2025. Müllerian Mimicry in Neotropical Butterflies: One Mimicry Ring to Bring Them All and in the Jungle Bind Them. Global Ecology and Biogeography, 34(9), p.e70127.
    • Kirchberger, Paul C., and Antoni Luque. “A novel mobile genetic element with virus-like characteristics is widespread in the world’s oceans.” bioRxiv (2025): 2025-08. https://doi.org/10.1101/2025.08.03.668216;
    • Aguilar, A., I. Miranda, O. Nadel, S. Nayfach, L. Ruiz Pestana, A. M. Segall, F. L. Rohwer, S. Roux, S. White, and A. Luque. “Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids.” bioRxiv (2025). https://doi.org/10.1101/2025.06.18.659913;
    • Cobo-López, Sergio, Lucas J. Carbajal, Matthew Witt, Forest L. Rohwer, and Antoni Luque. “Emergence of tipping points and transient dynamics in finite observations.” bioRxiv (2023): 2023-12. https://doi.org/10.1101/2023.12.27.573307
    • Podgorski, J.P., J. Podgorski, L. Abad, D. Jacobs-Sera, K.G. Freeman, C. Brown, G. Hatfull, A. Luque*, S.J. White*, “A novel stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids.” Nature Communications, 16, 3145 (2025) https://doi.org/10.1038/s41467-025-58298-0;
    • Wallace, B. A., Varona, N. S., Stiffler, A. K., Vermeij, M. J., & Silveira, C. High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao’s coral reefs. mSystems, e01208-25. 2025.
    • Wallace, B., Varona, N., Silveira, C. Viruses in Coral Reef Microbiome. Coral Reefs of the World; 20, 47-64. Springer. 2025.
    • Varona, N.S., Wallace, B.A., Bosco-Santos, A., Mullinax, J., Stiffler, A.K., O’Beirne, M.D., Werne, J.P., Gilhooly III, W.P., Silveira, C.B. Viral activity in lake analogs of anoxic early Earth oceans. Microbiome. 2025.
    • Ferretti, P., Martignoni, M.M., McManus, L.C., Sakal, T., Liaghat, A., Stevens, B., Dahlin, K.J.M., Souza, L.S., Cardon, Z.G., Silveira, C.B., Bordenstein, S.R. Theory of host-microbe symbioses: Challenges and opportunities. Cell Host and Microbe. 2025.
    • Golikova, A., Stiffler, A., Silveira, C. Identification of phage lysis from environmental samples based on 96-well plate screening. protocols.io. 2025.
    • Varona, N.S., Schellenberg, L., Barnes, W., Scholten, Y., Haas, A.F., Silveira, C.B. Bacteriophage replication strategies are associated with organic matter energy content on coral reefs. bioRxiv. 2025.
    • Chaudhary, V. B., Kim, S., Medina, M., Srivastava, D. S., Traylor-Knowles, N., Brito-Millan, M., Camargo-Cely, A., Chatterjee, S., Chen, N., Chen, Y. H., Gotanda, K. M., Halsey, S. J., Jack, C. N., McGuire, R. M., Miller, C. M. L., Moore, A. C., Noh, S., Ong, T. W., Peralta, A. L., Puitiza, A., Ramirez, L. N., Romero-Olivares, A. L., Pulido-Barriga, M. F., Sanchez, K. A., Sit, C. Y., Su, C., Vazquez-Cardona, J., Venkataraman, Y. R., Werner, C. M., & Khadempour, L. (2025). Protect US racial affinity groups. Science, 387(6737), 937. https://doi.org/10.1126/science.adq4733
    • Talice, S., Barkan, S. K., Snyder, G. A., Kozlovski, I., Sharoni, T., Levy, T., Lewandowska, M., Ehrens, D., Sultan, E., Azarov, A., Oisher, S., Yannai, R., Aharoni, R., Hadad, U., Davis, C., Moran, Y., Gershoni-Yahalom, O., Traylor-Knowles, N., & Rosental, B. (2025). Protocol for cell transplantation in Nematostella vectensis, a Hexacorallian model. STAR Protocols, 6(3), 103913. https://doi.org/10.1016/j.xpro.2025.103913

  • 2024

    • Almeida, B.K., E. Tran, and M.E. Afkhami. (2024) Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance. New Phytologist. 243: 2416-2429. doi: 10.1111/nph.19792
    • Rosser, N. and Mallet, J., 2024. Interactive maps for visualizing geographic distributions and phenotypes. Tropical Lepidoptera Research, pp.104-107.
    • Seixas, F., Dendy, S., Guan, S., Rosser, N., Grishin, N., Davies, N., Gilbert Jr, L.E., Owen McMillan, W. and Mallet, J., 2024. Ancient inversion polymorphisms are locally adaptive in a widespread butterfly species. bioRxiv, pp.2024-09.
    • Papudeshi, B., A.A. Vega, C. Souza, S.K. Giles, V. Mallawaarachchi, M.J. Roach, M. An, N. Jacobson, K. McNair, M.F. Mora, K. Pastrana, L. Boling, C. Leigh, C. Harker, W.S. Plewa, S.R. Grigson, G. Bouras, P. Decewicz, A. Luque, L. Droit, S.A. Handley, D. Wang, A.M. Segall, E.A. Dinsdale, R.A. Edwards, “Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2,” Microbial Genomics, 9(9):001100 (2023). https://doi.org/10.1099/mgen.0.001100;
    • Brown, C.G., A. Agarwal, A. Luque, “pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells,” Bioinformatics, 40(1), btad761 (2024). https://doi.org/10.1093/bioinformatics/btad761;
    • Luque, A. and D. Reguera, “Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses,” in M.G. Mateo (eds) Structure, and Physics of Viruses, Subcellular Biochemistry, 105, Springer (2024). https://doi.org/10.1007/978-3-031-65187-8_19 
    • Luza A, Bender MG, Ferreira CEL, Francini-Filho RB, Longo GO, Pinheiro HT, Quimbayo JP, Bastazini VAG. (2024). Coping with Collapse: Functional robustness of coral-reef fish network to simulated cascade extinction. Global Change Biology. 30 e17513.
    • Feng H, Wilson ACC (2024) Experimental uncoupling of hosts and endosymbionts, mBio, 15(8): e01116-24.
    • Varona, N., Hesketh-Best, P., Stiffler, A., Garcia, S., Scholten, Y., Haas, A., Little, M., Coutinho, F.H., Vermeij, M., Luque, A. and Silveira, C. Host-specific viral predation network on coral reefs. The ISME Journal, wrae240. 2024.
    • Gibbs, T., Dahlin, K.J-M., Brennan, J., Silveira, C.B., McManus, L.C. Coexistence of bacteria with a competition-colonization tradeoff on a dynamic coral host. BioRxiv. 2024.
    • Stiffler, A., Hesketh-Best, P., Varona, N., Zagame, A., Wallace, B., LaPointe, B., Silveira, C. Inducible prophages modulate symbiotic phenotypes in Sargassum-associated bacteria. Microbiome, 12, 143. 2024.
    • Wallace, B., Varona, N., Hesketh-Best, P., Stiffler, A., Silveira, C. Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions. The ISME Journal, wrae132. 2024.
    • Barno, A., K.H., Green, K., Rohwer, F., Silveira, C.B. Snow viruses and their implications on red snow algal blooms. mSystems 9:e00083-24. 2024.
    • Voolstra, C., Raina, J.B., Dorr, M., Cardenas, A., Pogoreutz, C., Silveira, C., Mohamed, A., Bourne, D., Luo, H., Amin, S., Peixoto, R. The coral microbiome in sickness, in health, and in a changing world. Nature Reviews Microbiology 22, 460–475. 2024. (Cover Article)
    • Young, B. D., Williams, D., Bright, A., Peterson, A., Traylor-Knowles, N., & Rosales, S. M. (2024). Genet identity and season drive gene expression in outplanted Acropora palmata at different reef sites. Scientific Reports, 14(1), 29444. https://doi.org/10.1038/s41598-024-29444 
    • Rosales, S. M., Young, B. D., Bright, A. J., Montes, E., Zhang, J., Traylor-Knowles, N., & Williams, D. E. (2024). It’s all about the reef: Reef site and habitat are important considerations for restoration of Acropora palmata based on the microbiome. Communications Earth & Environment, 5, 689. https://doi.org/10.1038/s43247-024-01816-7 
    • Talice, S., Kozlovski, I., Barkan, S. K., Snyder, G. A., Sharoni, T., Levy, T., Oisher, S., Ottolenghi, A., Eliachar, S., Ben-Romano, R., Berlyne, K., Yannai, R., Lewandowska, M., Sultan, E., Goldstein, O., Aharoni, R., Hadad, U., Davis, C., Moran, Y., Gershoni-Yahalom, O., Traylor-Knowles, N., & Rosental, B. (2024). Candidate stem cell isolation and transplantation in Hexacorallia. Cell Reports, 43(11), 114944. https://doi.org/10.1016/j.celrep.2024.114944
    • Hutchinson, A., Appeltant, R., Burdon, T., Bao, Q., Bargaje, R., Bodnar, A., Chambers, S., Comizzoli, P., Cook, L., Endo, Y., Harman, B., Hayashi, K., Hildebrandt, T., Korody, M. L., Lakshmipathy, U., Loring, J. F., Munger, C., Ng, A., Novak, B., Onuma, M., Ord, S., Paris, M., Pask, A., Pelegri, F., Pera, M., Phelan, R., Rosental, B., Ryder, O. A., Sukparangsi, W., Sullivan, G., Tay, N. L., Traylor-Knowles, N., Walker, S., Weberling, A., Whitworth, D. J., Williams, S. A., Wojtusik, J., Wu, J., Ying, Q., Zwaka, T. P., & Kohler, T. N. (2024). Advancing stem cell technologies for conservation of wildlife biodiversity. Development, 151(20), dev203116. https://doi.org/10.1242/dev.203116 
    • Wong, K. H., Andrade Rodriguez, N., & Traylor-Knowles, N. (2024). Exploring the unknown: How can we improve single-cell RNAseq cell type annotations in non-model organisms? Integrative and Comparative Biology, 64(5), 1291–1299. https://doi.org/10.1093/icb/icae112
    • Reimer, J. D., Peixoto, R. S., Davies, S. W., Traylor-Knowles, N., et al. (2024). The fourth global coral bleaching event: Where do we go from here? Coral Reefs. https://doi.org/10.1007/s00338-024-02504-w 
    • Vandepas, L. E., Stefani, C., Domeier, P. P., Traylor-Knowles, N., Goetz, F. W., Browne, W. E., & Lacy-Hulbert, A. (2024). Extracellular DNA traps in a ctenophore demonstrate immune cell behaviors in a non-bilaterian. Nature Communications. (accepted).
    • Young, B. D., Williamson, O. M., Kron, N. S., Andrade Rodriguez, N., Isma, L. M., MacKnight, N. J., Muller, E. M., Rosales, S. M., Sirotzke, S. M., Traylor-Knowles, N., Williams, S. D., & Studivan, M. S. (2024). Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing. BMC Genomics.
    • Papke, E., Carreiro, A., Dennison, C., Deutsch, J. M., Isma, L. M., Meiling, S. S., Rossin, A. M., Baker, A. C., Brandt, M. E., Garg, N., Holstein, D. M., Traylor-Knowles, N., Voss, J. D., & Ushijima, B. (2024). Stony coral tissue loss disease: A review of emergence, impacts, etiology, diagnostics, and intervention. Frontiers in Marine Science, 10, 1321271. https://doi.org/10.3389/fmars.2023.1321271

  • 2023

    • Duncan RP, Anderson CMH, ThwaitesDT, Luetje CW, Wilson ACC (2023) Co-option of a conserved host glutamine transporter facilitates aphid/Buchnera metabolic integration, Proceedings of the National Academy of Science, USA 120 (43) e2308448120.
    • Hesketh-Best, P., Bosco-Santos, A., Garcia, S., O’Beirne, M., G., Werne, J., Gilhooly, W., Silveira, C.B. Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms. Communications Earth and Environment 4, 126. 2023.
    • Silveira, C.B., Luque, A., Haas, A.F., Roach, T.N.F., George, E.E., Knowles, B., Sullivan, C., Little, M., Varona, N.S., Kelly, K.W., Brainard, R.E., Rohwer, F., Bailey, B. Viral predation pressure on coral reefs. BMC Biology 21, 77. 2023.
    • Coutinho, F.H., Silveira, C.B., Sebastián, M., Sánchez, P., M., Duarte, C.M., Vaqué, D., Gasol, J.M., Acinas, S.G. Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities. Microbiome 11, 118.
    • Ahmadi, R.A., Varasteh, T., Silveira, C.B., Walter, J., Siegle, E., Omachi, C., Rezende, C.E., Francini‑Filho, R.B., Thompson, C.C., Tschoeke, D., Bahiense, L., Thompson, F.L. Machine learning sheds light on physical-chemical and biological parameters leading to Abrolhos coral reef microbialization. Science of the Total Environment 891,164465.
    • Traylor-Knowles, N., Bedi de Silva, A., Boyd, A. D., Callwood, K. A., Davis, A. C. D., Hall, G., Moreno, V., & Scott, C. P. (2023). Experiences of and support for Black women in ecology, evolution, and marine science. Frontiers in Marine Science, 10, 1295931. https://doi.org/10.3389/fmars.2023.1295931
    • Boohar, R. T., Vandepas, L. E., Traylor-Knowles, N., & Browne, W. E. (2023). Phylogenetic and protein structure analyses provide insight into the evolution and diversification of the CD36 domain ‘apex’ among scavenger receptor class B proteins across eukarya. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evad218
    • Dieter, A. C., True, A. B. K., Gilbertson, E. A., Snyder, G., Lacy-Hulbert, A., Traylor-Knowles, N., Browne, W. E., & Vandepas, L. E. (2023). Flow cytometry methods for targeted isolation of ctenophore cells. Frontiers in Marine Science, 10, 1276041. https://doi.org/10.3389/fmars.2023.1276041
    • Morris, J. T., Enochs, I. C., Studivan, M. S., Young, B. D., Mayfield, A., Soderberg, N., Traylor-Knowles, N., & Manzello, D. K. (2023). Ocean acidification influences the gene expression and physiology of two Caribbean bioeroding sponges. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2023.1223380
    • Young, B. D., Rosales, S. M., Enochs, I. C., Kolodziej, G., Formel, N., Moura, A., D’Alonso, G., Traylor-Knowles, N., & Studivan, M. S. (2023). Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata. PLOS ONE, 18(5), e0286293. https://doi.org/10.1371/journal.pone.0286293
    • Connelly, M. T., Snyder, G., Palacio-Castro, A. M., Gillette, P. R., Baker, A. C., & Traylor-Knowles, N. (2023). Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption, and activate immune gene expression. Molecular Ecology, 32, 4677–4694. https://doi.org/10.1111/mec.17049
    • Davies, S. W., Gamache, M. H., Howe-Kerr, L. I., Kriefall, N. G., Baker, A. C., Banaszak, A. T., Bay, L. K., Bellantuono, A. J., Bhattacharya, D., Chan, C. X., Claar, D. C., Coffroth, M. A., Cunning, R., Davy, S. K., del Campo, J., Díaz-Almeyda, E. M., Frommlet, J. C., Fuess, L. E., González-Pech, R. A., Goulet, T. L., Hoadley, K. D., Howells, E. J., Hume, B. C. C., Kemp, D. W., Kenkel, C. D., Kitchen, S. A., LaJeunesse, T. C., Lin, S., McIlroy, S. E., McMinds, R., Nitschke, M. R., Oakley, C. A., Peixoto, R. S., Prada, C., Putnam, H. M., Quigley, K., Reich, H. G., Reimer, J. D., Rodriguez-Lanetty, M., Rosales, S. M., Saad, O. S., Sampayo, E. M., Santos, S. R., Shoguchi, E., Smith, E. G., Stat, M., Stephens, T. G., Strader, M. E., Suggett, D. J., Swain, T. D., Tran, C., Traylor-Knowles, N., Voolstra, C. R., Warner, M. E., Weis, V. M., Wright, R. M., Xiang, T., Yamashita, H., Ziegler, M., Correa, A. M. S., & Parkinson, J. E. (2023). Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ, 11, e15023. https://doi.org/10.7717/peerj.15023
    • Afkhami, M.E. (2023) Past microbial stress benefits tree resilience. Soil Microbiota from stressful environments provide an avenue for climate resilience. Science. 380 (6647): 798-799. doi: 10.1126/science.adi1594
    • Hernandez, D.J., K.N. Kiesewetter, B.K. Almeida, D.P. Revillini, M.E. Afkhami. (2023) Multidimensional specialization and generalization are pervasive in soil prokaryotes. Nature Ecology and Evolution. 7: 1408–1418. doi: 10.1038/s41559-023-02149-y
    • Revillini, D., A.S. David, A.L. Reyes Gonzalez, L.D. Knecht, P. Allen, C. Vigo, E.S. Menges, C.A. Searcy, and M.E. Afkhami. (2023) Allelopathy-selected microbiomes mitigate chemical inhibition of plant performance. New Phytologist. 240: 2007-2019. doi: 10.1111/nph.19249
    • David, A.S., D. Hernandez, E.S. Menges, V. Sclater, M.E. Afkhami, and C.A. Searcy. (2023) Heterogeneous landscape promotes distinct microbial communities in an imperiled scrub ecosystem. Mycologia. 115: 739-748. doi: 10.1080/00275514.2023.2258268
    • Kiesewetter, K.N., Otano Velazco, L. and M.E. Afkhami. (2023) Fragmentation disrupts microbial effects on native plant community productivity. 11: 1292–1307. Journal of Ecology. doi:10.1111/1365-2745.14097
    • Schardl, C., M.E. Afkhami, P. Gundel, L. Iannone, C. Young, R. Creamer, D. Cook. (2023) Diversity of seed endophytes: Causes and implications. The Mycota. Vol 5: Plant Relationships. Ed. B. Scott and C. Mesarich. Springer Press.
    • Almeida, B.K., E. Cline, F. Sklar, and M.E. Afkhami. (2023) Hydrology shapes microbial communities and microbiome-mediated growth of an Everglades tree island species. Restoration Ecology. e13677. doi:10.1111/rec.13677

  • 2022

    • Revillini, D., A.S. David, K. Main, E.S. Menges, M.E. Afkhami, C.A. Searcy. (2022) Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance. New Phytologist. 233: 2071-2082. doi:10.1111/nph.17689
    • Subedi, S.C., P. Allen, R. Vidales, L. Sternberg, M. Ross, M.E. Afkhami. (2022) Salinity legacy: Foliar microbiome history affects mutualist-conferred salinity tolerance. Ecology. 103: e3679. doi:10.1002/ecy.3679
    • James EB, Pan X, Schwartz O, Wilson ACC (2022) SymbiQuant: A Machine Learning Object Detection Tool for Polyploid Independent Estimates of Endosymbiont Population Size. Frontiers in Microbiology, 13: 816608.
    • Sandin, S. A., […], Silveira, C.B., et al. Benthic assemblages are more predictable than fish assemblages at an island scale. Coral Reefs. (2022)
    • Han, L., Yu, D., Li, B., Du, S., Silveira, C.B., Cobian-Guemes, A.G., Zhang, L., He, J., Rohwer, F. Distribution of soil viruses across China and their potential role in phosphorous metabolism. Environmental Microbiome 17(6), 1-11. 2022.
    • Eliachar, S., Snyder, G. A., Barkan, S. K., Talice, S., Otolenghi, A., Jaimes-Becerra, A., Sharoni, T., Sultan, E., Hadad, U., Levy, O., Moran, Y., Gershoni-Yahalom, O., Traylor-Knowles, N., & Rosental, B. (2022). Heat stress increases immune cell function in Hexacorallia. Frontiers in Immunology, 13, 1016097. https://doi.org/10.3389/fimmu.2022.1016097
    • Traylor-Knowles, N., Baker, A. C., Beavers, K. M., Garg, N., Guyon, J. R., Hawthorn, A., MacKnight, N. J., Medina, M., Mydlarz, L. D., Peters, E. C., Stewart, J. M., Studivan, M. S., & Voss, J. D. (2022). Advances in coral immunity ‘omics in response to disease outbreaks. Frontiers in Marine Science, 9, 952199. https://doi.org/10.3389/fmars.2022.952199
    • DeMerlis, A., Kirkland, A., Kaufman, M. L., Mayfield, A. B., Formel, N., Kolodziej, G., Manzello, D. P., Lirman, D., Traylor-Knowles, N., & Enochs, I. C. (2022). Pre-exposure to a variable temperature treatment improves the response of Acropora cervicornis to acute thermal stress. Coral Reefs. https://doi.org/10.1007/s00338-022-02232-z
    • Connelly, M. T., Cecily, M., McRae, C. J., Liu, P.-J., & Traylor-Knowles, N. (2022). Antibiotic treatments alter Pocillopora coral-symbiont bacteria interactions and cause microbial dysbiosis during acute heat stress. Frontiers in Marine Science, 8, 814124. https://doi.org/10.3389/fmars.2021.814124

  • 2021

    • Wilson ACC. (2021) A new protein protects a symbiotic relationship. Proceedings of the National Academy of Science, USA 118 (30): e2109637118.
    • Saurabh Singh K, Cordeiro EMG, Troczka BJ, Pym A, Mackisack J, Mathers TC, Duarte A, Legeai F, Robin S, Bielza P, Burrack HJ, Charaabi K, Denholm I, Figueroa CC, ffrench-Constant RH, Jander G, Margaritopoulos JT, Mazzoni E, Nauen R, Ramírez CC, Ren G, Stepanyan I, Umina PA, Voronova NV, Vontas J, Williamson MS, Wilson ACC, Xi-Wu G, Youn Y-N, Zimmer CT, Simon J-C, Hayward A, Bass C (2021) Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Communications Biology 4: 847.
    • Venincasa MJ, Randlett O, Sumathipala SH, Bindernagel R, Stark MJ, Yan Q, Sloan SA, Li C, Buglo E, Meng QC, Engert F, Züchner SL, Kelz MB, Syed S, and Dallman JE. (2021) Elevated preoptic brain activity in zebrafish glial glycine transporter mutants is linked to lethargy-like behaviors and delayed emergence from anesthesia. Scientific Reports 11:3148.
    • James DJ, Davidson E, Yanes J, Moshiree B, Dallman JE. (2021) The gut-brain-microbiome axis and its link to autism: emerging insights and the potential of zebrafish models. Frontiers in Cell and Developmental Biology 9:662916. doi: 10.3389/fcell.2021.662916
    • Kozol RA, James DJ, Varela I, Sumathipala SH, Züchner SL, and Dallman JE. (2021) Restoring Shank3 in the rostral brainstem of shank3ab-/- zebrafish autism models rescues sensory deficits. Communications Biology 4: 1411.
    • Snyder, G. A., Shir, E., Connelly, M. T., Talice, S., Gershoni-Yahalom, O., Hadad, U., William, E., Caroline, V., Palmer, B., Rosental, B., & Traylor-Knowles, N. (2021). Functional characterization of Hexacorallian phagocytic cells. Frontiers in Immunology, 12, 662803. https://doi.org/10.3389/fimmu.2021.662803
    • Davies, S. W., Hollie, M. P., Tracy, A., Julia, K. B., Colleen, B. B., Crosby, S., Isabelle, M. C., Anne, D., Robinson, W. F., Alyssa, J. G., Torrance, C. H., Tessa, H., Adriana, H., Anna, M., Laura, M. P., Hanny, E. R., Nyssa, J. S., Nicola, S. S., Ana, K. S., Traylor-Knowles, N., Brooke, L. W., Rachel, M. W., & Amanda, E. B. (2021). Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science. PLOS Biology. https://doi.org/10.1371/journal.pbio.3001282
    • Traylor-Knowles, N., Connelly, M. T., Young, B. D., Eaton, K., Muller, E., Paul, V., Ushijima, B., DeMerlis, A., Drown, M.K., Goncalves, A., Kron, N., Martin, C., Snyder, G.A., Rodriguez, K. (2021) Gene Expression Response to Stony Coral Tissue Loss Disease Transmission in M. cavernosa and O. faveolata from Florida, Frontiers in Marine Science. https://doi.org/10.3389/fmars.2021.681563.
    • Fulweiler, R.W.; Davies, S.W.; Biddle, J.F.; Burgin, A.J.; Cooperdock, E.H.; Hanley, T.C.; Kenkel, C.; Marcarelli, A.M.; Matassa, C.M.; Santiago-Vazquez, L.Z.; Traylor-Knowles, N.; Ziegler, M. (2021) Rebuilding the Academy: Strategies for Supporting Academic Mothers during the COVID-19 Global Pandemic and Beyond. PLOS Biology.19(3): e3001100.
    • Nowotny, J. D., Connelly, M.T., Traylor-Knowles N. (2021) Novel Methods to Establish Whole-Body Primary Cell Cultures for the Cnidarians Nematostella vectensis and Pocillopora damicornis. Scientific Reports.11 (1), 1-9.
    • Bonacolta A., Connelly, M.T., Rosales S., Del Campo J., Traylor-Knowles N. (2021) Micro-niche sampling of the bacteriome in the Starlet Sea Anemone, Nematostella vectensis, reveals a compartment-specific dominance of Spirochetes. FEMS Microbiology Ecology Letters. 368 (3), fnab002.
    • Forcone, K.H., Coutinho, F.H., Cavalcanci, G.S., Silveira, C.B. Prophage genomics and ecology in the family Rhodobacteraceae. 2021. Microorganisms 9(6):1115. 2021.
    • Ventero, M.P., Cuadrat, R., Vidal, I., Andrade, B., Molina-Pardines, C., Haro-Moreno, J.M., Coutinho, F., Merino, E., Regitano, L.C.A., Silveira, C.B., Afli, H., Lopez-Perez, M., Rodriguez, J.C. Nasopharingeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19. 2021. Frontiers in Microbiology 12:637430.
    • Little, M., George, E.E., Arts, M.G.I., Shivak, J., Huckeba, J., Benler, S., Quinlan, Z.A.D., Boscaro, V., Mueller, B., Cobián-Güemes, A.G., Rojas, M.I., White, B., Petras, D., Silveira, C.B., Haas, A.F., Kelly, L.W., Vermeij, M., Quinn, R.A., Keeling, P.J., Dorrestein, P.C., Rohwer F., Roach. T.N.F. Three-dimensional molecular cartography of the Caribbean reef-building coral Orbicella faveolata. 2021. Frontiers in Marine Science 8:627724.
    • George, E., Mullinix, J., Meng, F., Bailey, B., Edwards, C., Felts, B., Haas, A., Hartmann, A., Mueller, B., Nulton, J., Roach, T., Salamon, P., Silveira, C.B., Vermeij, M., Rohwer, F., Luque, A. Space-filling and benthic competition on coral reefs. 2021. PeerJ 9:e11213.
    • Silveira, C. B., Luque, A., Rohwer, F. The landscape of lysogeny across microbial community density, diversity and energetics. 2021. Environmental Microbiology 23(8), 4098–4111.
    • Voolstra, C.R., Suggett, D.J., Peixoto, R.S., Parkinson, J.E., Quigley, K.M., Silveira, C.B., Sweet, M., Muller, E.M., Barshis, D.J., Bourne, D.G., Aranda, M. Extending the natural adaptive capacity of coral holobionts. 2021. Nature Reviews Earth & Environment doi: https://doi.org/10.1038/s43017-021-00214-3
    • Quintana-Ascencio, P.F., E.S. Menges, G. Cook, J. Ehrlén, and M.E. Afkhami. (2021) Drivers of demography: past challenges and a promise for a changed future. Demographic Methods across the Tree of Life. Eds. R. Salguero-Gomez and M. Gamelon. Oxford University Press.
    • Kiesewetter, K.N and M.E. Afkhami (2021) Microbiome-mediated effects of habitat fragmentation on native plant performance. New Phytologist. 232: 1823-1838. doi:10.111/nph.17595
    • Hernandez, D.J., A.D. David, E.S. Menges, C.A. Sercy, and M.E. Afkhami. (2021) Environmental stress destabilizes microbial networks. The ISME Journal. doi: 10.1038/s41396-020-00882-x
    • Afkhami, M.E., M. Friesen & J.R. Stinchcombe. (2021) Multiple Mutualist Effects generate synergistic selection on host traits and strengthen fitness alignment in the interaction between legumes, nitrogen-fixing bacteria, and mycorrhizal fungi. Ecology Letters. 24: 1824-1834. doi:10.1111/ele.13814

  • 2020

    • Banfill CR, Wilson ACC, Lu HL (2020) Further evidence that mechanisms of host/symbiont integration are dissimiliar in the maternal versus embryonic Acyrthosiphon pisum bacteriome. EvoDevo 11:23.
    • Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao Y-M, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu H-L, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre R-F, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D (2020) The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biology, 18(1):90.
    • Wilson ACC (2020) Regulation of an insect symbiosis. In: Advances in Insect Physiology: Mechanisms Underlying Microbial Symbiosis. Vol.58, 207-232. Russell JA & Oliver KM eds., Academic Press, Elsevier, London U.K.
    • Silveira CB, Coutinho FH, Cavalcanti GS, Benler S, Doane MP, Dinsdale EA, Edwards RA, Francini-Filho RB, Thompson CC, Luque A, Rohwer FL, Thompson F (2020) Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC Genomics, 21(1):126.
    • Roach TNF, Little M, Arts MGI, Huckeba J, Haas AF, George EE, Quinn RA, Cobián-Güemes AG, Naliboff DS, Silveira CB, Vermeij MJA, Kelly LW, Dorrestein PC, Rohwer F (2020) A multiomic analysis of in situ coral-turf algal interactions. Proceedings of the National Academy of Sciences of the United States of America, 117(24):13588–13595.
    • Cortese A, Inherited Neuropathy Consortium, Zhu Y, Rebelo AP, Negri S, Courel S, Abreu L, Bacon CJ, Bai Y, Bis-Brewer DM, Bugiardini E, Buglo E, Danzi MC, Feely SME, Athanasiou-Fragkouli A, Haridy NA, Isasi R, Khan A, Laurà M, Magri S, Pipis M, Pisciotta C, Powell E, Rossor AM, Saveri P, Sowden JE, Tozza S, Vandrovcova J, Dallman J, Grignani E, Marchioni E, Scherer SS, Tang B, Lin Z, Al-Ajmi A, Schüle R, Synofzik M, Maisonobe T, Stojkovic T, Auer-Grumbach M, Abdelhamed MA, Hamed SA, Zhang R, Manganelli F, Santoro L, Taroni F, Pareyson D, Houlden H, Herrmann DN, Reilly MM, Shy ME, Grace Zhai R, Zuchner S (2020) Author Correction: Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes. Nature Genetics, 52(6):640–640. https://doi.org/10.1038/s41588-020-0649-7
    • Walters BM, Connelly MT, Young B, Traylor-Knowles N (2020) The Complicated Evolutionary Diversification of the Mpeg-1/Perforin-2 Family in Cnidarians. Frontiers in immunology, 11:1690.
    • Connelly MT, McRae CJ, Liu P-J, Traylor-Knowles N (2020) Lipopolysaccharide treatment stimulates Pocillopora coral genotype-specific immune responses but does not alter coral-associated bacteria communities. Developmental and comparative immunology, 109:103717.
    • Snyder GA, Browne WE, Traylor-Knowles N*, Rosental B* (2020) Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations. Journal of Visualized Experiments, (159) https://doi.org/10.3791/60446 *Co-senior authors
    • David AS, Thapa-Magar KB, Menges ES, Searcy CA, Afkhami ME (2020) Do plant-microbe interactions support the Stress Gradient Hypothesis? Ecology, 101(8):e03081.
    • Afkhami ME, Almeida BK, Hernandez DJ, Kiesewetter KN, Revillini DP (2020) Tripartite mutualisms as models for understanding plant–microbial interactions. Current Opinion in Plant Biology, 56:28–36. https://doi.org/10.1016/j.pbi.2020.02.003
    • Rudgers JA, Afkhami ME, Bell-Dereske L, Anny Chung Y, Crawford KM, Kivlin SN, Mann MA, Nuñez MA (2020) Climate Disruption of Plant-Microbe Interactions. Annual Review of Ecology, Evolution, and Systematics, 51(1) https://doi.org/10.1146/annurev-ecolsys-011720-090819
    • Carscadden KA, Emery NC, Arnillas CA, Cadotte MW, Afkhami ME, Gravel D, Livingstone SW, Wiens JJ (2020) Niche Breadth: Causes and Consequences for Ecology, Evolution, and Conservation. The Quarterly Review of Biology, 95(3):179–214. https://doi.org/10.1086/710388
    • Almeida BK, Garg M, Kubat M, Afkhami ME (2020) Not that kind of tree: Assessing the potential for decision tree-based plant identification using trait databases. Applications in plant sciences, 8(7):e11379.
    • Hernandez D, Kiesewetter KN, Palakurty S, Stinchcombe JR, Afkhami ME (2020) Synergism and symbioses: unpacking complex mutualistic species interactions using transcriptomic approaches. The Model Legume Medicago truncatula, :1045–1054. https://doi.org/10.1002/9781119409144.ch135
    • Buglo E, Sarmiento E, Martuscelli NB, Sant DW, Danzi MC, Abrams AJ, Dallman JE, Züchner S (2020) Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease. PloS one, 15(3):e0230566.

  • 2019

    • David AS, Quintana-Ascencio PF, Menges ES, Thapa-Magar KB, Afkhami ME*, Searcy CA* (2019) Soil Microbiomes Underlie Population Persistence of an Endangered Plant Species. The American Naturalist, in press. *Co-senior authors
    • Feng H, Edwards N, Anderson CMH, Althaus M, Duncan RP, Hsu Y-C, Luetje CW, Price DRG, Wilson ACC, Thwaites DT (2019) Trading amino acids at the aphid–Buchnera symbiotic interface. Proceedings of the National Academy of Sciences, 116(32):16003–16011. https://doi.org/10.1073/pnas.1906223116
    • Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL (2019) Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes. Nature Communications, 10(1):502.
    • Traylor-Knowles N (2019) Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus. PeerJ, 7:e6510.
    • Traylor-Knowles N, Vandepas LE, Browne WE (2019) Still enigmatic: innate immunity in the ctenophore Mnemiopsis leidyi. Integrative and comparative biology, https://doi.org/10.1093/icb/icz116
    • James DM, Kozol RA, Kajiwara Y, Wahl AL, Storrs EC, Buxbaum JD, Klein M, Moshiree B, Dallman JE (2019) Intestinal dysmotility in a zebrafish (Danio rerio) shank3a;shank3b mutant model of autism. Molecular Autism, 10(1) https://doi.org/10.1186/s13229-018-0250-4
    • Mintz KJ, Mercado G, Zhou Y, Ji Y, Hettiarachchi SD, Liyanage PY, Pandey RR, Chusuei CC, Dallman J, Leblanc RM (2019) Tryptophan carbon dots and their ability to cross the blood-brain barrier. Colloids and surfaces. B, Biointerfaces, 176:488–493.
    • Silveira CB, Luque A, Roach TN, Villela H, Barno A, Green K, Reyes B, Rubio-Portillo E, Le T, Mead S, Hatay M, Vermeij MJ, Takeshita Y, Haas A, Bailey B, Rohwer F (2019) Biophysical and physiological processes causing oxygen loss from coral reefs. eLife, 8 https://doi.org/10.7554/eLife.49114 *Article featured in an eLife Digest.
    • Rosales SM, Miller MW, Williams DE, Traylor-Knowles N, Young B, Serrano XM (2019) Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays. Scientific reports, 9(1):18279.

  • 2018

    • Palakurty SX, Stinchcombe JR, Afkhami ME (2018) Cooperation and coexpression: How coexpression networks shift in response to multiple mutualists. Molecular Ecology, 27(8):1860–1873.
    • Feng H, Wang L, Wuchty S, Wilson ACC (2018) microRNA regulation in an ancient obligate endosymbiosis. Molecular Ecology, 27(8):1777–1793.
    • David AS, Thapa-Magar KB, Afkhami ME (2018) Microbial mitigation–exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress. Ecology, 99(3):517–523.
    • Afkhami ME, Luke Mahler D, Burns JH, Weber MG, Wojciechowski MF, Sprent J, Strauss SY (2018) Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera. Ecology, 99(2):502–502.
    • Batstone RT, Carscadden KA, Afkhami ME, Frederickson ME (2018) Using niche breadth theory to explain generalization in mutualisms. Ecology, 99(5):1039–1050.
    • James EB, Feng H, Wilson ACC (2018) mTOR Complex 1 Implicated in Aphid/Buchnera Host/Symbiont Integration. G3, 8(9):3083–3091.
    • Nakajima R, Haas AF, Silveira CB, Kelly ELA, Smith JE, Sandin S, Kelly LW, Rohwer F, Nakatomi N, Kurihara H (2018) Release of dissolved and particulate organic matter by the soft coral Lobophytum and subsequent microbial degradation. Journal of experimental marine biology and ecology, 504:53–60.
    • Traylor-Knowles N (2018) In Situ Hybridization Techniques for Paraffin-Embedded Adult Coral Samples. Journal of visualized experiments: JoVE, (138) https://doi.org/10.3791/57853
    • Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N (2018) Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Scientific reports, 8(1):16134.
    • Cirrincione A, Rieger S (2018) Keratinocyte-specific mitochondrial H2O2 formation as possible cause of paclitaxel neurotoxicity. Journal of the peripheral nervous system, 23:389–390.
    • Waldron AL, Schroder PA, Bourgon KL, Bolduc JK, Miller JL, Pellegrini AD, Dubois AL, Blaszkiewicz M, Townsend KL, Rieger S (2018) Oxidative stress-dependent MMP-13 activity underlies glucose neurotoxicity. Journal of diabetes and its complications, 32(3):249–257.
    • Zhao H, Pullagura SRN, Rieger S, Lisse TS (2018) Vitamin D and MicroRNAs. Vitamin D, :245–267. https://doi.org/10.1016/b978-0-12-809965-0.00015-x
    • Bedell V, Buglo E, Marcato D, Pylatiuk C, Mikut R, Stegmaier J, Scudder W, Wray M, Züchner S, Strähle U, Peravali R, Dallman JE (2018) Zebrafish: A Pharmacogenetic Model for Anesthesia. Methods in enzymology, 602:189–209.

  • 2017

    • Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, Munster M van, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, Oosterhout C van, Swarbreck D, Hogenhout SA (2017) Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, 18(1):27.
    • Silveira CB, Cavalcanti GS, Walter JM, Silva-Lima AW, Dinsdale EA, Bourne DG, Thompson CC, Thompson FL (2017) Microbial processes driving coral reef organic carbon flow. FEMS microbiology reviews, 41(4):575–595.
    • Silveira CB, Gregoracci GB, Coutinho FH, Silva GGZ, Haggerty JM, Oliveira LS de, Cabral AS, Rezende CE, Thompson CC, Francini-Filho RB, Edwards RA, Dinsdale EA, Thompson FL (2017) Bacterial Community Associated with the Reef Coral Mussismilia braziliensis’s Momentum Boundary Layer over a Diel Cycle. Frontiers in microbiology, 8:784.
    • Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL (2017) Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nature communications, 8:15955.5.
    • Knowles B, Bailey B, Boling L, Breitbart M, Cobián-Güemes A, Del Campo J, Edwards R, Felts B, Grasis J, Haas AF, Katira P, Kelly LW, Luque A, Nulton J, Paul L, Peters G, Robinett N, Sandin S, Segall A, Silveira C, Youle M, Rohwer F (2017) Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature microbiology, 2:17064.
    • Traylor-Knowles N, Rose NH, Palumbi SR (2017) The cell specificity of gene expression in the response to heat stress in corals. The Journal of experimental biology, 220(Pt 10):1837–1845.
    • Traylor-Knowles N, Rose NH, Sheets EA, Palumbi SR (2017) Early Transcriptional Responses during Heat Stress in the Coral Acropora hyacinthus. The Biological bulletin, 232(2):91–100.
    • Rosental B, Kozhekbaeva Z, Fernhoff N, Tsai JM, Traylor-Knowles N (2017) Coral cell separation and isolation by fluorescence-activated cell sorting (FACS). BMC cell biology, 18(1):30.
    • Traylor-Knowles N, Connelly MT (2017) What Is Currently Known About the Effects of Climate Change on the Coral Immune Response. Current Climate Change Reports, 3(4):252–260.
    • Grover H, Rieger S (2017) Reactive oxygen species and neuroepithelial interactions during wound healing. Regenerative Engineering and Developmental Biology, :23–38. https://doi.org/10.1201/9781315120188-3
    • Lisse TS, Rieger S (2017) IKKα regulates human keratinocyte migration through surveillance of the redox environment. Journal of cell science, 130(5):975–988.
    • Yan Q, Zhai L, Zhang B, Dallman JE (2017) Spatial patterning of excitatory and inhibitory neuropil territories during spinal circuit development. The Journal of comparative neurology, 525(7):1649–1667.
    • Hung CY, Volkmar B, Baker JD, Bauer JW, Gussoni E, Hainzl S, Klausegger A, Lorenzo J, Mihalek I, Rittinger O, Tekin M, Dallman JE, Bodamer OA (2017) A defect in the inner kinetochore protein CENPT causes a new syndrome of severe growth failure. PloS one, 12(12):e0189324.

  • 2016

    • Afkhami ME, Stinchcombe JR (2016) Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi. Molecular ecology, 25(19):4946–4962.
    • Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobián-Güemes AG, Coutinho FH, Dinsdale EA, Felts B, Furby KA, George EE, Green KT, Gregoracci GB, Haas AF, Haggerty JM, Hester ER, Hisakawa N, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, Oliveira LS de, 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 (2016) Corrigendum: Lytic to temperate switching of viral communities. Nature, 539(7627):123.
    • Silveira CB, Rohwer FL (2016) Piggyback-the-Winner in host-associated microbial communities. npj Biofilms and Microbiomes, 2(1) https://doi.org/10.1038/npjbiofilms.2016.10
    • Lu H-L, Chang C-C, Wilson ACC (2016) Amino acid transporters implicated in endocytosis of Buchnera during symbiont transmission in the pea aphid. EvoDevo, 7:24.
    • Duncan RP, Feng H, Nguyen DM, Wilson ACC (2016) Gene Family Expansions in Aphids Maintained by Endosymbiotic and Nonsymbiotic Traits. Genome biology and evolution, 8(3):753–764.
    • Lu H-L, Price DRG, Wikramanayake A, Chang C-C, Wilson ACC (2016) Ontogenetic differences in localization of glutamine transporter ApGLNT1 in the pea aphid demonstrate that mechanisms of host/symbiont integration are not similar in the maternal versus embryonic bacteriome. EvoDevo, 7(1):1.
    • Afkhami ME, Strauss SY (2016) Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales. Ecology, 97(5):1159–1169.
    • Haas AF, Fairoz MFM, Kelly LW, Nelson CE, Dinsdale EA, Edwards RA, Giles S, Hatay M, Hisakawa N, Knowles B, Lim YW, Maughan H, Pantos O, Roach TNF, Sanchez SE, Silveira CB, Sandin S, Smith JE, Rohwer F (2016) Global microbialization of coral reefs. Nature Microbiology, 1(6) https://doi.org/10.1038/nmicrobiol.2016.429.
    • Somera TM, Bailey B, Barott K, Grasis J, Hatay M, Hilton BJ, Hisakawa N, Nosrat B, Nulton J, Silveira CB, Sullivan C, Brainard RE, Rohwer F (2016) Energetic differences between bacterioplankton trophic groups and coral reef resistance. Proceedings of the Royal Society B: Biological Sciences, 283(1829):20160467.
    • Quistad SD, Traylor-Knowles N (2016) Precambrian origins of the TNFR superfamily. Cell death discovery, 2:16058.
    • Traylor-Knowles N (2016) Distinctive wound-healing characteristics in the corals Pocillopora damicornis and Acropora hyacinthus found in two different temperature regimes. Marine biology, 163(11):231.
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Contact

Afkhami – michelle.afkhami@miami.edu

Dallman – j.dallman@miami.edu

Lariviere – pj.lariviere@miami.edu

Luque – antoni.luque@miami.edu

Quimbayo – quimbayojp@miami.edu

Rieger – srieger@miami.edu

Rosser – neil.rosser@miami.edu

Silveira – cynthiasilveira@miami.edu

Traylor-Knowles – ntraylorknowles@rsmas.miami.edu

Wilson – acwilson@miami.edu

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