![Dr Loan Nguyen](/sites/default/files/profiles/22854.jpeg)
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
2024
Journal Article
Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility
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
2024
Journal Article
Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis
Ong, Chian Teng, Mody, Karishma T., Cavallaro, Antonino S., Yan, Yakun, Nguyen, Loan T., Shao, Renfu, Mitter, Neena, Mahony, Timothy J. and Ross, Elizabeth M. (2024). Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis. International Journal of Molecular Sciences, 25 (14) 7824, 7824. doi: 10.3390/ijms25147824
2024
Journal Article
Whole-genome sequence of <i>Micrococcus</i> sp. strain HOU01 isolated from potato root
Dao, Van Hong Thi, Nguyen, Loan To, Tran, Phuong Minh Thi, Nguyen, Truong Xuan, Le, Ha Hai Thanh and Dinh, Son Truong (2024). Whole-genome sequence of Micrococcus sp. strain HOU01 isolated from potato root. Microbiology Resource Announcements, 13 (6). doi: 10.1128/mra.00268-24
2024
Journal Article
Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility
Forutan, Mehrnush, Engle, Bailey N., Chamberlain, Amanda J., Ross, Elizabeth M., Nguyen, Loan T., D’Occhio, Michael J., Snr, Alf Collins, Kho, Elise A., Fordyce, Geoffry, Speight, Shannon, Goddard, Michael E. and Hayes, Ben J. (2024). Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility. Communications Biology, 7 (1) 724, 724. doi: 10.1038/s42003-024-06403-2
2024
Journal Article
Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach
López-Catalina, Adrián, Reverter, Antonio, Alexandre, Pamela A., Nguyen, Loan T. and González-Recio, Oscar (2024). Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach. Epigenetics, 19 (1) 2381856. doi: 10.1080/15592294.2024.2381856
2023
Journal Article
Use of continuous genotypes for genomic prediction in sugarcane
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
2023
Journal Article
Imputation strategies for genomic prediction using nanopore sequencing
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
2023
Conference Publication
Protocol Modification for DNA Extraction from Human Faecal Samples
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.
2023
Journal Article
Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle
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
2023
Journal Article
Long-read Pore-C shows the 3D structure of the cattle genome
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
2023
Journal Article
In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants
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
2022
Conference Publication
The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy
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
2022
Conference Publication
Predicted isoforms of a Brahman cow revealed by full-length transcript sequencing
Nguyen, L.T., Cheng, Y., Kuo, R., Hayes, B.J. and Ross, E.M. (2022). Predicted isoforms of a Brahman cow revealed by full-length transcript sequencing. 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_513
2022
Conference Publication
Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis
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
2022
Conference Publication
Bos indicus genome percentage effects gene expression profile and differentially expressed genes in Brahman cattle whole blood
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
2022
Journal Article
Proteomic analysis of hypothalamus and pituitary gland in pre and postpubertal Brahman heifers
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
2022
Journal Article
Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle
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
2021
Journal Article
Genomic prediction using low-coverage portable Nanopore sequencing
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
2021
Journal Article
An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology
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
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.
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
Natural photosensitizers for photodynamic microbial inactivation i
Associate Advisor
Other advisors: Dr Michael Netzel, Professor Yasmina Sultanbawa
-
Doctor Philosophy
Understanding the genomic variation of methane producing ruminants
Associate Advisor
Other advisors: Dr Elizabeth Ross
-
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, Professor Mary Fletcher, Dr Natasha Hungerford
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: