Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

K-mer Assisted Reassortant Mapping Algorithm for Influenza

Estimating the generation time for influenza transmission using household data in the United States

Understanding spatiotemporal clustering of seasonal influenza in the United States

Kieran et al. 2024 - npj Viruses - influenza A transmission thersholds

Pulit-Penaloza et al. 2026 - Nature Communications. Advancing A(H5N1) influenza risk assessment in ferrets through comparative evaluation of airborne virus shedding patterns R code.

Kieran et al. 2025 - Scientific Reports. R code for lethality/morbidity machine learning with tissues.

A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.

Kieran et al. (under revision) - PLoS Computational Biology

Protein analysis pipeline for characterizing influenza antigenic drift

Kieran et al. 2024 - Communication Biology - R code for machine learning in influenza infected ferrets

Phylogenetic Analysis and Characterization of am4N1 Nueraminidases from North American A(H5N1) HPAI

For producing amino acid difference tables for other applications.

Code repository for published manuscript