J. Iranzo

Timescales and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

The paper examines how defense systems affect horizontal gene transfer (HGT) across different timescales and finds that CRISPR-Cas most often reduces MGE abundance and gene acquisition, but this effect is masked by recent co-transfer events.

Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome

The paper studies how CRISPR-Cas immunity in the human gut microbiome affects phage abundances and bacterial diversity using longitudinal metagenomic data.

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

The paper develops Coselens to quantify conditional selection of driver mutations in cancer, identifying 296 conditionally selected gene pairs across 16 cancer types and revealing modular epistasis networks.

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

The paper systematically analyzes UG and Abi RTs, classifies them into three major classes, and demonstrates their association with defense functions and antiphage roles.

Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

The paper shows homologous recombination delays sequence divergence but not gene content divergence in prokaryotic populations, explaining rapid gene turnover before significant sequence divergence.

Origins and Evolution of the Global RNA Virome

This study reconstructs the evolution of the global RNA virome using RdRp phylogenetics, revealing new insights into viral origins and gene exchange.

The cancer-mutation network and the number and specificity of driver mutations

The paper constructs a cancer-mutation network to analyze driver mutation specificity and estimates the number of drivers required for different cancers.

Disentangling The Effects Of Selection And Loss Bias On Gene Dynamics

The paper estimates the relative contributions of selection and loss bias to gene dynamics in prokaryotes using mathematical modeling and comparative genomics.