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January 2021
QCBio Research Seminar: Tevfik Umut Dincer (Ernst)
TITLE: "Genomewide supervised prediction of activating and repressive regions in over hundred cell and tissue types" ABSTRACT: While the vast majority of variants associated with common disease risk are distributed across the non-coding genome, our understanding of the regulatory elements contained within remains notably incomplete. Strategies for identifying and characterizing these regulatory elements, such as high-throughput reporter assays and CRISPR-dCas9 screens, have been essential in decoding this complex regulatory landscape, but they only provide information on the particular regions they…
Find out more »QCBio Research Seminar: Iris Dror (Plath)
TITLE: "XIST controls X chromosome dampening and autosomal genes in early human development" ABSTRACT: Female human pre-implantation embryos and naïve human pluripotent stem cells (hPSCs) equalize X-linked gene expression with males via X-chromosome dampening (XCD), a unique strategy of dosage compensation in mammals. The mechanisms controlling XCD are unknown. Here, we show that the long non-coding RNA XIST, which mediates X-chromosome inactivation (XCI), is required for XCD. XIST employs similar principles and protein partners, including SPEN, to execute XCD and XCI,…
Find out more »W16: Library Prep for NGS
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.
Find out more »QCBio Research Seminar: Ariel Wu (Sankararaman)
TITLE: "Fast estimation of genetic correlation for Biobank-scale data" ABSTRACT: Genetic correlation is an important parameter in understanding the shared genetic basis across pairs of complex traits with applications ranging across disease subtyping, genetic prediction, and causal inference. The availability of genome-wide genetic data has led to a number of methods that aim to estimate genetic correlation. Methods that analyze individual genotype data (typically using a bi-variate linear mixed model) are computationally expensive to be applied to large-scale datasets such as…
Find out more »QCBio Research Seminar: Diane Lefaudeux (Hoffmann)
TITLE: "Determining mRNA nuclear export kinetics reveals a wide range of values associated with innate immune response genes" ABSTRACT: The abundance and stimulus-responsiveness of mature mRNA is considered determined by nuclear synthesis and cytoplasmic decay. However, pre-mRNA processing and transport may also contribute, but have rarely been measured. We generated high spatio-temporal resolution RNA-seq data and developed a mathematical modeling workflow to infer kinetic parameters. We found that the effective chromatin-to-cytoplasm transport rate is gene-specific, varying 100-fold. Importantly, effective export…
Find out more »February 2021
W22: Advanced Cytoscape
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.
Find out more »QCBio Research Seminar: Lingyun (Ivy) Xiong (Garfinkel)
TITLE: "Oncogenic alterations in the p53 pathway abolish oscillatory competence" ABSTRACT: The tumor suppressor p53 displays concentration oscillations in response to DNA damage, a behavior that has been suggested to be essential to its anti-cancer function. Many genetic alterations in the p53 pathway have been shown to be oncogenic, whether by experiment or by clinical associations with various cancers. These oncogenic alterations include somatic mutations, copy number variations and inherited polymorphisms. Using a differential equation model of p53-Mdm2 dynamics, we employ…
Find out more »W20: Single-Cell RNA-Seq Analysis with Python
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.
Find out more »QCBio Research Seminar: Kexin Li (Li JJ)
TITLE: "Learning Sparse Representation of Single Cells using Projective Nonnegative Matrix Factorization (pNMF)"
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