Christopher W. Benner

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.

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.

Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

This study maps transcription initiation in mouse astrocytes to define how inflammatory signals drive cell-type-specific gene regulation and links enhancer activity to human disease risk.

Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon

The paper characterizes gene regulatory networks in human airway epithelial cells and identifies cell type-specific responses to type I interferon.

Mysm1 mutations in meander tail mice cause anterior-selective cerebellum malformation

This paper identifies Mysm1 mutations as the cause of meander tail mouse cerebellum malformation and links them to hematological and neurological defects.

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.

Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.

This study identifies AUTS2's dual DNA/RNA binding in human neural progenitors and shows its role in regulating Wnt pathway genes, linking its disruption to neurodevelopmental disorders.

Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors

The paper identifies regeneration-associated transitional progenitors (RATPs) in Cldn18 knockout mice, showing they are less fibrogenic and contribute to lung repair rather than fibrosis.

Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygen-inducedlung injury

The paper identifies TREM2-p53 signaling as a determinant of oxygen-induced lung injury in mice, showing that TREM2 loss reduces inflammation and improves lung development.

Gastric cancer treatment target identified from an accelerated Helicobacter-induced gastric cancer mouse model

The paper identifies PSMB8 as a potential therapeutic target in gastric cancer and shows carfilzomib's efficacy in reducing tumor growth and inducing apoptosis in a mouse model.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19

The paper profiles the active cistrome in peripheral leukocytes of critically ill COVID-19 patients to identify severity-associated cis-regulatory elements and their regulatory programs.

Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction

The paper investigates how drug exposure alters gene regulatory networks in the brain using multi-omics approaches, identifying enhancer repression and transcription factor involvement in addiction-related behaviors.

A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells

The paper revises transcription start site annotations in Chinese hamster genes using experimental data to improve gene engineering and glycosylation in CHO cells.

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function

MAGGIE identifies DNA sequence motifs mediating TF binding and function by linking genetic variation to epigenomic changes, improving sensitivity and specificity over existing methods.

LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signalling.

The paper shows LSD1-mediated enhancer silencing limits RA signaling duration during endocrine cell development by suppressing persistent enhancer activity.

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

The paper identifies non-redundant DNA binding activities of AP-1 family members in macrophages using ChIP-sequencing and machine learning, showing motif ensembles drive factor-specific binding.