R. Neher

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016.

The paper analyzes MPXV genomes to show evidence of APOBEC3 deaminase editing, suggesting sustained human transmission since 2016.

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates

The paper shows that HIV-1 reversion mutations are under positive selection and affect evolutionary rate estimates across different time scales.

Limited predictability of amino acid substitutions in seasonal influenza viruses

This study assesses the predictability of amino acid substitutions in seasonal influenza viruses and finds that current frequency is the strongest predictor of fixation, while other features like epitope occurrence or LBI have limited predictive power.

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

This study develops a forecasting framework for influenza A/H3N2 evolution by integrating phenotypic antigenic drift data with sequence-based fitness estimates, showing improved long-term predictions.

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

The paper shows that the timing mismatch between virus growth and antibody selection limits antigenic evolution within hosts, explaining global selectivity and local neutrality in influenza.

Complementation can maintain a quasispecies of drug sensitive and resistant HIV

The paper shows that complementation between drug-sensitive and resistant HIV genotypes maintains a stable quasispecies, preventing the resistant genotype from outcompeting the sensitive one.

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

This study maps influenza transmission in a city at high resolution, finding socioeconomic factors like income influence infection patterns and vaccination rates, independent of population density.

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

The paper develops an efficient algorithm to estimate site-specific substitution models and evaluates their accuracy using simulated data and HIV alignments, finding issues with identifiability and divergence saturation.

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

The paper analyzes seasonal influenza circulation patterns from September 2019 to September 2020, identifying dominant clades and antigenic changes in A/H3N2, A/H1N1pdm, B/Vic, and B/Yam viruses.

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

This study analyzes the intra- and interpatient evolution of EV-D68 using whole-genome sequencing, finding low intrapatient variability and evidence of dual infections, along with strong temporal evolution and local spread during the 2016 outbreak.

Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing

The paper uses single molecule sequencing to analyze genomic diversity of carbapenemase-producing bacteria and identifies patterns of carbapenemase movement and recombination.

Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen

The paper analyzes the phylodynamics of rapidly evolving pathogens, showing how extinction and speciation rates depend on evolutionary parameters and cross-immunity dynamics in Red Queen states.

Real-time analysis and visualization of pathogen sequence data

This paper reviews recent developments in real-time analysis of pathogen sequence data with a focus on visualization and integration of sequence and phenotypic data.

TreeTime: maximum likelihood phylodynamic analysis

TreeTime is a Python framework for phylodynamic analysis that uses an approximate Maximum Likelihood approach to estimate ancestral states, infer evolution models, and scale linearly with dataset size.