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X-WR-CALNAME:Institute for Quantitative and Computational Biosciences
X-ORIGINAL-URL:https://qcb.ucla.edu
X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210205T110000
DTEND;TZID=America/Los_Angeles:20210205T120000
DTSTAMP:20260518T060145
CREATED:20210107T162654Z
LAST-MODIFIED:20210205T203344Z
UID:15717-1612522800-1612526400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Lingyun (Ivy) Xiong (Garfinkel)
DESCRIPTION:TITLE: “Oncogenic alterations in the p53 pathway abolish oscillatory competence” \nABSTRACT: 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 Hopf bifurcation analysis to show that all of the oncogenic perturbations have a common effect\, to abolish the oscillatory competence of p53\, thereby impairing its tumor suppressor function. In this analysis\, these diverse genetic alterations\, widely observed in human cancers\, have a unified mechanistic explanation. \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Ivy-Xiong-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-lingyun-ivy-xiong-garfinkel/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/Lingyun-Ivy-Xiong.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210205T113000
DTEND;TZID=America/Los_Angeles:20210205T120000
DTSTAMP:20260518T060145
CREATED:20210129T140921Z
LAST-MODIFIED:20210226T201021Z
UID:16320-1612524600-1612526400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Marcus Gallagher-Jones (Rodriguez)
DESCRIPTION:TITLE: Structural interrogation of small open reading frame (sORF) encoded proteins \nABSTRACT: 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 2000s\, their gene products represent a kind of ‘dark matter’ of the proteome. Many sORF families encode sequences that do not resemble a known protein domain\, limiting our ability to correlate their sequence to a known function. Given the widespread roles previously characterized small proteins play in bacterial cells\, they hold great potential as future therapeutic targets. My current research is focussed on leveraging advances in protein structure prediction to discover sORF encoded proteins (SEP) with a compact tertiary structure and tease out the role they may be playing in cellular function. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Marcus-Gallagher-Jones-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminars-marcus-gallagher-jones-sankararaman/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/Marcus-Gallagher-Jones.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210205T120000
DTEND;TZID=America/Los_Angeles:20210205T130000
DTSTAMP:20260518T060145
CREATED:20210203T154838Z
LAST-MODIFIED:20210203T154841Z
UID:16436-1612526400-1612530000@qcb.ucla.edu
SUMMARY:COVID-19 Basic\, Translational and Clinical Research Seminar Series
DESCRIPTION:Swab-Seq: Massively scaling SARS-CoV-2 testing using genomic sequencing. \nThe 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 this will also be a venue to identify collaborations for larger projects and grant opportunities. \nPlease note zoom below requires pre-registration: \nhttps://uclahs.zoom.us/meeting/register/tJIsd-mpqDkuHNFCfaOEkKnLO0lALIGPQGpW \nAfter registering\, you will receive a confirmation email containing information about joining the meeting.
URL:https://qcb.ucla.edu/event/covid-19-basic-translational-and-clinical-research-seminar-series/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210212T110000
DTEND;TZID=America/Los_Angeles:20210212T113000
DTSTAMP:20260518T060145
CREATED:20210204T152332Z
LAST-MODIFIED:20210226T200938Z
UID:16453-1613127600-1613129400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Nicolas Rochette (Campbell-Staton)
DESCRIPTION:TITLE: Cis-regulatory divergence between highland and lowland deer mice populations highlight the essential role of pleiotropic genes for high-altitude adaptation. \nABSTRACT: 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 as allele-specific expression) as it intrinsically emphasizes cis-regulatory effects. Here\, we demonstrate the power of the allelic imbalance approach and use it to investigate the cis-regulatory landscape of local adaptation to high altitude in the deer mouse (Peromyscus maniculatus). We find evidence that freely segregating regulatory alleles are ubiquitous in wild populations. Then\, we detect strong cis-regulatory differentiation between highland and lowland populations in a small set of genes\, which comprises known adaptations as well as new candidates and underlines the role of integrative genes to explain the broad range of organismal changes observed in high altitude populations.
URL:https://qcb.ucla.edu/event/qcbio-research-seminars-nicolas-rochette-campbell-staton/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/02/Nicolas-Rochette.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210212T113000
DTEND;TZID=America/Los_Angeles:20210212T120000
DTSTAMP:20260518T060145
CREATED:20210112T233425Z
LAST-MODIFIED:20210215T163620Z
UID:15816-1613129400-1613131200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Kexin Li (Li JJ)
DESCRIPTION:TITLE: “scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling.” \nABSTRACT: 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.\, spatial) information; however\, they typically can only measure up to a few hundred genes. Then another challenging question is how to select genes for targeted gene profiling based on existing scRNA-seq data. Here we develop the single-cell Projective Non-negative Matrix Factorization (scPNMF) method to select informative genes from scRNA-seq data in an unsupervised way. Compared with existing gene selection methods\, scPNMF has two advantages. First\, its selected informative genes can better distinguish cell types. Second\, it enables the alignment of new targeted gene profiling data with reference data in a low-dimensional space to facilitate the prediction of cell types in the new data. Technically\, scPNMF modifies the PNMF algorithm for gene selection by changing the initialization and adding a basis selection step\, which selects informative bases to distinguish cell types. We demonstrate that scPNMF outperforms the state-of-the-art gene selection methods on diverse scRNA-seq datasets. Moreover\, we show that scPNMF can guide the design of targeted gene profiling experiments and cell-type annotation on targeted gene profiling data. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Kexin-Li-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-kexin-li-li-jj/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/KexinLi.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210219T110000
DTEND;TZID=America/Los_Angeles:20210219T113000
DTSTAMP:20260518T060145
CREATED:20210112T233728Z
LAST-MODIFIED:20210222T201152Z
UID:15821-1613732400-1613734200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Igor Nikolskiy (Wollman)
DESCRIPTION:TITLE: “A state space model to characterize the phenotypic variation in a panel of drug treatment time course experiments.” \nABSTRACT: 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 to generate hypotheses about the underlying drivers of behavior from global trends in the collected data.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-igor-nikolskiy-wollman/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/Igor-Nikolskiy.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210219T110000
DTEND;TZID=America/Los_Angeles:20210219T113000
DTSTAMP:20260518T060145
CREATED:20210128T192151Z
LAST-MODIFIED:20210222T150500Z
UID:16307-1613732400-1613734200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Maria Izabel Alves Cavassim (Lohmueller)
DESCRIPTION:TITLE: The evolution and co-evolution of PRDM9 across vertebrates \nABSTRACT: 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 independent PRDM9 losses to infer the co-evolution of PRDM9 with other meiosis-related genes. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Maria-Izabel-Alves-Cavassim-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-maria-izabel-alves-cavassim-lohmueller/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/Maria-Izabel-Alves-Cavassim.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210226T110000
DTEND;TZID=America/Los_Angeles:20210226T113000
DTSTAMP:20260518T060145
CREATED:20210106T171458Z
LAST-MODIFIED:20210226T202400Z
UID:15673-1614337200-1614339000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Amandine Gamble (Lloyd-Smith)
DESCRIPTION:TITLE: “Linking exposure dose to infectious disease development using mechanistic models” (using SARS-CoV-2 in a mouse model as an illustration) \nABSTRACT: 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 complex within-host models are generally parameterized with invasive data\, limiting their potential applications. I will present a modelling framework of the dose-dependence of disease development probability and incubation time using non-invasive data\, illustrated by experimental data collected in rodents exposed to SARS-CoV-2\, and the potential applications of such models. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Amandine-Gamble-edited.mp4\n 
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-amandine-gamble-lloyd-smith/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/01/Amandine-Gamble.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210226T113000
DTEND;TZID=America/Los_Angeles:20210226T120000
DTSTAMP:20260518T060145
CREATED:20210217T164027Z
LAST-MODIFIED:20210217T164031Z
UID:16662-1614339000-1614340800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Will Shoemaker (Garud)
DESCRIPTION:TITLE: “Inferring positive selection in the human gut microbiome using signatures of genetic linkage.” \nABSTRACT: 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 selection in microbial populations. I will then demonstrate how linkage can provide insight into the degree of positive and negative selection as well as the targets of adaptation across human microbiomes. Finally\, I will compare patterns of linkage disequilibria across hosts to the co-occurrence of mutations within a host. In sum\, the ability to examine linkage among large cohorts for many species provides an opportunity for researchers to examine novel patterns that are indicative of certain evolutionary dynamics.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-will-shoemaker-garud/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/02/Will-Shoemaker.jpeg
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