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January 2022

W16: Library Prep for NGS

January 25 @ 1:30 pm - January 27 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional, sign-up is required.

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W3: Intro to R and Data Visualization

January 25 @ 9:00 am - January 27 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This course is a pre-requisite for several other Collaboratory workshops. This workshop is geared towards researchers who have little or no experience with R who want to get started with importing data into R…

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Bioinformatics/Human Genetics Seminar Series: Jennifer Wilson, PhD, Assistant Professor, Bioengineering, UCLA

January 24 @ 4:00 pm - 5:00 pm
ZOOM CA United States

TITLE: "Deriving network parameters for understanding drug effects.” Hosted by Jason Ernst.

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CAPS/RISE Workshop: Copying with Stress

January 21 @ 11:00 am - 12:00 pm
ZOOM CA United States

QCBio Research Seminar: Dongyuan Song (Li JJ), Graduate Student in Bioinformatics

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

TITLE: "scDesign3: an all-in-one statistical framework that generates realistic single-cell omics data and infers cell heterogeneity structure." ABSTRACT: The generation of realistic synthetic data is essential for benchmarking numerous computation tools developed for single-cell omics data. Here we propose an all-in-one statistical framework that generates single-cell omics data from various cell heterogeneity structures, including discrete cell types, continuous cell trajectories, and spatial cell locations. Our framework uses a unified probabilistic model with accessible likelihood. This probabilistic formulation is advantageous in that…

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QCBio Research Seminar: Evan Maltz (Wollman), Graduate Student in BMSB (Biochemistry, Molecular and Structural Biology)

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

TITLE: "Phenotypic consequences of gene expression variability." ABSTRACT: The central dogma of biology proposes that information flows from genes to RNA to protein, determining protein identity and abundance. Single cell transcriptome measurements provide ample information about RNA abundance in cells. While the expression of individual genes clearly matters for determining phenotype, they do not work independently. How the information in RNA abundances is combined to determine cellular phenotype remains unclear. Here we address this question for a single cellular phenotype,…

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W18: Advanced Python

January 11 @ 1:30 pm - January 13 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming), use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets, and matplotlib for plotting results. At the end of this workshop, students will better understand the python data structures for handling large datasets and will have some knowledge of how to manipulate these data and plot…

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W2: Using NGS Analysis Tools

January 11 @ 9:00 am - January 13 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short…

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Bioinformatics/Human Genetics Seminar Series: Lauren McIntyre, PhD, Professor, Molecular Genetics & Microbiology, University of Florida

January 10 @ 4:00 pm - 5:00 pm
ZOOM CA United States

TITLE: "Climate change and maize response to pollutants: gene content, expression and regulation." Hosted by Kirk Lohmueller.

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QCBio Research Seminar: Jianxiao Yang (Suchard), Grad Student in Biomathematics

January 5 @ 12:00 pm - 12:30 pm
ZOOM CA United States

TITLE: "Massive parallelization of massive sample-size survival analysis." ABSTRACT: Large-scale observational health databases are increasingly popular for conducting comparative effectiveness and safety studies of medical products. However, increasing number of patients poses computational challenges when fitting survival regression models in such studies. In this paper, we use graphics processing units (GPUs) to parallelize the computational bottlenecks of massive sample-size survival analyses. Specifically, we develop and apply time andmemory efficient single-pass parallel scan algorithms for Cox proportional hazardsmodels and forward-backward parallel scan algorithms for…

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