Matthew Thomas Wheeler

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

The paper analyzes multi-omic, multi-tissue molecular responses to acute exercise in sedentary adults, identifying key pathways and exerkines involved in exercise effects.

This study identifies shared and sex-specific molecular responses to endurance training in skeletal muscle using multi-omics data from rats.

The paper develops a multidimensional assay to assess variant effects in MYBPC3, reclassifying variants and uncovering disease mechanisms in hypertrophic cardiomyopathy.

METAFORA calls depth-aware, covariate-adjusted methylation outlier regions from PacBio and Nanopore long reads; in 551 rare-disease genomes, outliers tracked structural variants, repeat expansions, and imprinting defects.

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

This study identifies tissue-specific lncRNA responses to endurance exercise in rats, revealing sex differences and potential therapeutic implications.

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The paper identifies biallelic variants in RNU2-2 as a common cause of recessive neurodevelopmental disorders, showing higher prevalence than the dominant form in England.

The paper identifies individuals with minor spliceopathies by analyzing transcriptome-wide splicing outliers in RNA-seq data from rare disease cohorts.

The paper identifies biallelic variants in RNU4-2 causing a recessive neurodevelopmental syndrome with distinct white matter changes, expanding the known genotypic and phenotypic spectrum of RNU4-2-related disorders.

This study identifies barriers and needs for genetic evaluation in dilated cardiomyopathy through a survey and discussion with cardiologists, highlighting the need for improved reimbursement, education, and infrastructure.

An LLM agent with a literature-mined environment of 150 tools, 105 packages and 59 databases plans in code, matching reported human accuracy on database and sequence question answering.

The paper integrates long-read sequencing and gene expression to prioritize functional structural variants and tandem repeats in rare disease patients, identifying potential causal variants in a neurodevelopmental disorder.

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 study examines how different genome builds affect RNA-seq results in rare disease samples and recommends cross-referencing with a database of build-dependent genes for more accurate transcriptomics analysis.

The paper explores researchers' perspectives on returning multi-omics results to participants in the MoTrPAC study, highlighting both support and concerns about ethical, logistical, and communication challenges.

The paper applies complete long read sequencing to undiagnosed patients, identifying a 16kb intragenic duplication in EHMT1 causing Kleefstra syndrome.

RExPRT predicts pathogenicity of tandem repeat expansions with high precision, identifying ~30,000 likely pathogenic TRs in the reference genome.

The paper identifies impactful rare variants by integrating multi-omic data from MESA, showing that combining expression and protein data increases the detection of rare stop and frameshift variants.

This study shows that loss of MECR causes elevated ceramide levels and impaired iron metabolism, linking mitochondrial fatty acid synthesis to neurodegeneration.

This study maps multi-omic mitochondrial changes across 19 tissues in rats after endurance exercise training, identifying tissue-specific adaptations and disease-related hubs.

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

The paper investigates how mono- and bi-allelic ACTN2 mutations cause cardiomyopathy through distinct mechanisms using patient-derived iPSC-cardiomyocytes and CRISPR-Cas9 editing.

The paper characterizes HNRNPA1 mutations in patients with neurodegenerative diseases, showing varied effects on fibrillization, phase separation, and stress granule dynamics.

The paper maps regulatory effects of human disease variants in pluripotent cells, identifying cis- and trans-QTL across 18,556 genes and linking them to GWAS traits.

AMELIE 3 automatically reanalyzes undiagnosed Mendelian disease patients using new literature, achieving 80% diagnostic yield with 0.5-1 alerts per patient per year.

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.

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