PhD Candidate in Bioinformatics at the University of Georgia.
I work at the intersection of avian influenza, wild bird ecology, poultry health, and machine learning.
🌐 Personal website: https://sachin-subedi.github.io/
-
Highly Pathogenic Avian Influenza (HPAI H5Nx)
- Ecological and evolutionary drivers of cross-species and cross-border spread
- Bayesian phylodynamics & phylogeography (discrete traits, GLMs, Markov jumps/rewards)
- Integrating wild bird occurrence, poultry density, trade, and environmental covariates into reproducible analysis pipelines
-
Bioinformatics & AI for poultry health
- Deep learning and computer vision (YOLO, CNNs) for cage-free hen monitoring
- Automated detection of mis-laying, feather pecking, and floor-egg behavior
- Translating image- and sequence-based models into decision-support tools for animal health and welfare
- Languages: R, Python, C++, Bash
- Bioinformatics & stats: tidyverse, data.table, scikit-learn, PyTorch, mixed models, Bayesian modeling
- Phylodynamics & evolution: BEAST / BEAST2, baltic, TreeAnnotator, LogCombiner
- Genomics / data wrangling: FASTA/metadata processing, custom pipeline scripts
- GIS & spatial modeling: sf, terra, raster, xarray, rioxarray
- Deep learning & CV: PyTorch, torchvision, YOLO variants
- Reproducibility & HPC: Git/GitHub, SLURM-based workflows, parameterized R/Python pipelines
- Ecological & evolutionary analysis of 2.3.4.4b H5Nx HPAI spread
- GLM-based and deep-learning models to predict spillover risk at fine spatial and temporal scales
- Designing transparent, well-documented workflows so others can reuse and extend my code and analyses
- 🌐 Website: https://sachin-subedi.github.io/
- 💼 GitHub: you’re already here 🙂
If you’re interested in HPAI, zoonotic spillover, wild bird ecology, or computational methods for infectious disease, feel free to open an issue or reach out!