Alan H. Beggs

This study identifies unique myofiber populations in XLMTM using transcriptomics and shows they respond to therapeutic interventions across species.

The paper evaluates incomplete penetrance in 4,325 rare disease families, finding 1.6% of diagnosed cases involve inherited variants from unaffected parents and showing divergent transcriptional effects in CHD8-related cases.

The paper identifies domain-specific phenotypic effects of MACF1 variants outside the GAR domain, revealing broader neurodevelopmental and craniofacial anomalies.

IsoRanker uses long-read transcriptomics to prioritize non-coding variants in Mendelian conditions by detecting expression outliers, allelic imbalance, and NMD, leading to the identification of pathogenic variants in one individual.

The paper identifies novel AXIN2 variants causing expanded phenotypes in humans and validates their pathogenicity using human, mouse, and fly models.

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

This paper demonstrates that ensilication preserves DNA integrity at ambient temperature, enabling diagnostic-quality long-read sequencing without cold-chain infrastructure.

The paper presents a framework for interpreting TTN missense variants by integrating clinical, computational, and functional evidence, identifying two variants as likely pathogenic.

This paper presents a mouse model of ADSS1 myopathy by knocking out Adss1 and characterizes its motor deficits and histopathological features.

The paper evaluates two self-phenotyping tools, showing that GenomeConnect provides more accurate phenotype profiles while Phenotypr offers greater precision and user preference for its autocomplete format.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The paper presents a joint genomic analysis of UDN patients using whole genome sequencing and new statistical methods to prioritize disease genes, revealing new disease associations and releasing a software tool for cohort analysis.

This paper develops a high-resolution kinematic method to quantify impaired mobility in dystrophic zebrafish larvae, finding significant differences in swimming performance between mutants and wild-types.

The paper identifies structural variants in the NEB gene across 35 families, showing large deletions cause dominant distal myopathy while recessive variants show no severity correlation.

The paper detects and classifies copy number variants in exome data from 6,633 families, identifying causal CNVs in 173 families and improving classification standards.

This study identifies novel embryonic and metabolic phenotypes in SelN-deficient zebrafish and myoblasts, linking SelN function to redox and metabolic pathways.

This study evaluates genome sequencing's diagnostic yield in a cohort of undiagnosed rare disease patients, finding it solves 29.3% of cases with specific variant types not detectable by exome sequencing.

This paper investigates the role of SPEG in skeletal muscle biology using multi-omics approaches, revealing its interaction with the myospryn complex and its impact on mitochondrial function and calcium signaling.

The paper evaluates unanticipated monogenic disease risks found in newborns through genomic screening, finding most risks are actionable and lead to medical interventions.

GEM, an AI-based tool, ranks causal genes highly for rare genetic diseases, improving diagnostic efficiency and reducing manual effort.

The paper identifies de novo PRKAR1B variants in six individuals with neurodevelopmental disorder, autism, apraxia, and reduced pain sensitivity.

The paper identifies RFX3, RFX4, and RFX7 mutations as causes of neurodevelopmental disorders including autism, ADHD, and intellectual disability, and links these genes to ASD risk genes through bioinformatic analysis.

AMELIE 2 improves Mendelian disorder diagnosis by matching patient phenotypes and genotypes to primary literature, achieving high accuracy and efficiency.

The paper identifies de novo variants in EIF2AK1 and EIF2AK2 associated with neurodevelopmental disorders and leukoencephalopathy, showing similar pathogenic mechanisms to CACH/VWM.

This study shows that sarcomere assembly via ACTN2 and MRTF-SRF signaling promotes cardiomyocyte maturation through a positive feedback loop.

ClinPhen automatically extracts and prioritizes patient phenotypes from medical records to improve genetic disease diagnosis efficiency.

This study identifies genetic mutations in 78% of Diamond-Blackfan anemia patients using whole exome sequencing, finds new RP genes, and reports genotype-phenotype associations.

This study identifies damaging variants in IRF2BPL associated with neurological phenotypes in humans and shows functional conservation in fruit flies.

This study identifies DDX27 as a regulator of skeletal muscle growth and regeneration by modulating translational processes and ribosome biogenesis in zebrafish.

Transcriptome sequencing improves the diagnostic rate for Mendelian disease in patients for whom genetic analysis has not returned a diagnosis.