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May 2022

QCBio Research Seminar: Jackson Chin (Meyer), Graduate Student in Bioengineering

May 18 @ 12:30 pm - 1:00 pm
ZOOM CA United States

TITLE: "Tensor Factorization for Interpreting the Mechanisms of MRSA Persistence." ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) bacteria is an increasingly common and life-threatening infection. While some antibiotics resolve MRSA infections in vitro, these same antibiotics often fail to clear an infection when used to treat patients, suggesting that MRSA persistence is a confluence of both host and bacterial factors. While recent research has identified critical genetic and proteomic determinants of MRSA persistence, the mechanisms that drive MRSA persistence are still poorly…

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QCBio Research Seminar: Yue Wang (Chou), Postdoc, Department of Computational Medicine

May 18 @ 12:00 pm - 12:30 pm
ZOOM CA United States

TITLE: "Stochastic Model and Optimization of SELEX." ABSTRACT: Systematic Evolution of Ligands by EXponential enrichment (SELEX) is a process to select the best aptamer sequence in a huge aptamer library that binds a specified target molecule with the highest affinity. There has been a deterministic model of SELEX, and we develop a fully discrete stochastic model to obtain more accurate results when the mass action law does not hold. Specifically, we find that the optimal SELEX protocol in the stochastic…

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W5a: RNA-seq I Analysis

May 17 @ 1:30 pm - May 19 @ 4:30 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq. To facilitate learning, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case…

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QCBio Research Seminar: Heather Zhou (Li JJ), Graduate Student in Statistics

May 11 @ 12:30 pm - 1:00 pm
ZOOM CA United States

TITLE: "PCA outperforms popular hidden variable inference methods for QTL mapping." ABSTRACT: Estimating and accounting for hidden variables is widely practiced as an important step in quantitative trait locus (QTL) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for this purpose. Here we benchmark popular hidden variable inference methods including surrogate variable analysis (SVA), probabilistic estimation of expression residuals (PEER), and hidden covariates with…

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QCBio Research Seminar: Keunseok Park (Park), Grad Student, Chemical and Bimolecular Engineering

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

TITLE: "G-Flux: a metabolic flux and free energy analysis software for interpreting 13C, 2H, 18O, and 15N isotope tracing data." ABSTRACT: Metabolic fluxes offer insights into pathway utilization, kinetics, and thermodynamics. Stable isotope tracing and metabolic footprinting are widely used for inferring metabolic fluxes. However, quantitative flux measurement across broad metabolism remains challenging due to our inability to convert multiple isotope distributions into fluxes and integrate exometabolomics data. Here we develop a software application, G-Flux, for computing metabolic fluxes by…

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W23: Advanced Cytoscape

May 10 @ 9:00 am - May 12 @ 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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W20: Single-Cell RNA-Seq Analysis with Python

May 3 @ 1:30 pm - May 6 @ 4:30 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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W17: Machine Learning with Python

May 3 @ 9:00 am - 12:00 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 basic principles involved in the applications mentioned above, such as pattern recognition, linear and non-linear regression and cluster analysis. The workshop will be oriented towards hands-on activities, starting from the basics of how to load and prepare biological datasets in a Python environment.

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April 2022

W15: Bacterial Genomics

April 26 @ 1:30 pm - April 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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W14: Intro to Modern Statistics with R

April 26 @ 9:00 am - April 28 @ 12:00 pm
529 Boyer Hall, 611 Charles E Young Dr E,
Los Angeles, CA 90095 United States
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Through this seminar, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course makes no assumptions about familiarity with traditional statistics – we will simply go through relatable experimental examples and ask how to test various hypotheses, introducing the relevant methods along the way. There will be homework assignments each night to solidify the concepts…

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