A5006169289- Cytomegalovirus and herpesvirus research
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Multiple Myeloma Research and Treatments
- Mycobacterium research and diagnosis
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Plant Pathogenic Bacteria Studies
- Housing Market and Economics
- Plant and Fungal Interactions Research
- Electrochemical sensors and biosensors
- Healthcare Policy and Management
- MicroRNA in disease regulation
- Fungal and yeast genetics research
- American Sports and Literature
- HIV Research and Treatment
- Silk-based biomaterials and applications
- Healthcare cost, quality, practices
- Glycosylation and Glycoproteins Research
- Genetic Neurodegenerative Diseases
University of Iowa
2022
Q2 Solutions (United States)
2016-2020
IQVIA (United States)
2013-2017
Duke University
2013
Duke University Hospital
2013
Duke Medical Center
2013
North Carolina State University
2008
University of Mississippi Medical Center
1993
State Street (United States)
1993
The question of how HIV-1 interfaces with cellular microRNA (miRNA) biogenesis and effector mechanisms has been highly controversial. Here, we first used deep sequencing small RNAs present in two different infected cell lines (TZM-bl C8166) types primary human cells (CD4(+) peripheral blood mononuclear [PBMCs] macrophages) to unequivocally demonstrate that does not encode any viral miRNAs. Perhaps surprisingly, also observed infection T by only a modest effect on the expression miRNAs at...
Abstract The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine effects of formalin fixation and delay (DTF) on analysis nucleic acids. By performing whole transcriptome sequencing small RNA profiling matched snap-frozen FFPE specimens exposed different delays fixation, this aimed acceptable proper workflow for accurate reliable Next-Generation Sequencing (NGS) specimens. In comparison snap-freezing, changed relative proportions...
The human leukocyte antigen (HLA) system is a genomic region involved in regulating the immune by encoding cell membrane major histocompatibility complex (MHC) proteins that are responsible for self-recognition. Understanding variation this provides important insights into autoimmune disorders, disease susceptibility, oncological immunotherapy, regenerative medicine, transplant rejection, and toxicogenomics. Traditional approaches to HLA typing low throughput, target only few genes, labor...
The cell-to-cell movement of Turnip crinkle virus (TCV) in Nicotiana benthamiana requires the presence its coat protein (CP), a known suppressor RNA silencing. transcripts TCV construct containing reporter gene (green fluorescent protein) (TCV-sGFP) place CP open reading frame generated foci three to five cells. delivered trans by Agrobacterium tumefaciens infiltration potentiated TCV-sGFP and increased diameter, on average, factor four. Deletion proteins (construct TCVDelta92-sGFP)...
With the price of next generation sequencing steadily decreasing, bacterial genome assembly is now accessible to a wide range researchers. It therefore necessary understand best methods for generating assembly, specifically, which combination and bioinformatics strategies result in most accurate assemblies. Here, we sequence three E. coli strains on Illumina MiSeq, Life Technologies Ion Torrent PGM, Pacific Biosciences RS. We then perform assemblies all datasets alone or determine...
Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical logistical issues, however, make it challenging to accurately detect abnormal in a cost-effective manner clinical studies.Here we present CNV Radar, software tool that utilizes next-generation sequencing read depth variant allele frequency patterns, infer the true status of genes genomic regions from whole exome data. Evaluation...
Novel treatments for Huntington's disease (HD), a progressive neurodegenerative disorder, include selective targeting of the mutant allele huntingtin gene (mHTT) carrying abnormally expanded disease-causing cytosine-adenine-guanine (CAG) repeat. WVE-120101 and WVE-120102 are investigational stereopure antisense oligonucleotides that enable suppression mHTT by single-nucleotide polymorphisms (SNPs) in haplotype phase with CAG repeat expansion. Recently developed long-read sequencing...
Abstract Genomic structural variation and associated RNA fusions are a common clinical feature known to be involved in the initiation pathogenesis of cancer. This complex class variants also has significant implications on therapeutic decisions emerging roles evidence-based applications. Consequently, fusion detection is an aspect precision medicine that enables utility as therapeutically-relevant target which includes small molecules, biologics, neoantigen-directed approaches.Here we...
Abstract Recent advances in library preparation methodology from limiting amounts of total RNA have facilitated the characterization rare cell-types various biological systems. The SMART-Seq v4 Ultra Low Input Kit incorporates a number workflow improvements, including fewer purifications to increase yield, locked nucleic acid (LNA) template-switching oligo enhance stability, and an improved polymerase designed reduce amplification bias GC-rich regions. Certain challenges remain however,...
Abstract The excitement surrounding immunotherapy is being driven by results in the clinic. Currently, autoimmunity an unfortunate side-effect for a large fraction of those treated. Consequently, understanding how self-antigens are recognized nearly as important characterizing immune repertoire efficacious delivery these promising new therapies. One approach to measuring tumor environment with RNA-Seq assays. Here we show that genes responsible presenting (HLA Class I and II) can also be...
Table S1. Counts for each population of real samples used in the current study. S2. Number alleles available and type simulated data set. S8. Novel identified by TruSight HLA 33 HapMap having discordances between Sanger sequencing RNA sequencing. S9. Accuracy KIR genotyping at two-field precision. Figure Representative taxonomy. Run times calling software. S3. HLAProfiler low number reads. S4. Sequencing read count accuracy. (PDF 584 kb)
Abstract RNA-sequencing (RNA-seq) is an effective tool for gene expression analysis, promising to be a diagnostic patient stratification and individualized therapy. However, it has been challenging apply RNA-seq low-quantity degraded RNA derived from formalin fixed paraffin embedded clinical samples. The Illumina TruSeq® Access approach, utilizing capture probes targeting known exons enrich coding RNAs, shown high performance profile poor quality samples at input amounts or above 20 ng....