A5006289887- Cancer Immunotherapy and Biomarkers
- Single-cell and spatial transcriptomics
- CAR-T cell therapy research
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- Immunotherapy and Immune Responses
- Olfactory and Sensory Function Studies
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Microtubule and mitosis dynamics
- Renal cell carcinoma treatment
- RNA modifications and cancer
- Immune cells in cancer
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Extracellular vesicles in disease
- Cytomegalovirus and herpesvirus research
- Health, Environment, Cognitive Aging
- Health disparities and outcomes
- Data Analysis with R
- Cancer-related molecular mechanisms research
- Biochemical Analysis and Sensing Techniques
- Advanced Chemical Sensor Technologies
University of Southern California
2023-2025
Keck Hospital of USC
2023-2024
Southern California University for Professional Studies
2023
Dana-Farber Cancer Institute
2019-2022
Harvard University
2020-2022
University of California, Berkeley
2015-2018
Berkeley Public Health Division
2017
Center for Environmental Health
2016
Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied stem cells and their descendants in order chart the progression from multipotent progenitors fully differentiated While a variety statistical computational methods have been proposed for inferring cell lineages, problem accurately characterizing multiple branching lineages remains difficult solve.We introduce Slingshot, novel method pseudotimes single-cell gene...
Abstract: Altered olfactory function is a common symptom of COVID-19, but its etiology unknown. A key question whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 affects olfaction directly, by infecting sensory neurons or their targets bulb, indirectly, through perturbation supporting cells. Here we identify cell types epithelium and bulb that express entry molecules. Bulk sequencing demonstrated mouse, non-human primate human mucosa expresses two genes involved CoV-2 entry, ACE2...
Abstract Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. Downstream trajectory inference, it is vital to discover genes that are (i) associated with lineages trajectory, or (ii) differentially expressed between lineages, illuminate underlying biological processes. Current data analysis procedures, however, either fail exploit continuous resolution provided pinpoint exact types differential We introduce...
Abstract Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in brain 1–3 . With proliferation multi-omics datasets, a major challenge is to validate and integrate results into biological understanding cell-type organization. Here we generated transcriptomes epigenomes from more than 500,000 individual cells mouse primary motor cortex, structure that has an evolutionarily conserved role locomotion. We developed...
Abstract Altered olfactory function is a common symptom of COVID-19, but its etiology unknown. A key question whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 affects olfaction directly by infecting sensory neurons or their targets bulb, indirectly, through perturbation supporting cells. Here we identify cell types epithelium and bulb that express entry molecules. Bulk sequencing revealed mouse, non-human primate human mucosa expresses two genes involved CoV-2 entry, ACE2 TMPRSS2....
Abstract In single-cell RNA sequencing (scRNA-Seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation regeneration, at unprecedented resolution. dynamic biological systems, states form a continuum, e.g., stem cells into mature cell types. This process often represented via trajectory in reduced-dimensional representation scRNA-Seq dataset. While many methods have been suggested...
Abstract Immune checkpoint inhibitors (ICI) targeting the PD-1 pathway have transformed treatment of advanced renal cell carcinoma (RCC), but mechanisms underlying therapeutic response remain largely unknown. Herein, we perform transcriptomic analysis on RCC biospecimens from 102 patients enrolled in a phase II clinical trial frontline nivolumab (NCT03117309) to investigate determinants anti-PD1 monotherapy. Through bulk analysis, identify an enrichment genes associated with tertiary...
Abstract Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. These methods can be applied stem cells and their descendants in order chart the progression from multipotent progenitors fully differentiated While a number statistical computational have been proposed for analyzing cell lineages, problem accurately characterizing multiple branching lineages remains difficult solve. Here, we introduce novel method, Slingshot, inferring...
People are exposed to phthalates through their wide use as plasticizers and in personal care products. Many endocrine disruptors have been associated with adverse health outcomes. However, knowledge gaps exist understanding the molecular mechanisms effects of exposure early late pregnancy. In this study, we examined relationship eleven urinary phthalate metabolites isoprostane, an established marker oxidative stress, among pregnant Mexican-American women from agricultural cohort. Isoprostane...
Abstract Single cell transcriptomics has transformed the characterization of brain identity by providing quantitative molecular signatures for large, unbiased samples populations. With proliferation taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful types. We used battery single-cell transcriptome epigenome measurements generated BRAIN Initiative Cell Census Network (BICCN) comprehensively assess types in...
Abstract The oncogenic MUC1-C protein promotes dedifferentiation of castrate-resistant prostate cancer (CRPC) and triple-negative breast (TNBC) cells. Chromatin remodeling is critical for the stem cell (CSC) state; however, there no definitive evidence that regulates chromatin accessibility thereby expression stemness-associated genes. We demonstrate drives global changes in architecture CRPC TNBC Our results show induces differentially accessible regions (DAR) across their genomes, which...
Allograft rejection is common following clinical organ transplantation, but defining specific immune subsets mediating alloimmunity has been elusive. Calcineurin inhibitor dose escalation, corticosteroids, and/or lymphocyte depleting antibodies have remained the primary options for treatment of episodes. Here, we developed a highly multiplexed imaging mass cytometry panel to study response in archival biopsies from 79 liver transplant (LT) recipients with either no (NR), acute T...
Recent genome- and epigenome-wide studies demonstrate that the DNA methylation is controlled in part by genetics, highlighting importance of integrating genetic epigenetic data. To better understand molecular mechanisms affecting gene expression, we used candidate susceptibility paraoxonase 1 (PON1) as a model to assess associations PON1 polymorphisms with arylesterase activity, marker expression. has been associated obesity, cardiovascular disease, pesticide exposure. In this study,...
BACKGROUND. In type 1 diabetes (T1D), impaired insulin sensitivity may contribute to the development of diabetic kidney disease (DKD) through alterations in oxidative metabolism.
<p>RNA expression (normalized matrix), related to Figure 1.</p>
<p>Differential gene expression analysis, including differentially expressed genes for ZNF683+ SLAMF7+ CD8+ Exhausted T cells compared to all other cell clusters, related Figure 5. Positive log fold-change (per cluster) indicates upregulation in cells.</p>
<p>Differential gene expression analysis, including top 1,000 differentially expressed genes for each cluster (compared with all other clusters) graph-based clustering of myeloid cells, related to Figure 4. Positive log fold-change (per cluster) indicates upregulation in interest compared clusters.</p>
<p>TCR specificity in advanced renal cell carcinoma.</p>
<div>Abstract<p>Immune checkpoint inhibitors targeting the PD-1 pathway have transformed treatment of advanced renal cell carcinoma (RCC), but mechanisms underlying therapeutic response remain largely unknown. In this study, we perform transcriptomic analysis on RCC biospecimens from 102 patients enrolled in a phase II clinical trial first-line nivolumab (NCT03117309) to investigate determinants anti–PD-1 monotherapy. Through bulk analysis, identify an enrichment genes associated...