Adam G. Diehl

The paper develops a targeted long-read method to profile haplotype-specific chromatin accessibility and DNA methylation at L1HS loci in human cells, revealing allele-specific patterns and non-Mendelian inheritance.

GPatch creates chromosome-scale, gap-free pseudoassemblies from fragmented draft genomes, enabling accurate Hi-C matrix construction.

LRphase is a tool for phasing long sequencing reads using known haplotypes to assign haplotype identity to variants.

The paper investigates why studies fail to find associations between de novo noncoding variants and complex disorders like ASD, identifying annotation quality and variant reliability as key issues.

OnRamp provides a cost-effective method for plasmid validation using nanopore sequencing, enabling full plasmid sequencing and detection of sequence variation in complex regions.

MapGL infers the evolutionary gain and loss of short genomic sequence features using phylogenetic maximum parsimony, simplifying the process with a unified software tool.

The paper shows transposable elements contribute significantly to species- and cell-specific chromatin looping variation through CTCF binding site expansions in human and mouse.

The paper identifies conserved regulatory grammar patterns between human and mouse that predict shared chromatin states and gene expression, and links these patterns to disease-associated variation.