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QCBio/BIG Summer Research Seminar: Dr. Eleazar Eskin, Professor and Chair Department of Computational Medicine, UCLA

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

TITLE: "Swab-Seq: Detecting COVID-19 with Genomic Sequencing: From bench to vending machine." ABSTRACT: At UCLA we developed one of the only novel technologies for COVID-19 diagnostic testing that was deployed on a large scale.  The assay, which we named SwabSeq, performs genomic sequencing of pooled samples tagged with sample-specific molecular barcodes and then uses computational […]

QCBio/BIG Summer Research Seminar: Dr. Xia Yang, Professor, Dept. Integrative Biology & Physiology, UCLA

Boyer 159 611 Charles E. Young Dr. E., Los Angeles, CA, United States

TITLE: “Integrative systems analysis, applications, and challenges of single cell multiomics.” ABSTRACT: Recent advances in single cell multiomics technologies such as single cell RNA-seq, single cell ATAC-seq, and spatial transcriptomics have brought enormous opportunities that enable our understanding of the molecular underpinnings of pathophysiology at a single cell resolution. However, integrative analysis across single cell […]

QCBio/BIG Summer Research Seminar: Dr. Michael Wells, Assistant Professor, Human Genetics, UCLA

Boyer 159

TITLE:  "Exploration of human genetic and phenotypic diversity through cell villages". ABSTRACT: Our species is characterized by an immense diversity in neurological and psychological traits. Common and rare genetic variants have been linked to trait differences and disease risk in human populations, though the underlying biology is poorly understood and difficult to study at large scales. […]

W22: Intro to Cytoscape

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

The workshop introduces Cytoscape (https://cytoscape.org/) – an open source platform for retrieval and visualization of complex biological interactions that are available from public interaction resources: The IMEx Consortium (https://www.imexconsortium.org/), STRING (https://string-db.org/) and BioGIRD (https://thebiogrid.org/). It covers querying for interactions data using built-in search interface, interaction data cleanup and visualization as well as overlying of the […]

W4: Galaxy for NGS Data Analysis

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

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 […]

W6: BS-DNA Methylation Analysis with Hoffman2 and R

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BS-Seq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will have the opportunity to work on real DNA methylation data provided […]

QCBio Research Seminar: Matthew Soldano, Staff Research Associate for the Pellegrini Bioinformatic’s Lab

ZOOM CA, United States

TITLE: "Predicting Biological Aging from Epigenetics." ABSTRACT: Epigenetics are a proven measure of cellular health. Therefore, a field of research has emerged that utilizes epigenetics to measure, treat, and potentially reverse biological age in humans. Specifically, DNA methylation, responsible for cell differentiation and gene expression, has the potential to be a barcode for measuring biological […]

QCBio Research Seminar: Jee Yun Han (Boutros), Graduate Student in Gene Regulation, Epigenomics, and Transcriptomics

ZOOM CA, United States

TITLE: "Comprehensive study of gene expression outliers and their regulation mechanisms in pan-cancer." ABSTRACT: Cancer is a disease characterized by remarkable heterogeneity. Gene expression varies drastically between tumours and within cells of a single. This variability can generate extreme outliers: transcripts that show atypically high gene expression in a small percentage of cancers. These outliers […]

QCBio Research Seminar: Mark Xiang (Hoffmann), Graduate Student in Bioinformatics

Boyer Hall 159

TITLE: "Heterogeneity in cell states: Is it important whether cell states are heritable or change rapidly?" ABSTRACT: Cells of the same cell type show molecular and phenotypic heterogeneity. Is the particular cell state of a given cell heritable from one generation to the next?  Previous work in liver cancer cells indicates that the molecular network […]

QCBio Research Seminar: Guanao Yan (Li JJ), Graduate Student in Statistics

Boyer 159 611 Charles E. Young Dr. E., Los Angeles, CA, United States

TITLE: "scReadSim: a single-cell RNA-seq and ATAC-seq read simulator." ABSTRACT: Rapid advances of single-cell RNA-seq and ATAC-seq technologies have propelled the development of many computational tools, benchmarking of which demands realistic simulators. However, few simulators can generate sequencing reads, and none of the existing read simulators aim to mimic real cells, hindering the benchmarking of […]