Email

hoa.nguyen-phuc@bcm.edu

Positions

Bioinformatics Analyst II

Molecular Virology & Microbiology - Estes
Baylor College of Medicine
Houston, US

Postdoc Associate

The Raptor Center & Plant Pathology
University of Minnesota
St.Paul, Minnesota United States
Developed RNAseq immune assays and bioinformatics analyses to investigate the effects of neonicotinoid insecticides in immune competence in wild birds. Biostatistical analysis of ecotoxicological models. Maintained bioinformatics pipelines to identify virus sequences for routine veterinary diagnoses. Developed population genomics models to understand epidemiology and pathogenicity evolution of rust fungi. DNAseq phylogenetic analyses of stem rust and crown rust fungi.

Postdoc Associate

Poultry Science
Texas A&M University
College Station, Texas United States
DNAseq phylogenetic analyses on Junglefowl species. RNAseq research design and analyses to understand Woody Breast Myopathy and circadian cycles in chickens. Raised endemic colony of 15 Red Junglefowl with successful hatching.

Research Assistant

Animal Sciences
University of Wisconsin - Madison
Madison, Wisconsin United States
Research projects in spatial genetic variation of Red Junglefowl and Sarus Cranes in Vietnam using molecular technologies, HPC Bayesian models, and spatial statistics.

Education

PhD from University of Wisconsin-Madison

08/2015 - Madison, Wisconsin United States

MS from University of Melbourne

06/2005 - Melbourne, Australia

Professional Interests

• Bioinformatics, Evolutionary Biology, Population Genetics, Conservation Genomics

Professional Statement

I use genomics and bioinformatics tools to study changes in genomes over time in non-model systems and at population levels. With my background in wildlife ecology and conservation, I am particularly interested in wildlife species and their related domesticated livestock as multiple aspects of structure changes in their genomes can yield interesting results relevant to phenotypic changes and understanding evolutionary rates. My previous postdoc projects involved working on an ecotoxicology project to evaluate the influences of neonicotinoid insecticides in wild birds and a plant disease genomics and pathogenicity project to broaden our understanding of virulence resistance in wild relatives of cereals. My current projects have studied viral infection in human gastrointestinal systems.

I have hand-on programming and statistical skills in R, Python, and Unix BASH scripting. My PhD minor was in Statistics with focus in Spatial Statistics. I have Bioinformatics skills in using general packages structural variation SAMtools, GATK; de novo assembly QUAST, VELVET; metagenomics packages MOTHUR, QIIME. Population genetics in GENELAND (R), STRUCTURE; RNAseq funcational variation trimGalore, STAR/HISAT2 mapping, featureCounts, GSEA analysis, ORA analysis; single-cell RNAseq cellranger, seurat; phylogenetics GProfileR, AxML, MrBayes, BEAUTi & BEAST; R ggplot2, Rmardown, Rshiny for data visualization. Wet bench skills - PCR, DNA and RNA extraction, dye-terminator sequencing, plasmid construct cloning, in vitro cell culture; Illumina and KASP (SNP) sequencing platforms.

Selected Publications

• Upadhyaya N., Mago R., Panwar V., Hewitt T., Luo M., Sperschneider J., Nguyen-Phuc H., Wang A., Ortiz D., Hac L., Chen J., Li F., Zhang J., Figueroa M., Kanyuka K., Ellis J., Dodds P "Genomics accelerated isolation of a new stem rust avirulence gene wheat resistance gene pair." Nat Plants. 2021; Pubmed PMID: 34294906
• Senner P., Barzen J., Silbernagel J., Larsen B., and Nguyen-Phuc H. "Changes in avian community composition at a restored floodplain grassland in the Mekong Delta." Waterbirds. 2022;44(4):520-532.
• Miller M, Nazareno E, Rottschaefer S, Li F, Nguyen-Phuc H, Henningsen E, Persoons A, Saunders D, Hirsch C, Dodds P, Stukenbrock E, Kianian S, Figueroa M "Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci.." PLoS Genet. 2020;16(12) Pubmed PMID: 33370783
• Franzen-Klein D., Jankowski M., Roy C., Nguyen-Phuc H., Chen D., Neuman-Lee L., Rediga P., and Ponder J. "Evaluation of Neurobehavioral Abnormalities and Immunotoxicity after Oral Imidacloprid Exposure in Domestic Chickens." J Toxicol Environ Health A. 2020;83(2) Pubmed PMID: 32024444