Nextstrain: real-time tracking of pathogen evolution J Hadfield, C Megill, SM Bell, J Huddleston, B Potter, C Callender, ... Bioinformatics 34 (23), 4121-4123, 2018 | 2990 | 2018 |
TreeTime: maximum likelihood phylodynamic analysis P Sagulenko, V Puller, R Neher Virus Evolution 4 (1), vex042, 2018 | 948 | 2018 |
Nextclade: clade assignment, mutation calling and quality control for viral genomes I Aksamentov, C Roemer, EB Hodcroft, RA Neher Journal of Open Source Software 6 (67), 3773, 2021 | 652 | 2021 |
COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation. M Salathé, CL Althaus, R Neher, S Stringhini, E Hodcroft, J Fellay, ... Swiss medical weekly 150 (11-12), w20225-, 2020 | 604 | 2020 |
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 EB Hodcroft, M Zuber, S Nadeau, TG Vaughan, KHD Crawford, ... Nature 595 (7869), 707-712, 2021 | 585 | 2021 |
Novel SARS-CoV-2 variants: the pandemics within the pandemic E Boehm, I Kronig, RA Neher, I Eckerle, P Vetter, L Kaiser Clinical Microbiology and Infection 27 (8), 1109-1117, 2021 | 395 | 2021 |
Potential impact of seasonal forcing on a SARS-CoV-2 pandemic RA Neher, R Dyrdak, V Druelle, EB Hodcroft, J Albert Swiss Medical Weekly 150 (1112), 2020 | 371 | 2020 |
Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States JR Fauver, ME Petrone, EB Hodcroft, K Shioda, HY Ehrlich, AG Watts, ... Cell 181 (5), 990-996. e5, 2020 | 363 | 2020 |
2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate–a word of caution M Battegay, R Kuehl, S Tschudin-Sutter, HH Hirsch, AF Widmer, ... Swiss Medical Weekly 150 (0506), 2020 | 312 | 2020 |
Cryptic transmission of SARS-CoV-2 in Washington state T Bedford, AL Greninger, P Roychoudhury, LM Starita, M Famulare, ... Science 370 (6516), 571-575, 2020 | 298 | 2020 |
panX: pan-genome analysis and exploration W Ding, F Baumdicker, RA Neher Nucleic Acids Research 46 (1), e5-e5, 2017 | 273 | 2017 |
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse F Konings, MD Perkins, JH Kuhn, MJ Pallen, EJ Alm, BN Archer, ... Nature Microbiology, 1-3, 2021 | 257 | 2021 |
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 E Alm, EK Broberg, T Connor, EB Hodcroft, AB Komissarov, ... Eurosurveillance 25 (32), 2001410, 2020 | 256 | 2020 |
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2 CBF Vogels, MI Breban, IM Ott, T Alpert, ME Petrone, AE Watkins, ... PLoS biology 19 (5), e3001236, 2021 | 245* | 2021 |
Population genomics of intrapatient HIV-1 evolution F Zanini, J Brodin, L Thebo, C Lanz, G Bratt, J Albert, RA Neher eLife 4, e11282, 2016 | 244 | 2016 |
Genealogies of rapidly adapting populations RA Neher, O Hallatschek Proceedings of the National Academy of Sciences 110 (2), 437-442, 2013 | 220 | 2013 |
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus C Happi, I Adetifa, P Mbala, R Njouom, E Nakoune, A Happi, N Ndodo, ... PLoS biology 20 (8), e3001769, 2022 | 215 | 2022 |
Recombination rate and selection strength in HIV intra-patient evolution RA Neher, T Leitner PLoS computational biology 6 (1), e1000660, 2010 | 211 | 2010 |
A global surveillance system for crop diseases M Carvajal-Yepes, K Cardwell, A Nelson, KA Garrett, B Giovani, ... Science 364 (6447), 1237-1239, 2019 | 196 | 2019 |
Predicting evolution from the shape of genealogical trees RA Neher, CA Russell, BI Shraiman eLife 3, e03568, 2014 | 194 | 2014 |