vydang.github.io

Vy Dang

Bioinformatics | Graduate Student

I am a computational biology researcher building cross-disciplinary expertise in transcriptomics, structural bioinformatics, and high-performance data pipelines. My work focuses on developing workflows across multiple domains of bioinformatics while strengthening both biological insight and computational rigor.

Current Focus

• Protein structure trajectory modeling

Featured Projects

:cherry_blossom: Genome Assembly and Annotation

De novo genome assembly using short-read sequencing data followed by structural and functional annotation.

Key results

• A 3.49 Mb draft genome was assembled across 286 contigs, consistent with expected genome size for C. thermocellum.
• Prokka identified:
  • 2,981 coding sequences (CDS)
  • 55 tRNAs
  • 4 rRNAs
  • 1 tmRNA
• 726 high-confidence matches (24.35%) in BLASTP against Swiss-Prot

Tools: SPAdes, QUAST, Prokka, BLAST, FastQC, Trimmomatic

View the full GitHub repository

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:cherry_blossom: WGS Germline Human Variant Calling & Functional Annotation

Germline variant discovery workflow following GATK Best Practices.

Key results

• Successful complete germline variant calling workflow using GATK4
• Generated high-confidence SNP and INDEL callsets from aligned WGS data
• Annotated variants using Funcotator to extract gene-level information

Tools: GATK4, samtools, fastqc, bwa, multiQC

View the full GitHub repository

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:cherry_blossom: RNA-Seq Differential Expression – NUDT21 Knockdown

End-to-end RNA-seq analysis pipeline for NUDT21 knockdown including gene set enrichment analysis.

Key results

• 11,450 genes significant (FDR < 0.05)
• Ribosome biogenesis & RNA processing pathways strongly affected
• Results suggest that NUDT21 regulates core proliferative and RNA-processing programs

Tools: HISAT2, samtools, Subread, FastQC, MultiQC, Trimmomatic, featureCounts, ggplot2, Bioconductor, EnhancedVolcano, limma-voom, clusterProfiler

View the full GitHub repository

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Protein Structural Trajectory Modeling

Trajectory inference of protein isoforms using RMSD-based clustering and structural similarity analysis.

Tools: Python, MDAnalysis, PyTorch

Technical Skills

Category	Details
Languages	Bash, Python, R
Bioinformatics	RNA-seq, alignment, gene quantification, differential expression
Tools	HISAT2, Samtools, featureCounts, FastQC, SRA Toolkit
Computing	Linux, HPC clusters, Conda environments
Data Analysis	DESeq2, PCA, clustering, statistical modeling