A5037708512- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Glioma Diagnosis and Treatment
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Immunotherapy and Immune Responses
- DNA Repair Mechanisms
- Cancer Genomics and Diagnostics
- Extracellular vesicles in disease
- DNA and Nucleic Acid Chemistry
- RNA regulation and disease
- MicroRNA in disease regulation
- Gene expression and cancer classification
- Viral Infections and Vectors
- Mosquito-borne diseases and control
- CRISPR and Genetic Engineering
- Endoplasmic Reticulum Stress and Disease
- Genomics and Phylogenetic Studies
- interferon and immune responses
- Evolutionary Algorithms and Applications
University of Colorado Anschutz Medical Campus
2013-2025
University of Colorado Denver
2016-2025
Molecular Biology Consortium
2020
The Medical Center of Aurora
2020
Georgia Institute of Technology
2015
University of Colorado Boulder
2015
University of Washington
2005-2010
Seattle University
2005-2006
The University of Texas at Austin
1999-2003
Rogers (United States)
1998
Human β-defensins (HBDs) are antimicrobial peptides that may play a role in mucosal defense. Diminished activity of these has been implicated the pathogenesis cystic fibrosis (CF) lung disease. We show HBD-1 and HBD-2 mRNAs expressed excised surface submucosal gland epithelia from non-CF CF patients. The pro-inflammatory cytokine interleukin-1β stimulated expression but not mRNA peptide primary cultures airway epithelia. was found bronchoalveolar lavage (BAL) fluid normal volunteers,...
Many lung diseases result from a failure of efficient regeneration damaged alveolar epithelial cells (AECs) after injury. During regeneration, AEC2s proliferate to replace lost cells, which proliferation halts and some transdifferentiate into AEC1s restore normal structure function. Although the mechanisms underlying AEC2 have been studied, responsible for halting inducing transdifferentiation are poorly understood. To identify candidate signaling pathways transdifferentiation, we performed...
<ns4:p>Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited reference often have rigid structure requirements. We developed the clustifyr R package to leverage several external types, including gene expression profiles assign likely using scRNA-seq, bulk RNA-seq, microarray data, or signature lists. benchmark various parameters correlation-based approach implement list...
During development in the thymus, invariant natural killer T (iNKT) cells commit to one of three major functionally different subsets, iNKT1, iNKT2, and iNKT17. Here, we show that cell antigen receptor (TCR) signal strength governs iNKT with strong signaling promoting iNKT2 iNKT17 development. Altering TCR diversity or diminishes subset a cell-intrinsic manner. Decreased affects persistence Egr2 expression upregulation PLZF. By genome-wide comparison chromatin accessibility, identify...
Abstract Background Medulloblastoma (MB) is a heterogeneous disease in which neoplastic cells and associated immune contribute to progression. We aimed determine the influence of cell diversity on MB biology patient samples animal models. Methods To better characterize cellular heterogeneity we used single-cell RNA sequencing, immunohistochemistry, deconvolution transcriptomic data profile populations models across childhood subgroups. Results Neoplastic cluster primarily according...
Abstract Transfer RNAs are the fundamental adapter molecules of protein synthesis and most abundant heterogeneous class noncoding RNA in cells. The study tRNA repertoires remains challenging, complicated by presence dozens post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both detection modifications; however, such studies have been limited throughput accuracy direct methods. Moreover, complete set modifications nanopore challenging. Here we...
Reagents for proteome research must of necessity be generated by high throughput methods. Apta mers are potentially useful as reagents to identify and quantitate individual proteins, yet currently produced the most part manual selection procedures. We have developed automated methods, but still individually purify protein targets. Therefore, we attempted select aptamers against targets in vitro transcription translation genes. In order specifically immobilize selection, they also...
The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions local content genomic DNA. combined vitro nucleobase excision with massively parallel sequencing (Excision-seq) to determine the locations applied Excision-seq method map uracil E. coli budding yeast discovered significant variation content, wherein is excluded from earliest latest replicating regions genome, possibly driven by changes nucleotide...
Abstract Regulation of hematopoietic stem cell proliferation, lineage commitment, and differentiation in adult vertebrates requires extrinsic signals provided by cells the marrow microenvironment (ME) located within bone marrow. Both secreted cell-surface bound factors critical to this regulation have been identified, yet control their expression ME has not addressed. Herein we hypothesize that microRNAs (miRNAs) contribute controlled expression. MiRNAs are small noncoding RNAs bind target...
<ns4:p>New tools for reproducible exploratory data analysis of large datasets are important to address the rising size and complexity genomic data. We developed valr R package enable flexible efficient interval analysis. leverages new available in ”tidyverse”, including dplyr. Benchmarks show it performs similar BEDtools can be used interactive analyses incorporated into existing pipelines.</ns4:p>
Liver lymphatic vessels support liver function by draining interstitial fluid, cholesterol, fat, and immune cells for surveillance in the lymph node. Chronic disease is associated with increased inflammation cell infiltrate. However, it currently unknown if or how respond to infiltrate during chronic disease. Here we demonstrate that vessel abundance increases patients areas of fibrosis infiltration. Using single-cell mRNA sequencing multi-spectral immunofluorescence analysis identified...
Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited reference often have rigid structure requirements. We developed the clustifyr R package to leverage several external types, including gene expression profiles assign likely using scRNA-seq, bulk RNA-seq, microarray data, or signature lists. benchmark various parameters correlation-based approach implement list...
ABSTRACT Influenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts replication; however, the RNAs targeted for cleavage under conditions have not been defined. In this study, we used deep-sequencing methods identify sites within host from PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of allowed us distinguish between L-dependent L-independent...
The cytotoxin ricin disables translation by depurinating a conserved site in eukaryotic rRNA. In vitroselection has been used to generate RNA ligands (aptamers) specific for the catalytic A-chain (RTA). anti-RTA aptamers bear no resemblance normal RTA substrate, sarcin-ricin loop (SRL), and were not depurinated RTA. An initial 80-nucleotide ligand was minimized 31-nucleotide aptamer that contained all sequences structures necessary interacting with This minimal formed high affinity complexes...