ncird

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.

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

K-mer Assisted Reassortant Mapping Algorithm for Influenza

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

Understanding spatiotemporal clustering of seasonal influenza in the United States

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

IRMA-Viz is a Rust command-line tool for rendering IRMA report plots

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

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.

Estimating the generation time for COVID-19 transmission using household data in the United States, December 2021 – May 2023

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

Protein analysis pipeline for characterizing influenza antigenic drift

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

Phylogenetics for Human H5N1 Cases

SSWSORT: a simple tool for classifying gene segments