Kaitavjeet Chowdhary
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View article: Deep genomic models of allele-specific measurements
Deep genomic models of allele-specific measurements Open
Allele-specific quantification of sequencing data, such as gene expression, allows for a causal investigation of how DNA sequence variations influence cis gene regulation. Current methods for analyzing allele-specific measurements for caus…
View article: Deep Genomic Models of Allele-Specific Measurements
Deep Genomic Models of Allele-Specific Measurements Open
View article: Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction
Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction Open
View article: An interwoven network of transcription factors, with divergent influences from FoxP3, underlies Treg diversity
An interwoven network of transcription factors, with divergent influences from FoxP3, underlies Treg diversity Open
FoxP3+CD4+ regulatory T cells (Tregs), essential for immunologic and organismal homeostasis, have diverse functions and corresponding gene expression programs. How the many controlling transcription factors (TFs) organize to determine Treg…
View article: Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets
Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets Open
Foxp3 + regulatory T cells (Tregs) in the colon are key to promoting peaceful co-existence with symbiotic microbes. Differentiated in either thymic or peripheral locations, and modulated by microbes and other cellular influencers, colonic …
View article: Establishment of an Inactivation Method for Ebola Virus and SARS-CoV-2 Suitable for Downstream Sequencing of Low Cell Numbers
Establishment of an Inactivation Method for Ebola Virus and SARS-CoV-2 Suitable for Downstream Sequencing of Low Cell Numbers Open
Technologies that facilitate the bulk sequencing of small numbers of cells as well as single-cell RNA sequencing (scRNA-seq) have aided greatly in the study of viruses as these analyses can be used to differentiate responses from infected …
View article: FoxP3 associates with enhancer-promoter loops to regulate T<sub>reg</sub>-specific gene expression.
FoxP3 associates with enhancer-promoter loops to regulate T<sub>reg</sub>-specific gene expression. Open
Gene expression programs are specified by higher-order chromatin structure and enhancer-promoter loops (EPLs). T regulatory cell (Treg) identity is dominantly specified by the transcription factor (TF) FoxP3, whose mechanism of …
View article: A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV-2 at the immune–epithelial interface
A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV-2 at the immune–epithelial interface Open
Significance By modeling in vitro the cross-talk between epithelial and immune cells, this work provides possible origins for the profound inflammatory perturbations that are a hallmark of COVID-19, and the relative protection of children …
View article: FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression Open
SUMMARY Gene expression programs are specified by higher-order chromatin structure and enhancer-promoter loops (EPL). T regulatory cells (Treg) identity is dominantly specified by the transcription factor FoxP3, whose mechanism of action i…
View article: A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV2 at the immune-epithelial interface
A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV2 at the immune-epithelial interface Open
Infection by SARS-CoV2 provokes a potentially fatal pneumonia with multiorgan failure, and high systemic inflammation. To gain mechanistic insight and ferret out the root of this immune dysregulation, we modeled by in vitro co-culture the …
View article: Profound Treg perturbations correlate with COVID-19 severity
Profound Treg perturbations correlate with COVID-19 severity Open
Summary The hallmark of severe COVID-19 disease has been an uncontrolled inflammatory response, resulting from poorly understood immunological dysfunction. We explored the hypothesis that perturbations in FoxP3+ T regulatory cells (Treg), …
View article: Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis
Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis Open
View article: Additional file 5: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients
Additional file 5: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients Open
Table S3. Genes significantly changes in RNA-seq analysis from ALS patients. (XLSX 52 kb)
View article: Additional file 9: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients
Additional file 9: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients Open
Figure S4. poly-GR expression results in the upregulation of heat shock response genes and dHSF1 in the adult fly nervous system. UAS-(GR)36 was expressed in the adult fly nervous system using the drug-inducible Gal4 driver, elavGS, for 16…