Publications

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2025

A systematic nomenclature for mpox viruses causing outbreaks with sustained human-to-human transmission
Christopher Ruis, Eddy Lusamaki, Aine O'Toole et al.
Nature Medicine, 31 2854--2858. 10.1038/s41591-025-03820-6 bibtex Sun 27 July 2025

2024

Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus Below the Subgroup Level
Stephanie Goya, Christopher Ruis, Richard A. Neher et al.
Emerging infectious diseases, 10.3201/eid3008.240209 bibtex Thu 11 July 2024

2023

SARS-CoV-2 evolution in the Omicron era
Cornelius Roemer, Daniel J. Sheward, Ryan Hisner et al.
Nature Microbiology, 10.1038/s41564-023-01504-w bibtex Sun 15 October 2023

Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal
Vitor Borges, Mariana Perez Duque, Joao Vieira Martins et al.
Nature Medicine, 1--9. 10.1038/s41591-023-02542-x bibtex Mon 11 September 2023

LAPIS is a fast web API for massive open virus sequencing data
Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer et al.
BMC bioinformatics, 24 232. 10.1186/s12859-023-05364-3 bibtex Mon 05 June 2023

Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses
Aiste Dijokaite-Guraliuc, Raksha Das, Daming Zhou et al.
Cell Reports, 42 112271. 10.1016/j.celrep.2023.112271 bibtex Tue 25 April 2023

2022

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Houriiyah Tegally, Monika Moir, Josie Everatt et al.
Nature Medicine, 28 1785--1790. 10.1038/s41591-022-01911-2 bibtex Thu 01 September 2022

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
Christian Happi, Ifedayo Adetifa, Placide Mbala et al.
PLOS Biology, 20 e3001769. 10.1371/journal.pbio.3001769 bibtex Tue 23 August 2022

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
Chaoran Chen, Sarah Nadeau, Michael Yared et al.
Bioinformatics (Oxford, England), 38 1735--1737. 10.1093/bioinformatics/btab856 bibtex Fri 04 March 2022

2021

Nextclade: clade assignment, mutation calling and quality control for viral genomes
Ivan Aksamentov, Cornelius Roemer, Emma B. Hodcroft and Richard A. Neher
Journal of Open Source Software, 6 3773. 10.21105/joss.03773 bibtex Mon 15 November 2021