A5010223887- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Gene expression and cancer classification
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Islamic Studies and History
- Cancer-related molecular mechanisms research
- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- Politics and Conflicts in Afghanistan, Pakistan, and Middle East
- RNA modifications and cancer
- Monoclonal and Polyclonal Antibodies Research
- Epigenetics and DNA Methylation
- Steroid Chemistry and Biochemistry
- Genomics and Phylogenetic Studies
- Radiopharmaceutical Chemistry and Applications
- RNA and protein synthesis mechanisms
- Jewish and Middle Eastern Studies
- Cytokine Signaling Pathways and Interactions
- Metabolomics and Mass Spectrometry Studies
- Middle East and Rwanda Conflicts
- Protein Tyrosine Phosphatases
University of North Carolina at Chapel Hill
2017-2025
Lung Institute
2017-2020
Indiana University School of Medicine
2017
Rutgers Sexual and Reproductive Health and Rights
2012
Rutgers, The State University of New Jersey
2007-2008
E-cigarettes vaporize propylene glycol/vegetable glycerin (PG/VG), nicotine, and flavorings. However, the long-term health effects of exposing lungs to vaped e-liquids are unknown.
Abstract Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops generally studied a finer scale, the impact looping on proximal interactions remains enigmatic. Here, we critically examine nuclear and loop-proximal using combination in situ Hi-C unparalleled depth, algorithm development, biophysical modeling. Producing large map with 33 billion contacts conjunction an for performing...
Abstract Motivation The R programming language is one of the most widely used languages for transforming raw genomic datasets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure tools developed Bioconductor project. However, existing plotting packages rely on relative positioning sizing plots, often sufficient exploratory but poorly suited creation publication-quality multi-panel images inherent to scientific...
The e-liquids used in electronic cigarettes (E-cigs) consist of propylene glycol (PG), vegetable glycerin (VG), nicotine, and chemical additives for flavoring. There are currently over 7,700 e-liquid flavors available, while some have been tested toxicity the laboratory, most not. Here, we developed a 3-phase, 384-well, plate-based, high-throughput screening (HTS) assay to rapidly triage validate multiple e-liquids. Our data demonstrated that PG/VG vehicle adversely affected cell viability...
Electronic nicotine delivery systems, or e-cigarettes, utilize a liquid solution that normally contains propylene glycol (PG) and vegetable glycerin (VG) to generate vapor act as carrier for flavorings. Evidence indicated these “carriers” reduced growth survival of epithelial cells including those the airway. We hypothesized 3% PG mixed with VG (3% PG/VG, 55:45) inhibited glucose uptake in human airway first step reducing cell survival. Exposure H441 bronchiolar (HBECs) PG/VG (30–60 min)...
To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly spaced time points of macrophage activation. Enhancers genes connected by loops exhibit stronger correlations histone H3K27 acetylation expression than can be explained genomic distance or physical proximity alone. At these looped enhancer-promoter pairs, changes at distal enhancers precede expression. Changes...
Abstract The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes promote tumorigenesis and resistance to therapy. This is especially true cancers have little or no known driver mutations within protein coding genes, ovarian cancer. Herein, we utilize an integrated set genomic epigenomic datasets identify clinically relevant super-enhancers preferentially amplified in patients. We systematically probe top 86...
Abstract Motivation Deriving biological insights from genomic data commonly requires comparing attributes of selected loci to a null set loci. The selection this is non-trivial, as it careful consideration potential covariates, problem that exacerbated by the non-uniform distribution features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow sets pool possible items while controlling for multiple covariates; however,...
Abstract Motivation 3D chromatin structure plays an important role in regulating gene expression and alterations to this can result developmental abnormalities disease. While genomic approaches like Hi-C Micro-C provide valuable insights architecture, the resulting datasets are extremely large difficult manipulate. Results Here, we present mariner, a rapid memory efficient tool extract, aggregate, plot data from matrices within R/Bioconductor environment. Mariner simplifies process of...
Abstract Megabase-scale intervals of active, gene-rich and inactive, gene-poor chromatin are known to segregate, forming the A B compartments. Fine mapping contents these compartments has been hitherto impossible, owing extraordinary sequencing depths required distinguish between long-range contact patterns individual loci, computational complexity associated calculations. Here, we generate largest published in situ Hi-C map date, spanning 33 billion contacts. We also develop a method,...
Abstract Motivation Enrichment analysis is a widely utilized technique in genomic that aims to determine if there statistically significant association between two sets of features. To conduct this type hypothesis testing, an appropriate null model typically required. However, the distribution commonly used can be overly simplistic and may result inaccurate conclusions. Results bootRanges provides fast functions for generation block bootstrapped ranges representing enrichment analysis. As...
Abstract Summary Exclusion regions are sections of reference genomes with abnormal pileups short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE Github. However, the variety sets creates uncertainty which to use. Furthermore, gap (e.g. centromeres, telomeres, arms) create additional considerations generating sets....
Implantation is a complex event demanding contributions from both embryo and endometrium. Despite advances in assisted reproduction, endometrial receptivity defects persist as barrier to successful implantation women with infertility. We previously demonstrated that maternal haploinsufficiency for the endocrine peptide adrenomedullin (AM) mice confers subfertility phenotype characterized by defective uterine sparse epithelial pinopode coverage. The strong link between AM suggested compelling...
The sequencing of the human genome and subsequent advances in DNA technology have created a need for computational tools to analyze manipulate genomic data sets.The bedtools software suite R programming language emerged as indispensable this purpose but lacked integration.Here we describe bedtoolsr, an package that provides simple intuitive access all functions from within environment.We provide several usability enhancements, support compatibility with past future versions bedtools, include...
Abstract Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome’s 3D structure and function. The diversity motifs has led to a fragmented landscape data. We collected position weight matrices defined strand-oriented sites in human mouse genomes, including recent Telomere mm39 assemblies. included selected experimentally determined predicted sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. recommend...
During mouse embryogenesis, expression of the long non-coding RNA (lncRNA) Airn leads to gene repression and recruitment Polycomb repressive complexes (PRCs) varying extents over a 15-Mb domain. The mechanisms remain unclear. Using high-resolution approaches, we show in trophoblast stem cells that induces long-range changes chromatin architecture coincide with PRC-directed modifications center around CpG island promoters contact locus even absence expression. Intensity between lncRNA...
ABSTRACT Investigating the relationship, particularly lead–lag effect, between time series is a common question across various disciplines, especially when uncovering biological processes. However, analyzing presents several challenges. Firstly, due to technical reasons, points at which observations are made not uniform intervals. Secondly, some effects transient, necessitating time-lag estimation based on limited number of points. Thirdly, external factors also impact these series,...
Abstract “Pod‐based” e‐cigarettes such as JUUL are currently the most prevalent electronic nicotine delivery systems (ENDS) in United States. JUUL‐type ENDS utilize salts protonated with benzoic acid rather than freebase nicotine. However, limited information is available on cellular effects of these products. Cytoplasmic Ca 2+ a universal second messenger that controls many functions including cell growth and death. Of note, dysregulation homeostasis has been linked several disease...
Background High tumor-infiltrating lymphocytes (TILs) and hemorrhage are important prognostic factors in patients who have undergone craniotomy for melanoma brain metastases (MBM) before 2011 at the University of Pittsburgh Medical Center (UPMC). We investigated or predictive role these histopathologic a more contemporary cohort from North Carolina Chapel Hill (UNC-CH). also sought to understand better how various immune cell subsets, angiogenic factors, blood vessels may be associated with...
In the past 5 years, e-cigarette use has been increasing rapidly, particularly in youth and young adults. Due to novelty of e-cigarettes (e-cigs) liquids (e-liquids), research on their chemo-physical properties is still its infancy. Here, we describe a previously unknown potentially useful property e-liquids, namely autofluorescence. We performed an emission scan at 9 excitation wavelengths common fluorescent microscopy found (i) that autofluorescence differs widely between (ii) e-liquids...
Abstract Genome-wide association studies have identified over 100 loci associated with osteoarthritis risk, but the majority of risk variants are noncoding, making it difficult to identify impacted genes for further study and therapeutic development. To address this need, we used a multiomic approach genome editing functionally characterize potential genes. Computational analysis genome-wide ChIP-seq data revealed that chondrocyte regulatory enriched variants. We constructed...
Abstract Introduction Alveolar macrophages (AMs) are lung-resident immune cells that phagocytose inhaled particles and pathogens, help coordinate the lung’s response to infection. Little is known about impact of chronic e-cigarette use (ie, vaping) on this important pulmonary cell type. Thus, we determined effect vaping AM phenotype gene expression. Aims Methods We recruited never-smokers, smokers, users (vapers) performed research bronchoscopies isolate AMs from bronchoalveolar lavage fluid...