Overview
Background
Dr. Nguyen is an expert in applying long-read Oxford Nanopore Sequencing Technologies (ONT) in agriculture, particularly livestock and other sectors. Her groundbreaking contributions include being the pioneer in sequencing the genomes of Brahman and Wagyu cattle, developing an innovative epigenetic clock for age prediction in cattle, and successfully implementing ONT portable sequencers for Blockchain traceability systems in Australia.
As a leader in the field, Dr. Nguyen spearheads the use of ONT long-read technology to scaffold genome assemblies in livestock, plants, protists, and insects. Her multidisciplinary expertise in molecular biology, advanced genomics, and animal sciences also empowers her to explore causative markers for commercial SNP arrays and identify significant DNA variants from low-coverage sequencing data sets.
Dr. Nguyen's exceptional achievements and expertise have been acknowledged through the prestigious ARC Industry Fellowship, recognising her as a promising early career researcher. Her work has significantly contributed to advancing genomic research in agriculture and has opened new avenues for utilising ONT sequencing technologies across diverse domains.
Availability
- Dr Loan Nguyen is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Doctor of Philosophy, The University of Queensland
Works
Search Professor Loan Nguyen’s works on UQ eSpace
2021
Conference Publication
Assessing the potential of parentage testing using portable long read sequencing technologies
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.
2021
Conference Publication
Genome wide analysis of bovine enhancers and promoters across developmental stages in liver
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.
2021
Conference Publication
Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing
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.
2021
Journal Article
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues
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
2021
Journal Article
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data
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
2021
Conference Publication
Genome-wide analysis of transcription start sites across Bos indicus tissues
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.
2021
Conference Publication
A Bos indicus epigenetic clock predicts age from tail hair
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.
2021
Conference Publication
Chromatin accessibility and regulatory vocabulary in indicine cattle
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.
2021
Conference Publication
Genomic prediction using low-coverage Nanopore sequencing
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.
2021
Journal Article
Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus
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
2021
Journal Article
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
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
2021
Journal Article
Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects
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
2021
Journal Article
Accuracy of genomic prediction of complex traits in sugarcane
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
2020
Journal Article
The future of livestock management: a review of real-time portable sequencing applied to livestock
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
2020
Journal Article
Genome-wide co-expression distributions as a metric to prioritize genes of functional importance
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
2020
Journal Article
X chromosome variants are associated with male fertility traits in two bovine populations
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
2020
Journal Article
Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers
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
2020
Journal Article
Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing
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
2019
Journal Article
Proteomics recapitulates ovarian proteins relevant to puberty and fertility in Brahman heifers (Bos indicus L.)
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
2019
Conference Publication
Pre- and post-puberty co-expression gene networks from RNA-sequencing of Brahman heifers
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.
Supervision
Availability
- Dr Loan Nguyen is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Available projects
-
Cas9 targeted enrichment of age-related sites
Tools to predict birthdates of cattle are desperately required by industry to ensure compliance with breed registration requirements and to increase the rate of genetic gain for traits such as growth rate and fertility. This study will use new methods of gene targeting and sequencing to investigate the predictive ability of the methylation status of key genes related to age in mammals. Several studies found age-related-conserved sites among species. From these a list of 43 age related genes in cattle has been derived. In this study these genes will be targeted for sequencing and methylation calling in cattle of varying ages. A predictive statistical approach will then the used to associated the methylation rates of those genes with animal age, which can then be used to calculate birthdate.
This project will apply long-read Oxford Nanopore Sequencing CAS9 targeted enrichment. The project aims to use this approach to target age-related-conversed genes among humans, dogs, and cattle. Finally, validation in large populations will be performed with the most significant age-related sites using quantitative methylation-specific PCR. The ultimate aim of this work is to develop an on farm diagnostic tool that will allows producers to record accurate birthdates and improve the profitability of the beef industry through genetic gain for key traits.
This project will develop skills in bioinformatics and molecular biology. Students will learn how to design experiments, perform sequencing, and manage very large sequence data sets.
-
A comparison of Full-length transcript sequencings methods
Precise gene annotations are essential to understanding the complexity of a species transcriptome and to connect genomic sequence to gene function and ultimately phenotype. RNA sequencing has been widely applied to build a reference transcriptome using short-read sequencing, followed by the assembly or mapping reads to accessible reference genomes. However, short-read sequencing is facing the challenge of lengthy transcripts, repetitive regions, and transposable elements. Long read-sequencing technology, represented by Pacbio Sequencing and Oxford Nanopore sequencing, has overwhelmed this challenge by generating full-length transcripts. Another advantage of Oxford Nanopore sequencing is the potential to direct sequence RNA molecules to remove PCR bias and identify the base modifications.
In this study, students will perform direct cDNA sequencing and direct RNA sequencing from the liver samples from two cattle genomes using Pacbio isoform sequencing and Nanopore sequencing. The generated sequencing datasets will be compared between technologies and published sequencing data from the same tissues (RNAseq and CAGEseq). The ultimate aim of this project is to advance our understanding of emerging technologies and deeping our understanding of the cattle transcriptome.
This project will developed molecular techniques (DNA extraction, library preparation and sequencing) and bioinformatics skills. Students will learn how to work with RNA samples and manage extensive sequencing data sets.
-
DNA extraction method for faecal metagenomics to assess cattle diet
Cattle diet history information can be obtained by studying non-invasive samples, like dried faecal samples. Additionally, the analysis of faecal samples can also provide the information about the digestive efficiency of an animal. The advent of improved sequencing methodologies has simplified the characterization of complex faecal DNA and allows for the characterization of diet profiles by matching the faecal sequence data with available sequence databases of potential food sources. In this study, student will employ different extraction protocols to isolate DNA from faecal samples using a variety of molecular techniques in the lab.
-
Predicting age using methylated sites
In humans, the methylation state of CpG sites changes with age and can therefore be utilized as an accurate biomarker for aging. In cattle, biological age prediction based on methylation status could provide key information for genetic improvement programs. Additionally, comparing chronological age with biological age (based on methylation status) can provide important information about the stress an animal has been under during its lifetime. However, relatively little is known about DNA methylation patterns in cattle. Students will use cutting edge data sources including reduce representation bisulphite sequencing data, whole genome bisulphite sequencing, long read sequencing and human methylation data to identify differentially methylated regions between old and young animals and validate those regions with modern molecular technologies.
-
Exploring tissue specific methylation sites in cattle
DNA methylation is an epigenetic mechanism driving the gene expression in specific tissues at a particular stage. However, the mechanism of how DNA-methylation regulates gene expression in cattle is still unknown. Here, the student will use two types of datasets, whole genome sequencing from Oxford Nanopore sequencing versus RNA sequencing, to explore the relationship between methylation and gene expression. This will be conducted in two tissues, lung and liver.
-
Discovering methane reducing pathways in seaweed
Cattle are a major source of methane, a potent greenhouse gas. Recently, it has been discovered that feeding some seaweeds to cattle, particularly red seaweed (Asparagopsis taxiformis) greatly reduces methane emissions. In this project, the successful candidate will sequence the red seaweed genome, and discover the gene pathways that led to the production of anti-methanogenic compounds. This knowledge could lead to new innovations to reduce methane emissions and so contribute to a large scale reduction in global warming. The student will learn skills in genome sequencing with state of the art (Nanopore) technology as well as cutting edge bioinformatics techniques.
Supervision history
Current supervision
-
Doctor Philosophy
Bovine Immunity from Novel Protozoan Vaccines
Associate Advisor
Other advisors: Dr Hannah Siddle, Dr Gry Boe-Hansen, Professor Ala Tabor
-
Doctor Philosophy
Stingless bee enzymes for biotransformation of cane sugar to a low GI sugar
Associate Advisor
Other advisors: Professor James De Voss, Emerita Professor Mary Fletcher, Dr Natasha Hungerford
-
Doctor Philosophy
Understanding the genomic variation of methane producing ruminants
Associate Advisor
Other advisors: Dr Elizabeth Ross
-
Doctor Philosophy
Assessing the effect of date fruit (Phoenix dactylifera L.) on human gut microbiota and metabolite production: an in vitro fermentation study
Associate Advisor
Other advisors: Dr Michael Netzel, Professor Yasmina Sultanbawa
Completed supervision
-
2023
Doctor Philosophy
The cellular and molecular foundations of antibody response kinetics and affinity maturation in giant grouper (Epinephelus lanceolatus)
Associate Advisor
Other advisors: Professor Andrew Barnes
Media
Enquiries
Contact Dr Loan Nguyen directly for media enquiries about their areas of expertise.
Need help?
For help with finding experts, story ideas and media enquiries, contact our Media team: