J. P. Gogarten

Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense

This study uses pan-genomics to identify 50 genomic islands in Halorubrum ezzemoulense, revealing rare accessory genes and homeocassettes that contribute to adaptability and speciation.

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability

The paper constructs a structural dendrogram of actinobacteriophage major capsid proteins to explore the evolution of capsid stability using cryo-EM, phylogenetic analysis, and AlphaFold predictions.

The evolutionary origins of extreme halophilic Archaea

This paper resolves conflicts in the evolutionary placement of Nanohaloarchaea and Methanonatronarchaeia using phylogenetic and phylogenomic data, showing Nanohaloarchaea share a sister relationship with Haloarchaea.

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon

The paper identifies genes and pathways associated with mating in Haloferax volcanii through transcriptomic analysis of gene expression during mating conditions.

Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life

This paper introduces the Evolutionary Similarity Index (IES) to identify co-evolving gene families in archaea, finding eight major clusters with compatible evolutionary trends and evidence of horizontal gene transfer.

Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

This paper introduces HoMer, a computational framework to detect multi-gene horizontal transfers in prokaryotes, revealing insights into gene function, phylogenetic distance, and transfer frequency.

The Impact of Restriction-Modification Systems on Mating in Haloferax volcanii

This study examines how restriction-modification systems affect genetic exchange in Haloferax volcanii, finding that they reduce but do not block recombination between incompatible strains.

Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum

This study shows that two divergent archaellins in Halorubrum lacusprofundi work together to stabilize archaellar structure and improve thermal and salinity resistance.

Identification and characterization of putative Aeromonas spp. T3SS effectors

This study identifies and validates T3SS effector proteins in Aeromonas spp. using a bioinformatics pipeline and experimental validation in yeast, finding 21 effector groups with 15 showing cytotoxicity.