Benjamin J. Mallory

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

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.

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

This paper introduces DAF-seq, a method for single-molecule and single-cell chromatin fiber sequencing, enabling precise analysis of protein occupancy and chromatin accessibility.

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.

This study shows plasmids can form chromatin structures in mammalian cells and uses plasmid Fiber-seq to map these structures and their functional consequences.

The paper uses Fiber-seq to show that regional centromeres have dichromatin organization, with accessible and compacted chromatin, which is conserved across species despite DNA sequence differences.

This paper introduces fibertools, a toolkit for DNA-m6A detection and integration of long-read genetic and epigenetic data, achieving high accuracy and speed.

This study uses targeted Fiber-seq to analyze the chromatin impact of mosaic variants, showing that pathogenic DMPK CTG expansions disrupt regulatory elements and that base editing can alter chromatin accessibility.

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.

This study demonstrates rapid whole-genome sequencing and targeted analysis within three hours to assess genetic risk in a newborn, showing they are not affected or a carrier for a specific Mendelian condition.

The paper evaluates DNA-m6A detection methods, finds most commercial antibodies are poorly selective, and identifies distinct DNA-m6A patterns in three eukaryotic species.

This paper describes a method to isolate C. elegans males by degrading DPY-27, enabling molecular and biochemical analyses of male-specific processes.