B Bernstein

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

This study identifies a loss of osteoblastic lineage fidelity in metastatic osteosarcoma through single-nucleus RNA sequencing, linking it to disease progression and potential therapeutic targets.

The paper identifies ZNF654 and JMJD6 as novel factors defining TAD boundaries through in silico screens and experimental validation.

This study shows mutant IDH reprograms neural progenitor cell fate by silencing Gsx2, promoting gliomagenesis through lineage switching.

This paper develops a CRISPRi approach using truncated guides to screen multiple transcription factor binding sites, showing they can disrupt enhancer activity and repress transcription factor binding.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

The paper develops a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and uses it to explore the function of genetic variants in both coding and non-coding regions.

This paper develops a platform to model and manipulate human microglial states in vitro using single-cell RNA sequencing and genetic tools, identifying disease-associated transcriptional signatures.

The paper identifies critical base-resolution regulatory elements in immune gene expression using base editing and deep learning.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper develops a method to detect mitochondrial mutations from single-cell RNA-seq to identify clonal expansions in human hematopoiesis.

Crosscheck detects mislabeled samples in NGS data by analyzing linkage disequilibrium, correcting errors in 1% of ENCODE datasets.

The paper predicts cancer cell-of-origin from DNA sequences by matching mutational landscapes to chromatin modification patterns in normal tissues.

This study identifies tau pathology-driven chromatin organization changes in aged human brains and shows these effects can be reversed with HSP90 inhibitors.

The paper uses gene expression data and GWAS summary statistics to identify disease-relevant tissues and cell types by detecting heritability enrichments in gene-specific expression regions.

This study shows that cohesin loss eliminates loop domains, causing superenhancer links and gene downregulation, which are reversible upon cohesin restoration.

MACS calls ChIP-Seq peaks by estimating tag shift from Watson/Crick strand offsets and testing enrichment against a locally adaptive Poisson background, improving specificity and binding-site resolution.