Zhang, Jia, Schneller, Nadja M., Field, Matt A., Chan, Cheong Xin, Miller, David J., Strugnell, Jan M., Riginos, Cynthia, Bay, Line, and Cooke, Ira (2024) Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Molecular Ecology, 33 (16). e17468.

Mason, Benjamin, Hayward, David C., Moya, Aurelie, Cooke, Ira, Sorenson, Alanna, Brunner, Ramona, Andrade Rodriguez, Natalia, Huerlimann, Roger, Bourne, David G., Schaeffer, Patrick, Grinblat, Mila, Ravasi, Timothy, Ueda, Nobuo, Tang, Sen-Lin, Ball, Eldon E., and Miller, David J. (2024) Microbiome manipulation by corals and other Cnidaria via quorum quenching. Current Biology, 34. pp. 3226-3232.

Horowitz, Jeremy, Quattrini, Andrea M., Brugler, Mercer R., Miller, David J., Pahang, Kristina, Bridge, Tom C.L., and Cowman, Peter F. (2023) Bathymetric evolution of black corals through deep time. Proceedings of the Royal Society of London Series B, Biological Sciences, 290 (2008). 20231107.

Grinblat, Mila, Eyal-Shaham, Lee, Eyal, Gal, Ben-Zvi, Or, Harii, Saki, Morita, Masaya, Sakai, Kazuhiko, Hirose, Mamiko, Miller, David J., and Loya, Yossi (2023) Energy allocation trade-offs as a function of age in fungiid corals. Frontiers in Marine Science, 10. 1113987.

Mason, Benjamin M., Koyanagi, Mitsumasa, Sugihara, Tomohiro, Iwasaki, Makoto, Slepak, Vladlen, Miller, David J., Sakai, Yusuke, and Terakita, Akihisa (2023) Multiple opsins in a reef-building coral, Acropora millepora. Scientific Reports, 13. 1628.

Cumming, Graeme S., Adamska, Maja, Barnes, Michele L., Barnett, Jon, Bellwood, David R., Cinner, Joshua E., Cohen, Philippa J., Donelson, Jennifer M., Fabricius, Katharina, Grafton, R. Quentin, Grech, Alana, Gurney, Georgina G., Hoegh-Guldberg, Ove, Hoey, Andrew S., Hoogenboom, Mia O., Lau, Jacqueline, Lovelock, Catherine E., Lowe, Ryan, Miller, David J., Morrison, Tiffany H., Mumby, Peter J., Nakata, Martin, Pandolfi, John M., Peterson, Garry D., Pratchett, Morgan S., Ravasi, Timothy, Riginos, Cynthia, Rummer, Jodie L., Schaffelke, Britta, Wernberg, Thomas, and Wilson, Shaun K. (2023) Research priorities for the sustainability of coral-rich western Pacific seascapes. Regional Environmental Change, 23 (2). 66.

O'Brien, Paul A., Tan, Shangjin, Frade, Pedro R., Robbins, Steven J., Engelberts, J. Pamela, Bell, Sara C., Vanwonterghem, Inka, Miller, David J., Webster, Nicole S., Zhang, Guojie, and Bourne, David G. (2023) Validation of key sponge symbiont pathways using genome-centric metatranscriptomics. Environmental Microbiology, 25 (12). pp. 3207-3224.

Xu, Jane, Mead, Oliver, Moya, Aurelie, Caglar, Cüneyt, Miller, David J., Adamski, Marcin, and Adamska, Maja (2023) Wound healing and regeneration in the reef building coral Acropora millepora. Frontiers in Ecology and Evolution, 10. 979278.

Kuek, Felicity, Motti, Cherie, Zhang, Jia, Cooke, Ira R., Todd, Jonathan D., Miller, David J., Bourne, David G., and Raina, Jean-Baptiste (2022) DMSP production by coral-associated bacteria. Frontiers in Marine Science, 9. 869574.

Zhang, Jia, Richards, Zoe T., Adam, Arne A.S., Chan, Cheong Xin, Shinzato, Chuya, Gilmour, James, Thomas, Luke, Strugnell, Jan M., Miller, David J., and Cooke, Ira (2022) Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum. Molecular Biology and Evolution, 39 (10). msac201.

Schmidt, Casey A., Cooke, Ira, Wilson, David T., Miller, David J., Peigneur, Steve, Tytgat, Jan, Field, Matthew, Takjoo, Rozita, Smout, Michael J., Loukas, Alex, and Daly, Norelle L. (2022) Newly Discovered Peptides from the Coral Heliofungia actiniformis Show Structural and Functional Diversity. Journal of Natural Products, 85 (7). pp. 1789-1798.

Ying, Hua, Hayward, David C., Klimovich, Alexander, Bosch, Thomas C.U., Baldassarre, Laura, Neeman, Teresa, Foret, Sylvain, Huttley, Gavin, Reitzel, Adam M., Fraune, Sebastian, Ball, Eldon E., and Miller, David (2022) The Role of DNA Methylation in Genome Defense in Cnidaria and Other Invertebrates. Molecular Biology and Evolution, 39 (2). msac018.

Rosenberg, Yaeli, Simon-Blecher, Noa, Lalzar, Maya, Yam, Ruth, Shemesh, Aldo, Alon, Shahar, Perna, Gabriela, Cardenas, Anny, Voolstra, Christian R., Miller, David J., and Levy, Oren (2022) Urbanization comprehensively impairs biological rhythms in coral holobionts. Global Change Biology, 28 (10). pp. 3349-3364.

Ball, Eldon E., Hayward, David C., Bridge, Tom C.L., and Miller, David J. (2021) Acropora - The most-studied coral genus. In: Boutet, Agnès, and Schierwater, Bernd, (eds.) Handbook of Marine Model Organisms in Experimental Biology: Established and Emerging. CRC Press, Boca Raton, FL, USA, pp. 173-193.

Mason, B., Cooke, I., Moya, A., Augustin, R., Lin, M.F., Satoh, N., Bosch, T.C.G., Bourne, D.G., Hayward, D.C., Andrade, N., Forêt, S., Ying, H., Ball, E.E., and Miller, D.J. (2021) AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones. Developmental and Comparative Immunology, 114. 103866.

Grinblat, Mila, Cooke, Ira, Shlesinger, Tom, Ben-Zvi, Or, Loya, Yossi, Miller, David J., and Cowman, Peter F. (2021) Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals). Molecular Phylogenetics and Evolution, 164. 107265.

Petrou, K., Nunn, B. L., Padula, M. P., Miller, D. J., and Nielsen, D. A. (2021) Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral acropora millepora. Scientific Reports, 11. p. 19061.

Praher, Daniela, Zimmermann, Bob, Dnyansagar, Rohit, Miller, David J., Moya, Aurelie, Modepalli, Vengamanaidu, Fridrich, Arie, Sher, Daniel, Friis-Møller, Lene, Sundberg, Per, Fôret, Sylvain, Ashby, Regan, Moran, Yehu, and Technau, Ulrich (2021) Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proceedings of the Royal Society B: Biological Sciences, 288 (1945). 20203169.

Pereira Luz, Bruna Louise, Miller, David, and Kitahara, Marcelo Visentini (2021) High regenerative capacity is a general feature within colonial dendrophylliid corals (Anthozoa, Scleractinia). Journal of Experimental Zoology. Part B: Molecular and Developmental Evolution, 336 (3). pp. 281-292.

O'Brien, Paul A., Andreakis, Nikolaos, Tan, Shangjin, Miller, David, Webster, Nicole S., Zhang, Guojie, and Bourne, David G. (2021) Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Molecular Ecology, 30 (15). pp. 3768-3782.

Andrade Rodriguez, N., Moya, A., Jones, R., Miller, D.J., and Cooke, I. (2021) The significance of genotypic diversity in coral competitive interaction: a transcriptomic perspective. Frontiers in Ecology and Evolution, 9. 659360.

Mohamed, Amin R., Chan, Cheong Xin, Ragan, Mark A., Zhang, Jia, Cooke, Ira, Ball, Eldon E., and Miller, David J. (2020) Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports, 12 (4). pp. 534-443.

O'Brien, Paul A., Tan, Shangjin, Yang, Chentao, Frade, Pedro R., Andreakis, Nikolaos, Smith, Hillary A., Miller, David J., Webster, Nicole S., Zhang, Guojie, and Bourne, David G. (2020) Diverse coral reef invertebrates exhibit patterns of phylosymbiosis. ISME Journal: multidisciplinary journal of microbial ecology, 14. pp. 2211-2222.

Mohamed, Amin R., Andrade, Natalia, Moya, Aurelie, Chan, Cheong Xin, Negri, Andrew P., Bourne, David G., Ying, Hua, Ball, Eldon E., and Miller, David J. (2020) Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Molecular Ecology, 29 (20). pp. 3921-3937.

Hehenberger, Elisabeth, Eitel, Michael, Fortunato, Sofia A.V., Miller, David J., Keeling, Patrick J., and Cahill, Michael A. (2020) Early eukaryotic origins and metazoan elaboration of MAPR family proteins. Molecular Phylogenetics and Evolution, 148. 106814.

Cooke, Ira, Ying, Hua, Forêt, Sylvain, Bongaerts, Pim, Strugnell, Jan M., Simakov, Oleg, Zhang, Jia, Field, Matt A., Rodriguez-Lanetty, Mauricio, Bell, Sara C., Bourne, David G., van Oppen, Madeleine J.H., Ragan, Mark A., and Miller, David J. (2020) Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. Science Advances, 6 (48). eabc6318.

Schmidt, Casey A., Wilson, David T., Cooke, Ira, Potriquet, Jeremy, Tungatt, Katie, Muruganandah, Visai, Boote, Chloe, Kuek, Felicity, Miles, John J., Kupz, Andreas, Ryan, Stephanie, Loukas, Alex, Bansal, Paramjit S., Takjoo, Rozita, Miller, David J., Peigneur, Steve, Tytgat, Jan, and Daly, Norelle (2020) Identification and characterization of a peptide from the stony coral Heliofungia actiniformis. Journal of Natural Products, 83 (11). pp. 3454-3463.

Suryawanshi, Ashwini, Schaefer, Karolin, Holz, Oliver, Apel, David, Lange, Ellen, Hayward, David C., Miller, David J., and Hassel, Monika (2020) What lies beneath: Hydra provides cnidarian perspectives into the evolution of FGFR docking proteins. Development Genes and Evolution, 230. pp. 227-238.

Fingerhut, Legana C. H. W., Miller, David J., Strugnell, Jan M., Daly, Norelle L., and Cooke, Ira R. (2020) ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics, 36 (21). btaa653.

Cowman, Peter F., Quattrini, Andrea M., Bridge, Tom C.L., Watkins-Colwell, Gregory J., Fadli, Nur, Grinblat, Mila, Roberts, T. Edward, McFadden, Catherine S., Miller, David J., and Baird, Andrew H. (2020) An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Molecular Phylogenetics and Evolution, 153. 106944.

Langlois, Tim, Goetze, Jordan, Bond, Todd, Monk, Jacquomo, Abesamis, Rene A., Asher, Jacob, Barrett, Neville, Bernard, Anthony T. F., Bouchet, Phil J., Birt, Matthew J., Cappo, Mike, Currey-Randall, Leanne M., Driessen, Damon, Fairclough, David V., Fullwood, Laura A.F., Gibbons, Brooke A., Harasti, David, Heupel, Michelle R., Hicks, Jamie, Holmes, Thomas H., Huveneers, Charlie, Ierodiaconou, Daniel, Jordan, Alan, Knott, Nathan A., Lindfield, Steve, Malcolm, Hamish A., McLean, Dianne, Meekan, Mark, Miller, David, Mitchell, Peter J., Newman, Stephen J., Radford, Ben, Rolim, Fernanda A., Saunders, Benjamin J., Stowar, Marcus, Smith, Adam N.H., Travers, Michael J., Wakefield, Corey B., Whitmarsh, Sasha K., Williams, Joel, and Harvey, Euan S. (2020) A field and video annotation guide for baited remote underwater stereo-video surveys of demersal fish assemblages. Methods in Ecology and Evolution, 11 (11). pp. 1401-1409.

Attenborough, Rosalind M.F., Hayward, David C., Wiedemann, Ursula, Foret, Sylvain, Miller, David J., and Ball, Eldon E. (2019) Expression of the neuropeptides RFamide and LWamide during development of the coral Acropora millepora in relation to settlement and metamorphosis. Developmental Biology, 446 (1). pp. 56-67.

Lehmann, Robert, Lightfoot, Damien, Schunter, Celia, Michell, Craig T., Ohyanagi, Hajime, Mineta, Katsuhiko, Foret, Sylvain, Berumen, Michael L., Miller, David J., Aranda, Manuel, Gojobori, Takashi, Munday, Philip L., and Ravasi, Timothy (2019) Finding Nemo's genes: a chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Molecular Ecology Resources, 19 (3). pp. 570-585.

O'Brien, Paul, Webster, Nicole S., Miller, David J., and Bourne, David G. (2019) Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio, 10 (1). e02241-18.

Cooke, Ira, Mead, Oliver, Whalen, Casey, Boote, Chloe, Moya, Aurelie, Ying, Hua, Robbins, Steven, Strugnell, Jan M., Darling, Aaron, Miller, David, Voolstra, Christian, and Adamska, Maya (2019) Molecular techniques and their limitations shape our view of the holobiont. Zoology, 137. 125695.

Jaspers, Cornelia, Fraune, Sebastian, Arnold, A. Elizabeth, Miller, David J., Bosch, Thomas C.G., Voolstra, Christian R., Adamska, Maja, Ainsworth, Tracy, Ball, Eldon, Boote, Chlöe, Bourne, David, Butterfield, Nicholas J., Chan, Cheong Xin, Cooke, Ira, Cowman, Peter F., Darling, Aaron, Davy, Simon K., Mohamed, Amin, Fabricius, Katharina, Valero Fortunato, Sofia V., Hernandez Agreda, Alejandra, Hoogenboom, Mia, Moya, Aurelie, Pita, Lucia, Ragan, Mark A., Robbins, Steven J., Andrade Rodriguez, Natalia R., Sakamaki, Kazuhiro, Schoepf, Verena, Seemann, Thorsten, Shinzato, Chuya, Stolarski, Jarosław, Strugnell, Jan, Takahashi, Shunichi, Tang, Sen-Lin, Webster, Nicole N, Whitelaw, Brooke, and Ying, Hua (2019) Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology, 133. pp. 81-87.

Lin, Mei-Fang, Takahashi, Shunichi, Foret, Sylvain, Davy, Simon K., and Miller, David J. (2019) Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species. Biology Open, 8 (3). bio038281.

Aguilar, Catalina, Raina, Jean-Baptiste, Fôret, Sylvain, Hayward, David C., Lapeyre, Bruno, Bourne, David G., and Miller, David J. (2019) Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress. BMC Genomics, 20. 148.

Robbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W., Bourne, David G., Ball, Eldon, Beeden, Roger, Berumen, Michael, Aranda, Manuel, Ravasi, Timothy, Bongaerts, Pim, Hoegh-Guldberg, Ove, Cooke, Ira, Leggat, Bill, Sprungala, Susanne, Fitzgerald, Anna, Shang, Catherine, Lundgren, Petra, Fyffe, Theresa, Rubino, Francesco, van Oppen, Madeleine, Weynberg, Karen, and Bells, Sara C. (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 (12). pp. 2090-2100.

Ying, Hua, Hayward, David C., Cooke, Ira, Wang, Weiwen, Moya, Aurelie, Siemering, Kirby R., Sprungala, Susanne, Ball, Eldon E., Foret, Sylvain, and Miller, David J. (2019) The whole-genome sequence of the coral Acropora millepora. Genome Biology and Evolution, 11 (5). pp. 1374-1379.

Ying, Hua, Cooke, Ira, Sprungala, Susanne, Wang, Weiwen, Hayward, David C., Tang, Yurong, Huttley, Gavin, Ball, Eldon E., Forêt, Sylvain, and Miller, David J. (2018) Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biology, 19. 175.

Mohamed, Amin R., Cumbo, Vivian R., Harii, Saki, Shinzato, Chuya, Chan, Cheong Xin, Ragan, Mark A., Satoh, Nori, Ball, Eldon E., and Miller, David J. (2018) Deciphering the nature of the coral-Chromera association. ISME Journal: multidisciplinary journal of microbial ecology, 12 (3). pp. 776-790.

Sorek, Michal, Schnytzer, Yisrael, Ben-Asher, Hiba Waldman, Caspi, Vered Chalifa, Chen, Chii-Shiarng, Miller, David J., and Levy, Oren (2018) Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium. Microbiome, 6. 83.

Liu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J.H., Voolstra, Christian R., Ragan, Mark A., and Chan, Cheong Xin (2018) Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1. 95.

Quattrini, Andrea M., Faircloth, Brant C., Dueñas, Luisa F., Bridge, Tom C.L., Brugler, Mercer R., Calixto-Botía, Iván F., DeLeo, Danielle M., Forêt, Sylvain, Herrera, Santiago, Lee, Simon M.Y., Miller, David J., Prada, Carlos, Rádis-Baptista, Gandhi, Ramírez-Portilla, Catalina, Sánchez, Juan A., Rodríguez, Estefanía, and McFadden, Catherine S. (2018) Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems. Molecular Ecology Resources, 18 (2). pp. 281-295.

Lin, Mei-Fang, Moya, Aurelie, Ying, Hua, Chen, Chaolun Allen, Cooke, Ira, Ball, Eldon E., Forȇt, Sylvain, and Miller, David J. (2017) Analyses of corallimorpharian transcriptomes provide new perspectives on the evolution of calcification in the Scleractinia (corals). Genome Biology and Evolution, 9 (1). pp. 150-160.

Chuang, Yaoyang, Kitahara, Marcelo, Fukami, Hironobu, Tracey, Dianne, Miller, David J., and Chen, Chaolun Allen (2017) Loss and gain of group I introns in the mitochondrial cox1 gene of the scleractinia (cnidaria; anthozoa). Zoological Studies, 56 (9).

Torda, Gergely, Donelson, Jennifer M., Aranda, Manuel, Barshis, Daniel J., Bay, Line, Berumen, Michael L., Bourne, David G., Cantin, Neal, Foret, Sylvain, Matz, Mikhail, Miller, David J., Moya, Aurelie, Putnam, Hollie M., Ravasi, Timothy, van Oppen, Madeleine J.H., Vega Thurber, Rebecca, Vidal-Dupiol, Jeremie, Voolstra, Christian R., Watson, Sue-Ann, Whitelaw, Emma, Willis, Bette L., and Munday, Philip L. (2017) Rapid adaptive responses to climate change in corals. Nature Climate Change, 7. pp. 627-636.

Aguilar, Catalina, Raina, Jean-Baptiste, Motti, Cherie A., Foret, Sylvain, Hayward, David C., Lapeyre, Bruno, Bourne, David G., and Miller, David J. (2017) Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals. BMC Genomics, 18. 612.

Wessels, Wiebke, Sprungala, Susanne, Watson, Sue-Ann, Miller, David J., and Bourne, David G. (2017) The microbiome of the octocoral Lobophytum pauciflorum: minor differences between sexes and resilience to short-term stress. FEMS Microbiology Ecology, 93 (5). pp. 1-13.

Moya, Aurelie, Sakamaki, Kazuhiro, Mason, Benjamin M., Huisman, Lotte, Forêt, Sylvain, Weiss, Yvonne, Bull, Tara, Tomii, Kentaro, Imai, Kenichiro, Hayward, David C., Ball, Eldon E., and Miller, David J. (2016) Functional conservation of the apoptotic machinery from coral to man: the diverse and complex Bcl-2 and caspase repertoires of Acropora millepora. BMC Genomics, 17. 62. pp. 1-20.

Capel, K.C.C., Migotto, A.E., Zilberberg, C., Lin, M.F., Forsman, Z., Miller, D.J., and Kitahara, M.V. (2016) Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): implications for species identification. Gene, 590 (2). pp. 270-277.

Lin, Mei Fang, Chou, Wen Hwa, Kitahara, Marcelo V., Chen, Chao Lun Allen, Miller, David John, and Forêt, Sylvain (2016) Corallimorpharians are not "naked corals": insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses. PeerJ, 4. e2463. pp. 1-16.

Bosch, Thomas C.G., and Miller, David J. (2016) The Holobiont Imperative: perspectives from early emerging animals. Springer, Vienna, Austria.

Moya, Aurelie, Howes, Ella L., Lacoue-Labarthe, Thomas, Foret, Sylvain, Hanna, Bishoy, Medina, Mónica, Munday, Philip L., Ong, Jue-Sheng, Teyssié, Jean-Louis, Torda, Gergely, Watson, Sue-Ann, Miller, David J., Bijma, Jelle, and Gattuso, Jean-Pierre (2016) Near-future pH conditions severely impact calcification, metabolism and the nervous system in the pteropod Heliconoides inflatus. Global Change Biology, 22 (12). pp. 3888-3900.

Mohamed, A.R., Cumbo, V., Harii, S., Shinzato, C., Chan, C.X., Ragan, M.A., Bourne, D.G., Willis, B.L., Ball, E.E., Satoh, N., and Miller, D.J. (2016) The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology, 25 (13). pp. 3127-3141.

Lutz, Adrian, Raina, Jean-Baptiste, Motti, Cherie A., Miller, David J., and van Oppen, Madeleine J.H. (2015) Host coenzyme Q redox state is an early biomarker of thermal stress in the coral Acropora millepora. PLoS ONE, 10 (10). e0139290. pp. 1-18.

Bertucci, A., Forêt, S., Ball, E.E., and Miller, D.J. (2015) Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals. Molecular Ecology, 24 (17). pp. 4489-4504.

Moya, A., Huisman, L., Fêret, S., Gattuso, J-P., Hayward, D.C., Ball, E.E., and Miller, D.J. (2015) Rapid acclimation of juvenile corals to CO2-mediated acidification by upregulation of heat shock protein and Bcl-2 genes. Molecular Ecology, 24 (2). pp. 438-452.

Sakamaki, Kazuhiro, Imai, Kenichiro, Tomii, Kentaro, and Miller, David J. (2015) Evolutionary analyses of caspase-8 and its paralogs: deep origins of the apoptotic signaling pathways. BioEssays, 37 (7). pp. 767-776.

Voolstra, Christian R., Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., Van Oppen, Madeleine J.H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra, Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva, and Fyffe, Theresa (2015) The ReFuGe 2020 Consortium: using "omics" approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2. 68. pp. 1-8.

Hayward, David C., Grasso, Lauretta C., Saint, Robert, Miller, David J., and Ball, Eldon E. (2015) The organizer in evolution–gastrulation and organizer gene expression highlight the importance of Brachyury during development of the coral, Acropora millepora. Developmental Biology, 399 (2). pp. 337-347.

Bosch, Thomas C.G., Adamska, Maja, Augustin, René, Domazet-Loso, Tomislav, Foret, Sylvain, Fraune, Sebastian, Funayama, Noriko, Grasis, Juris, Hamada, Mayuko, Hatta, Masayuki, Hobmayer, Bert, Kawai, Kotoe, Klimovich, Alexander, Manuel, Michael, Shinzato, Chuya, Technau, Uli, Yum, Seungshic, and Miller, David J. (2014) How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans. BioEssays, 36 (12). pp. 1185-1194.

Lutz, Adrian, Motti, Cherie A., Freckelton, Mamie L., Van Oppen, Madeleine J.H., Miller, David J., and Dunlap, Walter C. (2014) Simultaneous determination of coenzyme Q and plastoquinone redox states in the coral-Symbiodinium symbiosis during thermally induced bleaching. Journal of Experimental Marine Biology and Ecology, 455. pp. 1-6.

Kitahara, Marcelo V., Lin, Mei-Fang, Forêt, Sylvain, Huttley, Gavin, Miller, David J., and Chen, Chaolun Allen (2014) The "naked coral" hypothesis revisited: evidence for and against Scleractinian monophyly. PLoS One, 9 (4). e94774. pp. 1-13.

Lin, Mei-Fang, Kitahara, Marcelo Visentini, Luo, Haiwei, Tracey, Dianne, Geller, Jonathan, Fukami, Hironobu, Miller, David John, and Chen, Chaolun Allen (2014) Mitochondrial genome rearrangements in the Scleractinia/Corallimorpharia complex: implications for coral phylogeny. Genome Biology and Evolution, 6 (5). pp. 1086-1095.

Sakamaki, Kazuhiro, Shimizu, Kouhei, Iwata, Hiroaki, Imai, Kenichiro, Satou, Yutaka, Funayama, Noriko, Nozaki, Masami, Yajima, Mamiko, Nishimura, Osamu, Higuchi, Mayura, Chiba, Kumiko, Yoshimoto, Michi, Kimura, Haruna, Gracey, Andrew Y., Shimizu, Takashi, Tomii, Kentaro, Gotoh, Osamu, Akasaka, Koji, Sawasaki, Tatsuya, and Miller, David J. (2014) The apoptotic initiator Caspase-8: its functional ubiquity and genetic diversity during animal evolution. Molecular Biology and Evolution, 31 (12). pp. 3282-3301.

Richards, Z.T., Miller, D.J., and Wallace, C.C. (2013) Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Molecular Phylogenetics and Evolution, 69 (3). pp. 837-851.

Lin, Mei-Fang, Chen, Chaolun Allen, and Miller, David J. (2013) Asexual reproduction by marginal budding in the tropical corallimorpharian Ricordea yuma (Corallimorpharia; Ricordeidae). Galaxea, Journal of Coral Reef Studies, 15 (2). pp. 41-42.

Weiss, Yvonne, Forêt, Sylvain, Hayward, David C., Ainsworth, Tracy, King, Rob, Ball, Eldon E., and Miller, David J. (2013) The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants. BMC Genomics, 14. 400. pp. 1-12.

Kitahara, Marcelo V., Cairns, Stephen D., Stolarski, Jaroslaw, and Miller, David J. (2013) Deltocyathiidae, an early-diverging family of Robust corals (Anthozoa, Scleractinia). Zoologica Scripta, 42 (2). pp. 201-212.

Hamada, Mayuko, Shoguchi, Eiichi, Shinzato, Chuya, Kawashima, Takeshi, Miller, David J., and Satoh, Nori (2013) The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations. Molecular Biology and Evolution, 30 (1). pp. 167-176.

Ramos-Silva, Paula, Kaandorp, Jaap, Huisman, Lotte, Marie, Benjamin, Zanella-Cléon, Isabelle, Guichard, Nathalie, Miller, David J., and Marin, Frédéric (2013) The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling. Molecular Biology and Evolution, 30 (9). pp. 2099-2112.

Reyes-Bermudez, Alejandro, Miller, David J., and Sprungala, Susanne (2012) The neuronal calcium sensor protein acrocalcin: a potential target of calmodulin regulation during development in the coral Acropora millepora. PLoS ONE, 7 (12). 0051689. pp. 1-8.

Moya, A., Huisman, L., Ball, E.E., Hayward, D.C., Grasso, L.C., Chua, C.M., Woo, H.N., Gattuso, J.-P, Forêt, S., and Miller, D.J. (2012) Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification. Molecular Ecology, 21 (10). pp. 2440-2454.

Bellantuono, Anthony J., Granados-Cifuentes, Camila, Miller, David J., Hoegh-Guldberg, Ove, and Rodriguez-Lanetty, Mauricio (2012) Coral thermal tolerance: tuning gene expression to resist thermal stress. PLoS ONE, 7 (11). e50685. pp. 1-14.

Puill-Stephan, Eneour, Seneca, François O., Miller, David J., van Oppen, Madeleine J.H., and Willis, Bette L. (2012) Expression of putative immune response genes during early ontogeny in the coral Acropora millepora. PLoS ONE, 7 (7). e39099. pp. 1-5.

Kaniewska, Paulina, Campbell, Paul R., Kline, David I., Rodriguez-Lanetty, Mauricio, Miller, David J., Dove, Sophie, and Hoegh-Guldberg, Ove (2012) Major cellular and physiological impacts of ocean acidification on a reef building coral. PLoS ONE, 7 (4). e34659. pp. 1-12.

Emblem, Ase, Karlsen, Bard Ove, Evertsen, Jussi, Miller, David J., Moum, Truls, and Johansen, Steinar D. (2012) Mitogenome polymorphism in a single branch sample revealed by SOLiD deep sequencing of the Lophelia pertusa coral genome. Gene, 506 (2). pp. 344-349.

Lin, Mei-Fang, Kitahara, Marcelo Visentini, Tachikawa, Hiroyuki, Fukami, Hironobu, Miller, David John, and Chen, Chaolun Allen (2012) Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications. Molecular Phylogenetics and Evolution, 65 (1). pp. 323-328.

Kitahara, Marcelo V., Stolarski, Jaroslaw, Cairns, Stephen D., Benzoni, Francesca, Stake, Joel L., and Miller, David J. (2012) The first modern solitary Agariciidae (Anthozoa, Scleractinia) revealed by molecular and microstructural analysis. Invertebrate Systematics, 26 (3). pp. 303-315.

Attenborough, Rosalind M.F., Hayward, David C., V. Kitahara, Marcelo, Miller, David J., and Ball, Eldon E. (2012) A "neural" enzyme in nonbilaterian animals and algae: preneural origins for peptidylglycine α-amidating monooxygenase. Molecular Biology and Evolution, 29 (10). pp. 3095-3109.

Ainsworth, T.D., Wasmund, K., Ukani, L., Seneca, F., Yellowlees, D., Miller, D., and Leggat, W. (2011) Defining the tipping point. A complex cellular life/death balance in corals in response to stress. Scientific Report, 1. 160. pp. 1-9.

Miller, David, Ball, Eldon E., Foret, Sylvain, and Satoh, Nori (2011) Coral genomics and transcriptomics — ushering in a new era in coral biology. Journal of Experimental Marine Biology and Ecology, 408 (1-2). pp. 114-119.

Hayward, David C., Hetherington, Suzannah, Behm, Carolyn A., Grasso, Lauretta C., Forêt, Sylvain, Miller, David J., and Ball, Eldon E. (2011) Differential gene expression at coral settlement and metamorphosis: a subtractive hybridization study. PLoS ONE, 6 (10). e26411. pp. 1-18.

Shinzato, Chuya, Shoguchi, Eiichi, Kawashimi, Takeshi, Hamada, Mayuko, Hisata, Kanako, Tanaka, Makiko, Fujie, Manabu, Fujiwara, Mayuki, Koyanagi, Ryo, Ikuta, Tetsuro, Fujiyama, Asao, Miller, David J., and Satoh, Nori (2011) Using the Acropora digitifera genome to understand coral responses to environmental change. Nature, 476 (7360). pp. 320-323.

Iguchi, Akira, Shinzato, Chuya , Forêt, Sylvain, and Miller, David J. (2011) Identification of fast-evolving genes in the scleractinian Coral Acropora using comparative EST analysis. PLoS ONE, 6 (6). e20140. pp. 1-6.

Grasso, L.C., Negri, A.P., Fôret, S., Saint, R., Hayward, D.C., Miller, D.J., and Ball, E.E. (2011) The biology of coral metamorphosis: molecular responses of larvae to inducers of settlement and metamorphosis. Developmental Biology, 353 (2). pp. 411-419.

Lange, Christina, Hemmrich, Georg, Klostermeier, Ulrich C. , López-Quintero, Javier A. , Miller, David J., Rahn, Tasja, Weiss, Yvonne, Bosch, Thomas C.G., and Rosenstiel, Philip (2011) Defining the origins of the NOD-like receptor system at the base of animal evolution. Molecular Biology and Evolution, 28 (5). pp. 1687-1702.

Levy, O., Kaniewska, P., Alon, S., Eisenberg, E., Karako-Lampert , S., Bay, L.K., Reef, R., Rodriguez-Lanetty , M., Miller, D.J., and Hoegh-Guldberg, O. (2011) Complex diel cycles of gene expression in coral-algal symbiosis. Science, 331 (6014). p. 175.

Forêt, Sylvain, Seneca, François, De Jong, Danielle, Bieller, Annette, Hemmrich, Georg, Augustin, Rene, Hayward, David C., Ball, Eldon E., Bosch, Thomas C.G., Agata, Kiyokazu, Hassel, Monika, and Miller, David J. (2011) Phylogenomics reveals an anomalous distribution of USP genes in metazoans. Molecular Biology and Evolution, 28 (1). pp. 153-161.

Ball, Eldon E., de Jong, Danielle M., Schierwater, Bernd, Shinzato, Chuya, Hayward, David C., and Miller, David J. (2011) Cnidarian gene expression patterns and the origins of bilaterality – are cnidarians reading the same game plan as "higher" animals? In: DeSalle, Rob, and Schierwater, Bernd, (eds.) Key Transitions in Animal Evolution. Science Publishers, Enfield, NH, USA, pp. 197-216.

Stolarski, Jarosław, Kitahara, Marcelo V., Miller, David J., Cairns, Stephen D., Mazur, Maciej, and Meibom, Anders (2011) The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evolutionary Biology, 11. 316. pp. 1-10.

Kitahara, Marcelo V., Cairns, Stephen D., Stolarski, Jaroslaw, Blair, David, and Miller, David J. (2010) A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS ONE, 5 (7). e11490. pp. 1-9.

Ball, Eldon E., and Miller, David J. (2010) Putting placozoans on the (phylogeographic) map. Molecular Ecology, 19 (11). pp. 2181-2183.

Hartmann, Beata, Müller, Michael, Hislop, Nikki R., Roth , Bettina, Tomljenovic, Lucija, Miller, David J., and Reichert, Heinrich (2010) Coral emx-Am can substitute for Drosophila empty spiracles function in head, but not brain development. Developmental Biology, 340 (1). pp. 125-133.

Forêt, Sylvain, Knack, Brent, Houliston, Evelyn, Momose, Tsuyoshi, Manuel, Michael, Quéinnec, Eric, Hayward, David C., Ball, Eldon E., and Miller, David J. (2010) New tricks with old genes: the genetic bases of novel cnidarian traits. Trends in Genetics, 26 (4). pp. 154-158.

Kitahara, Marcelo V., Cairns, Stephen D., and Miller, David J. (2010) Monophyletic origin of Caryophyllia (Scleractinia, Caryophylliidae), with descriptions of six new species. Systematics and Biodiversity, 8 (1). pp. 91-118.

Miller, David J., and Technau, Ulrich (2010) Understanding the evolution of multicellularity; insights from basal metazoans. BioEssays, 32 (2). pp. 175-178.

Richards, Zoe T., Wallace, Carden C., and Miller, David J. (2010) Archetypal elkhorn coral discovered in the Pacific Ocean. Systematics and Biodiversity, 8 (2). pp. 281-288.

Seneca, Francois O., Forêt , Sylvain, Ball, Eldon E., Smith-Keune, Carolyn, Miller, David J., and van Oppen, Madeleine J.H. (2010) Patterns of gene expression in a scleractinian coral undergoing natural bleaching. Marine Biotechnology, 12 (5). pp. 594-604.

Reyes-Bermudez, A., and Miller, D.J. (2009) In vitro culture of cells derived from larvae of the staghorn coral Acropora millepora. Coral Reefs, 28 (4). pp. 859-864.

Miller, David J., and Ball, Eldon E. (2009) The gene complement of the ancestral bilaterian: was Urbilateria a monster? Journal of Biology, 8. 89. pp. 1-4.

Zhou, Yan, Zheng, Huajun, Chen, Yangyi, Zhang, Lei, Wang, Kai, Guo, Jing, Huang, Zhen, Guo, Jing, Huang, Zhen, Zhang, Bo, Huang, Wei, Jin, Ke, Dou, Tonghai, Hasegawa, Masami, Wang, Li, Zhang, Yuan, Zhou, Jie, Tao, Lin, Cao, Zhiwei, Li, Yixue, Vinar, Tomas, Brejova, Brona, Brown, Dan, Li, Ming, Miller, David, Blair, David, Zhong, Yang, Chen, Zhu, Liu, Feng, Hu, Wei, Wang, Zhi-Qin, Zhang, Qin-Hua, Song, Huai-Dong, Chen, Saijuan, Xu, Xuenian, Xu, Bin, Ju, Chuan, Huang, Yucheng, Brindley, Paul, McManus, Donald, Feng, Zheng, Han, Ze-Guang, Lu, Gang, Ren, Shuangxi, Wang, Yuezhu, Wenyi, Gu, Kang, Hui, Chen, Jie, Cheng, Xiaoyun, Chen, Shuting, Wang, Lijun, Yan, Jie, Wang, Biyun, Lv, Zinyan, Jin, Lei, Wang, Bofei, Pu, Shiyin, Zhang, Xianglin, Zhang, Wei, Hu, Qiuping, Zhu, Genfeng, Wang, Jun, Yu, Jun, Wang, Jian, Yang, Huamming, Ning, Zemin, Beriman, Matthew, Wei, Chia-Lin, Ruan, Yijuan, Zhao, Guoping, and Wang, Shengyue (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature, 460. pp. 345-352.

Bay, Line K., Ulstrup, Karin E., Nielsen, H. Bjorn, Jarmer, Hanne, Goffard, Nicolas, Willis, Bette L., Miller, David J., and van Oppen, Madeleine J.H. (2009) Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora. Molecular Ecology, 18 (14). pp. 3062-3075.

Reyes-Bermudez, Alejandro, Lin, Zhiyi, Hayward, David C., Miller, David J., and Ball, Eldon E. (2009) Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora. BMC Evolutionary Biology, 9 (178). - .

Iguchi, Akira, Morita, Masaya, Nakajima, Yuichi, Nishikawa, Akira, and Miller, David (2009) In vitro fertilization efficiency in Acropora digitifera. Zygote, 17. pp. 225-227.

Shinzato, Chuya, Iguchi, Akira, Hayward, David C., Technau, Ulrich, Ball, Eldon E., and Miller, David J. (2008) Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa. BMC Evolutionary Biology, 8. .

Miller, David J., and Ball, Eldon E. (2008) Animal evolution: Trichoplax, trees and taxonomic turmoil. Current Biology, 18 (21). pp. 1003-1005.

Knack, Brent A., Iguchi, Akira, Shinzato, Chuya, Hayward, David C., Ball, Eldon E., and Miller, David J. (2008) Unexpected diversity of cnidarian integrins: expression during coral gastrulation. BMC Evolutionary Biology, 8. - .

Miller, David J., and Ball, Eldon E. (2008) Cryptic complexity captured: the Nematostellar genome reveals its secrets. Trends in Genetics, 24 (1). pp. 1-4.

Schwarz, Jodi A., Brokstein, Peter B., Voolstra, Christian, Terry, Astrid Y., Miller, David J., Szmant , Alina M., Coffroth, Mary Alice, and Medina, Monica (2008) Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics, 9 (97). pp. 1-16.

Alieva, Naila O., Konzen, Karen A., Field, Steven F., Meleshkevitch, Ella A., Hunt, Marguerite E., Beltran Ramirez, Victor, Miller, David J., Wiedenmann, Jorg, Salih, Anya, and Matz, Mikhail V. (2008) Diversity and evolution of coral fluorescent proteins. Public Library of Science ONE , 3 (7). pp. 1-12.

Grasso, Lauretta, Maindonald, John, Rudd, Stephen, Hayward, David C., Saint, Robert, Miller, David J., and Ball, Eldon E. (2008) Microarray analysis identifies candidate genes for key roles in coral development. BMC Genomics, 9. pp. 540-557.

Richards, Zoe T., van Oppen, Madeleine J.H., Wallace, Carden C., Willis, Bette L., and Miller, David J. (2008) Some rare Indo-Pacific coral species are probable hybrids. Public Library of Science ONE , 3 (9). pp. 1-8.

Iguchi, Akira, Márquez, Luis M., Knack, Brent, Shinzato, Chuya, van Oppen, Madeleine J.H., Willis, Bette L., Hardie, Kate, Catmull, Julian, and Miller, David J. (2007) Apparent involvement of a β1 type integrin in coral fertilization. Marine Biotechnology, 9 (6). pp. 760-765.

Ball, Eldon E., de Jong, Danielle M., Schierwater, Bernd, Shinzato, Chuya, Hayward, David C., and Miller, David J. (2007) Implications of cnidarian gene expression patterns for the origins of bilaterality - is the glass half full or half empty? Integrative and Comparative Biology, 47. pp. 701-711.

Levy, O., Appelbaum, L., Leggat, W., Gothlif, Y., Hayward, D.C., Miller, D.J., and Hoegh-Guldberg, O. (2007) Light-responsive cryptochromes from a simple multicellular animal, the coral Acropora millepora. Science, 318 (5849). pp. 467-470.

Hemmrich, Georg, Miller, David J., and Bosch, Thomas C.G. (2007) The evolution of immunity: a low-life perspective. Trends in Immunology, 28 (10). pp. 449-454.

Forêt, S., Kassahn, K.S., Grasso, L.C., Hayward, D.C., Iguchi, A., Ball, E.E., and Miller, D.J. (2007) Genomic and microarray approaches to coral reef conservation biology. Coral Reefs, 26 (3). pp. 475-486.

Antil, Michel, Hayward, David C., Miller, David J., and Ball, Eldon E. (2007) Sequence and expression of four coral G protein-coupled receptors distinct from all classifiable members of the rhodopsin family. Gene, 392 (1-2). pp. 14-21.

Miller, David J., Hemmrich, Georg, Ball, Eldon E., Hayward, David C., Khalturin, Konstantin, Funayama, Noriko, Agata, Kiyokazu, and Bosch, Thomas C.G. (2007) The innate immune repertoire in Cnidaria - ancestral complexity and stochastic gene loss. Genome Biology, 8 (4). R59.1-R59.13.

Fukatsu, Takuya, Onodera, Ken-ichi, Ohta, Yuichiro, Oba, Yuichi, Nakamura, Hideshi, Shintani, Tomoaki, Yoshioka, Yukio, Okamoto, Tetsuji, ten Lohuis, Michael, Miller, David J., Kawachi, Masanobu, and Ojika, Makoto (2007) Zooxanthellamide D, a polyhydroxy polyene amide from a marine dinoflagellate, and chemotaxonomic perspective of the Symbiodinium polyols. Journal of Natural Products, 70 (3). pp. 407-411.

Willis, Bette L., van Oppen, Madeleine J.H., Miller, David J., Vollmer, Steve V., and Ayre, David J. (2006) The role of hybridization in the evolution of reef corals. Annual Review of Ecology, Evolution, and Systematics, 37. pp. 489-517.

de Jong, Danielle M., Hislop, Nikki R., Hayward, David C., Reece-Hoyes, John S., Pontynen, Patricia C., Ball, Eldon, and Miller, David J. (2006) Components of both major axial patterning systems of the Bilateria are differentially expressed along the primary axis of a 'radiate' animal, the anthozoan cnidarian Acropora millepora. Developmental Biology, 298 (2). pp. 632-643.

Kamm, Kai, Schierwater, Bernd, Jakob, Wolfgang, Dellaporta, Stephen L., and Miller, David J. (2006) Axial patterning and diversification in the Cnidaria predate the Hox System. Current Biology, 16 (9). pp. 920-926.

Ball, Eldon E., and Miller, David J. (2006) Phylogeny: the continuing classificatory conundrum of Chaetognaths. Current Biology, 16 (15). pp. 593-596.

Technau, Ulrich, Rudd, Stephen, Maxwell, Peter, Gordon, Paul M.K., Saina, Michael, Grasso, Lauretta C., Hayward, David C., Sensen, Christoph W., Saint, Robert, Holstein, Thomas W., Ball, Eldon E., and Miller, David J. (2005) Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends in Genetics, 21 (12). pp. 633-639.

Miller, David J., Catmull, Julian, Puskeiler, Robert, Tweedale, Helen, Sharples, Frank P., and Hiller, Roger G. (2005) Reconstitution of the peridinin–chlorophyll a protein (PCP): evidence for functional flexibility in chlorophyll binding. Photosynthesis Research, 86 (1-2). pp. 229-240.

Miller, David J., Ball, Eldon E., and Technau, Ulrich (2005) Cnidarians and ancestral genetic complexity in the animal kingdom. Trends in Genetics, 21 (10). pp. 536-539.

St. Pierre, Liam, Masci, Paul P., Filippovich, Igor, Sorokina, Natasha, Marsh, Neville, Miller, David J., and Lavin, Martin F. (2005) Comparative analysis of prothrombin activators from the venom of Australian elapids. Molecular Biology and Evolution, 22 (9). pp. 1853-1864.

Hislop, Nikki R., de Jong, Danielle, Hayward, David C., Ball, Eldon E., and Miller, David J. (2005) Tandem organization of independently duplicated homeobox genes in the basal cnidarian Acropora millepora. Development Genes and Evolution, 215 (5). pp. 268-273.

Miller, David J., and Ball, Eldon E. (2005) Animal evolution: the enigmatic phylum Placozoa revisited. Current Biology, 15 (1). R26-R28.

Ball, Eldon E., Hayward, David C., Saint, Robert, and Miller, David J. (2004) A simple plan: cnidarians and the origins of developmental mechanisms. Nature Reviews: Genetics, 5 (8). pp. 567-577.

Jolodar, Abbas, Fischer, Peter, Büttner, Dietrich W., Miller, David J., Schmetz, Christel, and Brattig, Norbert W. (2004) Onchocerca volvulus: expression and immunolocalization of a nematode cathepsin D-loike lysosomal aspartic protease. Experimental Parasitology, 107 (3-4). pp. 145-156.

Hayward, David C., Miller, David J., and Ball, Eldon E. (2004) Snail expression during embryonic development of the coral Acropora: blurring the diploblast/triplobalst divide. Development Genes and Evolution, 214 (5). pp. 257-260.

Mackenzie, J.B., Munday, P.L., Willis, B.L., Miller, D.J., and van Oppen, M.J.H. (2004) Unexpected patterns of genetic structuring among locations but not colour morphs in Acropora nasuta (Cnidaria; Scleractinia). Molecular Ecology, 13 (1). pp. 9-20.

Kortschak, R. Daniel, Samuel, Gabrielle, Saint, Robert, and Miller, David J. (2003) EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Current Biology, 13 (24). pp. 2190-2195.

Plaza, Serge, de Jong, Danielle M., Gehring, Walter J., and Miller, David J. (2003) DNA-binding characteristics of cnidarian Pax-C and Pax-B proteins in vivo and in vitro: no simple relationship with the Pax-6 and Pax-2/5/8 classes. Journal of Experimental Zoology Part B: molecular and developmental evolution, 299B (1). pp. 26-35.

Miller, Steven W., Hayward, David C., Bunch, Thomas A., Miller, David J., Ball, Eldon E., Bardwell, Vivian J., Zarkower, David, and Brower, Danny L. (2003) A DM domain protein from a coral, Acropora millepora, homologous to proteins important for sex determination. Evolution & Development, 5 (3). pp. 251-258.

Nordström, Karin, Scholten, Ingo, Nordström, Johanna, Larhammer, Dan, and Miller, David (2003) Mutational analysis of the Acropora millepora PaxD paired domain highlights the importance of the linker region for DNA binding. Gene, 320 (27). pp. 81-87.

Marquez, Luis M., Miller, David J., Mackenzie, Jason B., and van Oppen, Madeleine J.H. (2003) Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Molecular Biology and Evolution, 20 (7). pp. 1077-1086.

Miller, David J., and van Oppen, Madeleine J.H. (2003) A 'fair go' for coral hybridization. Molecular Ecology, 12 (4). pp. 805-807.

van Oppen, Madeleine J.H., Willis, Bette L., van Rheede, Teun, and Miller, David J. (2002) Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Molecular Ecology, 11 (8). pp. 1363-1376.

Hayward, David C., Samuel, Gabrielle, Pontynen, Patricia C., Catmull, Julian, Saint, Robert, Miller, David J., and Ball, Eldon E. (2002) Localized expression of a dpp/BMP2/4 ortholog in a coral embryo. National Academy of Sciences. Proceedings, 99 (12). pp. 8106-8111.

Jolodar, Abbas, and Miller, David J. (2002) Construction and expression of aspartic protease from Onchocerca volvulus as ompA fusion protein in a mutant strain of Salmonella typhimurium. Genetics and Molecular Biology, 25 (1). pp. 97-101.

Ball, Eldon E., Hayward, David C., Reece-Hoyes, John S., Hislop, Nikki R., Samuel, Gabrielle, Saint, Robert, Harrison, Peter L., and Miller, David J. (2002) Coral development: from classical embryology to molecular control. International Journal of Developmental Biology, 46 (4). pp. 671-678.

Ball, E.E, Hayward, D.C., Catmull, J., Reece-Hoyes, J.S., Hislop, N.R., Harrison, P.L., and Miller, D.J. (2002) Molecular control of development in the reef coral, Acropora millepora. In: Proceedings of the 9th International Coral Reef Symposium (1) pp. 395-401. From: 9th International Coral Reef Symposium: World Coral Reefs in the New Millenium, 23-27 October 2000, Bali, Indonesia.

Marquez, L.M., van Oppen, M.J.H., Willis, B.L., and Miller, D.J. (2002) Sympatric populations of the highly cross-fertile coral species Acropora hyacinthus and Acropora cytherea are genetically distinct. Proceedings of the Royal Society of London Series B, Biological Sciences, 269 (1497). pp. 1289-1294.

Marquez, L.M., van Oppen, M.J.H., Willis, B.L., Reyes, A., and Miller, D.J. (2002) The highly cross-fertile coral species, Acropora hyacinthus and Acropora cytherea, constitute statistically distinguishable lineages. Molecular Ecology, 11 (8). pp. 1339-1349.

van Oppen, Madeleine J. H., Catmull, Julian, McDonald, Brenda J, Hislop, Nikki R., Hageman, Paul J., and Miller, David J. (2002) The mitochondrial genome of Acropora tenuis (Cnidaria: Scleractinia) contains a large group I intron and a candidate control region. Journal of Molecular Evolution, 55 (1). pp. 1-13.

van Oppen, Madeleine, Palstra, Friso P., Piquet, Anouk M.-T., and Miller, David J. (2001) Patterns of coral-dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host-symbiont selectivity. Proceedings of the Royal Society of London Series B: biological sciences, 268 (1478). pp. 1759-1767.

Samuel, Gabrielle, Miller, David, and Saint, Robert (2001) Conservation of a DPP/BMP signaling pathway in the nonbilateral cnidarian Acropora millepora. Evolution & Development, 3 (4). pp. 241-250.

van Oppen, Madeleine J.H., McDonald, Brenda J., Willis, Bette, and Miller, David J. (2001) The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Molecular Biology and Evolution, 18 (7). pp. 1315-1329.

Hayward, David C., Catmull, Julian, Reece-Hoyes, John S., Berghammer, Heinrich, Dodd, Heather, Hann, Steven J., Miller, David J., and Ball, Eldon E. (2001) Gene structure and larval expression of cnox-2Am from the coral Acropora millepora. Development Genes and Evolution, 211 (1). pp. 10-19.

Van Oppen, M.J.H., Willis, B.L., Van Vugt, H.W.J., and Miller, D.J. (2000) Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyses. Molecular Ecology, 9 (9). pp. 1363-1373.

Miller, David J., Hayward, David C., Reece-Hoyes, John S., Scholten, Ingo, Catmull, Julian, Gehring, Walter J., Callaerts, Patrick, Larsen, Jill E., and Ball, Eldon E. (2000) Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): Implications for the evolution of the Pax gene family. Proceedings of the National Academy of Sciences of the United States of America, 97 (7). pp. 4475-4480.

Miller, David J., and Ball, Eldon E. (2000) The coral Acropora: what it can contribute to our knowledge of metazoan evolution and the evolution of developmental processes. BioEssays, 22 (3). pp. 291-296.

Galliot, Brigitte, and Miller, David (2000) Origin of anterior patterning: how old is our head? Trends in Genetics, 16 (1). pp. 1-5.

Chen, C.L., Miller, David J., Wei, Nuwei Vivian, Dai, Chang-Feng, and Yang, Hsiao-Pei (2000) The ETS/IGS region in a lower animal, the seawhip, Junceella fragilis (Cnidaria: Anthozoa: Octocorallia): compactness, low variation and apparent conservation of a pre-rRNA processing signal with fungi. Zoological Studies, 39 (2). pp. 138-143.

Ten Lohuis, Michael R., and Miller, David (1998) Genetic transformation of dinoflagellates (Amphidinium and Symbiodinium): expression of GUS in microalgae using heterologous promoter constructs. The Plant Journal, 13 (3). pp. 427-435.

Miller, David, and Miles, Annabel (1993) Homeobox genes and the zootype. Nature, 365. pp. 215-216.