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February 2021

QCBio Research Seminar: Maria Izabel Alves Cavassim (Lohmueller)

February 19 @ 11:00 am - 11:30 am
ZOOM CA United States

TITLE: The evolution and co-evolution of PRDM9 across vertebrates ABSTRACT: In sexually reproducing organisms, meiotic recombination is initiated by the deliberate infliction of numerous double-strand breaks (DSBs) in the genome, the repair of which yields crossover and non-crossover resolutions. In most mammals, these DSBs are specified through the binding of PRDM9 and the deposition of H3K4me3 and H3K36me3 marks. Despite its evolutionary importance, PRDM9 has been independently lost numerous times across vertebrate’s evolution. Here, we take advantage of the multiple…

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QCBio Research Seminar: Igor Nikolskiy (Wollman)

February 19 @ 11:00 am - 11:30 am
ZOOM CA United States

TITLE: "A state space model to characterize the phenotypic variation in a panel of drug treatment time course experiments." ABSTRACT: As new technologies enable high throughput collection of marker measurements in drug treatment time course experiments, we are faced with a need to characterize the observed cellular behaviors over time.  I will present a model that builds on previous approaches to produce cell state trajectories that emphasize the variation between cell lines and treatments.  The resulting approach provides another means…

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W14: Intro to Modern Statistics with R

February 16 @ 1:30 pm - February 18 @ 3:30 pm
ZOOM CA United States + Google Map

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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W11: Metagenomics Analysis with Python and R

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

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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W3: Intro to R and Data Visualization

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

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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QCBio Research Seminar: Kexin Li (Li JJ)

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

TITLE: "scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling." ABSTRACT: Single-cell RNA sequencing (scRNA-seq) captures whole transcriptome information of individual cells. While scRNA-seq measures thousands of genes, researchers are often interested in only dozens to hundreds of genes for a closer study. Then a question is how to select those informative genes from scRNA-seq data. Moreover, single-cell targeted gene profiling technologies are gaining popularity for their low costs, high sensitivity, and extra (e.g.,…

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QCBio Research Seminars: Nicolas Rochette (Campbell-Staton)

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

TITLE: Cis-regulatory divergence between highland and lowland deer mice populations highlight the essential role of pleiotropic genes for high-altitude adaptation. ABSTRACT: Variation in gene expression regulation contributes extensively to phenotypic diversity within and between species and plays a major role in complex trait evolution. However, the characterization of the genetic basis of regulatory variation is complicated by the inter-dependencies between the expressions of all genes. A promising approach to circumvent this issue is to measure gene-wise allelic imbalance (also known…

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W20: Single-Cell RNA-Seq Analysis with Python

February 9 @ 1:30 pm - February 12 @ 4:30 pm
ZOOM CA United States + Google Map

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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COVID-19 Basic, Translational and Clinical Research Seminar Series

February 5 @ 12:00 pm - 1:00 pm
ZOOM CA United States

Swab-Seq: Massively scaling SARS-CoV-2 testing using genomic sequencing. The COVID-19 Basic, Translational and Clinical Research Task Forces has created a seminar series each Friday at noon. The purpose of these seminars is to bring together people across campus working on SARS-CoV-2 from all angles to form a community and exchange information, both for expert virologists and those new to COVID-19 from other disciplines. Some presentations will focus on individual COVID-19 research projects and others on discussion of tools and reagents and campus resources. We hope…

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QCBio Research Seminars: Marcus Gallagher-Jones (Rodriguez)

February 5 @ 11:30 am - 12:00 pm
ZOOM CA United States

TITLE: Structural interrogation of small open reading frame (sORF) encoded proteins ABSTRACT: Advances in genomics and proteomics have unearthed sequences of a startling number of novel proteins. Despite this, our knowledge of their three-dimensional structure and function relies on only a small fraction of the known protein universe.  Small open reading frames (sORFs) encoding proteins less than 100 amino acids in length are an extreme example of this. With tens of thousands of newly discovered sORFs per year since the late…

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