Alon Goren

Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility

Improved spike-in normalization clarifies the relationship between active histone modifications and transcription

The paper introduces a novel dual-spike-in normalization method for ChIP-seq, demonstrating its ability to clarify the relationship between RNA polymerase II activity and histone modifications.

Trex-QTL: A mixture-model for identification of genetic effects with global effects on molecular phenotypes

Trex-QTL identifies trans-eQTLs with global effects on molecular phenotypes, showing improved power and replicating known loci in rat brain data.

The contribution of short tandem repeats to splicing variation in the human cortex

This study identifies STRs associated with alternative splicing in human brain tissue and links some to disease-related GWAS signals.

SETD5 dysfunction in human astrocytes drives IL-6-mediated neuronal impairments via the JAK/STAT signaling pathway

This study shows that SETD5 dysfunction in astrocytes increases IL-6, which harms neurons via JAK/STAT signaling, suggesting therapeutic targeting of this pathway for ASD and ID.

Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

Prod&PQ-seq detects and quantifies protein-protein interactions and protein abundance across different cellular conditions, showing changes in PRC2 interactions with EZH2 inhibition and H3 variants.

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

The paper introduces spa-ChIP-seq, an automated ChIP-seq protocol, showing it achieves comparable signal-to-noise ratios to manual methods and identifies sensitivity of weak signals to antibody-to-cell-number ratio changes.

Characterization of shared and ancestry-specific signals driving complex traits using multi-ancestry fine-mapping

The paper introduces PIPSORT, a method to detect shared and ancestry-specific genetic signals in complex traits, and applies it to GWAS data from diverse populations.

Systematic evaluation of the impact of promoter proximal short tandem repeats on expression

This study evaluates how promoter proximal short tandem repeats (STRs) affect gene expression using MPRA, identifying key factors like repeat unit sequence and copy number.

Polymorphic short tandem repeats make widespread contributions to blood and serum traits

The paper identifies 119 high-confidence STR-trait associations across 93 STRs for blood and serum traits using imputed genotypes from UK Biobank data.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

The paper identifies a quantitative trait locus on chromosome 13 associated with STR expansion propensity in mice, implicating Msh3 in genome-wide mutation patterns.

Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits

The paper identifies over 28,000 STRs associated with gene expression across 17 tissues and links them to complex traits like height and schizophrenia.

A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments

This paper introduces Tulip, a toolkit for simulating ChIP-seq data to evaluate analyses like peak calling and differential binding, enabling power analysis and benchmarking.

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns

The paper investigates mitotic bookmarking through histone modifications and nucleosome deposition patterns in human cells, showing that epigenomic landscapes and modified nucleosomes contribute to chromatin reestablishment after mitosis.

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq

This study compares monoclonal and polyclonal antibodies for ChIP-seq of histone modifications, finding monoclonals perform similarly in most cases but show differences for H3K27ac.