Stephanie C. Bohaczuk

Enhancer Tuning by Sequence-Specific Repressors

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

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions

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.

Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing

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.

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

Protamine lacunae preserve the paternal chromatin landscape in sperm

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.

Principles and functional consequences of plasmid chromatinization in mammalian cells

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

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

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

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

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.

Somatic epimutations cap genetic determinism in the human diploid chromatin epigenome

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.

3-hour genome sequencing and targeted analysis to rapidly assess genetic risk

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.