Benjamin P. Berman

The paper uses ATAC-Seq to study chromatin accessibility in neutrophils stimulated with inflammatory factors, finding stimulus-specific programs linked to sepsis transcriptional states.

This study improves ctDNA deconvolution in ULP-WGS data using CelFiE-ISH, achieving lower cancer fraction detection limits than CNA benchmarks.

The paper uses long-read sequencing to analyze cfDNA fragmentation patterns in cancer patients, identifying hypofragmentation and hyperfragmentation linked to elevated cfDNA levels.

This study compares chromatin accessibility changes during NET formation in whole blood versus isolated neutrophils, finding that whole blood responses show stronger immune pathway activation.

The paper examines chromatin dynamics in primary human neutrophils during PMA-induced NETosis, identifying early chromatin changes linked to NOX-dependent NET formation.

This paper develops a probabilistic model for cell type deconvolution using single-molecule DNA methylation haplotypes, showing improved accuracy in detecting rare cell types.

The paper identifies a sequence signature that predicts CpG methylation loss in healthy tissues and cancer, revealing slow-loss CpGs with minimal methylation loss in health but significant loss in cancer.

This study demonstrates the ability to detect cell-of-origin and cancer-specific methylation features from cell-free DNA using Oxford Nanopore sequencing.

This study uses comparative genomics to identify potential therapeutic targets for Rett syndrome by analyzing co-evolutionary relationships with MECP2 and testing drug candidates in neural cells.

This study shows that DNA methylation and gene expression patterns are preserved in recurrent high grade serous ovarian cancers, with BRCA1/2 carriers showing more shared methylation changes and improved survival.

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

ELMER v.2 reconstructs gene regulatory networks from DNA methylation and transcriptome data to identify Master Regulators in diseases like breast cancer.

TCGAbiolinksGUI provides a graphical interface for analyzing GDC cancer data, making the TCGAbiolinks package more accessible to non-R users.

The paper introduces StateHub and StatePaintR to provide rapid, reproducible chromatin state annotations for genome annotation, supporting variant prioritization and analysis.