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January 2021

QCBio Research Seminar: Tevfik Umut Dincer (Ernst)

January 22 @ 11:00 am - 11:30 am
ZOOM CA United States

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…

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QCBio Research Seminar: Iris Dror (Plath)

January 22 @ 11:30 am - 12:00 pm
ZOOM CA United States

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,…

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QCBio Research Seminar: Ariel Wu (Sankararaman)

January 29 @ 11:00 am - 11:30 am
ZOOM CA United States

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…

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QCBio Research Seminar: Diane Lefaudeux (Hoffmann)

January 29 @ 11:30 am - 12:00 pm
ZOOM CA United States

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…

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February 2021

QCBio Research Seminar: Lingyun (Ivy) Xiong (Garfinkel)

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

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…

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QCBio Research Seminar: Marcus Gallagher-Jones (Rodriguez)

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

TITLE: "TBD"

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QCBio Research Seminar: Kexin Li (Li JJ)

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

TITLE: "Learning Sparse Representation of Single Cells using Projective Nonnegative Matrix Factorization (pNMF)"

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QCBio Research Seminar: Igor Nikolskiy (Wollman)

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

TITLE: "TBD"

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QCBio Research Seminar: Amandine Gamble (Lloyd-Smith)

February 26 @ 11:00 am - 11:30 am
ZOOM CA United States

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…

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March 2021

QCBio Research Seminar: Katherine Sheu (Hoffmann)

March 5 @ 11:00 am - 11:30 am
ZOOM CA United States

TITLE: "TBD"

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