A

Alharbi, Adel B., Schmitz, Ulf, Bailey, Charles G., and Rasko, John E.J. (2021) CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Research, 49 (14). pp. 7825-7838.

Alharbi, Adel B., Schmitz, Ulf, Marshall, Amy D., Vanichkina, Darya, Nagarajah, Rajini, Vellozzi, Melissa, Wong, Justin J.L., Bailey, Charles G., and Rasko, John E.J. (2020) Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner. RNA Biology, 18 (1). pp. 93-103.

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.

B

Bernal, Moisés A., Schmidt, Elliott, Donelson, Jennifer M., Munday, Philip L., and Ravasi, Timothy (2022) Molecular Response of the Brain to Cross-Generational Warming in a Coral Reef Fish. Frontiers in Marine Science, 9. 784418. pp. 1-16.

Brady, Aisling K., Willis, Bette L., Harder, Lawrence D., and Vize, Peter D. (2016) Lunar phase modulates circadian gene expression cycles in the broadcast spawning coral Acropora millepora. Biological Bulletin, 230 (2). pp. 130-142.

Belpaire, Claude, Pujolar, José Martin, Geeraerts, Caroline, and Maes, Gregory E. (2016) Contaminants in eels and their role in the collapse of the eel stocks. In: Arai, Takaomi, (ed.) Biology and Ecology of Anguillid Eels. CRC Press, Boca Raton, FL, USA, pp. 225-250.

C

Chartrand, Katie, Rasheed, Michael, Bryant, Catherine, Pernice, Mathieu, and Ralph, Peter (2019) New science informing effective management of the often overlooked deep-water seagrasses of tropical Australia. In: [Presented at the Australian Marine Sciences Association 2019 Conference]. From: Australian Marine Sciences Association Conference 2019: Marine Science for a Blue Economy, 7-11 July 2019, Fremantle, WA, Australia.

D

De Meyer, J., Maes, G.E., Dirks, R.P., and Adriaens, D. (2017) Differential gene expression in narrow- and broad-headed European glass eels (Anguilla anguilla) points to a transcriptomic link of head shape dimorphism with growth rate and chemotaxis. Molecular Ecology, 26 (15). pp. 3943-3953.

Dixon, Groves B., Bay, Line K., and Matz, Mikhail V. (2016) Evolutionary consequences of DNA methylation in a basal Metazoan. Molecular Biology and Evolution, 33 (9). pp. 2285-2293.

G

Green, Immanuel D., Pinello, Natalia, Song, Renhua, Lee, Quitin, Halsted, James M., Kwok, Chau-To, Wong, Alex C. H., Nair, Shalima S., Clark, Susan J., Roediger, Ben, Schmitz, Ulf, Larance, Mark, Hayashi, Rippei, Rasko, John E. J., and Wong, Justin J.-L. (2020) Macrophage development and activation involve coordinated intron retention in key inflammatory regulators. Nucleic Acids Research, 48 (12). pp. 6513-6529.

Gierz, Sarah, Forêt, Sylvain, and Leggat, William (2017) Transcriptomic analysis of thermally stressed Symbiodinium reveals differential expression of stress and metabolism genes. Frontiers in Plant Science, 8. 271. pp. 1-20.

Gierz, Sarah L., Gordon, Benjamin R., and Leggat, William (2016) Integral light-harvesting complex expression in Symbiodinium within the coral Acropora aspera under thermal stress. Scientific Reports, 6. 25081.

H

Haydon, Trent D., Matthews, Jennifer L., Seymour, Justin R., Raina, Jean-Baptiste, Seymour, Jamie E., Chartrand, Kathryn, Camp, Emma F., and Suggett, David J. (2023) Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance. Proceedings of the Royal Society of London Series B, Biological Sciences, 290 (1992). 20221877.

Hendriks, W. Karen, Colleoni, Silvia, Galli, Cesare, Paris, Damien B.B.P., Colenbrander, Ben, and Stout, Tom A.E. (2019) Mitochondrial DNA replication is initiated at blastocyst formation in equine embryos. Reproduction, Fertility and Development, 31 (3). pp. 570-578.

Huerlimann, Roger, Wade, Nicholas M., Gordon, Lavinia, Montenegro, Juan D., Goodall, Jake, McWilliam, Sean, Tinning, Matthew, Siemering, Kirby, Giardina, Erika, Donovan, Dallas, Sellars, Melony J., Cowley, Jeff A., Condon, Kelly, Coman, Greg J., Khatkar, Mehar S., Raadsma, Herman W., Maes, Gregory E., Zenger, Kyall R., and Jerry, Dean R. (2018) De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Scientific Reports, 8. 13553.

Henstridge, Michelle A., Aulsebrook, Lucinda, Koyama, Takashi, Johnson, Travis K., Whisstock, James C., Tiganis, Tony, Mirth, Christen K., and Warr, Coral G. (2018) Torso-Like Is a Component of the Hemolymph and Regulates the Insulin Signaling Pathway in Drosophila. Genetics, 208 (4). pp. 1523-1533.

K

Kenkel, Carly D., Moya, Aurelie, Strahl, Julia, Humphrey, Craig, and Bay, Line K. (2018) Functional genomic analysis of corals from natural CO2‐seeps reveals core molecular responses involved in acclimatization to ocean acidification. Global Change Biology, 24 (1). pp. 158-171.

L

Leow, Melvin Khee Shing, Ang, Joshur, Bi, Xinyan, Koh, Ee Tzun, and McFarlane, Craig (2023) Alterations in SAMD9, AHSG, FRG2C, and FGFR4 Genes in a Case of Late-Onset Massive Tumoral Calcinosis. AACE Clinical Case Reports, 9 (5). pp. 153-157.

Luter, Heidi M., Kenkel, Carly D., Terzin, Marko, Peirce, Tyler, Laffy, Patrick W., Gibb, Karen, and Webster, Nicole S. (2020) Gene correlation networks reveal the transcriptomic response to elevated nitrogen in a photosynthetic sponge. Molecular Ecology, 29 (8). pp. 1452-1462.

Lau, Quintin, Igawa, Takeshi, Kosch, Tiffany, and Satta, Yoko (2018) Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs. PeerJ, 6.

M

Myers, Jaelen N., Dyce, Paul W., Chatakondi, Nagaraj G., Gorman, Sara A., Quiniou, Sylvie M.A., Su, Baofeng, Peatman, Eric, Dunham, Rex A., and Butts, Ian A.E. (2020) Analysis of specific mRNA gene expression profiles as markers of egg and embryo quality for hybrid catfish aquaculture. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology, 243. 110675.

Monteuuis, Geoffray, Schmitz, Ulf, Petrova, Veronika, Kearney, Padraic S., and Rasko, John E.J. (2020) Holding on to junk bonds: intron retention in cancer and therapy. Cancer Research, 81 (4). pp. 779-789.

McIntyre, Jenifer K., Edmunds, Richard C., Redig, Maria G., Mudrock, Emma M., Davis, Jay W., Incardona, John P., Stark, John D., and Scholz, Nathaniel L. (2016) Confirmation of stormwater bioretention treatment effectiveness using molecular indicators of cardiovascular toxicity in developing fish. Environmental Science and Technology, 50 (3). pp. 1561-1569.

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.

McIntyre, Jenifer K., Edmunds, Richard C., Analucion, Bernadita F., Davis, Jay W., Incardona, John P., Stark, John D., and Scholz, Nathaniel L. (2016) Severe coal tar sealcoat runoff toxicity to fish is prevented by bioretention filtration. Environmental Science and Technology, 50 (3). pp. 1570-1578.

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.

O

Oudot, Morgane, Neige, Pascal, Ben Shir, Ira, Schmidt, Asher, Strugnell, Jan M., Plasseraud, Laurent, Broussard, Cédric, Hoffmann, René, Lukeneder, Alexander, and Marin, Frédéric (2020) The shell matrix and microstructure of the Ram's Horn squid: molecular and structural characterization. Journal of Structural Biology, 211 (1). 107507.

P

Pewan, Shedrach Benjamin (2022) Genetic selection for health beneficial long-chain omega-3 fatty acids, intramuscular fat, and fat melting point in Australian white lambs. PhD thesis, James Cook University.

Pernice, Mathieu, Sinutok, Sutinee, Sablok, Gaurav, Commault, Audrey S., Schliep, Martin, Macreadie, Peter I., Rasheed, Michael A., and Ralph, Peter J. (2016) Molecular physiology reveals ammonium uptake and related gene expression in the seagrass Zostera muelleri. Marine Environmental Research, 122. pp. 126-134.

R

Rocker, Melissa M., Kenkel, Carly D., Francis, David S., Willis, Bette L., and Bay, Line K. (2019) Plasticity in gene expression and fatty acid profiles of Acropora tenuis reciprocally transplanted between two water quality regimes in the central Great Barrier Reef, Australia. Journal of Experimental Marine Biology and Ecology, 511. pp. 40-53.

Razaghi, Ali, Tan, Emylin, Lua, Linda H.L., Owens, Leigh, Karhikeyan, O.P., and Heimann, Kirsten (2017) Is Pichia pastoris a realistic platform for industrial production of recombinant human interferon gamma? Biologicals, 45. pp. 52-60.

S

Schmitz, Ulf, Monteuuis, Geoffray, Petrova, Veronika, Shah, Jaynish S., and Rasko, John E.J. (2021) Computational methods for intron retention identification and quantification. In: Wolkenhauer, Olaf, Cai, Yudong, and Rozman, Damjana, (eds.) Systems Medicine: integrative, qualitative and computational approaches. Academic Press, London Wall, United Kingdom, pp. 63-74.

Shiel, Brett P., Cooke, Ira R., Hall, Nathan E., Robinson, Nicholas A., and Strugnell, Jan M. (2020) Gene expression differences between abalone that are susceptible and resilient to a simulated heat wave event. Aquaculture, 526. 735317.

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A., and Strugnell, Jan M. (2017) Epipodial tentacle gene expression and predetermined resilience to summer mortality in the commercially important greenlip abalone, Haliotis laevigata. Marine Biotechnology, 19 (2). pp. 191-205.

Steinig, Eike J., Neuditschko, Markus, Khatkar, Mehar S., Raadsma, Herman W., and Zenger, Kyall R. (2016) NETVIEW P: a network visualization tool to unravel complex population structure using genome-wide SNPs. Molecular Ecology Resources, 16 (1). pp. 216-227.

V

Veilleux, Heather D., Donelson, Jennifer M., and Munday, Philip L. (2018) Reproductive gene expression in a coral reef fish exposed to increasing temperature across generations. Conservation Physiology, 6 (1). cox077.

W

Wong, Justin J.L., and Schmitz, Ulf (2022) Intron retention: importance, challenges, and opportunities. Trends in Genetics, 38 (8). pp. 789-792.

Whitelaw, Brooke (2021) The iridescent enigma: genome evolution and species boundaries of the blue-ringed octopus species complex (Octopodidae: Hapalochlaena). PhD thesis, James Cook University.

Whitelaw, Brooke L., Cooke, Ira R., Finn, Julian, da Fonseca, Rute R., Ritschard, Elena A., Gilbert, M. T. P., Simakov, Oleg, and Strugnell, Jan M. (2020) Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss. GigaScience, 9 (11). giaa120.