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May 2022
W5b: RNA-Seq II Analysis
RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).
Find out more »QCBio Research Seminar: Connor Razma (Hoffmann), Undergraduate Bioinformatics Researcher
TITLE: "Baseline MEthylation Patterns prior to flu vaccination." ABSTRACT: Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into subtypes specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how many antibodies are present in a sample, a hemagglutination inhibition assay (HAI) is used. DNA methylation is an epigenetic mechanism used to regulate gene expression…
Find out more »QCBio Research Seminar: Ha Vu (Ernst), Graduate Student in Bioinformatics
TITLE: "Universal annotation of the human genome through integration of over a thousand epigenomic datasets." ABSTRACT: Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative ‘stacked modeling’ approach was previously suggested, where chromatin states…
Find out more »June 2022
W4: Galaxy for NGS Data Analysis
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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