Christopher W. Benner

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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

The paper identifies host-virus chimeric proteins, called UFOs, generated during influenza virus infection through the translation of viral 5UTRs using host transcripts.

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.