TITLE: "Unbiased analysis of single cell RNA sequencing data reveals previously uncharacterized heterogeneity in small cell lung cancer cell lines." ABSTRACT: Small Cell Lung Cancer (SCLC) accounts for approximately 13% of all new lung cancer diagnoses. SCLC exhibits propensity for early metastasis, rapid cell division, high levels of replication stress, the ability to cope with […]
Associate Professor, Biostatistics & Bioinformatics, Center for Genomic and Computational Biology, Duke University “TBD” Hosted by Jason Ernst
TITLE: “Large uncertainty in individual PRS estimation impacts PRS-based risk stratification.” ABSTRACT: Large-scale genome-wide association studies have enabled polygenic risk scores (PRS), which estimate the genetic value of an individual for a given trait. Since PRS accuracy is typically assessed using cohort-level metrics, uncertainty in PRS estimates at individual level remains underexplored. In this talk, […]
TITLE: "Constructing a Functional Interactome from Published Work to Identify Underrepresented and Integrative Effects of Neuroinflammatory Cytokines on Neural Excitability." ABSTRACT: Maintaining normal excitability is a key function of our nervous system which is subject to ongoing perturbations such as aging and chronic neurodegeneration. Neuroinflammatory responses which are widely associated with injury and disease are […]
TITLE: "Metabolic dependencies of ecDNA and HSR focal amplification modes and plasticity." ABSTRACT: The focal amplification (FA) of genes that support the uncontrolled growth and proliferation of cells (i.e., oncogenes) on homogeneous chromosomal staining regions (HSRs, chromosomal) ans extrachromosomal DNA (ecDNA) is a hallmark of resistant cancers. However, it remains an open question whether oncogene […]
TITLE: "DoubletCollection: An R package that integrates cutting-edge computational doublet-detection methods." ABSTRACT: The existence of doublets is a key confounder in single-cell RNA sequencing (scRNA-seq) data analysis. There are several computational methods for detecting doublets from scRNA-seq data. We develop an R package DoubletCollection to integrate the installation and execution of those methods. DoubletCollection also […]
TITLE: “Applications of generalized additive models and copulas to single-cell RNAseq computational method development: PseudotimeDE and scDesign2” ABSTRACT: Part 1: PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes […]
TITLE: “Integrating single cell omics and deep phenotype data to discover genes underlying cardiometabolic disorders” ABSTRACT: Obesity predisposes to cardiometabolic disorders (CMDs), such as type 2 diabetes, multiple dyslipidemias, and non-alcoholic fatty liver disease (NAFLD). We are interested in how cell-type level gene expression contributes to CMDs and impacts cross talk between cardiometabolic tissues. We […]
TITLE: "Is there a Quiescence Histone Code?" ABSTRACT: Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and […]
TITLE: “Model driven design and analysis of quantitative phenotype screens” ABSTRACT: Increasingly, CRISPR screens are coupled with flow cytometry (FACS) to sort cells and quantify the impact of genetic perturbations on a continuous phenotype. While FACS provides much more quantitative information than simple survival screens, it introduces a number of experimental and statistical challenges. Furthermore, as experimentalists push […]
