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October 2021

W22: Intro to Cytoscape

October 26 @ 9:00 am - October 29 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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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 in-house generated data (eg. gene expression levels) on top of the imported reference interaction network. The workshop will also provide an overview of the experimental…

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W15: Bacterial Genomics

October 26 @ 1:30 pm - October 28 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence data and the assemble of a genome. Next, basic statistics will be explained to learn how to check the quality of assembledgenome (e.g., N50, #…

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QCBio Research Seminar: Giovanni Quinones Valdez (Xiao), Grad student in Bioengineering

October 27 @ 12:00 pm - 12:30 pm
ZOOM CA United States

TITLE: "scAllele, a versatile tool for the detection and analysis of variants in scRNA-seq." ABSTRACT: Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better…

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QCBio Research Seminar: Ulzee An (Sankararaman), Grad student in Computer Science

October 27 @ 12:30 pm - 1:00 pm
ZOOM CA United States

TITLE: "AutoComplete: Deep Learning-based Phenotype Imputation" ABSTRACT: Health data has become increasingly available, vast in scale, and highly missing. For many downstream applications, the ability to accurately impute missing features in health records may tap into additional analytical power which would be unrealized otherwise. While existing imputation methods are applicable, many fall short in one or more aspects of being reliable or scalable in the domain of massive, highly incomplete, and heterogenous population-scale data. We propose AutoComplete, a deep learning-based…

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November 2021

Bioinformatics/Human Genetics Seminar Series: Anya Prince, Associate Professor of Law, Genetic Cluster, University of Iowa College of Law

November 1 @ 11:00 am - 12:00 pm
ZOOM CA United States

“Regulating Insurer Use of Genetic Information” Hosted by Christina Palmer

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W20: Single-Cell RNA-Seq Analysis with Python

November 2 @ 9:00 am - November 5 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired scRNA-seq data and would like to learn about different analytical approaches.  

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W10: Mathematical Modeling of Cell Signaling

November 2 @ 1:30 pm - November 5 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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Molecular biology has taught us a great deal about what is happening inside a cell, that is that pathways can get very complicated and life is not just independent pathways but networks. Fortunately, we can use computational tools to understand dynamics of complex networks. This workshop introduces the basic concepts of modeling cell signaling pathways. In this workshop we will describe signaling pathways and network motifs using mathematical equations and will be using MATLAB to solve and plot dynamical solutions.…

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QCBio Research Seminar: Alexander Markowitz (Boutros), Postdoc in Human Genetics

November 3 @ 12:00 pm - 12:30 pm
Boyer 159, 611 Charles E. Young Dr. E.
Los Angeles, CA 90095 United States
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TITLE: "A pan-cancer multi-omic analysis of tumor proliferation." ABSTRACT: The underlying mechanisms of dysregulated cellular proliferation in cancer remain unclear; however, it is hypothesized that specific mutations, mutational signatures, evolutionary trajectories and other global (epi)genomic features may be linked to differing rates of proliferation. In this presentation, I will showcase a landscape analysis of cellular proliferation across primary cancers and cell lines using genome, transcriptome and proteome data from 11,597 primary tumors and 1,804 cell lines across six major consortia.  The…

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QCBio Research Seminar: Ricky Wolff (Garud), Graduate Student in Ecology & Evolutionary Biology

November 3 @ 1:00 pm - 1:30 pm
Boyer 159, 611 Charles E. Young Dr. E.
Los Angeles, CA 90095 United States
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TITLE: "Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome." ABSTRACT: The human gut microbiome is a complex community that harbors substantial ecological diversity at the species level, as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome community are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is…

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W11: Metagenomics Analysis with Python and R

November 8 @ 9:00 am - November 10 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

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