John M. Greally

This study quantifies how patient-level factors and site-level practices affect diagnostic yield in exome and genome sequencing across five clinical sites.

The paper integrates multi-omic QTLs and predictive models to identify regulatory variants in CD4+ T cells and their role in immune-related GWAS loci.

This study shows that Egr1 overexpression induces sex-specific changes in neuronal chromatin, gene expression, and behavior in female rodents, mimicking high-oestrogenic phases and affecting hormone-depleted females.

This study investigates the effect of a rare MYH11 variant in mice, finding it does not cause aortic disease but leads to cardiac hypertrophy and heart failure under pressure overload.

The paper identifies founder populations in New York City using genomic data and finds 202 likely disease-causing variants enriched in these under-represented groups, many of which are new discoveries.

The paper identifies de novo variants in RNU4-2 and RNU5B-1 as causes of neurodevelopmental disorders by disrupting splicing, with variant location and allele phase influencing clinical severity.

The paper identifies distinct CD4+ T cell subtypes in obese asthma linked to CDC42 upregulation, Th1 inflammation, and steroid resistance.

The paper introduces gaiaAssociation, a tool for Regulatory Landscape Enrichment Analysis (RLEA) to identify cell types mediating phenotypes from GWAS data by testing locus enrichment in cell type-specific open chromatin regions.

The paper shows how early-life stress and ovarian hormones affect transcriptional regulation in the nucleus accumbens, leading to sex-specific responses to cocaine in mice.

This study shows prenatal vitamin D deficiency changes immune cell proportions in offspring by altering hematopoietic stem cell transcriptional properties and confirms maternal vitamin D levels affect cord blood immune profiles.

The paper evaluates the impact of GUIA, a digital genetic counseling tool, on understanding of genetic test results in diverse families, finding improved understanding in the intervention group.

This study compares the diagnostic yield of genome sequencing and targeted gene panel testing in diverse pediatric patients, finding higher yields with genome sequencing in most groups but not all.

The paper develops NuHash, a method for multiplexing snATAC-seq using oligonucleotide-conjugated antibodies, achieving high demultiplexing accuracy with human and mouse samples.

This paper provides recommendations for interpreting non-coding variants in clinical settings, adapting existing guidelines to account for their role in disease.

This study investigates the obesogenic effects of tributyltin (TBT) during adipogenic differentiation and finds that cytoskeletal damage, not PPARγ activation, is the primary mechanism.

The paper links DNA methylation changes in HSCs from large for gestational age neonates to altered quiescence via transcriptional network disruption.

GenomeDiver improves genomic diagnosis by enabling clinicians to input structured phenotypic data to guide gene prioritization and enhance collaboration with diagnostic labs.

The paper evaluates three ATAC-seq protocols for neuronal chromatin accessibility analysis in mouse and human brains, showing consistent results across freezing methods and highlighting challenges in human post-mortem tissue.

GUIA is a web-based platform designed to improve the delivery of genomic results to patients and families, showing positive feedback from pilot users.

The NYCKidSeq project evaluates the clinical utility and communication of genomic testing in diverse children through a randomized controlled trial.

The paper evaluates epigenetic methods using reference materials, finding high concordance between assays and differences in performance across platforms.

This study shows that gene expression distributions in cancer data are often non-Normal, and using this information improves survival classification in cancer patients.

AptCompare identifies RNA aptamer motifs from HTS-SELEX data by integrating six algorithms and ranking candidates based on binding affinity validation.

This paper describes a protocol for efficient CRISPR-mediated genomic editing in Epstein-Barr virus-transformed lymphoblastoid B cells using ssODN, achieving 20% successful editing and identifying structural mutations missed by targeted sequencing.

Aneuvis is a web tool that quantifies numerical chromosomal variation in single cells and compares it between treatment groups.

The paper shows that estimating cell subtype proportions from functional genomic data improves interpretation of human phenotypic associations by revealing cellular events.

The paper develops a statistical method to model transcriptional heterogeneity in breast tumors, identifying CBX2 as an oncogene overexpressed in invasive breast carcinoma and linked to poorer survival.

The paper optimizes library preparation and sequencing for whole genome bisulphite sequencing on the Illumina HiSeq X system, eliminating an artefact affecting several percent of reads.