PhD · ML & Bioinformatics · UGA
I'm Utsav Lamichhane, a PhD researcher at the University of Georgia working on microbiome analysis, predictive modeling, and 16S & shotgun metagenomics — and the open-source software that makes those pipelines reproducible.
# 16S amplicon → insight, end to end qiime tools import \ --input-path manifest.tsv \ --output-path reads.qza mbx denoise --asv \ --classifier silva-138 mbx diversity --alpha --beta mbx ml --random-forest \ --target phenotype # → report.html ✓
Research focus
My work sits at the intersection of microbial ecology, sequencing, and machine learning — turning raw reads into models that explain host phenotypes.
Amplicon & shotgun metagenomic workflows — from primer detection and denoising through taxonomy, diversity, and differential abundance.
Supervised models (random forests, deep learning) that link microbial community structure to host phenotypes and traits.
Open-source R and Python packages, Shiny apps, and step-by-step pipelines so analyses run the same way on any machine.
Featured work
A toolkit for microbiome data wrangling and visualization, available in both R and Python. Published in Stats (MDPI, 2025).
An interactive Shiny app that writes correct QIIME 2 commands for your study design — no more syntax hunting across docs.
A 19-step, fully documented amplicon pipeline — primer ID, DADA2, taxonomy, diversity, ANCOM-BC2, PICRUSt2, ML and networks — each step with copy-ready code.
A pip-installable package bundling microbiome taxa helpers and machine-learning utilities used across my projects.
Toolbox
Get in touch
Reach out about microbiome analysis, ML for biology, or the tools above.
Contact me →