Shane J. Neph

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

The paper introduces CUT&TIME, a method to map historical chromatin accessibility in single cells during neurogenesis, revealing early changes in promoter accessibility linked to cell-fate commitment in retinal ganglion cells.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

This paper introduces FiberFold, a deep learning model that predicts haplotype-specific 3D chromatin organization using Fiber-seq data, revealing changes in TADs in a Mendelian disease.

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.