Research

I am a computational and molecular biologist working at the intersection of transcriptomics, evolutionary genetics, and multi-omic data integration. My research spans multiple biological systems: from human clinical cohort studies using patient-derived DNA samples during my Master’s training, to large-scale functional genomics in Drosophila melanogaster during my doctoral work. I combine rigorous experimental design with reproducible computational analysis to ask how gene expression is shaped by signaling pathways, sex, genetic background, and environmental context.

Dissertation Research — Graze Lab

Advisor: Dr. Rita M. Graze · Auburn University · 2017–Present

Mode of Sex-Differential Gene Regulation by Insulin Signaling

Does IIS regulate sex-differential expression through a gradual (dial-like) or threshold-like (switch-like) mechanism? I designed and analyzed a graded-perturbation RNA-seq experiment in adult D. melanogaster heads, building a fully reproducible pipeline with DESeq2, robust outlier detection, dose-response clustering, and functional enrichment analysis.

Sex-by-Genotype Effects Across Diverse Genetic Backgrounds

How does natural genetic variation shape sex-specific transcriptional responses to IIS perturbation? I designed a large multifactor experiment (genotype × sex × treatment × environment) across multiple DSPR-derived lines. Analysis includes differential expression, WGCNA co-expression network analysis, and cross-sex genetic correlations to quantify evolutionary constraint on IIS targets.

Isoform-Level Regulation of Sex-Differential IIS Response

Do sex-differential IIS responses arise through transcript abundance or alternative splicing? Using rMATS turbo across a 320-sample dataset, I quantified isoform usage and splicing patterns to determine the contribution of transcript-level regulation beyond total gene expression.

Summer 2026 — Stevison Lab

PI: Dr. Laurie Stevison · NIH-R35: “The Role of Oogenesis in Speciation”

Thermal Stress and Oogenesis in Drosophila

Analyzing previously collected RNA-seq and ATAC-seq data from two Drosophila species to characterize how thermal stress affects oogenesis, integrating transcriptomic and chromatin-accessibility approaches. I am also performing single-cell RNA-seq library preparation for collaborative Graze lab samples, contributing to a future co-authored publication.

Master’s Research — Population Genetics Lab

Advisor: Dr. A.H.M. Nurun Nabi · University of Dhaka · 2016–2017

Genetic Risk Factors for Type 2 Diabetes in the Bangladeshi Population

Using patient-derived human DNA samples from clinical case-control cohorts, I investigated genetic associations of GATA3, mitochondrial NADH dehydrogenase subunits, hTERT, and related loci with type 2 diabetes risk. I performed SNP genotyping, telomere length quantification, and bioinformatics annotation, contributing to five peer-reviewed publications.

Experimental and Computational Expertise

Experimental: RNA and DNA extraction, pre-sequencing QC (TapeStation, Qubit), PCR-based genotyping, molecular cloning, site-directed mutagenesis, bulk and single-cell RNA-seq library preparation (Illumina), Drosophila husbandry and BSL-2 lab work. Multifactor experimental designs incorporating sex, genotype, treatment, and environmental conditions.

Computational: R and Python on Linux/HPC environments with Git/GitHub version control. RNA-seq QC and alignment, differential expression (DESeq2, edgeR), multifactor modeling, k-means clustering, WGCNA, alternative splicing (rMATS turbo), ATAC-seq processing, SNP association analysis, and functional enrichment analysis.

Selected Publications and Presentations

See the Publications page for a full list.

Peer-Reviewed:

  • Huda, N. et al. (2021). MNS16A VNTR polymorphism of human telomerase gene. Journal of Diabetes and Its Complications, 35(10), 108018.
  • Huda, N. et al. (2018). Genetic variation of GATA3, not STAT4, is associated with type 2 diabetes risk. PLoS ONE, 13(7), e0198507.

Poster Presentations:

  • Huda, N., Graze, R.M. (2025). “Natural variation in regulation of sexually dimorphic gene expression by the insulin signaling pathway in Drosophila melanogaster.” 66th Annual Drosophila Research Conference, San Diego, CA.
  • Huda, N., Graze, R.M. (2023). “The role of insulin signaling in sex differences in gene expression.” 64th Annual Drosophila Research Conference, Chicago, IL.
  • Huda, N., Washburn, R.C., Williams, S.L., Graze, R.M. (2021). “Sex differences in the effects of insulin signaling on food consumption in adult Drosophila melanogaster.” 62nd Annual Drosophila Research Conference.