A5102842945- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Glycosylation and Glycoproteins Research
- Gene expression and cancer classification
- Cancer, Hypoxia, and Metabolism
- Bioinformatics and Genomic Networks
- CO2 Reduction Techniques and Catalysts
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Immunotherapy and Immune Responses
- Advanced Thermoelectric Materials and Devices
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Liver Disease Diagnosis and Treatment
- Advanced Proteomics Techniques and Applications
- Ionic liquids properties and applications
- Immune Cell Function and Interaction
- Circular RNAs in diseases
- Chromosomal and Genetic Variations
- Extracellular vesicles in disease
- Electrocatalysts for Energy Conversion
Virginia Commonwealth University
2021-2025
Virginia Cancer Institute
2021-2025
Cancer Research And Biostatistics
2023-2025
University Health System
2024
VCU Massey Comprehensive Cancer Center
2021-2024
Yanbian University
2024
Children's Hospital of Richmond at VCU
2022-2024
University of Richmond
2023
Jilin Agricultural University
2022-2023
Zhejiang University
2023
Circular RNAs composed of exonic sequence have been described in a small number genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe endogenous RNAs, we performed high-throughput sequencing (RNA-seq) libraries prepared ribosome-depleted with or without digestion exonuclease, RNase R. We identified >25,000 distinct human fibroblasts that contained non-colinear exons (a “backsplice”) and were reproducibly enriched by...
The accurate mapping of reads that span splice junctions is a critical component all analytic techniques work with RNA-seq data. We introduce second generation detection algorithm, MapSplice, whose focus high sensitivity and specificity in the splices as well CPU memory efficiency. MapSplice can be applied to both short (<75 bp) long (≥75 bp). not dependent on site features or intron length, consequently it detect novel canonical non-canonical splices. leverages quality diversity read...
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive bioprotective alkaloids. grass in the epichloae clade (Epichloë Neotyphodium species), which are extraordinarily diverse both their host interactions alkaloid profiles. Epichloae alkaloids of four distinct classes, all deter insects, some—including infamous ergot alkaloids—have potent effects on mammals. exceptional chemotypic diversity may relate to broad range interactions, whereby...
Significance A significant proportion of head and neck cancer is driven by human papillomavirus (HPV) infection, the expression viral oncogenes involved in development these tumors. However, role HPV integration primary tumors beyond increasing oncoproteins not understood. Here, we describe how impacts host genome amplification disruption tumor suppressors as well driving inter- intrachromosomal rearrangements. Tumors that do have integrants display distinct gene profiles DNA methylation...
Abstract The electrochemical reduction of carbon dioxide (CO 2 ) to high‐value liquid fuel with high selectivity is appealing for energy conversion and storage. Here we report a bismuth phosphate (BiPO 4 derived 2D nanosheet‐like electrocatalyst that efficiently converts CO into liquid‐phase formate. catalyst presents formate Faradaic efficiency over 90 % cathodic 73 at an industrially relevant current density 200 mA cm −2 in the flow cell. situ generation Bi‐O active species on surface was...
The RNA transcriptome varies in response to cellular differentiation as well environmental factors, and can be characterized by the diversity abundance of transcript isoforms. Differential transcription analysis, detection differences between transcriptomes different cells, may improve understanding cell development enable identification biomarkers that classify disease types. availability high-throughput short-read sequencing technologies provides in-depth sampling transcriptome, making it...
Pt-based cocatalysts with positive valence states achieve efficient photocatalytic water splitting.
Abstract Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application high-dimensionality reduction/spatial clustering and histopathological annotation matrix datasets to assess tissue metabolic heterogeneity in human lung diseases. Using features identified from this pipeline, hypothesize that channeling between glycogen N-linked...
Periodontitis affects billions of people worldwide. To address relationships periodontal niche cell types and microbes in periodontitis, we generated an integrated single-cell RNA sequencing (scRNAseq) atlas human periodontium (34-sample, 105918-cell), including sulcular junctional keratinocytes (SK/JKs). SK/JKs displayed altered differentiation states were enriched for effector cytokines periodontitis. Single-cell metagenomics revealed 37 bacterial species with cell-specific tropism....
Activating cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) holds great potential for cancer immunotherapy by eliciting type-I (IFN-I) responses. Yet, current approaches to cGAS-STING activation rely on STING agonists, which suffer from difficult formulation, poor pharmacokinetics, and marginal clinical therapeutic efficacy. Here, we report nature-inspired oligonucleotide, Svg3, as a cGAS agonist in tumor combination immunotherapy. The hairpin-shaped Svg3 strongly binds...
Background and Aims: The disease progression of nonalcoholic fatty liver (NAFLD) from simple steatosis (NAFL) to steatohepatitis (NASH) is driven by multiple factors. Berberine (BBR) an ancient Chinese medicine has various beneficial effects on metabolic diseases, including NAFLD/NASH. However, the underlying mechanisms remain incompletely understood due limitation NASH animal models used. Methods: A high-fat high-fructose diet-induced mouse model NAFLD, best available preclinical model, was...
Significance Alu elements, comprising more than 10% of the human genome, propagate via retrotransposition. This genomic expansion requires enzymatic activity L1 that reverse transcribes RNA into cDNA in nucleus. We report also undergoes L1-mediated transcription self-priming cytoplasm independent retrotransposition, providing evidence DNA synthesis this cellular compartment. newly discovered shunt molecule replication cycle induces death retinal pigmented epithelium, a hallmark atrophic...
Copper (Cu), as the most important and efficient catalyst, has been widely studied for electrochemically reducing carbon dioxide (CO 2 ) into multi-carbon (C 2+ products.
Copper (Cu)-based metal-organic frameworks (MOFs) and MOF-derived catalysts are well studied for electroreduction of carbon dioxide (CO2 ); however, the effects organic linkers selectivity CO2 reduction still unrevealed. Here, a series Cu-based is investigated with different appended, named X-Cu-BDC (BDC = 1,4-benzenedicarboxylic acid, X NH2 , OH, H, F, 2F). It found that affect faradaic efficiency (FE) C2 products an order < OH bare Cu-BDC F 2F, thus tuning FEC2 :FEC1 ratios from 0.6...
Abstract Two important factors that contribute to resistance immune checkpoint inhibitors (ICI) are an immune-suppressive microenvironment and limited antigen presentation by tumor cells. In this study, we examine whether inhibition of the methyltransferase enhancer zeste 2 (EZH2) can increase ICI response in lung squamous cell carcinomas (LSCC). Our vitro experiments using two-dimensional human cancer lines as well three-dimensional murine patient-derived organoids treated with two EZH2...
Abstract The neurobiological origins of social behaviors are incompletely understood. Here we utilized synthetic biology approaches to reprogram the function ZFP189, a transcription factor whose expression and in rodent prefrontal cortex was previously demonstrated be protective against stress-induced deficits. We created novel ZFP189 factors including VPR , which activates target genes therefore exerts opposite functional control from endogenous, transcriptionally repressive WT . Following...
Histones serve as a major carrier of epigenetic information in the form post-translational modifications which are vital for controlling gene expression, maintaining cell identity, and ensuring proper cellular function. Loss histones aging genome can drastically impact landscape leading to altered chromatin structure changes expression profiles. In this study, we investigated age-related on histone levels acetylation retinal pigment epithelium (RPE) retina mice. We observed global reduction...
Dysregulated metabolism of bioactive sphingolipids, including ceramides and sphingosine-1-phosphate, has been implicated in cardiovascular disease, although the specific species, disease contexts, cellular roles are not completely understood. Sphingolipids produced by serine palmitoyltransferase enzyme, canonically composed 2 subunits, SPTLC1 (serine long chain base subunit 1) SPTLC2 2). Noncanonical sphingolipids a more recently described subunit, SPTLC3 3).
Abstract Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts and plays an important role in tissue-specific differentiation, can be misregulated disease. To understand these processes, there is a great need for methods to detect differential transcription between samples. Our focus on samples observed using short-read sequencing (RNA-seq). Methods: We characterize two as difference relative abundance transcript isoforms present The magnitude gene...
Identifying variants using high-throughput sequencing data is currently a challenge because true biological can be indistinguishable from technical artifacts. One source of artifact results incorrectly aligning experimentally observed sequences to their genomic origin (‘mismapping’) and inferring differences in mismapped variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq DNA whole exome derived the reference genome, aligns these by custom parameters,...
We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min 19.1 GB memory conduct a global survey 11,658 fusion events 10,113 TCGA Pan-Cancer datasets. The recovers 92.7% tier-1 fusions curated by Fusion Gene Database reveals 270 novel occurrences, all which are as tumor-specific. By providing reference-free, alignment-free, parameter-free search system, will...