Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data. - Fabian J. Theis; Richard A. Neher; Andre Zeug (ICA, 2009)

Recombination Rate and Selection Strength in HIV Intra-patient Evolution. - Richard A. Neher; Thomas Leitner (PLoS Comput. Biol., 2010)

FFPopSim: an efficient forward simulation package for the evolution of large populations. - Fabio Zanini; Richard A. Neher (Bioinform., 2012)

nextflu: real-time tracking of seasonal influenza virus evolution in humans. - Richard A. Neher; Trevor Bedford (Bioinform., 2015)

Estimating time of HIV-1 infection from next-generation sequence diversity. - Vadim Puller; Richard A. Neher; Jan Albert (PLoS Comput. Biol., 2017)

Nextstrain: real-time tracking of pathogen evolution. - James Hadfield; Colin Megill; Sidney M. Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A. Neher (Bioinform., 2018)

Nextclade: clade assignment, mutation calling and quality control for viral genomes. - Ivan Aksamentov; Cornelius Roemer; Emma B. Hodcroft; Richard A. Neher (J. Open Source Softw., 2021)

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. - John Huddleston; James Hadfield; Thomas R. Sibley; Jover Lee; Kairsten Fay; Misja Ilcisin; Elias Harkins; Trevor Bedford; Richard A. Neher; Emma B. Hodcroft (J. Open Source Softw., 2021)

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. - Pierre Barrat-Charlaix; Timothy G. Vaughan; Richard A. Neher (PLoS Comput. Biol., 2022)

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. - Jover Lee; James Hadfield; Allison Black; Thomas R. Sibley; Richard A. Neher; Trevor Bedford; John Huddleston (Frontiers Bioinform., 2023)

Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. - Emma B. Hodcroft; Martin Wohlfender; Richard A. Neher; Julien Riou; Christian L. Althaus (PLoS Comput. Biol., 2025)