J. W. Hammond

Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity

This study presents a multi-omic atlas of the siphonophore Physalia utriculus, revealing the regulatory mechanisms of colonial division of labour and the molecular basis of venom activity.

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

Sex chromosome dosage compensation in a sex reversing skink is not influenced by sexual phenotype

The paper investigates dosage compensation in the eastern three-lined skink, finding that X chromosome expression in sex-reversed individuals matches their genotype rather than phenotype.

Targeted sequencing and iterative assembly of near-complete genomes

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies

This paper presents a high-quality chromosome-scale genome assembly for the Australian alpine skink Bassiana duperreyi using long-read technologies, achieving high completeness and providing a resource for sex determination and thermolabile sex reversal studies.

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

The paper presents a high-quality, telomere-to-telomere genome assembly and annotation for the central bearded dragon, providing insights into its sex determination mechanisms.

Repeat-rich regions cause false positive detection of NUMTs - a case study in amphibians using an improved cane toad reference genome

Somatic instability of the FGF14-SCA27B GAA·TTC repeat reveals a marked expansion bias in the cerebellum

This study examines somatic instability of the FGF14 GAA·TTC repeat in SCA27B, finding a cerebellar-specific expansion bias and increased instability in cerebellar regions compared to other brain areas.

Extensive DNA methylome rearrangement during early lamprey embryogenesis

This study investigates DNA methylation dynamics during lamprey embryogenesis, revealing extensive maternal-to-paternal epigenome remodeling and its link to programmed genome rearrangement.

The landscape of genomic structural variation in Indigenous Australians

This study profiles genomic structural variation in Indigenous Australians using whole genome long-read sequencing, revealing abundant and previously unannotated variants and unique STR diversity.

Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition.

The paper analyzes sex-specific transcriptomic and epitranscriptomic changes in mouse amygdala during PTSD-like fear acquisition using RNA-seq and dRNA-seq.

SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

The paper introduces SLOW5, a new file format for nanopore sequencing data that accelerates analysis on HPC systems by enabling efficient parallelization.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

This study evaluates the analytical validity of nanopore sequencing for SARS-CoV-2 genome analysis, finding high accuracy for SNVs but limitations in detecting short indels and low-frequency variants.