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.

Aghajani, Marra Jai, Yang, Tao, Schmitz, Ulf, James, Alexander, McCafferty, Charles Eugenio, de Souza, Paul, Niles, Navin, and Roberts, Tara L. (2020) Epithelial-to-mesenchymal transition and its association with PD-L1 and CD8 in thyroid cancer. Endocrine Connections, 9. pp. 1028-1041.

Amirkhah, Raheleh, Naderi-Meshkin, Hojjat, Shah, Jaynish S., Dunne, Philip D., and Schmitz, Ulf (2019) The intricate interplay between epigenetic events, alternative splicing and noncoding RNA deregulation in colorectal cancer. Cells, 8 (8). 929.

Amirkhah, Raheleh, Meshkin, Hojjat Naderi, Farazmand, Ali, Rasko, John E.J., and Schmitz, Ulf (2017) Computational and experimental identification of tissue-specific MicroRNA targets. In: Dalmay, Tamas, (ed.) MicroRNA Detection and Target Identification: methods and protocols. Methods in Molecular Biology, 1580 . Humana Press Inc., New York, NY, USA, pp. 127-147.

Amirkhah, Raheleh, Schmitz, Ulf, Linnebacher, Michael, Wolkenhauer, Olaf, and Farazmand, Ali (2015) MicroRNA-mRNA interactions in colorectal cancer and their role in tumor progression. Genes, Chromosomes and Cancer, 54 (3). pp. 129-141.

Amirkhah, Raheleh, Farazmand, Ali, Gupta, Shailendra K., Ahmadi, Hamed, Wolkenhauer, Olaf, and Schmitz, Ulf (2015) Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer. Molecular BioSystems, 11. pp. 2126-2134.

Amirkhah, R., Farazmand, A., Irfan-Maqsood, M., Wolkenhauer, O., and Schmitz, U. (2015) The role of microRNAs in the resistance to colorectal cancer treatments. Cellular and Molecular Biology, 61 (6). pp. 17-23.

B

Brennan, Sonja, Watson, David, Schneider, Michal, Rudd, Donna, and Kandasamy, Yogavijayan (2022) Fetal renal artery blood flow – Normal ranges. Ultrasound, 30 (1). pp. 62-71.

Blazev, Ronnie, Ashwood, Christopher, Abrahams, Jodie L., Chung, Long H., Francis, Deanne, Yang, Pengyi, Watt, Kevin I., Qian, Hongwei, Quaife-Ryan, Gregory A., Hudson, James E., Gregorevic, Paul, Thaysen-Andersen, Morten, and Parker, Benjamin L. (2021) Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development. Molecular and Cellular Proteomics, 20. 100030.

Bailey, Charles G., Gupta, Shailendra, Metierre, Cynthia, Amarasekera, Punkaja M.S., O'Young, Patrick, Kyaw, Wunna, Laletin, Tatyana, Francis, Habib, Semaan, Crystal, Sharifi Tabar, Mehdi, Singh, Krishna P., Mullighan, Charles G., Wolkenhauer, Olaf, Schmitz, Ulf, and Rasko, John (2021) Structure–function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cellular and Molecular Life Sciences, 78. pp. 7519-7536.

Bangaru, Sandhya, Lang, Shanshan, Schotsaert, Michael, Vanderven, Hillary A., Zhu, Xueyong, Kose, Nurgun, Bombardi, Robin, Finn, Jessica A., Kent, Stephen J., Gilchuk, Pavlo, Gilchuk, Iuliia, Turner, Hannah L., García-Sastre, Adolfo, Li, Sheng, Ward, Andrew B., Wilson, Ian A., and Crowe, James E. (2019) A site of vulnerability on the influenza virus hemagglutinin head domain trimer interface. Cell, 177 (5). e.18. pp. 1136-1152.

Banks, D.J.D., Copeman, D.B., Skerratt, L.F., and Molina, E.C. (2006) Echinococcus granulosus in northern Queensland 1. Prevalence in cattle. Australian Veterinary Journal, 84 (9). pp. 303-307.

C

Chartrand, K.M., Fletcher-Leonhardt, J.D., and Rasheed, M.A. (2020) Green Island Jetty Repairs Coral Monitoring Report – December 2020. Report. TropWATER, James Cook University, Cairns, QLD, Australia.

Cui, Cheng, Chatterjee, Bishwanath, Lozito, Thomas P., Zhang, Zhen, Francis, Richard J., Yagi, Hisato, Swanhart, Lisa M., Sanker, Subramaniam, Francis, Deanne, Yu, Qing, San Agustin, Jovenal T., Puligilla, Chandrakala, Chatterjee, Tania, Tansey, Terry, Liu, Xiaoqin, Kelley, Matthew W., Spiliotis, Elias T., Kwiatkowski, Adam V., Tuan, Rocky, Pazour, Gregory J., Hukriede, Neil A., and Lo, Cecilia W. (2013) Wdpcp, a PCP Protein Required for Ciliogenesis, Regulates Directional Cell Migration and Cell Polarity by Direct Modulation of the Actin Cytoskeleton. PLoS Biology, 11. e1001720.

Cui, Cheng, Chatterjee, Bishwanath, Francis, Deanne, Yu, Qing, SanAgustin, Jovenal T., Francis, Richard, Tansey, Terry, Henry, Charisse, Wang, Baolin, Lemley, Bethan, Pazour, Gregory J., and Lo, Cecilia W. (2011) Disruption of Mks1 localization to the mother centriole causes cilia defects and developmental malformations in Meckel-Gruber syndrome. Disease Models & Mechanisms, 4. pp. 43-56.

E

Emran, Abdullah Al, Nsengimana, Jérémie, Punnia-Moorthy, Gaya, Schmitz, Ulf, Gallagher, Stuart J., Newton-Bishop, Julia, Tiffen, Jessamy C., and Hersey, Peter (2020) Study of the female sex survival advantage in melanoma—a focus on x-linked epigenetic regulators and immune responses in two cohorts. Cancers, 12. 2082.

Edwards, Christopher R., Ritchie, William, Wong, Justin J-L., Schmitz, Ulf, Middleton, Robert, An, Xiuli, Mohandas, Narla, Rasko, John E.J., and Blobel, Gerd A. (2016) A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Blood, 127 (17). e24-e34.

Eales, Katie, Ketheesan, Natkunam, and Norton, Robert (2011) Problems with the use of a lateral flow assay in the serodiagnosis of brucellosis. Pathology, 43 (7). pp. 755-757.

F

Francis, Deanne, Krycer, James R, Cooney, Gregory J, and James, David E (2019) A modified gas-trapping method for high-throughput metabolic experiments in Drosophila melanogaster. BioTechniques, 67. pp. 123-125.

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.

Grech, A., Bos, M., Brodie, J., Coles, R., Dale, A., Gilbert, R., Hamann, M., Marsh, H., Neil, K., Pressey, R.L., Rasheed, M.A., Sheaves, M., and Smith, A. (2013) Guiding principles for the improved governance of port and shipping impacts in the Great Barrier Reef. Marine Pollution Bulletin, 75 (1). pp. 8-20.

Gutierrez, J., Navarro, I., Planas, J.V., Monserrat, N., Rojas, P., Castillo, J., Chystiakova, O.V., Gabillard, J.C., Smith, A., Chan, S.J., and Leibush, N.B. (2006) Insulin and IGF receptors in fish. In: Reinecke, Manfred, Zaccone, Giacomo, and Kapoor, B.G., (eds.) Fish Endocrinology. Science Publishers, Enfield, New Hampshire, USA, pp. 131-163.

H

Havula, E., Ghazanfar, S., Lamichane, N., Francis, D., Hasygar, K., Liu, Y., Alton, L.A., Johnstone, J., Needham, E.J., Pulpitel, T., Clark, T., Niranjan, H.N., Shang, V., Tong, V., Jiwnani, N., Audia, G., Alves, A.N., Sylow, L., Mirth, C., Neely, G.G., Yang, J., Hietakangas, V., Simpson, S.J., and Senior, A.M. (2022) Genetic variation of macronutrient tolerance in Drosophila melanogaster. Nature Communications, 13. 1637.

Hokke, Stacey, de Zoysa, Natasha, Carr, Bethany L., Abruzzo, Veronica, Coombs, Peter R., Allan, Carolyn A., East, Christine, Ingelfinger, Julie R., Puelles, Victor P., Black, Mary J., Ryan, Danica, Armitage, James A., Wallace, Euan M., Bertram, John F., and Cullen‐McEwen, Luise A. (2019) Normal foetal kidney volume in offspring of women treated for gestational diabetes. Endocrinology, Diabetes & Metabolism, 2 (4). e00091. pp. 1-9.

J

Jensen, Sacha A., Atwa, Ondine, and Handford, Penny A. (2021) Assembly assay identifies a critical region of human fibrillin-1 required for 10 - 12 nm diameter microfibril biogenesis. PLoS ONE, 16 (3). e0248532.

K

Kuddus, Md Abdul, McBryde, Emma S., Adekunle, Adeshina I., White, Lisa J., and Meehan, Michael T. (2022) Mathematical analysis of a two-strain tuberculosis model in Bangladesh. Scientific Reports, 12. 3634.

L

Lai, Xin, Eberhardt, Martin, Schmitz, Ulf, and Vera, Julio (2019) Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Research, 47 (15). pp. 7753-7766.

Lai, Xin, Gupta, Shailendra K., Schmitz, Ulf, Marquardt, Stephan, Knoll, Susanne, Spitschak, Alf, Wolkenhauer, Olaf, Pützer, Brigitte M., and Vera, Julio (2018) MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics, 8 (4). pp. 1106-1120.

M

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.

Munday, J.S., French, A.F., Smith, A., Wang, J., and Squires, R.A. (2008) Probable malignant catarrhal fever presented as transient generalised crusting dermatitis in a cow. New Zealand Veterinary Journal, 56 (2). pp. 89-93.

Mϋnch, G. (2005) Glycation and physiological mechanisms of its prevention in Alzheimer's disease. In: Sames, Klaus, Sethe, Sebastian, and Stolzing, Alexandra, (eds.) Extending the Lifespan: biotechnical, gerontological and social problems. LIT Verlag, Mϋnster, Germany, pp. 103-106.

N

Nugraha, Ari, Wongso, Hendris, Pratoko, Dwi Koko, and Wangchuk, Phurpa (2023) Enokitake (Flammulina velutipes). In: Sharma, Ajay, Bhardwaj, Garima, and Nayik, Gulzar Ahmad, (eds.) Phytochemistry and Nutritional Composition of Significant Wild Medicinal and Edible Mushrooms: Traditional Uses and Pharmacology. Royal Society of Chemistry, London, UK, pp. 165-200.

O

Owens, Leigh, and Busico-Salcedo, Nancy (2006) Vibrio harveyi: pretty problems in paradise. In: Thompson, Fabiano L., Austin, Brian, and Swings, Jean, (eds.) The Biology of Vibrios. ASM Press, Washington, DC, pp. 266-280.

P

Pertiwi, Kartika R., Hillman, Rachael M., Scott, Coralie A., and Chilton, Lisa (2019) Ischemia Reperfusion Injury Produces, and Ischemic Preconditioning Prevents, Rat Cardiac Fibroblast Differentiation: Role of KATP Channels. Journal of Cardiovascular Development and Disease, 6 (2). 22.

Paris, D.B.B.P., Taggart, D.A., Paris, M.C.J., Temple-Smith, P.D., and Renfree, M.B. (2005) Distribution of spermatozoa and copulatory plug in relation to the time of mating and ovulation in the female tammar wallaby (Macropus eugenii). Reproduction, Fertility and Development, 17 (2). p. 249.

Paris, D.B.B.P., Taggart, D.A., Shimmin, G.A., Renfree, M.B., and Paris, M.C.J. (2003) Anatomical considerations for the development of artificial insemination by catheter in two marsupials. Theriogenology, 59 (1). p. 401.

Paris, Damien B.B.P., Taggart, David A., Temple-Smith, Peter D., Shaw, Geoffrey, and Renfree, Marilyn B. (2003) Timing of intrauterine artificial insemination (IUAI) in relation to ovulation in the tammar wallaby, Macropus eugenii. In: Abstracts from the Australian Mammal Society Annual General Meeting. p. 25. From: 49th Australian Mammal Society Annual General Meeting, 7-9 July 2003, Sydney, NSW, Australia.

R

Robertson, Ian B., Dias, Hans F., Osuch, Isabelle H., Lowe, Edward D., Jensen, Sacha A., Redfield, Christina, and Handford, Penny A. (2017) The N-terminal region of Fibrillin-1 mediates a bipartite interaction with LTBP1. Structure, 25 (8). 1208-1221.e5.

Ryan, Danica, and Black, Mary Jane (2015) Preterm birth and/or factors that lead to preterm delivery: effects on the neonatal kidney. Journal of Neonatal Biology, 4 (1). pp. 93-104.

S

Sarker, Subir, Talukder, Saranika, Bhuiyan, Md Safiul Alam, and Haque, Md Hakimul (2024) Genomic characterization of parvovirus and beak and feather disease virus in cockatiel (Nymphicus hollandicus). Microbiology Resource Announcements, 13 (12). e00820-24.

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.

Sutherland, Megan R., Vojisavljevic, Danica, and Black, Mary Jane (2020) A practical guide to the stereological assessment of glomerular number, size, and cellular composition. The Anatomical Record, 303 (10). pp. 2679-2692.

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.

Schmitz, Ulf, Pinello, Natalia, Jia, Fangzhi, Alasmari, Sultan, Ritchie, William, Keightley, Maria-Cristina, Shini, Shaniko, Lieschke, Graham J., Wong, Justin J-L., and Rasko, John E.J. (2017) Intron retention enhances gene regulatory complexity in vertebrates. Genome Biology, 18. 216.

Sutherland, Megan R., Ryan, Danica, Dahl, Mar Janna, Albertine, Kurt, and Black, Mary Jane (2016) Effects of preterm birth and ventilation on glomerular capillary growth in the neonatal lamb kidney. Journal of Hypertension, 34 (10). pp. 1988-1997.

Schmitz, Ulf, and Wolkenhauer, Olaf (2016) Systems medicine. Methods in Molecular Biology, 1386 . Springer, New York, USA.

Sutherland, Megan, Ryan, Dana, Black, Mary Jane, and Kent, Alison (2014) Long-term renal consequences of preterm birth. Clinics in Perinatology, 41 (3). pp. 561-573.

Smith, A., Bourdeau, I., Wang, J., and Bondy, C.A. (2005) Expression of Catenin family members CTNNA1, CTNNA2, CTNNB1 and JUP in the primate prefrontal cortex and hippocampus. Molecular Brain Research, 135 (1-2). pp. 225-231.

Smith, A., Wang, J., Cheng, C.M., Weickert, C.S., and Bondy, C.A. (2004) High-level expression of Dok-1 in neurons of the primate prefrontal cortex and hippocampus. Journal of Neuroscience Research, 75 (2). pp. 218-224.

Shinzato, Chuya (2007) Cnidarian Sox genes and the evolution of function in the Sox gene family. PhD thesis, James Cook University.

V

Vanichkina, Darya P., Schmitz, Ulf, Wong, Justin J.-L., and Rasko, John E.J. (2018) Challenges in defining the role of intron retention in normal biology and disease. Seminars in Cell and Developmental Biology, 75. pp. 40-49.

W

Wong, Justin J.-L., Au, Amy Y.M., Gao, Dada, Pinello, Natalia, Kwok, Chau-To, Thoeng, Annora, Lau, Katherine A., Gordon, Jane E.A., Schmitz, Ulf, Feng, Yue, Nguyen, Trung V., Middleton, Robert, Bailey, Charles G., Holst, Jeff, Rasko, John E.J., and Ritchie, William (2016) RBM3 regulates temperature sensitive miR-142-5p and miR-143 (thermomiRs), which target immune genes and control fever. Nucleic Acids Research, 44 (6). pp. 2888-2897.

Wang, J., Cheng, C.M., Zhou, J., Smith, A., Shannon Weickert, C., Perlman, W.R., Becker, K.G., Powell, D., and Bondy, C.A. (2004) Estradiol alters transcription factor gene expression in primate prefrontal cortex. Journal of Neuroscience Research, 76 (3). pp. 306-314.