Alan Hunter Shain

WRN deficiency generates oncogenic rearrangements at TA-rich tandem repeats

This study shows WRN deficiency causes oncogenic rearrangements at TA-rich tandem repeats by destabilizing them, leading to chromosomal breaks and activation of TERT in melanoma.

Somatic mutations distinguish melanocyte subpopulations in human skin

The paper identifies distinct melanocyte subpopulations in human skin based on mutation burden, showing LowMut cells are stem-like and spatially distinct from HighMut cells.

Molecular effects of indoor tanning

This study examines the molecular effects of indoor tanning by analyzing mutation patterns in melanocytes from tanning bed users and finds increased mutation burdens and distinct mutational signatures.

Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma

This study uses multi-omic profiling to trace molecular changes in skin cells during carcinogenesis, identifying key mutations and spatial gene expression patterns in keratinocytes, actinic keratoses, and squamous cell carcinomas.

Visualizing somatic alterations in spatial transcriptomics data of skin cancer

The paper develops software to infer copy number and detect single nucleotide variants in spatial transcriptomics data, applied to skin cancer to reveal genetic patterns and clonal populations.

Tracing cancer evolution and heterogeneity using Hi-C

The paper develops HiDENSEC to analyze Hi-C data in heterogeneous cancer samples, identifying chromosomal rearrangements and their impact on melanoma progression.

The genomic landscapes of individual melanocytes from human skin

This study genotypes individual melanocytes from human skin, revealing mutation patterns linked to sun exposure, skin cancer risk, and melanoma origins.

CNVkit-RNA: Copy number inference from RNA-Sequencing data

CNVkit-RNA infers copy number from RNA-sequencing data by correcting technical biases and prioritizing stable, highly expressed genes, showing high concordance with aCGH in melanoma samples.