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prem-p-singh/README.md

Typing SVG

Postdoctoral Scholar @ Plan Pathology @ UC Davis

I study crop disease from the first field observation to the final model, combining molecular diagnostics, multi-omics, and reproducible data science to find signals that can improve crop decisions.

Website LinkedIn Google Scholar Email

Open to roles


🌱 How I Work

🍇 FIELD  →  🧬 MEASURE  →  💻 MODEL  →  🌱 DECIDE

🌿 Crop scientist: I begin with the plant, the field pattern, and the biological question.

🧬 Molecular scientist: I measure the signal with RT-qPCR, digital PCR, RNA-seq, and metabolomics.

📊 Data scientist: I build reproducible pipelines, integrate evidence, test models, and communicate uncertainty.

🎯 Translator: I turn results into diagnostic markers, biological mechanisms, and crop-improvement questions.

Vineyard samples Sequencing reads Journal articles Book chapters Citations


🔬 What I Work On

🍇 Grapevine–virus interactions · Transcriptomic and metabolomic profiling across commercial-vineyard samples, seasons, cultivars, and maturity stages

🧬 Molecular diagnostics · RT-qPCR and digital PCR assay development, validation, and quality control for plant pathogens

📊 Multi-omics data science · Differential expression, pathway analysis, biomarker discovery, causal analysis, Bayesian inference, and machine learning

🧪 Food safety and formulation · Plant-derived nano-formulations, toxin control, release modeling, and mechanism-of-action studies


⚡ Toolbox

🔬 Measure

RT-qPCR Digital PCR RNA-seq GC-MS LC-MS/MS

📊 Analyze

R Python Bioconductor DESeq2 scikit-learn Bayesian modeling Causal mediation

⚙️ Reproduce

Snakemake Bash SLURM Linux and HPC Git Conda Containers

✦ Communicate

ggplot2 Plotly Markdown Technical writing Research visualization


🚀 Featured Builds

🆕 Latest build

RNASeq pipeline v2: raw reads to traceable bulk RNA-seq results

⚙️ RNASeq pipeline · v2.1.1

Snakemake with Salmon or STAR limma-voom, edgeR and DESeq2 Excel intake, SLURM ready

A bulk RNA-seq pipeline that takes raw FASTQs to QC reports, gene counts, and differential-expression results. The study design is checked for estimability before any compute runs, and every project keeps its own configuration, logs, and results.

Explore the pipeline →

🧬 GRBV Transcriptomics

300+ samples across two seasons

An RNA-seq workflow for studying Grapevine Red Blotch Virus across vineyard samples, seasons, and maturity stages.

Explore the analysis →

📊 RGraphMaker

50 graph types from plain-language requests

An AI-ready R visualization skill with three plotting engines and PNG, PDF, and interactive HTML output.

Make a graph →

🌐 Research Portfolio

Crop biology and data stories

A visual portfolio connecting publications, methods, reproducible analyses, and research communication.

Visit the portfolio →


📚 Research Record

38 peer-reviewed journal articles · 22 book chapters · 2,300+ citations · h-index 25

View all publications


🌾 Grew up on a farm in India. Still trying to make science useful for agriculture.

🌿 Field  ➜  🔬 Bench  ➜  💻 Data  ➜  📊 Evidence  ➜  🎯 Crop decision

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