Dr Loan Nguyen
Research Fellow
Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI)
| Featured projects | Duration |
|---|---|
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Multi-contact Pore-C Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2022 |
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Cas9 targeted enrichment for Nanopore sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2023 |
Journal Articles
Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Nguyen, Loan, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2024). Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility. Scientific Reports, 14 (1) 4419, 1-14. doi: 10.1038/s41598-024-54577-w
Lamb, H. J., Nguyen, L. T., Copley, J. P., Engle, B. N., Hayes, B. J. and Ross, E. M. (2023). Imputation strategies for genomic prediction using nanopore sequencing. BMC Biology, 21 (1) 286, 1-18. doi: 10.1186/s12915-023-01782-0
Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Liu, Shouye, Nguyen, Loan To, Powell, Owen, Hickey, Lee T., Deomano, Emily, Atkin, Felicity, Voss‐Fels, Kai P. and Hayes, Ben J. (2023). Use of continuous genotypes for genomic prediction in sugarcane. The Plant Genome, 17 (1) e20417, e20417. doi: 10.1002/tpg2.20417
Lamb, H. J., Nguyen, L. T., Briody, T. E., Ambrose, R. K., Hayes, B. J., Mahony, T. J. and Ross, E. M. (2023). Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle. Animal Production Science, 63 (11), 1074-1085. doi: 10.1071/an22451
Nguyen, Loan T., Jung, Hyungtaek, Ma, Jun, Andersen, Stacey and Ross, Elizabeth (2023). Long-read Pore-C shows the 3D structure of the cattle genome. Animal Production Science, 63 (11), 1-11. doi: 10.1071/an22479
Nguyen, Tuan V., Vander Jagt, Christy J., Wang, Jianghui, Daetwyler, Hans D., Xiang, Ruidong, Goddard, Michael E., Nguyen, Loan T., Ross, Elizabeth M, Hayes, Ben J., Chamberlain, Amanda J. and MacLeod, Iona M. (2023). In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genetics Selection Evolution, 55 (1) 9, 1-15. doi: 10.1186/s12711-023-00783-5
Nguyen, Loan To, Lau, Li Yieng and Fortes, Marina Rufino Salinas (2022). Proteomic analysis of hypothalamus and pituitary gland in pre and postpubertal Brahman heifers. Frontiers in Genetics, 13 935433, 1-15. doi: 10.3389/fgene.2022.935433
Ross, Elizabeth M., Sanjana, Hari, Nguyen, Loan T., Cheng, YuanYuan, Moore, Stephen S. and Hayes, Ben J. (2022). Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle. Frontiers in Genetics, 13 784663, 784663. doi: 10.3389/fgene.2022.784663
Lamb, Harrison J., Hayes, Ben J., Randhawa, Imtiaz A. S., Nguyen, Loan T. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage portable Nanopore sequencing. PLoS One, 16 (12) e0261274, e0261274. doi: 10.1371/journal.pone.0261274
Hayes, Ben J., Nguyen, Loan T., Forutan, Mehrnush, Engle, Bailey N., Lamb, Harrison J., Copley, James P., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology. Frontiers in Genetics, 12 760450, 760450. doi: 10.3389/fgene.2021.760450
Alexandre, Pâmela A., Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T., Porto-Neto, Laercio R., Fortes, Marina R. S. and Reverter, Antonio (2021). Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. Genome Biology, 22 (1) 273, 273. doi: 10.1186/s13059-021-02489-7
Lee, Simon, Nguyen, Loan T., Hayes, Ben J. and Ross, Elizabeth (2021). Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics, 37 (21), 3936-3937. doi: 10.1093/bioinformatics/btab630
Forutan, Mehrnush, Ross, Elizabeth, Chamberlain, Amanda J., Nguyen, Loan, Mason, Brett, Moore, Stephen, Garner, Josie B., Xiang, Ruidong and Hayes, Ben J. (2021). Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Communications Biology, 4 (1) 829, 1-14. doi: 10.1038/s42003-021-02340-6
Trigo, Beatriz B., Utsunomiya, Adam T. H., Fortunato, Alvaro A. A. D., Milanesi, Marco, Torrecilha, Rafaela B. P., Lamb, Harrison, Nguyen, Loan, Ross, Elizabeth M., Hayes, Ben, Padula, Romulo C. M., Sussai, Thayla S., Zavarez, Ludmilla B., Cipriano, Rafael S., Caminhas, Maria M. T., Lopes, Flavia L., Pelle, Cassiano, Leeb, Tosso, Bannasch, Danika, Bickhart, Derek, Smith, Timothy P. L., Sonstegard, Tad S., Garcia, Jose F. and Utsunomiya, Yuri T. (2021). Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution, 53 (1) 40, 40. doi: 10.1186/s12711-021-00633-2
Yadav, Seema, Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Sun, Yue, Nguyen, Loan T., Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S., Hayes, Ben J. and Voss-Fels, Kai P. (2021). Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. Theoretical and Applied Genetics, 134 (7), 2235-2252. doi: 10.1007/s00122-021-03822-1
Hayes, Ben J., Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Yue, Jenny, Nguyen, Loan, Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S. and Voss-Fels, Kai P. (2021). Accuracy of genomic prediction of complex traits in sugarcane. Theoretical and Applied Genetics, 134 (5), 1455-1462. doi: 10.1007/s00122-021-03782-6
Lamb, Harrison J., Hayes, Ben J., Nguyen, Loan T. and Ross, Elizabeth M. (2020). The future of livestock management: a review of real-time portable sequencing applied to livestock. Genes, 11 (12) 1478, 1-27. doi: 10.3390/genes11121478
Alexandre, Pâmela A., Hudson, Nicholas J., Lehnert, Sigrid A., Fortes, Marina R. S., Naval-Sánchez, Marina, Nguyen, Loan T., Porto-Neto, Laercio R. and Reverter, Antonio (2020). Genome-wide co-expression distributions as a metric to prioritize genes of functional importance. Genes, 11 (10) 1231, 1231-13. doi: 10.3390/genes11101231
Fortes, Marina R. S., Porto-Neto, Laercio R., Satake, Nana, Nguyen, Loan T., Freitas, Ana Claudia, Melo, Thaise P., Scalez, Daiane Cristina Becker, Hayes, Ben, Raidan, Fernanda S. S., Reverter, Antonio and Boe-Hansen, Gry B. (2020). X chromosome variants are associated with male fertility traits in two bovine populations. Genetics Selection Evolution, 52 (1) 46, 46. doi: 10.1186/s12711-020-00563-5
Lau, Li Yieng, Nguyen, Loan T., Reverter, Antonio, Moore, Stephen S., Lynn, Aaron, McBride‐Kelly, Liam, Phillips‐Rose, Louis, Plath, Mackenzie, Macfarlane, Rhys, Vasudivan, Vanisha, Morton, Lachlan, Ardley, Ryan, Ye, Yunan and Fortes, Marina R. S. (2020). Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers. Veterinary Medicine and Science, 6 (4) vms3.278, 695-710. doi: 10.1002/vms3.278
Lamb, Harrison J., Ross, Elizabeth M., Nguyen, Loan T., Lyons, Russell E., Moore, Stephen S. and Hayes, Ben J. (2020). Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing. Journal of Animal Science, 98 (5) skaa127, skaa127. doi: 10.1093/jas/skaa127
Tahir, Muhammad S., Nguyen, Loan T., Schulz, Benjamin L., Boe-Hansen, Gry A., Thomas, Milton G., Moore, Stephen S., Lau, Li Yieng and Fortes, Marina R S (2019). Proteomics recapitulates ovarian proteins relevant to puberty and fertility in Brahman heifers (Bos indicus L.). Genes, 10 (11) 923, 923. doi: 10.3390/genes10110923
Fonseca, Pablo Augusto de Souza, Id-Lahoucine, Samir, Reverter, Antonio, Medrano, Juan F., Fortes, Marina S., Casellas, Joaquim, Miglior, Filippo, Brito, Luiz, Carvalho, Maria Raquel S., Schenkel, Flávio S., Nguyen, Loan T., Porto-Neto, Laercio R., Thomas, Milton G. and Cánovas, Angela (2018). Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle. PLOS ONE, 13 (10) e0205295, e0205295. doi: 10.1371/journal.pone.0205295
Fortes, M. R.S., Zacchi, L. F., Nguyen, L. T., Raidan, F., Weller, M. M.D.C.A., Choo, J. J.Y., Reverter, A., Rego, J. P.A., Boe-Hansen, G. B., Porto-Neto, L. R., Lehnert, S. A., Cánovas, A., Schulz, B. L., Islas-Trejo, A., Medrano, J. F., Thomas, M. G. and Moore, S. S. (2018). Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty. Animal Genetics, 49 (6), 539-549. doi: 10.1111/age.12721
Nguyen, L. T., Zacchi, L. F., Schulz, B. L., Moore, S. S. and Fortes, M. R. S. (2018). Adipose tissue proteomic analyses to study puberty in Brahman heifers. Journal of Animal Science, 96 (6), 2392-2398. doi: 10.1093/jas/sky128
Nguyen, Loan T., Reverter, Antonio, Cánovas, Angela, Venus, Bronwyn, Anderson, Stephen T., Islas-Trejo, Alma, Dias, Marina M., Crawford, Natalie F., Lehnert, Sigrid A., Medrano, Juan F., Thomas, Milt G., Moore, Stephen S. and Fortes, Marina R.S. (2018). STAT6, PBX2, and PBRM1 emerge as predicted regulators of 452 differentially expressed genes associated with puberty in Brahman heifers. Frontiers in Genetics, 9 (MAR) 87, 1-13. doi: 10.3389/fgene.2018.00087
Dias, M. M., Cánovas, A, Mantilla-Rojas, C, Riley, D. G., Luna-Nevarez, P, Coleman, S. J., Speidel, S. E., Enns, R. M., Islas-Trejo, A., Medrano, J. F., Moore, S. S., Fortes, M. R. S., Nguyen, L. T., Venus, B., Diaz, I. S. D. P., Souza, F. R. P., Fonseca, L. F. S., Baldi, F., Albuquerque, L. G., Thomas, M. G. and Oliveira, H. N. (2017). SNP detection using RNA-sequences of candidate genes associated with puberty in cattle. Genetics and Molecular Research, 16 (1) gmr16019522. doi: 10.4238/gmr16019522
Nguyen, L. T., Reverter, A., Canovas, A., Venus, B., Islas-Trejo, A., Porto-Neto, L. R., Lehnert, S. A., Medrano, J. F., Moore, S. S. and Fortes, M. R. S. (2017). Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers. Journal of Animal Science, 95 (2), 599-615. doi: 10.2527/jas.2016.0921
Fortes, M. R. S., Nguyen, L. T., Weller, M. M. D. C. A., Canovas, A., Islas-Trejo, A., Porto-Neto, L. R., Reverter, A., Lehnert, S. A., Boe-Hansen, G. B., Thomas, M. G., Medrano, J. F. and Moore, S. S. (2016). Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post-versus prepubertal Brahman heifers. Journal of Animal Science, 94 (9), 3693-3702. doi: 10.2527/jas.2016-0471
Fortes, Marina R.S., Nguyen, Loan To, Porto Neto, Laercio R., Reverter, Antonio, Moore, Stephen S., Lehnert, Sigrid A. and Thomas, Milton G. (2016). Polymorphisms and genes associated with puberty in heifers. Theriogenology, 86 (1), 333-339. doi: 10.1016/j.theriogenology.2016.04.046
Lyons, Russell E., Loan, Nguyen To, Dierens, Leanne, Fortes, Marina R. S., Kelly, Matthew, McWilliam, Sean S., Li, Yutao, Bunch, Rowan J., Harrison, Blair E., Barendse, William, Lehnert, Sigrid A. and Moore, Stephen S. (2014). Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle. BMC Genetics, 15 (1) 6, 6.1-6.10. doi: 10.1186/1471-2156-15-6
Conference Papers
Madani, Khalil Saber H., Nguyen, Loan, Phan, Anh Dao Thi, Netzel, Michael E. and Sultanbawa, Yasmina (2023). Protocol Modification for DNA Extraction from Human Faecal Samples. Queensland Annual Chemistry Symposium (QACS), Brisbane, QLD, Australia, 24 November 2023.
Ross, E.M., Nguyen, L.T., Engle, B.N., Chamberlain, A.J., Kho, E. and Hayes, B.J. (2022). Bos indicus genome percentage effects gene expression profile and differentially expressed genes in Brahman cattle whole blood. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_628
Mantilla Valdivieso, E. , Nguyen, L., Ross, E., Raza, A., James, P., Hayes, B., Jonsson, N. and Tabor, A. (2022). Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_557
Lamb, H.J., Nguyen, L.T., Randhawa, I.A.S., Hayes, B.J. and Ross, E.M. (2022). The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_279
Lamb, H. J. , Nguyen, L. T., Engle, B. N., Hayes, B. J. and Ross, E. M. (2021). Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.
Ross, E. M., Lamb, H. J., Engle, B. N. , Nguyen, L. T. and Hayes, B. J. (2021). Assessing the potential of parentage testing using portable long read sequencing technologies. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.
Forutan, M., Vander Jagt, C.J., Ross, E., Chamberlain, A. J., Mason, B., Nguyen, L., Moore, S., Garner, J. B., Xiang, R. and Hayes, B. J. (2021). Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.
Forutan, Mehrnush, Ross, Elizabeth, Nguyen, Loan and Hayes, Ben (2021). Genome-wide analysis of transcription start sites across Bos indicus tissues. 38th International Conference on Animal Genetics, Online, 26 - 30 July 2021.
Nguyen, Loan T., Forutan, Mehrnush, Hayes, Ben J. and Ross, Elizabeth M. (2021). A Bos indicus epigenetic clock predicts age from tail hair. 38th International Society of Animal Genetics (ISAG), Virtual, 26 - 30 July 2021.
Lamb, Harrison, Nguyen, Loan T., Hayes, Ben J., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage Nanopore sequencing. 38th International Society of Animal Genetics, Virtual, 26 - 30 July 2021.
Alexandre, Pâmela A., Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T., Porto-Neto, Laercio, Fortes, Marina R.S. and Reverter, Antonio (2021). Chromatin accessibility and regulatory vocabulary in indicine cattle. 38th International Society of Animal Genetics (ISAG), Virtual, 26-30 July 2021. Champaign, IL United States: ISAG.
Nguyen, Loan T., Reverter, Antonio, Cánovas, Angela, Porto-Neto, L.R., Venus, Bronwyn, Islas-Trejo, Alma, Lehnert, Sigrid A., Medrano, Juan F., Thomas, Milton G., Moore, Stephen S. and Fortes, Marina R.S. (2019). Pre- and post-puberty co-expression gene networks from RNA-sequencing of Brahman heifers. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, Armidale, NSW, Australia, 27 October - 1 November 2019.
Fonseca, P. A. D. S., Id-Lahoucine, S., Casellas, J., Miglior, F., Reverter, A., Fortes, M. R., Nguyen, L. T., Porto-Neto, L. R., Sargolzaei, M., Brito, L. F., Miller, S. P., Schenkel, F. S., Lohuis, M., Medrano, J. F. and Canovas, A. (2018). Functional Characterization of Genes Mapped in Transmission Ratio Distortion Regions of the Bovine Genome Affecting Reproduction. CARY: OXFORD UNIV PRESS INC.
Nguyen, Loan To, Fortes, Marina R.S. and Reverter, Antonio (2017). A pipeline for the analysis of multi-omics data. The Association for the Advancement of Animal Breeding and Genetics, Townsville, QLD, Australia, 2-5 July 2017.
Nguyen, L. T., Reverter-Gomez, A., Canovas, A., Venus, B., Islas-Trejo, A., Lehnert, S. A., Medrano, J. F., Moore, S. S. and Fortes, M. R. (2016). Liver transcriptome from pre versus post-pubertal Brahman heifers. Animal Genomes (FAANG) ASAS-ISAG Joint Symposium, Salt Lake City, UT United States, 23 July 2016. Cary, NC United States: Oxford University Press. doi: 10.1093/ansci/94.supplement4.20
Nguyen, L. T., Camargo, G. M. F. D, Lyons, R. E., Lehnert, S. A. and Fortes, M. R. S. (2015). Effects of TEX11 and AR polymorphisms on reproduction and growth traits in Australian beef cattle. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Bundoora, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.
Fortes, M. R. S., Almughlliq, F. B., Nguyen, L. T., Porto Neto, L. R. and Lehnert, S. A. (2015). Non-synonimous polymorphism in helb is associated with male and female reproductive traits in cattle. Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Bundoora, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.
Thesis
Nguyen, Loan To (2018). Using transcriptomic and proteomic analysis to characterize the biological basis of puberty in Brahman heifers. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/uql.2018.857