DENcode estimates transmission probabilities between dengue cases using genetic and epidemiological data, revealing key transmission roles and network structures.

PLoS Computational Biology · May 20, 2026Peer-reviewedBioinformatics

Between- and within-host mutation of dengue virus

Sachith Maduranga, Braulio M. Valencia, Chathurani Sigera, Praveen Nilendra Weeratunga, Deepika Fernando, Senaka Rajapakse, Melissa Rapadas, Ira W. Deveson, Andrew R. Lloyd, Rowena Anne Bull, Chaturaka Rodrigo

This study analyzes mutation patterns in dengue virus genomes from acute infections, showing higher haplotype diversity than consensus sequences.

Virology · Nov 26, 2025Peer-reviewedBioinformatics

Temporal dynamics of viral fitness and the adaptive immune response in HCV infection

Melanie Rose Walker, Preston Leung, Elizabeth Keoshkerian, Mehdi R Pirozyan, Andrew R. Lloyd, Fabio Luciani, Rowena Anne Bull

This study examines how viral fitness and immune responses interact in HCV infection, showing fitness decreases early but rebounds with mutations, and strong CD8+ T-cell responses drive chronic infection.

bioRxiv · Sep 7, 2024Immunology

HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies

Hang Zhang, Rowena Anne Bull, Ahmed Abdul Quadeer, Matthew R. McKay

The paper investigates how E1-E2 interactions in HCV affect viral fitness and antibody escape, identifying mutations and antibodies with implications for vaccine development.

Virus Evolution · Jul 1, 2023Peer-reviewedBioinformatics

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA (BNT162b2/mRNA-1273) and adenovirus vectored vaccines (ChAdOx1-S) after the first, second and third doses

Feargal J. Ryan, Todd S. Norton, Conor McCafferty, Stephen J. Blake, Natalie E. Stevens, Jane James, Georgina L. Eden, Yee C. Tee, Saoirse C. Benson, Makutiro Ghislain Masavuli, Arthur Eng Lip Yeow, Arunasingam Abayasingam, David Agapiou, Hannah Stevens, Jana Zecha, , David John Lynn

This study compares innate and adaptive immune responses to two COVID-19 vaccines in adults after multiple doses, identifying differences linked to antibody, T cell responses, and reactogenicity.

medRxiv · Sep 22, 2022 · PreprintGenetic & Genomic Medicine

Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak

Charles S. P. Foster, Rowena Anne Bull, Nicodemus T. Tedla, Fernando S. Santiago, David Agapiou, Anurag Adhikari, Gregory J. Walker, Lok Bahadur Shrestha, Sebastiaan J. van Hal, Ki Wook Kim, William D. Rawlinson

The paper identifies a SARS-CoV-2 variant with an ORF7a deletion that persisted during a major outbreak but shows no clear fitness advantage in cell culture.

medRxiv · Sep 6, 2022 · PreprintGenetic & Genomic Medicine

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

Rowena Anne Bull, Thiruni N. Adikari, James M. Ferguson, J. W. Hammond, Igor Stevanovski, Alicia G. Beukers, Zin Naing, Malinna Yeang, Andrey Verich, Hasindu Gamaarachchi, Ki Wook Kim, Fabio Luciani, Sacha Stelzer‐Braid, John‐Sebastian Eden, William D. Rawlinson, , Ira W. Deveson

This study evaluates the analytical validity of nanopore sequencing for SARS-CoV-2 genome analysis, finding high accuracy for SNVs but limitations in detecting short indels and low-frequency variants.

Nature Communications · Dec 9, 2020Peer-reviewedGenomics

Impact Of Sequencing Depth And Read Length On Single Cell RNA Sequencing Data: Lessons From T Cells

Simone Rizzetto, Auda A. Eltahla, Peijie Lin, Rowena Anne Bull, Andrew R. Lloyd, Joshua W. K. Ho, Vanessa Venturi, Fabio Luciani

This study examines how sequencing depth and read length affect scRNA-seq data quality, finding that sufficient depth and length improve TCRβ reconstruction and gene expression accuracy in T cells.

Scientific Reports · Oct 2, 2017Peer-reviewedBioinformatics