Publications

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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

Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant
Khadija Khan, Gila Lustig, Kajal Reedoy et al.
medRxiv, 10.1101/2023.09.08.23295250 bibtex Fri 08 September 2023

Fitness effects of mutations to SARS-CoV-2 proteins
Jesse D. Bloom and Richard A. Neher
Virus Evolution, in press, 10.1101/2023.01.30.526314 bibtex Sat 19 August 2023

Visualizing and quantifying structural diversity around mobile AMR genes
Liam P. Shaw and Richard A. Neher
bioRxiv, 10.1101/2023.08.07.551646 bibtex Mon 07 August 2023

PanGraph: scalable bacterial pan-genome graph construction
Nicholas Noll, Marco Molari, Liam Shaw and Richard Neher
Microbial Genomics, in press., 2022.02.24.481757. 10.1101/2022.02.24.481757 bibtex Mon 17 April 2023

Evolution of the SARS-CoV-2 mutational spectrum
Jesse D Bloom, Annabel C Beichman, Richard A Neher and Kelley Harris
Molecular Biology and Evolution, msad085. 10.1093/molbev/msad085 bibtex Mon 10 April 2023

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Bernadeta Dadonaite, Katharine H. D. Crawford, Caelan E. Radford et al.
Cell, 186 1263--1278.e20. 10.1016/j.cell.2023.02.001 bibtex Fri 10 February 2023

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016
Aine O'Toole, Richard A. Neher, Nnaemeka Ndodo et al.
bioRxiv, 10.1101/2023.01.23.525187 bibtex Tue 24 January 2023

2022

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates
Valentin Druelle and Richard A Neher
Virus Evolution, 9 veac118. 10.1093/ve/veac118 bibtex Thu 15 December 2022

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution
Richard A Neher
Virus Evolution, 8 veac113. 10.1093/ve/veac113 bibtex Sat 10 December 2022

Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021
Martina L. Reichmuth, Emma B. Hodcroft, Julien Riou et al.
Epidemics, 41 100654. 10.1016/j.epidem.2022.100654 bibtex Fri 25 November 2022

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
Sarah A. Nadeau, Timothy G. Vaughan, Christiane Beckmann et al.
Science Translational Medicine, 0 eabn7979. 10.1126/scitranslmed.abn7979 bibtex Tue 08 November 2022

Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2
Jana S Huisman, Jeremie Scire, Daniel C Angst et al.
eLife, 11 e71345. 10.7554/eLife.71345 bibtex Fri 16 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

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
Pierre Barrat-Charlaix, Timothy G. Vaughan and Richard A. Neher
PLOS Computational Biology, 18 e1010394. 10.1371/journal.pcbi.1010394 bibtex Fri 19 August 2022

Evolution, geographic spreading, and demographic distribution of Enterovirus D68
Emma B. Hodcroft, Robert Dyrdak, Cristina Andres et al.
PLOS Pathogens, 18 e1010515. 10.1371/journal.ppat.1010515 pdf bibtex Fri 20 May 2022

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates
Valentin Druelle and Richard Neher
Virus Evolution, in press, 2022.02.13.480259. 10.1101/2022.02.13.480259 bibtex Mon 14 February 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

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Frank Konings, Mark D. Perkins, Jens H. Kuhn et al.
Nature Microbiology, 1--3. 10.1038/s41564-021-00932-w bibtex Wed 09 June 2021

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Emma B. Hodcroft, Moira Zuber, Sarah Nadeau et al.
Nature, 1--9. 10.1038/s41586-021-03677-y bibtex Mon 07 June 2021

Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe
Kimberley S.M. Benschop, Eeva K. Broberg, Emma Hodcroft et al.
Emerging Infectious Diseases, 27 1616--1626. 10.3201/eid2706.203096 bibtex Tue 01 June 2021

Novel SARS-CoV-2 variants: the pandemics within the pandemic
Erik Boehm, Ilona Kronig, Richard A. Neher et al.
Clinical Microbiology and Infection, 10.1016/j.cmi.2021.05.022 bibtex Tue 25 May 2021

Investigate the origins of COVID-19
Jesse D. Bloom, Yujia Alina Chan, Ralph S. Baric et al.
Science, 372 694--694. 10.1126/science.abj0016 bibtex Fri 14 May 2021

Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Chantal B. F. Vogels, Mallery I. Breban, Isabel M. Ott et al.
PLOS Biology, 19 e3001236. 10.1371/journal.pbio.3001236 bibtex Fri 07 May 2021

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
Ana Rita Goncalves Cabecinhas, Tim Roloff, Madlen Stange et al.
Microorganisms, 9 677. 10.3390/microorganisms9040677 bibtex Thu 25 March 2021

Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses
Pierre Barrat-Charlaix, John Huddleston, Trevor Bedford and Richard A Neher
Molecular Biology and Evolution, 10.1093/molbev/msab065 bibtex Fri 05 March 2021

Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020
Robert Dyrdak, Emma B. Hodcroft, Martina Wahlund, Richard A. Neher and Jan Albert
Journal of Clinical Virology, 136 104754. 10.1016/j.jcv.2021.104754 bibtex Mon 01 February 2021

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
John Huddleston, James Hadfield, Thomas R. Sibley et al.
Journal of Open Source Software, 6 2906. 10.21105/joss.02906 bibtex Thu 07 January 2021

2020

Asynchrony between virus diversity and antibody selection limits influenza virus evolution
Dylan H Morris, Velislava N Petrova, Fernando W Rossine et al.
eLife, 9 e62105. 10.7554/eLife.62105 bibtex Wed 11 November 2020

Cryptic transmission of SARS-CoV-2 in Washington state
Trevor Bedford, Alexander L. Greninger, Pavitra Roychoudhury et al.
Science, 10.1126/science.abc0523 bibtex Thu 10 September 2020

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
John Huddleston, John R Barnes, Thomas Rowe et al.
eLife, 9 e60067. 10.7554/eLife.60067 bibtex Wed 02 September 2020

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
Erik Alm, Eeva K. Broberg, Thomas Connor et al.
Eurosurveillance, 25 2001410. 10.2807/1560-7917.ES.2020.25.32.2001410 bibtex Wed 26 August 2020

Efficient inference, potential, and limitations of site-specific substitution models
Vadim Puller, Pavel Sagulenko and Richard A. Neher
Virus Evolution, 10.1093/ve/veaa066 pdf bibtex Thu 20 August 2020

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Carla Mavian, Sergei Kosakovsky Pond, Simone Marini et al.
Proceedings of the National Academy of Sciences, 10.1073/pnas.2007295117 bibtex Wed 06 May 2020

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
Joseph R. Fauver, Mary E. Petrone, Emma B. Hodcroft et al.
Cell, 181 990--996.e5. 10.1016/j.cell.2020.04.021 pdf bibtex Thu 26 March 2020

COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation
Marcel Salathe, Christian L. Althaus, Richard Neher et al.
Swiss Medical Weekly, 150 10.4414/smw.2020.20225 pdf bibtex Thu 19 March 2020

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
Richard A. Neher, Robert Dyrdak, Valentin Druelle, Emma B. Hodcroft and Jan Albert
Swiss Medical Weekly, 150 10.4414/smw.2020.20224 pdf bibtex Sat 15 February 2020

2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate – a word of caution
Manuel Battegay, Richard Kuehl, Sarah Tschudin-Sutter et al.
Swiss Medical Weekly, 150 10.4414/smw.2020.20203 pdf bibtex Wed 12 February 2020

2019

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017–2018 influenza season
Barney I. Potter, Rebecca Kondor, James Hadfield et al.
Virus Evolution, 5 10.1093/ve/vez046 bibtex Wed 04 December 2019

Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens
Le Yan, Richard A Neher and Boris I Shraiman
eLife, 8 e44205. 10.7554/eLife.44205 pdf bibtex Thu 19 September 2019

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Robert Dyrdak, Monika Mastafa, Emma B. Hodcroft, Richard A. Neher and Jan Albert
Virus Evolution, 5 10.1093/ve/vez007 pdf bibtex Mon 15 April 2019

Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains
Olivier Cunrath, Dominik M. Meinel, Pauline Maturana et al.
EBioMedicine, 10.1016/j.ebiom.2019.02.061 bibtex Thu 07 March 2019

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses
Daniel Wuthrich, Daniela Lang, Nicola F. Muller et al.
Journal of Virological Methods, 266 30--33. 10.1016/j.jviromet.2019.01.009 bibtex Sat 19 January 2019

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform
Adrian Egli, Dominique S. Blanc, Gilbert Greub et al.
Swiss Medical Weekly, 148 w14693. 10.4414/smw.2018.14693 bibtex Fri 04 January 2019

2018

Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing
Nicholas Noll, Eric Ulrich, Daniel Wuthrich et al.
bioRxiv, 456897. 10.1101/456897 pdf bibtex Wed 31 October 2018

Real-Time Analysis and Visualization of Pathogen Sequence Data
Richard A. Neher and Trevor Bedford
Journal of Clinical Microbiology, 56 e00480--18. 10.1128/JCM.00480-18 pdf bibtex Wed 24 October 2018

Efficient estimation of evolutionary rates by covariance aware regression
Richard A. Neher
bioRxiv -- won't submit, 408005. 10.1101/408005 pdf bibtex Tue 04 September 2018

Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device
Mumina Javed, Viola Ueltzhoeffer, Maximilian Heinrich et al.
Journal of Antimicrobial Chemotherapy, 10.1093/jac/dky337 bibtex Tue 28 August 2018

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales
Talia L. Karasov, Juliana Almario, Claudia Friedemann et al.
Cell Host & Microbe, 24 168--179.e4. 10.1016/j.chom.2018.06.011 pdf bibtex Wed 11 July 2018

Nextstrain: real-time tracking of pathogen evolution
James Hadfield, Colin Megill, Sidney M. Bell et al.
Bioinformatics, 10.1093/bioinformatics/bty407 pdf bibtex Sat 26 May 2018

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death
Laurelle Jackson, Jessica Hunter, Sandile Cele et al.
eLife, 7 e30134. 10.7554/eLife.30134 pdf bibtex Sun 18 March 2018

2017

TreeTime: Maximum-likelihood phylodynamic analysis
Pavel Sagulenko, Vadim Puller and Richard A. Neher
Virus Evolution, 4 vex042. 10.1093/ve/vex042 pdf bibtex Sun 10 December 2017

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
Dylan H. Morris, Katelyn M. Gostic, Simone Pompei et al.
Trends in Microbiology, 10.1016/j.tim.2017.09.004 bibtex Mon 30 October 2017

panX: pan-genome analysis and exploration
Wei Ding, Franz Baumdicker and Richard A. Neher
Nucleic Acids Research, 10.1093/nar/gkx977 pdf bibtex Wed 25 October 2017

Estimating time of HIV-1 infection from next-generation sequence diversity
Vadim Puller, Richard Neher and Jan Albert
PLOS Computational Biology, 13 e1005775. 10.1371/journal.pcbi.1005775 pdf bibtex Mon 02 October 2017

Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture
Bianca Doesselmann, Matthias Willmann, Matthias Steglich et al.
Antimicrobial Agents and Chemotherapy, AAC.00043--17. 10.1128/AAC.00043-17 pdf bibtex Mon 19 June 2017

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering
Yuan You, Aneta Sawikowska, Manuela Neumann et al.
Nature Communications, 8 15120. 10.1038/ncomms15120 pdf bibtex Wed 17 May 2017

In vivo mutation rates and the landscape of fitness costs of HIV-1
Fabio Zanini, Vadim Puller, Johanna Brodin, Jan Albert and Richard A. Neher
Virus Evol, 3 10.1093/ve/vex003 pdf bibtex Thu 02 March 2017

2016

Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing.
Fabio Zanini, Johanna Brodin, Jan Albert and Richard A. Neher
Virus research, 10.1016/j.virusres.2016.12.009 bibtex Tue 27 December 2016

Establishment and stability of the latent HIV-1 DNA reservoir.
Johanna Brodin, Fabio Zanini, Lina Thebo et al.
eLife, 5 10.7554/eLife.18889 pdf bibtex Tue 15 November 2016

HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell.
Mikael Boulle, Thorsten G. Muller, Sabrina Dahling et al.
PLoS pathogens, 12 e1005964. 10.1371/journal.ppat.1005964 pdf bibtex Tue 15 March 2016

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.
Richard A. Neher, Trevor Bedford, Rodney S. Daniels, Colin A. Russell and Boris I. Shraiman
Proceedings of the National Academy of Sciences of the United States of America, 113 E1701--1709. 10.1073/pnas.1525578113 pdf bibtex Mon 07 March 2016

2015

Population genomics of intrapatient HIV-1 evolution.
Fabio Zanini, Johanna Brodin, Lina Thebo et al.
eLife, 4 10.7554/eLife.11282 pdf bibtex Tue 15 December 2015

nextflu: real-time tracking of seasonal influenza virus evolution in humans.
Richard A. Neher and Trevor Bedford
Bioinformatics (Oxford, England), 31 3546--3548. 10.1093/bioinformatics/btv381 pdf bibtex Fri 26 June 2015

Challenges with using primer IDs to improve accuracy of next generation sequencing.
Johanna Brodin, Charlotte Hedskog, Alexander Heddini et al.
PloS one, 10 e0119123. 10.1371/journal.pone.0119123 pdf bibtex Sun 15 March 2015

2014

Predicting evolution from the shape of genealogical trees.
Richard A. Neher, Colin A. Russell and Boris I. Shraiman
eLife, 3 10.7554/eLife.03568 pdf bibtex Tue 11 November 2014

Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.
Christian Rodelsperger, Richard A. Neher, Andreas M. Weller et al.
Genetics, 196 1153--1165. 10.1534/genetics.113.159855 pdf bibtex Tue 01 April 2014

Genetic diversity in the interference selection limit.
Benjamin H. Good, Aleksandra M. Walczak, Richard A. Neher and Michael M. Desai
PLoS genetics, 10 e1004222. 10.1371/journal.pgen.1004222 pdf bibtex Sat 15 March 2014

2013

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation
Richard A. Neher
Annual Review of Ecology, Evolution, and Systematics, 44 195--215. 10.1146/annurev-ecolsys-110512-135920 bibtex Wed 09 October 2013

Inferring HIV Escape Rates from Multi-Locus Genotype Data.
Taylor A. Kessinger, Alan S. Perelson and Richard A. Neher
Frontiers in immunology, 4 252. 10.3389/fimmu.2013.00252 pdf bibtex Mon 09 September 2013

Coalescence and genetic diversity in sexual populations under selection.
Richard A. Neher, Taylor A. Kessinger and Boris I. Shraiman
Proceedings of the National Academy of Sciences of the United States of America, 110 15836--15841. 10.1073/pnas.1309697110 pdf bibtex Tue 03 September 2013

Quantifying selection against synonymous mutations in HIV-1 env evolution.
Fabio Zanini and Richard A. Neher
Journal of virology, 87 11843--11850. 10.1128/JVI.01529-13 pdf bibtex Wed 28 August 2013

Quantifying the range of a lipid phosphate signal in vivo.
Amrita Mukherjee, Richard A. Neher and Andrew D. Renault
Journal of cell science, 126 5453--5464. 10.1242/jcs.136176 pdf bibtex Mon 19 August 2013

Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses.
Vitaly V. Ganusov, Richard A. Neher and Alan S. Perelson
Journal of statistical mechanics (Online), 2013 P01010. 10.1088/1742-5468/2013/01/P01010 pdf bibtex Wed 16 January 2013

Emergence of clones in sexual populations
Richard A. Neher, Marija Vucelja, Mark Mezard and Boris I. Shraiman
Journal of Statistical Mechanics: Theory and Experiment, 2013 P01008. 10.1088/1742-5468/2013/01/P01008 pdf bibtex Wed 16 January 2013

Genealogies of rapidly adapting populations.
Richard A. Neher and Oskar Hallatschek
Proceedings of the National Academy of Sciences of the United States of America, 110 437--442. 10.1073/pnas.1213113110 pdf bibtex Tue 01 January 2013

2012

FFPopSim: an efficient forward simulation package for the evolution of large populations.
Fabio Zanini and Richard A. Neher
Bioinformatics (Oxford, England), 28 3332--3333. 10.1093/bioinformatics/bts633 pdf bibtex Wed 24 October 2012

Dynamic mutation-selection balance as an evolutionary attractor.
Sidhartha Goyal, Daniel J. Balick, Elizabeth R. Jerison et al.
Genetics, 191 1309--1319. 10.1534/genetics.112.141291 bibtex Sun 16 September 2012

Estimating the strength of selective sweeps from deep population diversity data.
Philipp W. Messer and Richard A. Neher
Genetics, 191 593--605. 10.1534/genetics.112.138461 bibtex Sun 16 September 2012

2011

Target search on a dynamic DNA molecule.
Thomas Schotz, Richard A. Neher and Ulrich Gerland
Physical review. E, Statistical, nonlinear, and soft matter physics, 84 051911. 10.1103/PhysRevE.84.051911 bibtex Thu 17 November 2011

Statistical genetics and evolution of quantitative traits
Richard A. Neher and Boris I. Shraiman
Reviews of Modern Physics, 83 1283--1300. 10.1103/RevModPhys.83.1283 bibtex Thu 10 November 2011

Correlated evolution of nearby residues in Drosophilid proteins.
Benjamin Callahan, Richard A. Neher, Doris Bachtrog, Peter Andolfatto and Boris I. Shraiman
PLoS genetics, 7 e1001315. 10.1371/journal.pgen.1001315 pdf bibtex Thu 24 February 2011

2010

Recombination rate and selection strength in HIV intra-patient evolution.
Richard A. Neher and Thomas Leitner
PLoS computational biology, 6 e1000660. 10.1371/journal.pcbi.1000660 pdf bibtex Fri 29 January 2010

2009

Blind source separation techniques for the decomposition of multiply labeled fluorescence images.
Richard A. Neher, Miso Mitkovski, Frank Kirchhoff et al.
Biophysical journal, 96 3791--3800. 10.1016/j.bpj.2008.10.068 bibtex Wed 06 May 2009

Competition between recombination and epistasis can cause a transition from allele to genotype selection.
Richard A. Neher and Boris I. Shraiman
Proceedings of the National Academy of Sciences of the United States of America, 106 6866--6871. 10.1073/pnas.0812560106 pdf bibtex Thu 09 April 2009

2007

Force-induced DNA slippage.
Ferdinand Kuhner, Julia Morfill, Richard A. Neher, Kerstin Blank and Hermann E. Gaub
Biophysical journal, 92 2491--2497. 10.1529/biophysj.106.095836 bibtex Sun 16 September 2007

Optimal flexibility for conformational transitions in macromolecules.
Richard A. Neher, Wolfram Mobius, Erwin Frey and Ulrich Gerland
Physical review letters, 99 178101. 10.1103/PhysRevLett.99.178101 bibtex Sun 16 September 2007

2006

Kinetic accessibility of buried DNA sites in nucleosomes.
Wolfram Mobius, Richard A. Neher and Ulrich Gerland
Physical review letters, 97 208102. 10.1103/PhysRevLett.97.208102 bibtex Sat 16 September 2006

Intermediate phase in DNA melting.
Richard A. Neher and Ulrich Gerland
Physical review. E, Statistical, nonlinear, and soft matter physics, 73 030902. 10.1103/PhysRevE.73.030902 bibtex Sat 16 September 2006

2005

DNA as a programmable viscoelastic nanoelement.
Richard A. Neher and Ulrich Gerland
Biophysical journal, 89 3846--3855. 10.1529/biophysj.105.068866 bibtex Fri 16 September 2005

2004

Dynamics of force-induced DNA slippage.
Richard A. Neher and Ulrich Gerland
Physical review letters, 93 198102. 10.1103/PhysRevLett.93.198102 bibtex Thu 16 September 2004

Applying spectral fingerprinting to the analysis of FRET images.
Richard A. Neher and Erwin Neher
Microscopy research and technique, 64 185--195. 10.1002/jemt.20078 bibtex Tue 01 June 2004