Christopher Benner
YOU?
Author Swipe
View article: Improved spike-in normalization clarifies the relationship between active histone modifications and transcription
Improved spike-in normalization clarifies the relationship between active histone modifications and transcription Open
Spike-in normalization enables quantitative analysis of ChIP-sequencing (ChIP-seq) signal. Here we introduce a novel robust dual-spike-in normalization approach for ChIP-seq (ChIP-wrangler). We identify optimal conditions, such as the rati…
View article: Kaiso (ZBTB33) engages with non-canonical binding motifs to regulate DNA damage responses in breast cancer cells
Kaiso (ZBTB33) engages with non-canonical binding motifs to regulate DNA damage responses in breast cancer cells Open
In breast cancer, nuclear localization of Kaiso (ZBTB33), a dual specificity transcription factor, is a hallmark of high grade ductal-type carcinomas, especially in estrogen receptor negative disease. Regulation of gene expression by Kaiso…
View article: Repurposing Carfilzomib as a Promising Drug for Targeted Therapy in Gastric Cancer
Repurposing Carfilzomib as a Promising Drug for Targeted Therapy in Gastric Cancer Open
Background/Objectives: Identifying novel targets to treat gastric cancer (GC) has become a focus of research in recent years. Our accelerated Helicobacter-induced gastric cancer mouse model allowed us to identify several differentially exp…
View article: Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding
Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding Open
The AUTS2 gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2’s chromatin-and RNA-related functions are recognized,…
View article: Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors
Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors Open
SUMMARY Persistence of senescent alveolar transitional progenitors following lung injury is implicated in the pathogenesis of fibrosis. We identified transitional cells in uninjured Cldn18 knockout (KO) mouse lungs distinct from previously…
View article: Integrative multi-omics analysis in vivo identifies influenza virus host factors
Integrative multi-omics analysis in vivo identifies influenza virus host factors Open
View article: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations Open
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and…
View article: Zika but not Dengue virus infection limits NF-κB activity in human monocyte-derived dendritic cells and suppresses their ability to activate T cells
Zika but not Dengue virus infection limits NF-κB activity in human monocyte-derived dendritic cells and suppresses their ability to activate T cells Open
Understanding flavivirus immunity is critical for the development of pan-flavivirus vaccines. Dendritic cells (DC) coordinate antiviral innate and adaptive immune responses, and they can be targeted by flaviviruses as a mechanism of immune…
View article: The Wild West of spike-in normalization
The Wild West of spike-in normalization Open
View article: Protocol to establish an accelerated murine model for Helicobacter-induced gastric cancer
Protocol to establish an accelerated murine model for Helicobacter-induced gastric cancer Open
View article: Position-dependent function of human sequence-specific transcription factors
Position-dependent function of human sequence-specific transcription factors Open
View article: Author Correction: Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Author Correction: Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing Open
View article: Retraction Notice to: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers
Retraction Notice to: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers Open
View article: Triclosan administration to humanized UDP-glucuronosyltransferase 1 neonatal mice induces UGT1A1 through a dependence on PPARα and ATF4
Triclosan administration to humanized UDP-glucuronosyltransferase 1 neonatal mice induces UGT1A1 through a dependence on PPARα and ATF4 Open
Triclosan (TCS) is an antimicrobial toxicant found in a myriad of consumer products and has been detected in human tissues, including breastmilk. We have evaluated the impact of lactational TCS on UDP-glucuronosyltransferase 1A1 (UGT1A1) e…
View article: A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats Open
View article: TRIF-IFN-I pathway in Helicobacter-induced gastric cancer in an accelerated murine disease model and patient biopsies
TRIF-IFN-I pathway in Helicobacter-induced gastric cancer in an accelerated murine disease model and patient biopsies Open
Helicobacter pylori (H. pylori) infection is a known cause of many digestive diseases, including gastritis, peptic ulcers, and gastric cancer. However, the underlying mechanisms by which H. pylori infection triggers th…
View article: Drug target prediction through deep learning functional representation of gene signatures
Drug target prediction through deep learning functional representation of gene signatures Open
Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative an…
View article: Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian hamsters
Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian hamsters Open
Hybrid immunity (vaccination + natural infection) to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity indu…
View article: Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation
Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation Open
Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expressi…
View article: Drug target prediction through deep learning functional representation of gene signatures
Drug target prediction through deep learning functional representation of gene signatures Open
Many machine learning applications in bioinformatics currently rely on gene identities extracted from input gene signatures, and fail to take advantage of preexisting knowledge about gene functions. We developed the Functional Representati…
View article: Effects of Early Life Oral Arsenic Exposure on Intestinal Tract Development and Lipid Homeostasis in Neonatal Mice: Implications for NAFLD Development
Effects of Early Life Oral Arsenic Exposure on Intestinal Tract Development and Lipid Homeostasis in Neonatal Mice: Implications for NAFLD Development Open
Exposure to iAs in neonatal mice resulted in excessive accumulation of fat in enterocytes, disrupting lipid homeostasis in the serum and liver, revealing the importance of the gut-liver axis and endoplasmic reticulum stress in mediating iA…
View article: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation
Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation Open
Cis-regulatory elements (CREs) can be classified by the shapes of their transcription start site (TSS) profiles, which are indicative of distinct regulatory mechanisms. Massively parallel reporter assays (MPRAs) are increasingly being used…
View article: Strain and sex-related behavioral variability of oxycodone dependence in rats
Strain and sex-related behavioral variability of oxycodone dependence in rats Open
View article: Activation of the TRIF pathway and downstream targets results in the development of precancerous lesions during infection with<i>Helicobacter</i>
Activation of the TRIF pathway and downstream targets results in the development of precancerous lesions during infection with<i>Helicobacter</i> Open
Helicobacter pylori ( H. pylori) infection is an established cause of many digestive diseases, including gastritis, peptic ulcers, and gastric cancer. However, the mechanism by which infection with H. pylori causes these disorders is still…
View article: Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters
Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters Open
Hybrid immunity to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. mRNA vaccine, BNT162b2, was…
View article: SARS-CoV-2 Ancestral and Variant of Concern Breakthrough infections boost both cross-reactive cellular and humoral immune responses in mRNA-vaccinated Hamsters
SARS-CoV-2 Ancestral and Variant of Concern Breakthrough infections boost both cross-reactive cellular and humoral immune responses in mRNA-vaccinated Hamsters Open
When mRNA vaccines were rolled out under EUA, it was observed that a single vaccination, already protected vaccinees from severe disease, even before neutralizing antibodies appearded. To better understand the underlying mechanism of prote…
View article: A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats Open
Summary The seventh iteration of the reference genome assembly for Rattus norvegicus — mRatBN7.2—corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to it…
View article: Supplementary Figures S1-19 and legends from Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis
Supplementary Figures S1-19 and legends from Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis Open
Supplementary Figures S1-19 and legends. Figure S1: Overexpression of HIF-1α enhances BTIC characteristics. Figure S2: Characterizations of isolated BTICs by different parameters. Figure S3: The expression of TET1 and TET3 is upregulated b…
View article: Supplementary Table 4 from General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to <i>De novo</i> DNA Methylation in Cancer Cells
Supplementary Table 4 from General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to <i>De novo</i> DNA Methylation in Cancer Cells Open
Supplementary Table 4 from General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells
View article: Table S2 from Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis
Table S2 from Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis Open
Table S2: Sequence of the oligonucleotides for shRNA, real-time PCR, and ChIP assay.