ncird-id

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

MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation

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

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

Lineage and clade classifier for influenza sequences

Bioinformatics related user-defined functions for Cloudera Impala.

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

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

Understanding spatiotemporal clustering of seasonal influenza in the United States

Modeling the potential impacts of outpatient antiviral treatment in reducing influenza-associated hospitalizations in the United States

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

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

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.