P. S. Pennings

SCIP provides an online summer coding program for students, enhancing coding confidence and community engagement during the pandemic.

This study uses phylogenetic methods to analyze how antibiotic resistance in E. coli evolves within hosts versus spreads between hosts for different antibiotics.

The paper compares sequence-type diversity between antibiotic-resistant and susceptible bacterial strains across multiple datasets and finds resistant strains are less diverse in most cases.

This study estimates in vivo fitness costs of HCV mutations using frequency-based analysis across 195 patients, revealing mutation type and genomic location effects on fitness costs.

The paper analyzes HIV resistance evolution patterns under temporal and spatial drug heterogeneity models, showing resistance develops even after long-term therapy and in predictable sequences.

This study shows that high mutation rates increase reversion to wild type when compensation is partial, but fully compensatory mutations reduce reversion probability.

The paper investigates genetic adaptation in New York City rats by analyzing whole-genome sequences to identify signatures of selection related to urban living.

This study uses modeling to show how migration and selection interact to create non-monotonic FST patterns in adapting populations and estimates high migration rates in a Simian-HIV population.

The paper examines HIV drug resistance evolution in the late 1990s, showing patterns like soft and hard sweeps, clonal interference, and mutation accumulation in treated patients.

This paper uses time series data to show that soft sweeps drove early HIV treatment failure, contrasting with harder sweeps associated with better drugs.

This paper introduces FITS, a computational framework for inferring virus population genetics parameters from time-series data, demonstrating high accuracy in classifying mutations as advantageous, neutral, or deleterious.

The paper examines patterns and probabilities of selection footprints under rapid adaptation, showing that soft sweeps are frequent but complex footprints remain inadequately explained by current models.

The paper estimates the fitness costs of 870 HIV mutations in vivo by analyzing mutation frequencies in the pol gene across 160 patients, finding higher costs for non-synonymous, drastic amino acid changes, and CpG-creating mutations.