Shane McCarthy

This study uses PacBio HiFi sequencing to assemble complete Plasmodium falciparum genomes from natural infections, revealing full repertoires of immune-related genes.

This study shows hybridisation enables Amazonian trees to rapidly evolve chemical defences against herbivores, driving diversification in response to shifting herbivore communities.

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

This study investigates genomic convergence in Mediterranean clingfishes adapting to intertidal gravel beaches, finding no large-scale convergence but identifying candidate regions associated with morphological traits.

This study identifies molecular adaptations in Onychomys species that confer toxin resistance through genome analysis and positive selection detection.

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

This study examines two Neotropical butterfly radiations, revealing high rates of hybridization and chromosomal rearrangements as drivers of diversification.

The paper presents the reference genome of Cheirolophus tagananensis, providing tools for studying genetic adaptation and supporting conservation strategies.

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

The paper presents genome assemblies of two Hypolimnas species and analyzes the evolution of W chromosomes in Lepidoptera, suggesting a common origin despite conflicting hypotheses.

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

YaHS, a C command-line Hi-C scaffolder, normalises inter-contig contacts by intra-contig medians, yielding more contiguous, accurate chromosome-scale scaffolds than SALSA2 and pin_hic.

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

The paper identifies a rare variant that lowers ACE2 expression and reduces COVID-19 risk, and develops a genetic risk score predicting severe disease.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

The paper presents a high-quality chromosome-level genome assembly of the Black Soldier Fly and identifies genomic features and inbreeding patterns in a lab population.

The paper characterizes proteome variation across 202 human iPSC lines, identifies 700 pQTLs, and links pQTLs to disease-associated GWAS variants.

The paper presents a haplotype-resolved genome assembly for the wood tiger moth using trio binning, revealing population structure insights.

The paper reports the high-quality genome assembly of Pecten maximus, revealing gene duplicates and highlighting Nav1 as a candidate for toxin resistance.

This study presents 929 high-coverage human genome sequences from 54 populations, revealing new insights into genetic variation and population history.

The paper uses single-cell RNA-seq of differentiating iPS cells from 125 donors to identify expression quantitative trait loci influencing gene expression during endoderm differentiation.

The paper introduces a tool to identify and remove haplotypic duplication in genome assemblies, improving continuity and completeness.

This study identifies 111 genetic loci and 163 risk variants associated with atrial fibrillation using a GWAS of over 1 million individuals.

Crumble compresses sequence quality values in CRAM files to reduce storage while preserving variant calling accuracy.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.