Shen, Xueyan, Hu, Jie, Yáñez, José M., Bastos Gomes, Giana, Poon, Zhi Weng Josiah, Foster, Derick, Alarcon, Jorge F., Shao, Libin, Guo, Xinyu, Shao, Yunchang, Huerlimann, Roger, Li, Chengze, Goulden, Evan, Anderson, Kelli, Fan, Guangyi, and Domingos, Jose A. (2024) Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers. GigaScience, 13. giae034.

Clark-Shen, N., Chin, A., Domingos, J., and Hutchinson, N. (2024) The life (history), diet and death of the blackspot shark (Carcharhinus sealei) from South-east Asia. Marine and Freshwater Research, 75. MF24099.

Shen, Xueyan, Yáñez, José M., Gomes, Giana, Poon, Zhi Weng Josiah, Foster, Derick, Alarcon, Jorge, and Domingos, Jose A. (2023) Comparative gonad transcriptome analysis in cobia (Rachycentron canadum). Frontiers in Genetics, 14. 1128943.

Poon, Zhi Weng Josiah, Shen, Xueyan, Angelo, Joseph, Terence, Celestine, Chua, Shi Wei Gavin, and Domingos, Jose A. (2022) Comparative transcriptome analysis reveals factors involved in the influence of dietary astaxanthin on body colouration of Malabar Snapper (Lutjanus malabaricus). Aquaculture, 562. 738874.

Budd, Alyssa M., Guppy, Jarrod L., Thepot, Valentin, Domingos, Jose A., and Jerry, Dean R. (2022) Delayed effect of low rearing temperature on gonadal DNA methylation in juvenile barramundi (Lates calcarifer). Aquaculture, 560. 738541.

Ong, Jun Kiat Edwin, Nair, Thiviya, Ng, Tze Hann, Domingos, Jose A., and Gomes, Giana Bastos (2022) Identification of scale drop disease virus based on environment DNA in an aquaculture facility of Singapore. Aquaculture, 563. 738993.

Nghia, Nguyen Huu, Van, Phan Thi, Giang, Pham Thai, Hanh, Nguyen Thi, St‐Hilaire, Sophie, and Domingos, Jose A. (2021) Control of Vibrio parahaemolyticus (AHPND strain) and improvement of water quality using nanobubble technology. Aquaculture Research, 52 (6). pp. 2727-2739.

Banh, Quyen Q.T., Domingos, Jose A., Pinto, Ricardo C.C., Nguyen, Kien T., and Jerry, Dean R. (2021) Dietary 17 β-oestradiol and 17 α-ethinyloestradiol alter gonadal morphology and gene expression of the two sex-related genes, dmrt1 and cyp19a1a, in juvenile barramundi (Lates calcarifer Bloch). Aquaculture Research, 52 (4). pp. 1414-1430.

Tsang, Hin Hung, Domingos, Jose A., Westaway, Jacob A.F., Kam, Maximilian H.Y., Huerlimann, Roger, and Bastos Gomes, Giana (2021) Digital droplet PCR-based environmental DNA tool for monitoring Cryptocaryon irritans in a marine fish farm from Hong Kong. Diversity, 13 (8). 350.

Terence, Celestine, Domingos, Jose A., Angelo Uichanco, Joseph, Monteil, Yann, Monteil, Loïc, De Braux, Emmanuel, Banh, Quyen Q.T., Gibson-Kueh, Susan, and Jerry, Dean R. (2021) Early sex change of barramundi Lates calcarifer farmed in Singapore. Aquaculture Reports, 20. 100712.

Domingos, Jose A., Goldsbury, Julie A., Bastos Gomes, Giana, Smith, Brett G., Tomlinson, Christopher, Bade, Tim, Sander, Corey, Forrester, Justin, and Jerry, Dean R. (2021) Genotype by environment interactions of harvest growth traits for barramundi (Lates calcarifer) commercially farmed in marine vs. freshwater conditions. Aquaculture, 532. 735989.

Banh, Quyen Q. T., Guppy, Jarrod L., Domingos, Jose A., Budd, Alyssa M., Pinto, Ricardo C. C., Marc, Adrien F., and Jerry, Dean R. (2021) Induction of precocious females in the protandrous barramundi (Lates calcarifer) through implants containing 17β-estradiol - effects on gonadal morphology, gene expression and DNA methylation of key sex genes. Aquaculture, 539. 736601.

Domingos, Jose A., Shen, Xueyan, Terence, Celestine, Senapin, Saengchan, Dong, Ha Thanh, Tan, Marie R., Gibson-Kueh, Susan, and Jerry, Dean R. (2021) Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) coinfection downregulate immune-relevant pathways and cause splenic and kidney necrosis in barramundi under commercial farming conditions. Frontiers in Genetics, 12. 666897.

Meemetta, Watcharachai, Domingos, Jose A., Dong, Ha Thanh, and Senapin, Saengchan (2020) Development of a SYBR Green quantitative PCR assay for detection of Lates calcarifer herpesvirus (LCHV) in farmed barramundi. Journal of Virological Methods, 285. 113920.

Mangott, A., Nappi, J., Delli Paoli Carini, A., Goncalves, P., Hua, K., Domingos, J.A., de Nys, R., and Thomas, T. (2020) Ulva lactuca as a functional ingredient and water bioremediator positively influences the hepatopancreas and water microbiota in the rearing of Litopenaeus vannamei. Algal Research, 51. 102040.

Konovalov, Dmitry A., Saleh, Alzayat, Efremova, Dina B., Domingos, Jose A., and Jerry, Dean R. (2019) Automatic weight estimation of harvested fish from images. In: Proceedings of the International Conference on Digital Image Computing. pp. 308-314. From: DICTA 2019: International Conference on Digital Image Computing: Techniques and Applications, 2-4 December 2019, Perth, WA, Australia.

Gomes, Giana Bastos, Hutson, Kate S., Domingos, Jose A., Infante Villamil, Sandra, Huerlimann, Roger, Miller, Terrence L., and Jerry, Dean (2019) Parasitic protozoan interactions with bacterial microbiome in a tropical fish farm. Aquaculture, 502. pp. 196-201.

Munday, Philip L., Schunter, Celia, Allan, Bridie M.J., Nicol, Simon, Pether, Stephen M.J., Pope, Stephen, Ravasi, Timothy, Setiawan, Alvin N., Smith, Neville, and Domingos, Jose A. (2019) Testing the adaptive potential of yellowtail kingfish to ocean warming and acidification. Frontiers in Ecology and Evolution, 7. 253.

Konovalov, D.A., Domingos, J.A., White, R.D., and Jerry, D.R. (2018) Automatic scaling of fish images. In: Proceedings of the 2nd International Conference on Advances in Image Processing. pp. 48-53. From: ICAIP 18: 2nd International Conference on Advances in Image Processing, 16-18 June 2018, Chengdu, China.

Konovalov, Dmitry A., Saleh, Alzayat, Domingos, Jose A., White, Ron D., and Jerry, Dean R. (2018) Estimating mass of harvested Asian seabass Lates calcarifer from images. World Journal of Engineering and Technology, 6 (3). pp. 15-23.

Domingos, Jose A., Budd, Alyssa M., Banh, Quyen Q., Goldsbury, Julie A., Zenger, Kyall R., and Jerry, Dean R. (2018) Sex-specific dmrt1 and cyp19a1 methylation and alternative splicing in gonads of the protandrous hermaphrodite barramundi. PLoS ONE, 13 (9). e0204182.

Konovalov, D.A., Domingos, J.A., Bajema, C., White, R.D., and Jerry, D.R. (2017) Ruler detection for automatic scaling of fish images. In: Proceedings of the International Conference on Advances in Image Processing. pp. 90-95. From: ICAIP 2017: International Conference on Advances in Image Processing, 25-27 August 2017, Bangkok, Thailand.

Banh, Quyen Q., Domingos, Jose A., Zenger, Kyall R., and Jerry, Dean R. (2017) Morphological changes and regulation of the genes dmrt1 and cyp11b during the sex differentiation of barramundi (Lates calcarifer Bloch). Aquaculture, 479. pp. 75-84.

Bastos Gomes, Giana, Hutson, Kate S., Domingos, Jose A., Chung, Catherine, Hayward, Scott, Miller, Terrance L., and Jerry, Dean R. (2017) Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms. Aquaculture, 479. pp. 467-473.

Munday, Philip L., Donelson, Jennifer M., and Domingos, Jose A. (2016) Potential for adaptation to climate change in a coral reef fish. Global Change Biology, 23 (1). pp. 307-317.

Budd, Alyssa M., Banh, Quyen Q., Domingos, Jose A., and Jerry, Dean R. (2015) Sex control in fish: approaches, challenges and opportunities for aquaculture. Journal of Marine Science and Engineering, 3 (2). jmse3020329. pp. 329-355.

Domingos, Jose A., Zenger, Kyall R., and Jerry, Dean R. (2015) Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi, Lates calcarifer. Animal Genetics, 46 (4). pp. 468-469.

Domingos, Jose A., Smith-Keune, Carolyn, Harrison, Paul, and Jerry, Dean R. (2014) Early prediction of long-term family growth performance based on cellular processes: a tool to expedite the establishment of superior foundation broodstock in breeding programs. Aquaculture, 428-429. pp. 88-96.

Domingos, Jose A., Smith-Keune, Carolyn, and Jerry, Dean R. (2014) Fate of genetic diversity within and between generations and implications for DNA parentage analysis in selective breeding of mass spawners: a case study of commercially farmed barramundi, Lates calcarifer. Aquaculture, 424-425. pp. 174-182.

Domingos, Jose A.S. (2014) Filling in the gaps impeding the instigation of selective breeding programs in barramundi Lates calcarifer: fate of genetic diversity through to harvest, estimation of genetic parameters and early prediction of family growth based on cellular processes. PhD thesis, James Cook University.

Loughnan, Shannon R., Domingos, Jose A., Smith-Keune, Carolyn, Forrester, Justin P., Jerry, Dean R., Beheregaray, Luciano B., and Robinson, Nicholas A. (2013) Broodstock contribution after mass spawning and size grading in barramundi (Lates calcarifer, Bloch). Aquaculture, 404-405. pp. 139-149.

Domingos, Jose A., Smith-Keune, Carolyn, Robinson, Nicholas, Loughnan, Shannon, Harrison, Paul, and Jerry, Dean R. (2013) Heritability of harvest growth traits and genotype–environment interactions in barramundi, Lates calcarifer (Bloch). Aquaculture, 402-403. pp. 66-75.

Domingos, J.A., Fromm, P., Smith-Keune, C., and Jerry, D.R. (2012) A robust flow-cytometric protocol for assessing growth rate of hatchery-reared barramundi Lates calcarifer larvae. Journal of Fish Biology, 80 (6). pp. 2253-2266.

Bastos Gomes, Giana, Domingos, José Antonio Santos, Oliveira, Karine Kelly Cavalcanti, Mendes, Paulo de Paula, Da Silva, Veronica Arns, and Mendes, Emiko Shinozaki (2010) Diagnosis of necrotizing hepatopancreatitis in Pacific White Shrimp, Litopenaeus vannamei, through wet mount, histopathology and PCR techniques. Journal of the World Aquaculture Society, 41 (5). pp. 816-822.