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February 2021
QCBio Research Seminar: Will Shoemaker (Garud)
TITLE: “Inferring positive selection in the human gut microbiome using signatures of genetic linkage.” ABSTRACT: The human gut microbiome is composed of hundreds of simultaneously evolving species that can affect human health. However, fundamental features of genetic diversity have yet to be leveraged to identify genes that contribute towards microbial adaptation. One such feature is the statistical association of mutations, otherwise known as linkage disequilibria. In this seminar, I will describe how patterns of linkage disequilibria can reflect the direction of…
Find out more »QCBio Research Seminar: Amandine Gamble (Lloyd-Smith)
TITLE: "Linking exposure dose to infectious disease development using mechanistic models" (using SARS-CoV-2 in a mouse model as an illustration) ABSTRACT: Disease development after exposure to a pathogen does not follow a yes/no process, but rather a spectrum of disease manifestations influenced by host, pathogen and environmental factors. In particular, exposure dose can impact incubation time, shedding intensity and disease severity. However, classical dose-response models only consider the probability of disease development, neglecting the diversity of disease manifestations. In contrast, more…
Find out more »W5a: RNA-seq I Analysis
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…
Find out more »W6: DNA Methylation Analysis with R and Unix
This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BSseq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will have the opportunity to work on real DNA methylation data provided by the instructor and run the analysis on Hoffman2 and locally. Attendees need to have a basic knowledge in UNIX commands and R programming for…
Find out more »QCBio Research Seminar: Maria Izabel Alves Cavassim (Lohmueller)
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…
Find out more »QCBio Research Seminar: Igor Nikolskiy (Wollman)
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…
Find out more »W14: Intro to Modern Statistics with R
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…
Find out more »W11: Metagenomics Analysis with Python and R
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.
Find out more »W3: Intro to R and Data Visualization
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…
Find out more »QCBio Research Seminar: Kexin Li (Li JJ)
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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