Selected recent publications

Genetic disease risks of under-represented founder populations in New York City. A study from Mariko Isshiki and Sri Raj showing that what’s rare globally may be common locally, a study of rare disease risks in fine-scale ancestry groups in New York City.

Isshiki M, Griffen AJ, Meissner P, Spencer P, Cabana MD, Klugman SD, Colón M,
Maksumova Z, Suglia S, Isasi CR, Greally JM, Raj SM. Genetic disease risks of
under-represented founder populations in New York City. PLoS Genet. 2025 Jun
24;21(6):e1011755. doi: 10.1371/journal.pgen.1011755. PMID: 40554605; PMCID:
PMC12208467.

Using epigenomics to understand cellular responses to environmental influences in diseases. A how-to review for those considering using epigenomic studies to understand how environmental influences affect cellular physiology. We bring the reader from ‘epigenomic’ (transcriptional regulatory) patterns progressively upstream to transcription factors, and cell signalling, involving the role of non-coding DNA sequence variants.

Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to
understand cellular responses to environmental influences in diseases. PLoS
Genet. 2023 Jan 19;19(1):e1010567. doi: 10.1371/journal.pgen.1010567. PMID:
36656803; PMCID: PMC9851565.

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. An ingenious software package developed by Sam Rosean and Eric Sosa to infer the cell type(s) mediating a common, complex disease, using genome-wide association study (GWAS) data and ATAC-seq profiles.

Rosean S, Sosa EA, O’Shea D, Raj SM, Seoighe C, Greally JM. Regulatory
landscape enrichment analysis (RLEA): a computational toolkit for non-coding
variant enrichment and cell type prioritization. BMC Bioinformatics. 2024 May
7;25(1):179. doi: 10.1186/s12859-024-05794-7. PMID: 38714913; PMCID:
PMC11075237.