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July 2021

QCBio Research Seminar in collaboration with B.I.G. Summer: David Wong

July 30 @ 2:00 pm - 2:30 pm
ZOOM CA United States

TITLE: “Salivary exRNA for Gastric Cancer Detection” ABSTRACT: Biomarkers are needed for non-invasive early detection of gastric cancer (GC). We investigated whether salivary extracellular RNA (exRNA) biomarkers can be used as an efficient and economical clinical evaluation tool for GC. Unstimulated whole saliva samples were prospectively collected from 294 subjects (163 GC and 131 non-GC controls) who underwent endoscopic evaluation at the Samsung Medical Center in Korea. The salivary transcriptomes of 63 GC and 31 non-GC controls were profiled, and mRNA biomarker candidates were verified with RT-qPCR.…

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QCBio Research Seminar in collaboration with B.I.G. Summer: Harold Pimentel

July 24 @ 2:00 pm - 2:30 pm
ZOOM CA United States

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 these screens in limited primary cells or in vivo, they lack principled guidelines on how experimental parameters including multiplicity of infection, guide RNA coverage, or…

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QCBio Research Seminar in collaboration with B.I.G. Summer: Hilary Coller

July 16 @ 2:00 pm - 2:30 pm
ZOOM CA United States

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 out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Histone modifications have been shown…

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QCBio Research Seminar in collaboration with B.I.G. Summer: Paivi Pajukanta

July 9 @ 2:00 pm - 2:30 pm
ZOOM CA United States

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 hypothesized that obesity-induced inflammatory changes in adipose tissue alter the cell-type composition and key functions of this obesity responsive tissue, which drives ectopic deposition of…

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QCBio Research Seminar in collaboration with B.I.G. Summer: Jingyi Jessica Li

July 2 @ 2:00 pm - 2:30 pm
ZOOM CA United States

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 along the pseudotime inferred from single-cell RNA-sequencing data. However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posed p-values or…

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June 2021

QCBio Research Seminar: Nan (Miles) Xi (Li JJ)

June 4 @ 11:30 am - 12:00 pm
ZOOM CA United States

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 provides a unified interface to perform and visualize downstream analysis after doublet detection. In this talk, we will introduce a protocol of using DoubletCollection to…

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QCBio Research Seminar: Amelia Palermo (Graeber)

June 4 @ 11:00 am - 11:30 am
ZOOM CA United States

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 FA is affected by cellular metabolism and by the composition of the tumor microenvironment. This is important because cancers carrying oncogene focal amplifications, particularly on…

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QCBio Academic Jobs – Postdoc Career Development Series: “Starting a New Lab”

June 3 @ 3:00 pm - 4:00 pm
ZOOM CA United States

Panelist: Elaine Hsiao

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W4: Galaxy for NGS Data Analysis

June 1 @ 1:30 pm - June 2 @ 3:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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Galaxy (https://usegalaxy.org/) is a web-based infrastructure for bioinformatics application. First, this workshop introduces participants to using Galaxy for analysis of Next-Generation Sequencing data. Next, this workshop covers the structure of Galaxy, data format and manipulation, obtaining and sharing data, and building and sharing workflows. We will use the tools installed on the UCLA galaxy to perform a few types of NGS analysis.

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W23: Advanced Cytoscape

June 1 @ 9:00 am - June 3 @ 12:00 pm
ZOOM CA United States + Google Map

The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources, and the role of interaction data in the interpretation of large scale datasets. Highly encourage: Students should working knowledge of python scripting.

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