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X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences
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DTSTART:20200308T100000
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210305T110000
DTEND;TZID=America/Los_Angeles:20210305T113000
DTSTAMP:20260518T151416
CREATED:20210112T233946Z
LAST-MODIFIED:20210317T143543Z
UID:15824-1614942000-1614943800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Katherine Sheu (Hoffmann)
DESCRIPTION:TITLE: “Quantifying response-specificity to diverse immune threats from single cell transcriptomes” \nABSTRACT: Innate immune sentinel cells such as macrophages upregulate over a thousand genes in the minutes to hours following an encounter with pathogen invaders or damage signals. Previous bulk transcriptomic studies suggest there is stimulus-specificity in the combinations of genes that are activated. However\, bulk measurements do not reveal the distribution of responses\, precluding a quantification of response-specificity. Here\, we measure time-series single cell transcriptomic profiles of macrophages responding to diverse bacterial\, viral\, and host cytokine stimuli. We employ information theoretic and machine learning approaches to quantify how faithfully macrophage gene expression profiles relay information about the ligand encountered\, and which genes are important for distinguishing ligands\, based on their expression distributions across single cells. We find that microenvironmental context alters response-specificity\, and thus quantifying response-specificity may identify marks of inflammatory disease.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-katherine-sheu-hoffmann-2/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2020/04/Katherine-Sheu.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210305T113000
DTEND;TZID=America/Los_Angeles:20210305T120000
DTSTAMP:20260518T151416
CREATED:20210106T165755Z
LAST-MODIFIED:20210226T200911Z
UID:15662-1614943800-1614945600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Ali Pazokitoroudi (Sankararaman)
DESCRIPTION:TITLE: “Efficient variance components analysis across millions of genomes.” \nABSTRACT: While variance components analysis has emerged as a powerful tool in complex trait genetics\, existing methods for fitting variance components do not scale well to large-scale datasets of genetic variation. I will present a method for variance components analysis that is accurate and efficient: capable of estimating one hundred variance components on a million individuals genotyped at a million SNPs in a few hours. We illustrate the utility of our method in estimating and partitioning variation in a trait explained by genotyped SNPs (SNP-heritability). Analyzing 22 traits with genotypes from 300\,000 individuals across about 8 million common and low frequency SNPs\, we observe that per-allele squared effect size increases with decreasing minor allele frequency (MAF) and linkage disequilibrium (LD) consistent with the action of negative selection. Partitioning heritability across 28 functional annotations\, we observe enrichment of heritability in FANTOM5 enhancers in asthma\, eczema\, thyroid and autoimmune disorders.
URL:https://qcb.ucla.edu/event/qcbio-research-seminars-ali-pazokitoroudi-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/Ali-Pazakitoroudi.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210312T110000
DTEND;TZID=America/Los_Angeles:20210312T113000
DTSTAMP:20260518T151416
CREATED:20210304T173959Z
LAST-MODIFIED:20210316T003949Z
UID:17294-1615546800-1615548600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Sam Christensen (Roper)
DESCRIPTION:TITLE: “Asymptotic-Numerical Method For Cell Focusing in Microfluidic Channel.” \nABSTRACT: Inertial microfluidic devices use inertial lift forces to organize the spacing and positions of cells carried by flow.  A hybrid asymptotic-numerical method is presented that can calculate the migration velocities of cells in a channel by representing them as a combination singularities and discontinuities. Refinements to asymptotic analysis are given that improve the regularity of the PDE solution\, increasing the order of convergence for polynomial based numerical solvers. \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Sam-Christensen-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-sam-christensen-roper/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Sam-Christensen.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210312T113000
DTEND;TZID=America/Los_Angeles:20210312T120000
DTSTAMP:20260518T151416
CREATED:20210210T231400Z
LAST-MODIFIED:20210226T200841Z
UID:16525-1615548600-1615550400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Alexander Markowitz (Boutros)
DESCRIPTION:TITLE: “A pan-cancer landscape analysis of molecular and functional genomics in tumor proliferation.” \nABSTRACT: Rapid proliferation is a central hallmark of cancer and is associated with poor prognosis in most cancer types. My overall goal is to understand the mechanisms by which specific driver mutations and mutational signatures influence rates of tumor proliferation within and between cancer types and subtypes. I will do so by integrating model-system and patient data\, providing both descriptive and mechanistic insights into the origins\, consequences and targetability of unregulated proliferation in cancer.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-alexander-markowitz-boutros/
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/Alexander-Markowitz.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210329T110000
DTEND;TZID=America/Los_Angeles:20210329T120000
DTSTAMP:20260518T151416
CREATED:20210318T171239Z
LAST-MODIFIED:20210318T173825Z
UID:17542-1617015600-1617019200@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Vivian Li\, PhD
DESCRIPTION:Assistant Professor-Biostatistics\, Department of Biostatistics and Epidemiology\, Rutgers University\n“Model-based analysis of alternative polyadenylation using 3′ end reads” \nHosted by Jessica Li
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-vivian-li-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/1-1.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210402T110000
DTEND;TZID=America/Los_Angeles:20210402T110000
DTSTAMP:20260518T151416
CREATED:20210322T152126Z
LAST-MODIFIED:20210402T202258Z
UID:17594-1617361200-1617361200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Arjun Bhattacharya (Pasaniuc)
DESCRIPTION:TITLE: “Distal mediator-enriched placental transcriptome-wide association studies reveal genetic mechanisms supporting the  Developmental Origins of Health and Disease.” \nABSTRACT: As the master regulator of the intrauterine environment\, the placenta is core to the Developmental Origins of Health and Disease (DOHaD) but is understudied in large consortia of tissue-specific gene and trait regulation. We performed distal mediator-enriched transcriptome-wide association studies for 40 health outcomes across 5 categories\, using gene expression models trained from multi-omic data from the Extremely Low Gestational Age Newborn Study. I will discuss some of the novel methods we leverage in this analysis and the implications our computational and experimental results suggest on placental biology and health outcomes. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Arjun-Bhattacharya-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-arjun-bhattacharya-pasaniuc/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Arjun-Bhattacharya.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210402T113000
DTEND;TZID=America/Los_Angeles:20210402T120000
DTSTAMP:20260518T151416
CREATED:20210210T165325Z
LAST-MODIFIED:20210402T200850Z
UID:16520-1617363000-1617364800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Xinzhou Ge (Li JJ)
DESCRIPTION:TITLE: “Clipper: p-value-free FDR control on high-throughput data from two conditions.” \nABSTRACT: High-throughput biological data analysis commonly involves identifying “interesting” features (e.g.\, genes\, genomic regions\, and proteins)\, whose values differ between two conditions\, from numerous features measured simultaneously. The most widely-used criterion to ensure the analysis reliability is the false discovery rate (FDR). Existing bioinformatics tools primarily control the FDR based on p-values. However\, obtaining valid p-values relies on either reasonable assumptions of data distribution or large numbers of replicates under both conditions\, two requirements that are often unmet in biological studies. To address this issue\, we propose Clipper\, a general statistical framework for FDR control without relying on p-values or specific data distributions. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/02/Xinzhou-Ge-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminars-zinzhou-ge-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/14/2021/02/Zinzhou-Ge.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210405T110000
DTEND;TZID=America/Los_Angeles:20210405T120000
DTSTAMP:20260518T151416
CREATED:20210318T171819Z
LAST-MODIFIED:20210318T171819Z
UID:17548-1617620400-1617624000@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Nanibaa’ Garrison\, PhD
DESCRIPTION:Associate Professor\, UCLA Institute for Society and Genetics\n“TBD” \nHosted by Paivi Pajukanta
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-nanibaa-garrison-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/2.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210409T110000
DTEND;TZID=America/Los_Angeles:20210409T113000
DTSTAMP:20260518T151416
CREATED:20210323T144802Z
LAST-MODIFIED:20210409T225858Z
UID:17601-1617966000-1617967800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Casey Barkan (Wang)
DESCRIPTION:TITLE: “Critical slowing down signals quasi-species extinction in an evolutionary model with environmental heterogeneity.” \nABSTRACT: Environmental heterogeneity can significantly affect the evolutionary dynamics of a population. A key parameter that determines the influence of heterogeneity is the migration rate–the rate at which organisms explore their heterogeneous environment. We study a model of a population which migrates between two habitats that exert distinct selection pressure on the population. We find that the system undergoes multiple phase transitions\, each associated with the extinction of a quasispecies. The dynamics exhibit critical slowing down near each transition. Our results may be relevant to the evolution of antibiotic resistance in bacteria and evolution of gut microbiota. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Casey-Barkan-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-casey-barkan-wang/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Casey-Barkan.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210409T113000
DTEND;TZID=America/Los_Angeles:20210409T120000
DTSTAMP:20260518T151416
CREATED:20210323T144940Z
LAST-MODIFIED:20210409T195622Z
UID:17604-1617967800-1617969600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Aliya Lakhani (Park)
DESCRIPTION:TITLE: “Integrating metabolomics and fluxomics to study cancer metabolism in low glucose environments.” \nABSTRACT: Metabolomics and fluxomics are integral tools for quantitative metabolic analysis. By combining mass spectrometry\, isotope tracing\, and mathematical modeling\, we can quantify metabolite concentrations and fluxes in cancer cells. Using these tools\, we are investigating the coordination of bioenergetics\, biosynthesis\, and redox metabolism of cancer cells in the tumor microenvironment. We hypothesize that the tumor microenvironment plays a significant role in dictating cancer cell survival and proliferation. To shed light on how cancer cells use the tumor microenvironment\, we assessed their adaptability to high levels of lactate. While cancer cells did not have a growth advantage over healthy cells in the high-lactate environment\, we found that an intermittent supply of glucose allowed cancer cells to proliferate faster than healthy cells. By tracing stable isotopes from lactate and glutamine across metabolism\, we elucidate the role of lactate in cancer cell survival via gluconeogenesis and energy metabolism. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Aliya-Lakhani-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-aliya-lakhani-park/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Aliya-Lakhani.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210412T110000
DTEND;TZID=America/Los_Angeles:20210412T120000
DTSTAMP:20260518T151416
CREATED:20210318T172007Z
LAST-MODIFIED:20210318T172007Z
UID:17552-1618225200-1618228800@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Martin Kampmann\, PhD
DESCRIPTION:Associate Professor\, Department of Biochemistry and Biophysics\, UCSF\n“TBD” \nHosted by David Eisenberg
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-martin-kampmann-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/3.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210416T110000
DTEND;TZID=America/Los_Angeles:20210416T113000
DTSTAMP:20260518T151416
CREATED:20210323T145202Z
LAST-MODIFIED:20210409T061938Z
UID:17608-1618570800-1618572600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Juan de la Hoz Gomez (Olde Loohuis & Freimer)
DESCRIPTION:TITLE:“Longitudinal phenotyping of Severe Mental Illness from Electronic Health Records.” \nABSTRACT:Electronic Health Records (EHRs) offer an exciting avenue for large-scale genetic studies of psychiatric disorders in globally diverse populations. As a potential source of inexpensive and longitudinal phenotypes\, they are key for the study of severe mental illness trajectories. The Clinica San Juan de Dios is the only psychiatric hospital in Caldas\, Colombia\, serving a population of 1M people. We leverage their 15+ years of EHRs in order to 1) validate diagnoses of severe mental illness\, 2) extract trans-diagnostic symptom information from free text using clinical NLP\, and 3) explore patterns of temporal phenotypic variation. In addition to providing insights into the trajectory of psychiatric diagnoses\, this dataset serves as a valuable resource for genetic investigation of mental illness in admixed populations.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-juan-de-la-hoz-gomez-olde-loohuis-freimer/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Juan-de-la-Hoz-Gomez.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210416T113000
DTEND;TZID=America/Los_Angeles:20210416T120000
DTSTAMP:20260518T151416
CREATED:20210323T145340Z
LAST-MODIFIED:20210416T225835Z
UID:17611-1618572600-1618574400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Alec Chiu (Sankararaman)
DESCRIPTION:TITLE: “Population structure inference for biobank-scale data.” \nABSTRACT: Inferring the structure of human populations from genetic variation data is a key task in population and medical genomic studies. While a number of methods for population structure inference have been proposed\, current methods are impractical to run on biobank-scale genomic datasets containing millions of individuals and genetic variants. We introduce SCOPE\, a method that can infer population structure from biobank-scale data. We show that SCOPE is as or more accurate than existing methods while being orders of magnitude faster. SCOPE able to infer population structure in about a day on a dataset consisting of one million individuals and SNPs. Furthermore\, SCOPE is able to incorporate allele frequencies from previous studies in a supervised fashion to further aid interpretability of estimated admixture proportions.  \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Alec-Chiu-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-alec-chiu-sankararaman/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Alec-Chiu-scaled.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210419T110000
DTEND;TZID=America/Los_Angeles:20210419T120000
DTSTAMP:20260518T151416
CREATED:20210318T172226Z
LAST-MODIFIED:20210318T172226Z
UID:17556-1618830000-1618833600@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Smita Krishnaswamy\, PhD
DESCRIPTION:Associate Professor of Genetics and of Computer Science\, Yale School of Medicine\n“TBD” \nHosted by Jason Ernst
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-smita-krishnaswamy-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/4.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210423T110000
DTEND;TZID=America/Los_Angeles:20210423T120000
DTSTAMP:20260518T151416
CREATED:20210416T190850Z
LAST-MODIFIED:20210416T190850Z
UID:17846-1619175600-1619179200@qcb.ucla.edu
SUMMARY:Townhall on Diversity\, Equity & Inclusion
DESCRIPTION:
URL:https://qcb.ucla.edu/event/townhall-on-diversity-equity-inclusion/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/04/DEI-Townhall-Flyer-4.23.21-without-zoom-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210426T110000
DTEND;TZID=America/Los_Angeles:20210426T120000
DTSTAMP:20260518T151416
CREATED:20210318T172428Z
LAST-MODIFIED:20210318T173922Z
UID:17560-1619434800-1619438400@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Jennifer E. Phillips-Cremins\, PhD
DESCRIPTION:Assistant Professor of Bioengineering\, University of Pennsylvania\n“Genome folding\, unfolding\, and refolding in the mammalian brain” \nHosted by Hilary Coller
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-jennifer-e-phillips-cremins-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/5.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210430T110000
DTEND;TZID=America/Los_Angeles:20210430T113000
DTSTAMP:20260518T151416
CREATED:20210422T144613Z
LAST-MODIFIED:20210621T163019Z
UID:17955-1619780400-1619782200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Ashfaq Ahmed (Venugopal)
DESCRIPTION:TITLE: “Mechanisms of robust entrainment of biological oscillators involved in gastric peristalsis.”\nABSTRACT: Oscillator entrainment is a widely observed phenomenon in natural systems. Using a computational modeling approach\, we decipher the essential intrinsic and extrinsic mechanisms of robust entrainment of biological oscillators involved in gastric peristalsis. Specifically\, we show that the constitutive intercellular IP3-facilitated pacemaker pathway in these cells stabilizes cellular frequencies\, extends longitudinal entrainment range\, and enables rostro-caudal spread of a gastric slow-wave in a realistic multi-cellular coupled network. Our comprehensive model and the novel predictions offer directions for future experiments and theoretical work. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/04/Ashfaq-Ahmed-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-ashfaq-ahmed-venugopal/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/04/Ashfaq-Ahmed.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210430T113000
DTEND;TZID=America/Los_Angeles:20210430T120000
DTSTAMP:20260518T151416
CREATED:20210331T002943Z
LAST-MODIFIED:20210504T033951Z
UID:17713-1619782200-1619784000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Alexis Weber (Geschwind & de la Torre-Ubieta)
DESCRIPTION:TITLE: “Defining chromatin accessibility and molecular dysregulation in Down Syndrome.” \nABSTRACT: Despite accumulating almost two centuries of medical information\, the exact mechanisms underlying Down Syndrome (DS) developmental pathology remain unknown. DS is caused by trisomy of chromosome21 (T21)\, but without pinpointing the way in which T21 confers molecular dysfunctions and subsequently impairs neurodevelopment\, it has been difficult to devise medical interventions that will reduce cognitive deficits.  In order to identify these mechanisms in DS and deconvolute the inherent complexity of the developing brain\, we are leveraging single cell technologies to contrast DS and healthy expression profiles and chromatin accessibility in midgestation brain tissue and patient-derived primary human neural progenitor cells (phNPCs). Based on previous bulk RNA and chromatin analyses in DS samples and our preliminary data\, we anticipate 1) changes in cell composition and 2) altered gene-regulatory networks affecting neurogenesis pathways in neural progenitors\, oligodendrocyte precursor cells\, and astrocytes. By uncovering these cytological and molecular aberrations\, we hope to progress the understanding of neurodevelopment and DS to promote medical advances in the future. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Alexis-Weber-edited-1.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-alexis-weber-geschwind-de-la-torre-ubieta/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/HG-Weber.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210503T110000
DTEND;TZID=America/Los_Angeles:20210503T120000
DTSTAMP:20260518T151416
CREATED:20210318T172822Z
LAST-MODIFIED:20210318T172822Z
UID:17564-1620039600-1620043200@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Aaron Panofsky\, PhD
DESCRIPTION:Associate Professor and Vice Chair of Academic Personnel\, UCLA Institute for Society and Genetics \n “Citizen Scientific Racism: White Nationalist Appropriations of Genetic Research” \nHosted by Christina Palmer \n 
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-aaron-panofsky-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/6.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210507T110000
DTEND;TZID=America/Los_Angeles:20210507T113000
DTSTAMP:20260518T151416
CREATED:20210427T022748Z
LAST-MODIFIED:20210510T164035Z
UID:17994-1620385200-1620387000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Erin Molloy (Sankararaman)
DESCRIPTION:TITLE: “Advancing admixture graph estimation via maximum likelihood network orientation.” \nABSTRACT: Admixture\, the interbreeding between previously distinct populations\, is a pervasive force in evolution. The evolutionary history of populations in the presence of admixture can be modeled by augmenting phylogenetic trees with additional nodes that represent admixture events. However\, these admixture graphs present formidable inferential challenges. Exhaustively evaluating all admixture graphs can be prohibitively expensive\, so heuristics have been developed to enable efficient search. One heuristic\, implemented in the popular method TreeMix\, consists of adding edges to a starting tree while optimizing a suitable objective function. In this talk\, we will present a demographic model (with one admixed population incident to a leaf) where TreeMix and any other starting-tree-based maximum likelihood heuristic using its likelihood function is guaranteed to get stuck in a local optimum and return an incorrect network topology. We will then demonstrate how this issue can be addressed using our new search strategy: maximum likelihood network orientation (MLNO).\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/04/Erin-Molloy-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-erin-molloy-sankararaman/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/04/erin-molloy.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210507T113000
DTEND;TZID=America/Los_Angeles:20210507T120000
DTSTAMP:20260518T151416
CREATED:20210427T022301Z
LAST-MODIFIED:20210510T164111Z
UID:17990-1620387000-1620388800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Ruochen Jiang (Li JJ)
DESCRIPTION:TITLE: “Sources of zeros in single-cell RNA-seq data and how they affect data analysis.” \nABSTRACT: Single-cell RNA sequencing (scRNA-seq) technologies have revolutionized biomedical sciences by enabling genome-wide profiling of gene expression levels at an unprecedented single-cell resolution. A distinct characteristic of scRNA-seq data is the vast proportion of zeros unseen in bulk RNA-seq data. Researchers view these zeros differently: some regard zeros as biological signals representing no or low gene expression\, while others regard zeros as false signals or missing data to be corrected. As a result\, the scRNA-seq field faces much controversy regarding how to handle zeros in data analysis. In this paper\, we first discuss the sources of biological and non-biological zeros in scRNA-seq data. Second\, we summarize the advantages\, disadvantages\, and suitable users of three input data types: original counts\, imputed counts\, and binarized counts. Third\, we evaluate the impacts of non-biological zeros on cell clustering and differential gene expression analysis. Finally\, we discuss the open questions regarding non-biological zeros\, the need for benchmarking\, and the importance of transparent analysis.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/04/Ruochen-Jiang-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-ruochen-jiang-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/14/2021/04/Ruochen-Jiang.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210510T110000
DTEND;TZID=America/Los_Angeles:20210510T120000
DTSTAMP:20260518T151416
CREATED:20210318T173032Z
LAST-MODIFIED:20210318T173032Z
UID:17568-1620644400-1620648000@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Alexandra Stern\, PhD
DESCRIPTION:Associate Dean for the Humanities\, University of Michigan-Ann Arbor \n“TBD: History of genetic counseling” \nHosted by Christina Palmer
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-alexandra-stern-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/7.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210514T110000
DTEND;TZID=America/Los_Angeles:20210514T113000
DTSTAMP:20260518T151416
CREATED:20210331T001923Z
LAST-MODIFIED:20210514T192335Z
UID:17706-1620990000-1620991800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Brian Orcutt-Jahns (Meyer)
DESCRIPTION:TITLE: “A simple\, two-step\, multivalent binding model predicts IL-2 mutein cell signaling profiles.” \nABSTRACT: The common γ-chain cytokines are promising immune therapies\, but have been limited in their efficacy due to their induction of non-specific immune activation. Here\, we visualized immune cell response to both mono- and multivalent γ-chain muteins using a structured dimensionality reduction scheme. We then used a simple multivalent binding model to predict cell type-specific signaling with high accuracy. Finally\, we use this model to generate guidelines for engineering more effective γ-chain therapeutics. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Brian-Orcutt-Jahns-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-brian-orcutt-jahns-meyer/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Brian-Orcutt-Jahns.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210514T110000
DTEND;TZID=America/Los_Angeles:20210514T120000
DTSTAMP:20260518T151416
CREATED:20210503T185337Z
LAST-MODIFIED:20210514T193804Z
UID:18011-1620990000-1620993600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Rina Ding (Hsu)
DESCRIPTION:TITLE: “Multimodal radiomic analysis of biparametric MRI to predict biochemical recurrence after radical prostatectomy.” \nABSTRACT: Integration of information across multiple modalities and biological scales has the potential to improve the prediction of disease outcomes and response to treatments. In this talk\, I will discuss our ongoing work to predict prostate cancer aggressiveness by combining information from biparametric MRI. We predict biochemical recurrence (BCR) in 343 men post radical prostatectomy by fusing quantitative image features extracted from T2- and diffusion-weighted scans. We found the fused features improved the prediction of BCR when compared to various baseline models and clinical assessments. In the future\, we intend to incorporate genomic data\, relating imaging phenotypes to underlying tumor biology.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/05/Rina-Ding-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-rina-ding-hsu/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/05/Rina-Ding-1-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210517T110000
DTEND;TZID=America/Los_Angeles:20210517T120000
DTSTAMP:20260518T151416
CREATED:20210318T173219Z
LAST-MODIFIED:20210318T173219Z
UID:17572-1621249200-1621252800@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Viktor Adalsteinsson\, PhD
DESCRIPTION:Associate director\, Gerstner Center for Cancer Diagnostics\, Broad Institute \n“Ultrasensitive detection of minimal residual disease” \nHosted by Jasmine Zhou
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-viktor-adalsteinsson-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/8.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210521T110000
DTEND;TZID=America/Los_Angeles:20210521T113000
DTSTAMP:20260518T151416
CREATED:20210325T232203Z
LAST-MODIFIED:20210522T164828Z
UID:17676-1621594800-1621596600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Olga Schubert (Kruglyak)
DESCRIPTION:TITLE: “Genome-wide survey of mutations influencing protein abundances in yeast” \nABSTRACT: Our understanding of how protein-level regulation is encoded in the genome and how protein abundances are affected by DNA sequence variation remains sparse. I will discuss our genetic screen based on large-scale pooled base editing that allows us to capture the effects of thousands of mutations on the abundance of individual proteins in yeast. We applied this screen to 11 proteins and gained new insights into the components\, scale and connectedness of genetic networks underlying the regulation of protein abundances.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/03/Olga-Schubert-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-olga-schubert-kruglyak/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/Olga-Schubert.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210521T113000
DTEND;TZID=America/Los_Angeles:20210521T120000
DTSTAMP:20260518T151416
CREATED:20210409T062722Z
LAST-MODIFIED:20210522T164914Z
UID:17753-1621596600-1621598400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Shamus Cooley (Deeds)
DESCRIPTION:TITLE: “Unbiased analysis of single cell RNA sequencing data reveals previously uncharacterized heterogeneity in small cell lung cancer cell lines.” \nABSTRACT: Small Cell Lung Cancer (SCLC) accounts for approximately 13% of all new lung cancer diagnoses.  SCLC exhibits propensity for early metastasis\, rapid cell division\, high levels of replication stress\, the ability to cope with certain oxidative and metabolic stresses\, and evasion of apoptosis and the effector cells of the immune system. Together\, these factors contribute to an exceedingly poor prognosis with patient survival measured in months\, not years\, that has led to a recalcitrant cancer designation for SCLC by the National Cancer Institute.  Nevertheless\, systemic therapies that include immunotherapy are beginning to show promise in the clinic. Although\, these results are encouraging\, many patients do not respond to\, or rapidly recur after\, current regimens\, necessitating alternative or complementary therapeutic strategies.  Heterogeneity of cancer cells is a key factor by which tumors resist treatment\, and It is increasingly appreciated that there are discrete molecular subtypes of SCLC that can differ in their response to different therapies.  In my talk\, I will describe how we use gene expression data obtained from single-cell RNA sequencing of eight immortalized SCLC cell lines to characterize heterogeneity in SCLC.  I will show that\, in addition to established classification of cancer sub-types\, there is an orthogonal axis of heterogeneity in which exist distinct subpopulations\, each with its own unique gene expression profile.  One such subpopulation is characterized by stem-like properties and decreased expression of key signaling proteins. This finding suggests that SCLC tumors are highly heterogeneous in make-up\, and that consideration of this stem-like subpopulation will be critical for the development of effective therapeutics.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/04/Shamus-Cooley-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-shamus-cooley-deeds/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/04/Shamus-Cooley.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210524T110000
DTEND;TZID=America/Los_Angeles:20210524T120000
DTSTAMP:20260518T151416
CREATED:20210318T173355Z
LAST-MODIFIED:20210318T173355Z
UID:17576-1621854000-1621857600@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Raluca Gordân\, PhD
DESCRIPTION:Associate Professor\, Biostatistics & Bioinformatics\, Center for Genomic and Computational Biology\, Duke University \n“TBD” \nHosted by Jason Ernst
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-raluca-gordan-phd/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/03/9.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210528T110000
DTEND;TZID=America/Los_Angeles:20210528T113000
DTSTAMP:20260518T151416
CREATED:20210512T184047Z
LAST-MODIFIED:20210601T154745Z
UID:18164-1622199600-1622201400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Yi Ding (Pasaniuc)
DESCRIPTION:TITLE: “Large uncertainty in individual PRS estimation impacts PRS-based risk stratification.”\nABSTRACT: Large-scale genome-wide association studies have enabled polygenic risk scores (PRS)\, which estimate the genetic value of an individual for a given trait. Since PRS accuracy is typically assessed using cohort-level metrics\, uncertainty in PRS estimates at individual level remains underexplored. In this talk\, we will first introduce a Bayesian framework that can estimate the variance of an individual’s PRS and can yield well-calibrated credible intervals for the genetic value of a single individual. Then we will discuss the impact of PRS uncertainty on risk stratification and present a probabilistic PRS-based risk stratification approach to incorporate the uncertainty in individual PRS estimates. Finally\, we’ll present a theoretical estimate of individual PRS variance as a function of heritability\, number of causal SNPs and sample size.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/05/Yi-Ding-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-yi-ding-pasaniuc/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/05/Yi-Ding.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20210528T110000
DTEND;TZID=America/Los_Angeles:20210528T113000
DTSTAMP:20260518T151416
CREATED:20210520T191323Z
LAST-MODIFIED:20210527T021150Z
UID:18199-1622199600-1622201400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Jakob Von Morgenland (Venugopal)
DESCRIPTION:TITLE: “Constructing a Functional Interactome from Published Work to Identify Underrepresented and Integrative Effects of Neuroinflammatory Cytokines on Neural Excitability.” \nABSTRACT: Maintaining normal excitability is a key function of our nervous system which is subject to ongoing perturbations such as aging and chronic neurodegeneration. Neuroinflammatory responses which are widely associated with injury and disease are often disregarded as ongoing modulators of brain excitability. Indeed\, neuroinflammatory cytokines such as TNF-α released by resident glial cells in the nervous system can modify ionic conductivity in neurons at nano-molar concentrations at acute and chronic timescales and in turn can mediate emergence of neural dysfunctions observed during disease development. This suggests that understanding how and when cytokines act on neurons could represent targets for therapeutic modulation. Therefore\, we set out to examine in existing literature how strong are the evidence for neuroinflammatory modulation of neural excitability. Surprisingly\, neither the database search using popular bioinformatics tools such as the STRING\, nor the top hits on Pubmed search using keywords such as “cytokine” AND “ion channels” revealed strong evidence for molecular interactions between inflammatory cytokines in the brain and voltage-gated ion channel proteins responsible for neural signaling. However\, a more detailed examination of the literature uncovered a few yet convincing mechanistic studies demonstrating that cytokines can induce changes in ionic conductivity\, ion channel protein expression as well as action potential frequencies. Driven by these findings\, we set out to develop a novel functional interaction score (FIS) to quantitate the strength of evidence for cytokine actions on neural excitability. We then used such scores to generate a protein-protein interactome to enable further application of graph theory-based approaches to analyze the functional links between neuroinflammation and neural excitability. Our analysis and novel scoring also revealed 1-to-N associations between cytokines and ion channel proteins. In my talk\, I will discuss this journey and also share our ongoing innovative approach using the cytokine-ion channel associations in dynamic neuron models as predictive tools to test integrative actions of cytokines on neuronal excitability.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-jakob-von-morgenland-venugopal/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/05/Jakob-von-Morgenland.jpg
END:VEVENT
END:VCALENDAR