Ira Cooke

This study examines how thermal stress affects microbial symbiosis and host activity in the sponge Ianthella basta, showing tissue regression, symbiont loss, and microbial shifts under elevated temperatures.

This study identifies microRNAs expressed during early development of Acropora digitifera and shows their dynamic regulation across developmental stages.

The paper provides a comprehensive transcriptomic dataset and visualization tool for Acropora millepora development, revealing major gene expression transitions during gastrulation and post-settlement.

This study tests assisted gene flow in corals during a marine heatwave, finding AGF offspring had 4x greater survival odds than controls and 2x greater than northern juveniles.

This paper presents the first chromosome-scale genome assembly of the tropical abalone Haliotis asinina using long-read and Hi-C sequencing, providing a high-quality reference for comparative genomics and ecological studies.

The paper identifies chromosomal inversions in Acropora kenti with excess mutational load, suggesting they are under balancing selection and may impact adaptation and genetic decline.

This study shows that AMP prediction benchmarks are biased due to negative data selection and introduces a web server for fair benchmarking.

The paper investigates mechanisms of ecological divergence with gene flow in corals by combining genomic, transcriptomic, and symbiont analyses to understand adaptation to environmental stress.

The paper identifies genetic adaptations in coral holobionts from the Great Barrier Reef's inshore regions linked to Holocene climate change.

The paper introduces ampir, an R package for fast genome-wide prediction of antimicrobial peptides, showing higher classification accuracy than existing methods.

The paper compares transcriptomes of Chromera and Symbiodiniaceae algae to assess their genetic relationships and thermal tolerance.

The paper presents draft genomes of two Symbiodinium species and identifies genes under positive selection related to symbiosis functions.