G. A. Wray

Hybrid epigenomes reveal extensive local genetic changes to chromatin accessibility contribute to divergence in embryonic gene expression between species

The paper quantifies cis and trans influences on chromatin accessibility divergence between two sea urchin species, finding cis effects more numerous and larger, and highlighting distinct regulatory mechanisms near GRN genes.

Genomic insights into Plasmodium vivax population structure and diversity in central Africa

This study sequenced a Plasmodium vivax isolate from the Democratic Republic of the Congo and found it closely related to other African P. vivax populations, not to non-human primate parasites.

Recent Reconfiguration Of An Ancient Developmental Gene Regulatory Network In Heliocidaris Sea Urchins

This study shows how natural selection rapidly reshapes developmental gene regulatory networks in sea urchins with divergent life histories, revealing evolutionary changes in gene regulation and chromatin status.

Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene regulatory network during rapid life history divergence in sea urchins

This study identifies evolutionary changes in chromatin configuration and regulatory elements in sea urchins, showing how these modifications contribute to life history divergence and phenotypic evolution.

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

The paper identifies positive selection in SARS-CoV-2 and other coronaviruses, including non-protein-coding regions, using mutation patterns and RNA structure analysis.

An early cell shape transition drives evolutionary expansion of the human forebrain

The paper uses cerebral organoids to show that a delayed cell shape transition in human neuroepithelial cells drives brain expansion compared to apes.

Evaluating chromatin accessibility differences across multiple primate species using a joint modelling approach

The paper develops a joint modeling approach to identify chromatin accessibility differences across primate species and finds distinct classes of DHS sites with varying conservation and regulatory features.

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate neutral proxy

The paper introduces adaptyPhy, a method for detecting branch-specific positive selection in regulatory DNA, validated using simulations and human genomic data.