List of works by Richard A. Neher

2019-novel Coronavirus (2019-nCoV): estimating the case fatality rate - a word of caution

scientific article published on 01 January 2020

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

scientific article published on 02 November 2023

Applying spectral fingerprinting to the analysis of FRET images

scientific article published on 01 June 2004

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

scientific article published on 01 July 2018

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

scientific article published on 11 November 2020

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

scientific article published on 07 January 2021

Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data

Blind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images

Blind source separation techniques for the decomposition of multiply labeled fluorescence images

scientific article published on May 2009

COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2

scientific article published on 08 May 2020

COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation ⬇️

scientific article published on 19 March 2020

Challenges with using primer IDs to improve accuracy of next generation sequencing

scientific article published on 5 March 2015

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

scientific article published on 29 April 2020

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics

scientific article published on 19 November 2020

Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data

scientific article

Coalescence and genetic diversity in sexual populations under selection

scientific article published on 09 September 2013

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

scientific article published on 4 May 2020

Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

scientific article (preprint)

Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device

scientific article published on 01 December 2018

Competition between recombination and epistasis can cause a transition from allele to genotype selection

scholarly article

Correlated evolution of nearby residues in Drosophilid proteins

scientific article

Cryptic transmission of SARS-CoV-2 in Washington State

scientific article published on 06 April 2020

Cryptic transmission of SARS-CoV-2 in Washington state

scientific article published on 10 September 2020

DNA as a programmable viscoelastic nanoelement

scientific article published on 30 September 2005

Dynamic mutation-selection balance as an evolutionary attractor

scientific article

Dynamics of Force-Induced DNA Slippage

scientific article published in Physical Review Letters

Efficient inference, potential, and limitations of site-specific substitution models

scientific article published on 01 July 2020

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

scientific article published on 27 November 2020

Emergence of clones in sexual populations

Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

scientific article published on 27 December 2016

Establishment and stability of the latent HIV-1 DNA reservoir

article

Establishment and stability of the latent HIV-1 DNA reservoir.

scientific article published on 15 November 2016

Estimating Time Of HIV-1 Infection From Next-Generation Sequence Diversity

article

Estimating the strength of selective sweeps from deep population diversity data.

scientific article

Estimating time of HIV-1 infection from next-generation sequence diversity

scientific article published on 2 October 2017

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

scientific article published on 21 January 2019

FFPopSim: an efficient forward simulation package for the evolution of large populations

scientific article

Fitness effects of mutations to SARS-CoV-2 proteins

scientific article published in July 2023

Fluctuations of fitness distributions and the rate of Muller's ratchet.

scientific article

Force-induced DNA slippage

scientific article published on 11 January 2007

Genealogies of rapidly adapting populations

scientific article published on 26 December 2012

Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation

article

Genetic diversity in the interference selection limit.

scientific article

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

scientific article published on 01 August 2020

HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell

scientific article (publication date: 3 November 2016)

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

scientific article published on 05 April 2020

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform

scientific article published on 15 December 2018

In vivo mutation rates and the landscape of fitness costs of HIV-1.

scientific article

In-vivo mutation rates and fitness landscape of HIV-1

article

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death.

scientific article published on 20 March 2018

Inferring HIV Escape Rates from Multi-Locus Genotype Data

scientific article

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

scientific article published on 02 September 2020

Intermediate phase in DNA melting

scientific article published on 23 March 2006

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing

scientific article published on 01 January 2019

Investigate the origins of COVID-19

scientific article

Kinetic accessibility of buried DNA sites in nucleosomes

scientific article published on 14 November 2006

Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses.

scientific article published on January 2013

Nextclade: clade assignment, mutation calling and quality control for viral genomes

scientific article published on 30 November 2021

Nextstrain: real-time tracking of pathogen evolution.

scientific article

Novel SARS-CoV-2 variants: the pandemics within the pandemic

scientific article

Optimal Flexibility for Conformational Transitions in Macromolecules

scientific article published in Physical Review Letters

PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern

Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens

scientific article published on 18 September 2019

Population genomics of intrapatient HIV-1 evolution ⬇️

scientific article

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic

scientific article

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic

scientific article published on 16 March 2020

Predicting evolution from the shape of genealogical trees ⬇️

scientific article

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. ⬇️

scientific article

Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology.

scientific article published on 30 October 2017

Quantifying selection against synonymous mutations in HIV-1 env evolution.

scientific article published on 28 August 2013

Quantifying the range of a lipid phosphate signal in vivo

scientific article published on 4 September 2013

Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains

scientific article published on 07 March 2019

Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture

scientific article published on 19 June 2017

Rapid and consistent evolution of colistin resistance in Pseudomonas aeruginosa during morbidostat culture

article

Real-time analysis and visualization of pathogen sequence data

scientific article published on 25 October 2018

Recombination rate and selection strength in HIV intra-patient evolution

scientific article

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

scientific article published on 07 May 2020

Seasonal influenza circulation patterns and projections for 2016-2017

Seasonal influenza circulation patterns and projections for 2017-2018

Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

Stability of association between Arabidopsis thaliana and Pseudomonas pathogens over evolutionary time scales

scientific article published on 15 January 2018

Statistical genetics and evolution of quantitative traits

article

Symposium report: One Health meets sequencing

scientific article published on 08 August 2019

Target search on a dynamic DNA molecule.

scientific article

Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering

scientific article

Topological estimation of percolation thresholds

TreeTime: Maximum-likelihood phylodynamic analysis

scientific article published on 8 January 2018

TreeTime: maximum likelihood phylodynamic analysis

scholarly article published 21 June 2017

nextflu: real-time tracking of seasonal influenza virus evolution in humans

scientific article

panX: pan-genome analysis and exploration

scientific article published on 25 October 2017

panX: pan-genome analysis and exploration

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