Vu, Nguyen Thanh, Shen, Xueyan, Kueh, Susan, Carrai, Maura, Terence, Celestine, Poon, Zhi Weng Josiah, Nelson, Sarah Priyanka, Senapin, Saengchan, Dong, Ha Thanh, Loh, James, Jerry, Dean R., and Domingos, Jose A. (2026) Microbiome and Pathobiome Characterization in Farmed Barramundi (Lates calcarifer) During and Post Scale Drop Disease Outbreaks. Journal of Fish Diseases. e70225. (In Press)

Poon, Zhi Weng Josiah, Vu, Nguyen Thanh, Shen, Xueyan, Gibson-Kueh, Susan, Carrai, Maura, Nelson, Sarah Priyanka, Terence, Celestine, Oh, Joseph, Seah, Theophilus, Tan, Ying Quan, Awate, Sunita, Dong, Ha Thanh, Senapin, Saengchan, Tan, Marie R., Vij, Shubha, Jones, David B., Jerry, Dean R., and Domingos, Jose A. (2026) Cross-environment genomic prediction of scale drop disease resistance in barramundi (Lates calcarifer) using laboratory challenge and farm survival data. Aquaculture, 621. 744030.

Dong, Xiaojing, Li, Fangxi, Zhao, Mengjie, Wang, Jianqiao, Shen, Xueyan, Zhang, Guangyang, Li, Ao, Fu, Yuanyuan, Fan, Hongying, Wang, Anran, Miao, Shuyan, and Du, Xuedi (2026) Dietary betaine enhances muscle quality in largemouth bass: Insights into texture property, nutrient deposition, and lipid metabolic regulation under high-fat feeding. Aquaculture, 623. 744180.

Ruethers, Thimo, Sean, Afifah, Karnaneedi, Shaymaviswanathan, Chin, Renee, Leeming, Michael G., Nguyen, Vu, Huerlimann, Roger, Nugraha, Roni, Bade, Patrizia, Vij, Shubha, Shen, Xueyan, Limviphuvadh, Vachiranee, Williamson, Nicholas A., Domingos, Jose A., Jerry, Dean R., Maurer-Stroh, Sebastian, Andiappan, Anand K., and Lopata, Andreas L. (2026) Fish size matters – Variable food allergen profiles in farmed and wild Malabar red snapper (Lutjanus malabaricus). Food Chemistry, 505. 147950.

Liang, Bing, Jerry, Dean R., Koh, Joyce, Kathiresan, Purushothaman, Terence, Celestine, Shen, Xueyan, Loo, Grace, Vij, Shubha, and Domingos, Jose A. (2026) Histological characterisation of gonadal sex differentiation in Malabar red snapper (Lutjanus malabaricus) for aquaculture advancement. Journal of Fish Biology, 109 (1). pp. 246-256.

Kathiresan, Purushothaman, Vu, Nguyen Thanh, Liang, Bing, Qing, Saraphina Dianne Tneo Rwei, Mohamed, Muhammad Hazim bin, Wen, Rachel Ho Jia, Shen, Xueyan, Jones, David B., Loo, Grace, Jerry, Dean R., Domingos, Jose A., and Vij, Shubha (2026) Investigating genomic prediction accuracies for muscle fatty acids composition in Malabar red snapper (Lutjanus malabaricus). Aquaculture, 613. 743398.

Liang, Bing, Jerry, Dean R., Nguyen, Vu, Kathiresan, Purushothaman, Jones, David B., Shen, Xueyan, Koh, Joyce, Terence, Celestine, Nayfa, Maria G., Carrai, Maura, Ho, Rachel Jia Wen, Mohamed, Hazim, Tneo, Saraphina Dianne Rwei Qing, Loo, Grace, Vij, Shubha, and Domingos, Jose A. (2026) Optimisation of genomic selection for harvest traits of Malabar red snapper (Lutjanus malabaricus). Aquaculture, 613. 743314.

Thanh Vu, Nguyen, Purushothaman, Kathiresan, Nayfa, Maria G., Vu, Nga Thi Thanh, Liang, Bing, Koh, Joyce, Tsang, Hin Hung, Nahid, Sk Ahmad Al, Loo, Grace, Shen, Xueyan, Domingos, Jose A., Jerry, Dean R., and Vij, Shubha (2026) Population Structure and Genetic Connectivity of Malabar Red Snapper (Lutjanus malabaricus) Across the South China Sea and Northern Australia: Implications for Aquaculture and Broodstock Management. Aquaculture Journal, 6 (2). 17.

Shen, Xueyan, Gibson-Kueh, Susan, Nelson, Sarah Priyanka, Poon, Zhi Weng Josiah, Terence, Celestine, Vu, Nguyen Thanh, Carrai, Maura, Awate, Sunita, Vij, Shubha, Tan, Marie R., Jerry, Dean R., and Domingos, Jose A. (2026) Scale Drop Disease Virus (SDDV) infection induces intestinal dysbiosis and secondary Vibrio expansion in Asian seabass (Lates calcarifer). Fish and Shellfish Immunology, 174. 111344.

Shen, Xueyan, Yu, Xiong Da, Xie, Shangzhe, Hsu, Chia Da, Domingos, Jose A., and Gibson-Kueh, Susan (2026) Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore. Frontiers In Microbiology, 17. 1739391.

Sean, Afifah, Lim, Tzer Shyun, Domingos, Jose A., Uichanco, Joseph A., Shen, Xueyan, and Gibson-Kueh, Susan (2025) Air Nanobubbles Enhance Viable Bacteria Counts, Abundance of Nitrifying Bacteria, and Reduce Nitrite Levels in Marine Recirculation Aquaculture Systems. Fishes, 10 (11). 550. pp. 1-16.

Terence, Celestine, Poon, Zhi Weng Josiah, Senapin, Saengchan, Dong, Ha Thanh, Clarke, Shannon M., Brauning, Rudiger, Dodds, Ken G., Thanh Vu, Nguyen, Shen, Xueyan, Gibson-Kueh, Susan, Jerry, Dean R., and Domingos, Jose A. (2025) Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer). Aquaculture Reports, 46. 103273.

Ngoh, Si Yan, Shen, Xueyan, Chan, Tai Lok, Nankervis, Leo, and Hua, Katheline (2025) Effects of digestible protein and energy on growth, amino acid requirements and protein utilisation in juvenile Malabar snapper (Lutjanus malabaricus): A four-protein by three-energy factorial design study. Aquaculture, 600. 742200.

Ngoh, Si Yan, Shen, Xueyan, Nankervis, Leo, Chia, Isaiah, and Hua, Katheline (2025) Evaluation of nutritional value and quality of aquafeed ingredients for Malabar snapper (Lutjanus malabaricus). Aquaculture, 600. 742253.

Liang, Bing, Jerry, Dean R., Nguyen, Vu, Shen, Xueyan, Koh, Joyce, Terence, Celestine, Nayfa, Maria, Carrai, Maura, Kathiresan, Purushothaman, Jia Wen Ho, Rachel, Mohamed, Hazim, Rwei Qing Tneo, Saraphina Dianne, Loo, Grace, Vij, Shubha, and Domingos, Jose A. (2025) Genetic parameters and genotype by environment interaction for harvest traits of Malabar red snapper (Lutjanus malabaricus). Aquaculture, 600. 742247.

Poon, Zhi Weng Josiah, Vu, Nguyen Thanh, Shen, Xueyan, Gibson-Kueh, Susan, Carrai, Maura, Nelson, Sarah Priyanka, Terence, Celestine, Tan, Ying Quan, Awate, Sunita, Dong, Ha Thanh, Senapin, Saengchan, Tan, Marie R., Vij, Shubha, Jones, David B., Jerry, Dean R., and Domingos, Jose A. (2025) Genomic prediction of scale drop disease resistance in barramundi Lates calcarifer under controlled laboratory conditions. Aquaculture, 612. 743250.

Goh, Charlene, Gibson-Kueh, Susan, Bal, David, Chen, I.-Tung, Nuez-Ortín, Waldo, Domingos, Jose A., and Shen, Xueyan (2025) A synergistic blend of dietary organic acids, monoglycerides and phytobiotics enhance growth performance, intestinal mucosal height, and anti-viral immune gene expression in juvenile Barramundi (Lates calcarifer). Aquaculture Reports, 41. 102692.

Ngoh, Si Yan, Shen, Xueyan, Nankervis, Leo, and Hua, Katheline (2024) Evaluation of Energy Utilisation Efficiencies of Digestible Macronutrients in Juvenile Malabar Snapper (Lutjanus malabaricus) Reveals High Protein Requirement for Optimal Growth Using Both Factorial and Multifactorial Approaches. Aquaculture Nutrition, 2024 (1). 5467206.

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.

Chew, Xian Zhe, Carrai, Maura, Shen, Xueyan, and Gibson-Kueh, Susan (2024) Impact of transport conditions and underlying disease on post-stocking survival of juvenile Lates calcarifer. Journal of Fish Diseases, 47 (8). e13963.

Liang, Bing, Jerry, Dean R., Shen, Xueyan, Koh, Joyce, Terence, Celestine, Nayfa, Maria G., Nguyen, Vu, Loo, Grace, Vij, Shubha, and Domingos, Jose A. (2024) Transcriptomic analysis of gonads in Malabar red snapper (Lutjanus malabaricus) reveals genes associated with gonad development. Aquaculture, 592. 741258.

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.

Chew, Xian Zhe, Gibson-Kueh, Susan, Jerry, Dean R., and Shen, Xueyan (2023) Comparison of intestinal bacterial communities in asymptomatic and diseased Asian seabass (Lates calcarifer) with chronic enteritis and mixed bacterial infections. Aquaculture, 572. 739516.

Shen, Xueyan, Niu, Yong Chao, Uichanco, Joseph Angelo V., Phua, Norman, Bhandare, Pranjali, Thevasagayam, Natascha May, Prakki, Sai Rama Sridatta, and Orbán, László (2023) Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer). BMC Genomics, 24. 449.

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.

Gibson-Kueh, Susan, Terence, Celestine, Chew, Xian Zhe, Uichanco, Joseph Angelo, and Shen, Xueyan (2021) PCR, in-situ hybridization, and phylogenetic analysis suggest that ‘big belly’ disease in barramundi, Lates calcarifer (Bloch), is caused by a novel Vibrio species. Journal of Fish Diseases, 44 (12). pp. 1985-1992.

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.

Orbán, László, Shen, Xueyan, Phua, Norman, and Varga, László (2021) Toward genome-based selection in Asian seabass: what can we learn from other food fishes and farm animals? Frontiers in Genetics, 12. 506754.

Vij, Shubha, Kuhl, Heiner, Kuznetsova, Inna S., Komissarov, Aleksey, Yurchenko, Andrey A., Van Heusden, Peter, Singh, Siddharth, Thevasagayam, Natascha M., Prakki, Sai Rama Sridatta, Purushothaman, Kathiresan, Saju, Jolly M., Jiang, Junhui, Mbandi, Stanley Kimbung, Jonas, Mario, Hin Yan Tong, Amy, Mwangi, Sarah, Lau, Doreen, Ngoh, Si Yan, Liew, Woei Chang, Shen, Xueyan, Hon, Lawrence S., Drake, James P., Boitano, Matthew, Hall, Richard, Chin, Chen-Shan, Lachumanan, Ramkumar, Korlach, Jonas, Trifonov, Vladimir, Kabilov, Marsel, Tupikin, Alexey, Green, Darrell, Moxon, Simon, Garvin, Tyler, Sedlazeck, Fritz J., Vurture, Gregory W., Gopalapillai, Gopikrishna, Kumar Katneni, Vinaya, Noble, Tansyn H., Scaria, Vinod, Sivasubbu, Sridhar, Jerry, Dean R., O'Brien, Stephen J., Schatz, Michael C., Dalmay, Tamás, Turner, Stephen W., Lok, Si, Christoffels, Alan, and Orbán, László (2016) Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12 (4). pp. 1-35.

Shen, Xueyan, Ngoh, Si Yan, Thevasagayam, Natascha May, Prakki, Sai Rama Sridatta, Bhandare, Pranjali, Tan, Andy Wee Kiat, Tan, Gui Quan, Singh, Siddharth, Phua, Norman Chun Han, Vij, Shubna, and Orbán, László (2016) BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Scientific Reports, 6. 36647.

Li, Jia, Bian, Chao, Hu, Yinchang, Mu, Xidong, Shen, Xueyan, Ravi, Vydianathan, Kuznetsova, Inna S., Sun, Ying, Xinxin, You, Qui, Ying, Zhang, Xinhui, Yu, Hui, Huang, Yu, Xu, Pao, Gu, Ruobo, Xu, Junmin, Orban, Laszlo, Venkatesh, Byrappa, and Shi, Qiong (2016) A chromosomelevel genome assembly of the Asian arowana, Scleropages formosus. Scientific Data, 3. 160105.