A5067945000- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- Neuroblastoma Research and Treatments
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Cancer Immunotherapy and Biomarkers
- Genomics and Phylogenetic Studies
- Ubiquitin and proteasome pathways
- Ferroptosis and cancer prognosis
- Glioma Diagnosis and Treatment
- CAR-T cell therapy research
- Lung Cancer Treatments and Mutations
- Immunotherapy and Immune Responses
- MicroRNA in disease regulation
- vaccines and immunoinformatics approaches
- Sarcoma Diagnosis and Treatment
- Immune Cell Function and Interaction
- Cancer, Lipids, and Metabolism
- Cancer therapeutics and mechanisms
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Advanced Biosensing Techniques and Applications
- Circular RNAs in diseases
- Viral Infections and Vectors
AbbVie (United States)
2022-2025
University of California, Santa Cruz
2016-2022
University of California System
2019
Genomics (United Kingdom)
2019
Santa Cruz County Office of Education
2017
Denison University
2015-2017
University of California, San Francisco
2015-2017
American Red Cross
2015
Global Viral
2015
Abbott (United States)
2015
Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving diagnosis relapsed disease, limited therapeutic options. To systematically prioritize rationally test novel agents in preclinical murine models, researchers the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)—many which refractory to current...
Abstract The tumor microenvironment (TME) is complex and significantly influences how patients respond to immunotherapy. Despite decades of research generating numerous gene signatures describe the TME, there no consensus on best way capture meaningful variation, as commonly used are heavily T cell-biased with high degrees collinearity. To better understand TME dynamics represent them consistently interpretably, we developed a framework for immunophenotyping using disparate immuno-oncology...
Predictive biomarkers of immune checkpoint inhibitor (ICI) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from Anti-PD-1 Response Prediction DREAM Challenge, a crowdsourced initiative that enabled assessment predictive models by using data two randomized controlled clinical trials (RCTs) ICIs in first-line metastatic NSCLC.
<h3>Importance</h3> Pediatric cancers are epigenetic diseases; therefore, considering tumor gene expression information is necessary for a complete understanding of the tumorigenic processes. <h3>Objective</h3> To evaluate feasibility and utility incorporating comparative into precision medicine framework difficult-to-treat pediatric young adult patients with cancer. <h3>Design, Setting, Participants</h3> This cohort study was conducted as consortium between University California, Santa Cruz...
Abstract A newly developed transcription-mediated amplification assay was used to detect chikungunya virus infection in 3 of 557 asymptomatic donors (0.54%) from Puerto Rico during the 2014–2015 Caribbean epidemic. Viral detection confirmed by using PCR, microarray, and next-generation sequencing. Molecular clock analysis dated emergence strains early 2013.
Although increasingly recognized as critical to genomic research, data sharing is hindered by an absence of standards regarding timing, patient privacy, use agreement standards, and characterization quality. Only after months identifying, permissioning for use, committing terms restricting sharing, downloading, assessing quality, it possible know whether or not a dataset can be used. In this paper, we evaluate the barriers based on Treehouse experience offer recommendations metadata...
ABSTRACT Toil is portable, open-source workflow software that supports contemporary definition languages and can be used to securely reproducibly run scientific workflows efficiently at large-scale. To demonstrate Toil, we processed over 20,000 RNA-seq samples create a consistent meta-analysis of five datasets free computational batch effects make freely available. Nearly all the were analysed in under four days using commercial cloud cluster 32,000 preemptable cores.
Chronic fatigue syndrome (CFS) remains poorly understood. Although infections are speculated to trigger the syndrome, a specific infectious agent and underlying pathophysiological mechanism remain elusive. In previous study, we described similar clinical phenotypes in CFS patients alternatively diagnosed chronic Lyme (ADCLS) patients—individuals with disease by testing from private specialty laboratories but who test negative reference 2-tiered serologic analysis.
Somatic mutations in cancers affecting protein coding genes can give rise to potentially therapeutic neoepitopes. These neoepitopes guide Adoptive Cell Therapies and Peptide- RNA-based Neoepitope Vaccines selectively target tumor cells using autologous patient cytotoxic T-cells. Currently, researchers have independently align their data, call somatic haplotype the patient's HLA use existing neoepitope prediction tools. We present ProTECT, a fully automated, reproducible, scalable, efficient...
Abstract Background Diffuse midline gliomas with histone H3 K27M (H3K27M) mutations occur in early childhood and are marked by an invasive phenotype global decrease H3K27me3, epigenetic mark that regulates differentiation development. H3K27M mutation timing effect on embryonic brain development not fully characterized. Results We analyzed multiple publicly available RNA sequencing datasets to identify differentially expressed genes between non-K27M pediatric gliomas. found involved the...
Accelerating cures for children with cancer remains an immediate challenge due to extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving diagnosis relapsed disease, limited therapeutic options. To systematically prioritize rationally test novel agents in preclinical murine models, researchers the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs) from high-risk childhood cancers, many...
Abstract Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and identify biomarkers of response therapeutic agents. Advances in genomic sequencing made possible large-scale characterizations collections primary tumors, such as the Cell Line Encyclopedia (CCLE) The Genome Atlas (TCGA). These studies allow first time a comprehensive evaluation comparability tumors on proteomic level. Here we employ bulk mRNA micro-RNA data from...
Gliomatosis peritonei is a rare pathologic finding that associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of gliomatosis as mature glial implant can impart an improved prognosis to patients immature teratoma, making prompt accurate diagnosis important. We describe case recurrent teratoma in 10-yr-old female patient, which comparative analysis the RNA sequencing gene expression data from patient's tumor was used effectively aid peritonei.
Histone post-translational modifications play vital roles in a variety of nuclear processes, including DNA repair. It has been previously shown that histone H3K79 methylation is important for the cellular response to damage caused by ultraviolet (UV) radiation, with evidence specific states distinct UV Here, we report reduced exposure Saccharomyces cerevisiae This reduction dimethylated state, as trimethylation levels are minimally altered exposure. Inhibition this deleterious effect on...
Abstract Purpose Predictive biomarkers of immune checkpoint inhibitors (ICIs) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from Anti–PD-1 Response Prediction DREAM Challenge, a crowdsourced initiative that enabled assessment predictive models by using data two randomized controlled clinical trials (RCTs) ICIs in first-line metastatic NSCLC. Methods Participants developed and trained public resources. These were evaluated with CheckMate...
Summary Accelerating cures for children with cancer remains an immediate challenge due to extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving diagnosis relapsed disease, limited therapeutic options. To systematically prioritize rationally test novel agents in preclinical murine models, researchers the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs) from high-risk childhood cancers,...
The reproducibility of gene expression measured by RNA sequencing (RNA-Seq) is dependent on the depth. While unmapped or non-exonic reads do not contribute to quantification, duplicate quantification but are informative for reproducibility. We show that mapped, exonic, non-duplicate (MEND) a useful measure RNA-Seq datasets used analysis.
Abstract Machine learning algorithms identify patterns that would otherwise be difficult to observe in high-dimensional molecular and clinical data. For this reason, machine has the potential have a profound impact on decision making drug target discovery. Nevertheless, there remain considerable technical challenges adapting these tools for use. These include feature engineering, model selection, defining optimal strategies training. cancer care, RNA sequencing of patient tumor biopsies...
Abstract Gene expression analysis of single samples shows increasing promise for clinical applications. However, obtaining high quality RNA from a human tumor sample can be challenging because medical, surgical, and pathological requirements often lead to sparse or degraded RNA. The variability in presents challenges defining input requirements, which are required calculate sensitivity, specificity reference ranges as Clinical Laboratory Improvement Amendments (CLIA)-approved test. RNA-Seq...
10559 Background: One of the hallmarks neuroblastoma is molecular heterogeneity, which leads to spontaneous remission in some patients and aggressive, resistant disease others. Patients with low or intermediate risk have a high 5-year survival rate (90-95%), but high-risk 40% despite receiving intensity therapies. Methods: Genome-wide transcriptome profiling can be used stratify identify opportunities for molecularly targeted We developed gene expression analysis identifying subtypes large...
Abstract Somatic mutations in cancers affecting protein coding genes can give rise to potentially therapeutic neoepitopes. These neoepitopes guide Adoptive Cell Therapies (ACTs) and Peptide Vaccines (PVs) selectively target tumor cells using autologous patient cytotoxic T-cells. Currently, researchers have independently align their data, call somatic haplotype the patient’s HLA use existing neoepitope prediction tools. We present ProTECT, a fully automated, reproducible, scalable, efficient...
Precision oncology has primarily relied on coding mutations as biomarkers of response to therapies. While transcriptome analysis can provide valuable information, incorporation into workflows been difficult. For example, the relative rather than absolute gene expression level needs be considered, requiring differential across samples. However, programs related cell-of-origin and tumor microenvironment effects confound search for cancer-specific changes. To address these challenges, we...