Projects 12
Publications 30
Awards 17

Biography

Dr. Xueyan Shen obtained her M.Sc in Aquaculture and Ph.D. in Biochemistry and Molecular Biology from the Ocean University of China in 2004 and 2007, respectively. After that, she started her Postdoctoral work on maintenance of genomic resources for the National BioResource Project Medak in NIBB (Okazaki, Japan). From 2010, she worked in the Temasek Life Sciences Laboratory (TLL), Singapore, where as a Research Fellow, she led several research teams towards increasing Singapore’s food fish supply through application of aquaculture genomics R&D. She has now joined James Cook University in Singapore where she will continue to apply her state-of-the-art teaching and genetic research approaches to help Singapore as well as other Asia counties achieve their aquaculture related food security strategy.

Research Focus

Dr. Shen’s research focus is on the development of “robust” aquaculture strains to boost seafood production. She has conducted genomics-assisted selection on two economically important fish, namely Asian seabass/barramundi and Mozambique tilapia, and also the ornamental fish Asian arowana. Specific areas of her research interest include: 1) Developing genomic resources and genetic tools like whole genome sequencing, high-density SNP arrays, etc., to support selective breeding; 2) Exploring genetic basis of important traits (growth, disease resistance) using RNA sequencing, QTL mapping, GWAS and genomic selection; 3) Conducting functional feed trials and specific pathogen tests to evaluating feed additives' impact on fish immunity; 4) Investigating nutrition, gene expression, gut microbiome and immunity in various fish species using omics approaches. As an Associate Professor at JCU Singapore, Dr. Shen is keen to continue to collaborate with partners from commercial industry, government universities/institutes to create ‘State of the art’genomic platforms to further improve the productivity and quality of food fish species.

Impact of Research

Her research into the genetic improvement of Asian seabass, Red Snapper and Tilapia have allowed for a ‘quantum leap’ in generation of more superior broodstock leading to more efficient and greater productivity of foodfish products. In addition, tools she has developed will be easily applicable and adaptable to the aquaculture systems of other tropical marine fish species, advancing their production systems from the current most traditional methods into modern, science-assisted aquaculture.

Research

Projects

Teaching

Research Advisor Accreditation

Advisor Type

Primary

Research Advisor Accreditation

Role

Chair; Independent Academic


Taught Modules

Current JCU Research Students

Genomic selection of barramundi (Lates calcarifer) for improved scale drop disease virus resistance
Doctor of Philosophy (Agriculture, Environmental and Related Studies)
Molecular Epidemiology: Mapping pathogen trends and host immunity to inform disease management in Tropical Aquaculture food fish species.
Doctor of Philosophy (Agriculture, Environmental and Related Studies)
The Epidemiology of 'Scale Drop Disease' in Farmed Lates Calcarifer in Singapore
Doctor of Philosophy (Agriculture, Environmental and Related Studies)

Completed JCU Research Students

Nutritional requirements and optimised feed development for juvenile Malabar snapper (Lutjanus malabaricus)
Doctor of Philosophy (Agriculture, Environmental and Related Studies)- 2025
Biomarkers as early indicators of disease in farmed Asian seabass (lates calcarifer)
Doctor of Philosophy (Agriculture, Environmental and Related Studies)- 2025

Activities

Media

Awards

Associations

Output

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; Domingos, Jose A. (2026) 'Optimisation of genomic selection for harvest traits of Malabar red snapper (Lutjanus malabaricus)'. Aquaculture, 613 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; 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). [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; Vij, Shubha (2026) 'Investigating genomic prediction accuracies for muscle fatty acids composition in Malabar red snapper (Lutjanus malabaricus)'. Aquaculture, 613 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Shen, Xueyan; Yu, Xiong Da; Xie, Shangzhe; Hsu, Chia Da; Domingos, Jose A.; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; Domingos, Jose A. (2026) 'Microbiome and Pathobiome Characterization in Farmed Barramundi (Lates calcarifer) During and Post Scale Drop Disease Outbreaks'. Journal of Fish Diseases, . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Dong, Xiaojing; Li, Fangxi; Zhao, Mengjie; Wang, Jianqiao; Shen, Xueyan; Zhang, Guangyang; Li, Ao; Fu, Yuanyuan; Fan, Hongying; Wang, Anran; Miao, Shuyan; 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 . [DOI]
Journal Publication ResearchOnline@JCU
Liang, Bing; Jerry, Dean R.; Koh, Joyce; Kathiresan, Purushothaman; Terence, Celestine; Shen, Xueyan; Loo, Grace; Vij, Shubha; 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):246-256. [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; Lopata, Andreas L. (2026) 'Fish size matters – Variable food allergen profiles in farmed and wild Malabar red snapper (Lutjanus malabaricus)'. Food Chemistry, 505 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; Domingos, Jose A. (2025) 'Genomic prediction of scale drop disease resistance in barramundi Lates calcarifer under controlled laboratory conditions'. Aquaculture, 612 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Ngoh, Si Yan; Shen, Xueyan; Chan, Tai Lok; Nankervis, Leo; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Ngoh, Si Yan; Shen, Xueyan; Nankervis, Leo; Chia, Isaiah; Hua, Katheline (2025) 'Evaluation of nutritional value and quality of aquafeed ingredients for Malabar snapper (Lutjanus malabaricus)'. Aquaculture, 600 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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; Domingos, Jose A. (2025) 'Genetic parameters and genotype by environment interaction for harvest traits of Malabar red snapper (Lutjanus malabaricus)'. Aquaculture, 600 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Goh, Charlene; Gibson-Kueh, Susan; Bal, David; Chen, I.-Tung; Nuez-Ortín, Waldo; Domingos, Jose A.; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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.; Domingos, Jose A. (2025) 'Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer)'. Aquaculture Reports, 46 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Sean, Afifah; Lim, Tzer Shyun; Domingos, Jose A.; Uichanco, Joseph A.; Shen, Xueyan; 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):1-16. [DOI]
Journal Publication Open Access ResearchOnline@JCU
Chew, Xian Zhe; Carrai, Maura; Shen, Xueyan; 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). [DOI]
Journal Publication Open Access ResearchOnline@JCU
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; Domingos, Jose A. (2024) 'Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers'. GigaScience, 13 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Ngoh, Si Yan; Shen, Xueyan; Nankervis, Leo; 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). [DOI]
Journal Publication Open Access ResearchOnline@JCU
Liang, Bing; Jerry, Dean R.; Shen, Xueyan; Koh, Joyce; Terence, Celestine; Nayfa, Maria G.; Nguyen, Vu; Loo, Grace; Vij, Shubha; Domingos, Jose A. (2024) 'Transcriptomic analysis of gonads in Malabar red snapper (Lutjanus malabaricus) reveals genes associated with gonad development'. Aquaculture, 592 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Shen, Xueyan; Yáñez, José M.; Gomes, Giana; Poon, Zhi Weng Josiah; Foster, Derick; Alarcon, Jorge; Domingos, Jose A. (2023) 'Comparative gonad transcriptome analysis in cobia (Rachycentron canadum)'. Frontiers in Genetics, 14 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Shen, Xueyan; Niu, Yong Chao; Uichanco, Joseph Angelo V.; Phua, Norman; Bhandare, Pranjali; Thevasagayam, Natascha May; Prakki, Sai Rama Sridatta; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Chew, Xian Zhe; Gibson-Kueh, Susan; Jerry, Dean R.; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Poon, Zhi Weng Josiah; Shen, Xueyan; Angelo, Joseph; Terence, Celestine; Chua, Shi Wei Gavin; 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 . [DOI]
Journal Publication ResearchOnline@JCU
Gibson-Kueh, Susan; Terence, Celestine; Chew, Xian Zhe; Uichanco, Joseph Angelo; 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):1985-1992. [DOI]
Journal Publication ResearchOnline@JCU
Orbán, László; Shen, Xueyan; Phua, Norman; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
Domingos, Jose A.; Shen, Xueyan; Terence, Celestine; Senapin, Saengchan; Dong, Ha Thanh; Tan, Marie R.; Gibson-Kueh, Susan; 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 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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; Shi, Qiong (2016) 'A chromosomelevel genome assembly of the Asian arowana, Scleropages formosus'. Scientific Data, 3 . [DOI]
Journal Publication Open Access ResearchOnline@JCU
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; Orbán, László (2016) 'BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome'. Scientific Reports, 6 . [DOI]
Journal Publication Open Access ResearchOnline@JCU