TITLE: "Multimodal radiomic analysis of biparametric MRI to predict biochemical recurrence after radical prostatectomy." ABSTRACT: Integration of information across multiple modalities and biological scales has the potential to improve the prediction of disease outcomes and response to treatments. In this talk, I will discuss our ongoing work to predict prostate cancer aggressiveness by combining information from biparametric […]
Associate director, Gerstner Center for Cancer Diagnostics, Broad Institute “Ultrasensitive detection of minimal residual disease” Hosted by Jasmine Zhou
TITLE: "Genome-wide survey of mutations influencing protein abundances in yeast" ABSTRACT: Our understanding of how protein-level regulation is encoded in the genome and how protein abundances are affected by DNA sequence variation remains sparse. I will discuss our genetic screen based on large-scale pooled base editing that allows us to capture the effects of thousands […]
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 […]
