Robin D. Dowell

The paper identifies airway epithelial transcriptional mechanisms linked to air pollutant exposure and lung disease risk using a functional genomics pipeline, highlighting hyaluronic acid metabolism and TOMM7 regulation as potential therapeutic targets.

This study identifies attenuated estrogen signaling and NRIP1 as key factors in trophoblast defects in Down syndrome using patient-derived stem cells.

This paper integrates multiple transcriptomics assays to identify cancer biomarkers, finding GBP4 as a predictor of recurrence and immune remodeling.

The paper introduces two algorithms, Mu Counts and TFEA-LE, to improve the identification of differentially transcribed regulatory elements by integrating motif information and enhancing precision and recall.

The paper identifies two types of Pol II disassociation regions, differing in base composition and sensitivity to cellular perturbations.

The paper identifies four types of fragile nucleosomes that facilitate RNA Polymerase II transcription in human cells by analyzing histone modifications and Pol II activity.

This study identifies CDK7-dependent mechanisms regulating RNAPII function at gene 5'- and 3'-ends through biochemical reconstitution and multi-omics analysis.

The paper introduces the LIET model to analyze RNA polymerase kinetics across transcription stages and applies it to human cell-types and perturbation experiments to detect changes in transcription dynamics.

This study shows that inhibiting Mediator kinases CDK8/CDK19 suppresses hyperactive IFN signaling in Down syndrome by affecting transcription, splicing, and lipid metabolism.

This study shows largazole suppresses superenhancer accessibility by inhibiting SP1 and BRD4, leading to mitotic chromosome misalignment and cell cycle arrest.

The paper uses single nucleus RNA-sequencing to show transcriptional synchrony between prairie voles in social relationships, identifying genes in oligodendrocyte progenitor cells linked to dyadic behavior.

TF profiler infers transcription factor activity from PRO-seq and GRO-seq data, identifying three distinct TF classes based on regulatory roles.

The paper identifies over 800,000 bidirectional transcription regions in human samples and links them to genes through correlated transcription, enriched for disease SNPs and supported by 3D data.

This paper develops a method for supervised deconvolution of nascent sequencing data and finds enhancer RNAs are informative, while undifferentiated cell types complicate deconvolution.

The paper shows that changes in labile zinc levels affect chromatin accessibility and TP53 binding to DNA.

The paper shows that transcriptional dosage compensation is absent in Down syndrome using real and simulated data, and highlights issues with standard analysis methods.

The paper investigates the heat shock response in lymphoblastoid cell lines with and without trisomy 21, finding a more robust response in trisomy 21 cells.

The paper uses ATAC-seq and PRO-seq to study transcriptional and epigenetic responses to Afghan desert particulate matter in human small airway epithelial cells, identifying key pathways and transcription factors involved.

This study investigates the temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation, showing rapid and persistent effects on gene expression.

The paper develops a stapled peptide that inhibits p53-Mediator interaction, suppressing p53 transcriptional activity in cancer cells.

The paper investigates myonuclear maturation dynamics in aged and adult regenerating mouse skeletal muscle, finding that transcriptional heterogeneity arises during maturation and is altered in aged muscle.

TFEA quantifies transcription factor activity changes from perturbation data, identifying key regulators and temporal regulatory networks.

The paper applies a bioinformatic pipeline to RNA-seq data from ALS patients and controls to identify novel virus-like sequences.

The paper uses genomics techniques to analyze transcriptional responses to wood smoke particles and identifies rapid AHR signaling dynamics and interactions with NFkB.

The paper introduces MechSpy, a framework that generates mechanistic hypotheses of toxicity by combining gene expression data with biological knowledge, and validates predictions experimentally.

The paper shows heat shock in C. elegans increases antisense transcripts and downstream of gene transcripts, which accumulate as dsRNA foci overlapping with HSF-1 granules.

The paper uses ATAC-seq signal processing and recurrent neural networks to classify transcriptional activity from chromatin accessibility data.

The paper uses GRO-seq to show glucocorticoids rapidly repress transcription without local GR occupancy and induce anti-inflammatory effects through GR-NF-kB cooperation.

The paper demonstrates a method to detect differential transcription factor activity using ATAC-seq data by analyzing TF recognition motifs relative to open chromatin regions.