Andre L. M. Reis

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.

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

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

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

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

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

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

This paper introduces chimeric RNA standards for SARS-CoV-2 testing to simultaneously validate positive and negative controls in diagnostic assays.