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utsabghimire/README.md

Hi, I'm Dr. Utsab Ghimire

Plant scientist working where molecular biology meets data science.
CRISPR gene editing · plant transformation · multi-omics · machine learning

🌱 About me

I build more resilient crops — from a single edited gene to thousands analyzed at once. At Soilcea, I develop transgene-free, CRISPR-edited citrus to fight Huanglongbing (citrus greening), and I use multi-omics and machine learning to understand how plants grow, age, and defend themselves.

  • 🔬 At the bench: CRISPR/Cas9 & base editing, Agrobacterium-mediated transformation, tissue culture & regeneration, molecular cloning.
  • 💻 At the keyboard: bulk & single-cell RNA-seq, whole-genome sequencing, proteomics, metabolomics, and reproducible HPC pipelines.
  • 🤖 For prediction: gradient-boosted trees and neural networks for crop traits, biomass, and the signals hidden in omics data.
  • 🎓 PhD, Horticultural Sciences — University of Florida.

🧰 Tech stack

Languages
Python R Bash

ML & data
scikit-learn PyTorch TensorFlow pandas NumPy XGBoost CatBoost

Bioinformatics & omics
RNA-seq WGS Seurat WGCNA Proteomics

Tools
Docker Git Linux Jupyter Streamlit

🚀 Featured projects

Project What it does
broccoli-scRNA-seq Single-cell RNA-seq pipeline for broccoli inflorescences — senescence & developmental trajectories.
bulk-rnaseq-postharvest-pipeline QC, trimming, alignment & HPC workflow for bulk RNA-seq from postharvest tissue.
biomass-ml-prediction ML models for cover-crop biomass & C:N ratio (CatBoost, XGBoost, neural nets) with weather features.
broccoli-proteomics-senescence TMT-based proteomics pipeline — preprocessing, PCA, volcano plots, differential testing.
rnaseq-interactive-demo Interactive notebook + Streamlit app — RNA-seq from raw data to differential expression.

📚 Research

Peer-reviewed work in plant postharvest biology, senescence genomics, and ML for agriculture — published in Postharvest Biology and Technology, Vegetable Research, and Agricultural & Environmental Letters. 👉 Full publication list on Google Scholar

📈 GitHub stats

Thanks for stopping by. If our interests overlap — crop biotech, omics, or ML for plants — I'd love to connect.
🌐 utsabghimire.github.io

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  1. broccoli-scRNA-seq broccoli-scRNA-seq Public

    Single‑cell RNA‑seq analysis pipeline for broccoli inflorescences, focusing on senescence and developmental trajectories.

    R

  2. bulk-rnaseq-postharvest-pipeline bulk-rnaseq-postharvest-pipeline Public

    Processing bulk RNA-seq from postharvest broccoli: QC, trimming, alignment, and HPC.

    1

  3. Postharvest_RNAseq Postharvest_RNAseq Public

    Analyses exploring gene expression changes during postharvest senescence

    R

  4. biomass-ml-prediction biomass-ml-prediction Public

    Machine learning models for cover crop biomass and C:N ratio prediction using XGBoost, CatBoost, and neural networks.

    Python

  5. broccoli-proteomics-senescence broccoli-proteomics-senescence Public

    Proteomics data analysis pipeline for TMT-based postharvest senescence study in broccoli; Python scripts for loading, preprocessing, analysis and visualisation.

    Python

  6. rnaseq-interactive-demo rnaseq-interactive-demo Public

    Interactive notebook and Streamlit app demonstrating an RNA-seq analysis pipeline from raw data to differential expression and visualisation.

    Python