Ira W. Deveson

The paper develops a thermodynamic model linking transcriptome organization to growth state by analyzing RNA folding free energies across cell cycle and stress adaptation.

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

This paper introduces open-source GPU-accelerated basecalling tools for nanopore sequencing that are hardware-independent and competitive with proprietary solutions.

SVlog provides a logic programming framework for analyzing structural variants in genomic disease by applying deterministic rules to genomic data and annotations.

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.

This study uses proteomics to identify a cryptic JPH2 loss-of-function in a paediatric DCM patient, revealing a novel mechanism of recessive disease.

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.

The paper investigates how transcriptionally active HIV-1 reservoirs with APOBEC3-associated mutational signatures affect neuroaxonal integrity in individuals on suppressive antiretroviral therapy.

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.

This study analyzes mutation patterns in dengue virus genomes from acute infections, showing higher haplotype diversity than consensus sequences.

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.

This paper introduces minimod, a tool for analyzing base modifications in long-read sequencing data, showing significant speed improvements over existing tools.

This paper introduces ex-zd, a compression strategy for nanopore sequencing data that reduces file sizes by removing redundant bits without affecting downstream analyses.

This paper uses long-read sequencing to simultaneously detect genetic variation and methylation, enabling phenotypic classification of inherited and acquired genetic diseases.

Realfreq provides real-time base modification analysis for nanopore sequencing, enabling live data analysis during sequencing.

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.

This paper demonstrates that targeted long-read sequencing improves genetic diagnosis of spastic-ataxia disorders by identifying causative variants in 41% of undiagnosed cases using a single assay.

The paper uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

This paper compares POD5 and SLOW5 file formats for nanopore sequencing data, finding SLOW5 offers better performance, lower cost, and easier management.

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.

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.

This paper develops a lightweight k-mer model for RNA004 chemistry using basecaller move tables, achieving high alignment rates and comparable m6A detection performance to default models.

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

Squigulator simulates nanopore sequencing signals with tunable noise parameters to test and improve analysis methods.

The paper identifies a deep intronic MME variant causing CMT through aberrant splicing, highlighting the importance of considering deep intronic variants in CMT diagnosis.

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

Squigualiser provides an interactive visualization tool for nanopore signal data, enabling alignment to reference genomes and comparison of multiple datasets.

slow5curl enables efficient retrieval of specific nanopore reads from large datasets, reducing storage and transfer costs for reanalysis.

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.

This paper introduces Buttery-eel, an open-source tool that accelerates nanopore basecalling by leveraging the SLOW5 data format for efficient data access on HPC and cloud environments.