A5068851971- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Blood properties and coagulation
- Mosquito-borne diseases and control
- Viral Infections and Vectors
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Circular RNAs in diseases
- Cell Adhesion Molecules Research
- Diabetes Management and Research
- MicroRNA in disease regulation
- CAR-T cell therapy research
- Cancer Genomics and Diagnostics
- Monoclonal and Polyclonal Antibodies Research
- Glycosylation and Glycoproteins Research
- Malaria Research and Control
- Protease and Inhibitor Mechanisms
- Platelet Disorders and Treatments
- Venous Thromboembolism Diagnosis and Management
- Insect symbiosis and bacterial influences
- Genetic Mapping and Diversity in Plants and Animals
- Hepatitis C virus research
- Antiplatelet Therapy and Cardiovascular Diseases
- Coronary Interventions and Diagnostics
Children's Hospital of Philadelphia
2019-2024
Integral Molecular (United States)
2020-2022
University of Pennsylvania
2005-2011
Abstract Circular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, inherent limitation short-read RNA-seq that it does not experimentally determine the full-length sequences and exact exonic compositions Here, we report isoCirc, for circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe integrated computational pipeline...
Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read platforms poses a major challenge. We present ESPRESSO, computational tool robust discovery quantification isoforms from error-prone long reads. ESPRESSO jointly considers alignments all reads aligned to gene uses profiles individual improve identification splice junctions their corresponding isoforms....
Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely unexplored repertoire of novel immunotherapy targets. We describe
Abstract Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read platforms limits transcript coverage. One strategy overcoming this bottleneck targeted RNA-seq preselected gene panels. We present TEQUILA-seq, versatile, easy-to-implement, and low-cost method utilizing isothermally linear-amplified capture probes. When performed on Oxford nanopore platform with multiple panels varying sizes, TEQUILA-seq...
Summary Diabetic subjects have been shown to altered fibrin network structures. One proposed mechanism for this is non-enzymatic glycation of fibrinogen due high blood glucose. We investigated whether glycaemic control would result in structures decreased glycation. Twenty uncontrolled type 2 diabetic were treated with insulin order achieve control. age- and body mass index (BMI)-matched non-diabetic included as a reference group. Purified fibrinogen, isolated from plasma samples was used...
A major question in human genetics is how sequence variants of broadly expressed genes produce tissue- and cell type-specific molecular phenotypes. Genetic variation alternative splicing a prevalent source transcriptomic proteomic diversity populations. We investigated quantitative trait loci (sQTLs) 1,209 samples from 13 brain regions, using RNA sequencing (RNA-seq) genotype data the Genotype-Tissue Expression (GTEx) project. Hundreds sQTLs were identified each region. Some shared across...
The E1 and E2 envelope proteins of hepatitis C virus (HCV) form a heterodimer that drives virus-host membrane fusion. Here, we analyze the role each amino acid in E1E2 function, expressing 545 individual alanine mutants human cells, incorporating them into infectious viral pseudoparticles, testing against 37 different monoclonal antibodies (MAbs) to ascertain full-length translation, folding, assembly, CD81 binding, pseudoparticle incorporation, infectivity. We propose model describing...
The development of vaccines against flaviviruses, including Zika virus (ZIKV) and dengue (DENV), continues to be a major challenge, hindered by the lack efficient reliable methods for screening neutralizing activity sera or antibodies. To address this need, we previously developed plasmid-based, replication-incompetent DENV reporter particle (RVP) production system as an safe alternative Plaque Reduction Neutralization Test (PRNT). As part response 2015–2016 ZIKV outbreak, pseudo-infectious...
Abstract Aberrant alternative splicing (AS) is widespread in cancer, leading to an extensive but largely unexploited repertoire of potential immunotherapy targets. Here we describe IRIS, a computational platform leveraging large-scale cancer and normal transcriptomics data discover AS-derived tumor antigens for T-cell receptor (TCR) chimeric antigen (CAR-T) therapies. Applying IRIS RNA-Seq from 22 glioblastomas resected patients, identified candidate epitopes validated their recognition by...
ABSTRACT The development of vaccines against flaviviruses, including Zika virus (ZIKV) and dengue (DENV), continues to be a major challenge, hindered by the lack efficient reliable methods for screening neutralizing activity sera or antibodies. To address this need, we previously developed plasmid-based, replication-incompetent DENV reporter particle (RVP) production system as an safe alternative Plaque Reduction Neutralization Test (PRNT). As part response 2015-2016 ZIKV outbreak, recently...