Plant Biotechnology · Genome Editing · Multi-omics

Dr. Utsab
Ghimire.

Bridging the wet lab and the command line to build more resilient crops.

I'm a plant scientist working where molecular biology meets data science. I develop transgene-free, gene-edited crops and use CRISPR, multi-omics, and machine learning to understand how plants grow, age, and defend themselves — then turn that into traits that matter in the field.

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Dr. Utsab Ghimire in a lab coat in front of a plant tissue-culture rack DR. UTSAB GHIMIRE · IN THE LAB
About

A scientist comfortable at the bench and in the terminal.

Most problems in crop biology don't sit neatly on one side of that line — so I try not to either.

My work lives at the intersection of molecular biology and computation. On the bench, I run CRISPR gene editing and Agrobacterium-mediated transformation to develop gene-edited plants — including work on disease-resistant citrus. At the keyboard, I integrate high-throughput sequencing, proteomics, and metabolomics, and build predictive models with machine learning.

My doctoral research, completed at the University of Florida, focused on the gene regulatory networks behind senescence and stress responses in plants — asking why crops like broccoli decline so fast after harvest, and what we can do about it. That same question — how do we keep more of what we grow? — still drives the applied, food-security framing of everything I work on.

I care about reproducible science: open code, documented pipelines, and results that hold up.

RoleScientist, Soilcea
FieldAgricultural biotech
PhDHorticultural Sciences
UniversityUniv. of Florida
Based inTampa, Florida
FocusCRISPR · Multi-omics · ML
Experience

From the postharvest lab to the citrus biotechnology.

A path through academic research, federal science, and agricultural biotech.

Jan 2026 — Present

Scientist · Soilcea (Soil Culture Solutions, LLC)

Tampa, Florida
  • Develop transgene-free, CRISPR-edited citrus rootstocks for resistance to Huanglongbing (citrus greening) via Agrobacterium-mediated transformation.
  • Build and run genomics pipelines for edited lines — whole-genome sequencing, BWA-MEM alignment, variant calling, and CRISPR on/off-target and transgene-integration analysis.
  • Optimize tissue culture and regeneration across citrus rootstocks (Carrizo, Swingle, US-812), including contamination control and germination workflows.
  • Maintain reproducible multi-omics workflows on a dedicated Linux genomics workstation, with SOPs, plasmid maps, and genotyping records.
Jan 2022 — Dec 2025

Graduate Research Assistant · Postharvest Genomics Lab

University of Florida · Gainesville, Florida
  • Engineered Dex-inducible (pJAN33-GR) and 35S overexpression constructs; designed gRNAs and Gateway cloning strategies for target genes.
  • Established Agrobacterium-mediated transformation in broccoli and lettuce, optimizing tissue culture and regeneration to ~28% transformation efficiency in broccoli.
  • Built bulk RNA-seq, proteomics, and metabolomics pipelines — plus single-nuclei RNA-seq — to identify and resolve senescence regulators across cell types.
  • Developed large-scale HPC workflows on UF HiPerGator and interactive Streamlit apps for volcano plots, Venn diagrams, and pathway enrichment.
May 2025 — Aug 2025

AI/ML Intern · USDA-ARS SCINet / AI Center of Excellence

Adaptive Cropping Systems Laboratory · Beltsville, Maryland
  • Developed machine-learning models (CatBoost, XGBoost, scikit-learn) for biological yield prediction, improving accuracy ~10% through feature engineering and multi-environment variables.
  • Applied deep learning (TensorFlow, PyTorch) and parallelized workflows on SCINet HPC, cutting compute time ~40%.
  • Resulting work was published in Agricultural & Environmental Letters (2026) and featured in the USDA SCINet newsletter.
Apr 2021 — Nov 2021

Agriculture Technician · Sappros Nepal

Support Activities for Poor Producers of Nepal · Setī, Nepal
  • Provided field-level agricultural support to smallholder producers, including on-site training, data collection, and reporting.
Mar 2021 — Apr 2021

Enumerator · CIMMYT

International Maize and Wheat Improvement Center · Kosi Zone, Nepal
  • Conducted field surveys and recorded research data for maize and wheat improvement programs.
Education
Jan 2022 — Dec 2025

PhD, Horticultural Sciences

University of Florida · Gainesville, FL
Dissertation: Identification and functional characterization of novel senescence-associated genes in broccoli.

Dec 2020

B.Sc., Agriculture

Agriculture and Forestry University · Rampur, Nepal

Focus

Four threads, one through-line.

From editing a single gene to modeling thousands at once — all aimed at crops that grow stronger and last longer.

/ EDIT

CRISPR & plant transformation

Developing transgene-free, gene-edited plants through CRISPR base editing and Agrobacterium-mediated transformation — including disease-resistant citrus.

CRISPRbase editingtissue culture
/ AGE

Postharvest biology & senescence

Mapping the molecular and biochemical pathways that drive crops to decline after harvest, to extend shelf life and cut food loss.

physiologygene regulationshelf life
/ READ

Multi-omics & bioinformatics

Integrating RNA-seq, single-cell, proteomics, and whole-genome sequencing into pipelines that turn raw reads into biological insight.

RNA-seqscRNA-seqWGS
/ PREDICT

Machine learning for crops

Building predictive models — gradient-boosted trees and neural networks — for plant traits, biomass, and the signals hidden in omics data.

XGBoostCatBoostCNNs
Selected work

Peer-reviewed research.

Five published, peer-reviewed studies. Full list on Google Scholar.

2026

Machine learning–based prediction of cereal rye cover crop biomass across diverse agroecosystems

Ghimire U., Mitra A., Fleisher D., Park J., Barnaby J.Y., Kim Y., Han E. · Agricultural & Environmental Letters 11(1), e70055
View →
2026

Transcriptomic insights into postharvest senescence in artichoke for enhanced shelf life

Kaur A., Olmedo G.M., Ghimire U., Wang W., Tseung C., Yu F., Bai J., et al. · Postharvest Biology and Technology 240, 114421
View →
2024

Unique molecular mechanisms revealed for the effects of temperature, CA, ethylene exposure, and 1-MCP on postharvest senescence of broccoli

Ghimire U., Abeli P., Brecht J.K., Pliakoni E., Liu T. · Postharvest Biology and Technology 213, 112919
DOI →
2024

Postharvest senescence profiling in broccoli using Tandem Mass Tag–based proteomics

Ahlawat Y.K., Ghimire U., Li S., Timilsena P., Pliakoni E.D., Brecht J.K., Liu T. · Vegetable Research 4(1)
DOI →
2023

Identifying genes regulated during natural, on-plant senescence in broccoli (Brassica oleracea) in contrast to postharvest senescence

Ghimire U., Pliakoni E., Yu F., Brecht J.K., Liu T. · Postharvest Biology and Technology 206, 112535
DOI →
Beyond the bench

Talks, teaching & outreach.

Conferences & workshops

  • Plant & Animal Genome (PAG32) — poster & oral, 2025
  • Plant Cell Atlas Symposium — 2024
  • Florida Genetics Symposium — 2023
  • ASHS Annual Conference — oral presentations, 2022 & 2023

Teaching & mentoring

  • Mentored six undergraduate researchers (2022–2025) in bioinformatics and molecular biology.
  • Trained students in RNA-seq analysis, molecular cloning, CRISPR/Cas9, and tissue culture.

Public outreach

  • UF Finger Lime Field Day — 2025
  • UF Extension Passion Fruit Field Day — 2024
  • UF Grape Field Day — 2023
Code

Open pipelines & analysis.

Reproducible workflows for the analyses behind the research — all public on GitHub.

broccoli-scRNA-seq

Single-cell RNA-seq pipeline for broccoli inflorescences — senescence and developmental trajectories.

● R
 bulk-rnaseq-postharvest-pipeline

QC, trimming, alignment, and HPC workflow for bulk RNA-seq from postharvest plant tissue.

● Shell / R
 biomass-ml-prediction

ML models for cover-crop biomass and C:N ratio — CatBoost, XGBoost, and neural networks with weather features.

● Python
 broccoli-proteomics-senescence

TMT-based proteomics pipeline: preprocessing, PCA, volcano plots, and differential testing.

● Python
 rnaseq-interactive-demo

Interactive notebook and Streamlit app — RNA-seq from raw data to differential expression.

● Python
 more on github →

Explore the full set of repositories, pipelines, and experiments.

● @utsabghimire
PythonRBashHPC / UnixDockerGitSeuratWGCNAscikit-learnPyTorchBWAsamtoolsIGV
Gainesville, 2025
Dr. Utsab Ghimire at the University of Florida arch on graduation day Dr. Utsab Ghimire in doctoral regalia by the University of Florida Gator statue Dr. Utsab Ghimire walking through the University of Florida campus in doctoral regalia Dr. Utsab Ghimire celebrating PhD graduation at the University of Florida
PhD, Horticultural Sciences · University of Florida
Contact

Let's build something that grows.