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

IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.

A tool to aid virus sequencing and accelerate IRMA.

Zoe provides both broad and highly specialized implementations for bioinformatics. In particular, we focus on common data formats and methods relevant for the sequencing of RNA viruses.

K-mer Assisted Reassortant Mapping Algorithm for Influenza

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

Evaluating potential impacts of a preferential vaccine recommendation for adults 65 years of age and older on US influenza burden

Understanding spatiotemporal clustering of seasonal influenza in the United States

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. 2024 - npj Viruses - influenza A transmission thersholds

Kieran et al. (2026) - PLoS Computational Biology. R code for weight-based measurements in flu ferrets.

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

Phylogenetics for Human H5N1 Cases

Modeling the impacts of antiviral prophylaxis strategies in mitigating seasonal influenza outbreaks in nursing homes

Detection of novel influenza viruses through community and healthcare testing: Implications for surveillance efforts in the United States

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

Protein analysis pipeline for characterizing influenza antigenic drift

DAIS-ribosome annotates CDS and protein products for supported virus genomes into database-oriented output.