Murray P. Cox

The paper uses sequence-to-function models to predict the functional impact of archaic hominin introgression in Papuan individuals, identifying genes associated with introgressed haplotypes.

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

The paper investigates the regulatory effects of Neanderthal and Denisovan introgression in Papuan populations using a massively parallel reporter assay, finding differential activity in immune-related genes.

This study identifies eQTLs and environmental influences on immune cell diversity in Indonesian populations, highlighting the role of ancestry and environment in shaping immunity.

The paper uses genomic and morphometric analyses to show that pigs in Wallacea and Oceania have diverse ancestries linked to Austronesian dispersal 4,000-3,000 years ago.

The paper examines Crozier's Paradox in Dictyostelium discoideum by analyzing tgrB1 and tgrC1 genes, finding no strong evidence for the paradox and suggesting recombination generates genetic variation.

This paper uses whole-genome sequencing of kakapo to analyze genetic diversity and breeding values, showing how conservation management has maintained genetic diversity and providing tools for future recovery efforts.

The paper identifies and characterizes two genes, Bcvic1 and Bcvic2, in Botrytis cinerea that are involved in vegetative incompatibility, a fungal allorecognition system.

The paper shows that admixture in modern European genomes has masked over 50 historic hard sweeps, suggesting underappreciation of historical selection in human evolution.

The paper identifies Indonesia-specific eQTLs and methylQTLs linked to local ancestry and archaic introgression, showing their impact on gene regulation and hematological traits.

This paper identifies histone methyltransferases SetB and ClrD as essential for the infection capability of the grass-symbiotic fungus Epichloë festucae, showing their catalytic activity is required for successful colonization.

The paper identifies Denisovan introgression in Papuan genomes that influences immune-related processes and regulatory elements, with experimental validation of functional impacts.

The paper analyzes DNA methylation and gene expression in Indonesian populations to show genetic ancestry, environmental influences, and immune-related differences across regions.

The paper presents a chromosome-level genome assembly of Venturia effusa, identifying a frameshift mutation in ALM1 associated with the albino phenotype.

The paper investigates how repeat elements shape 3D genome structure and transcription in the fungus Epichloë festucae, revealing a unique patchwork genome with repeat-rich blocks that regulate gene expression in symbiosis.