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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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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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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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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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January 2021

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 known to be determined by nuclear synthesis and cytoplasmic decay. However, nuclear processing and export events and may also contribute.  Here, we investigated the role nuclear export rates in innate immune gene expression. We generated high spatio-temporal resolution RNA-seq data from endotoxin-stimulated macrophages and developed a mathematical modeling workflow to infer kinetic parameters…

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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: 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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