Publications

---

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