BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Institute for Quantitative and Computational Biosciences - ECPv6.16.2//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-ORIGINAL-URL:https://qcb.ucla.edu X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:America/Los_Angeles BEGIN:DAYLIGHT TZOFFSETFROM:-0800 TZOFFSETTO:-0700 TZNAME:PDT DTSTART:20200308T100000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0700 TZOFFSETTO:-0800 TZNAME:PST DTSTART:20201101T090000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:-0800 TZOFFSETTO:-0700 TZNAME:PDT DTSTART:20210314T100000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0700 TZOFFSETTO:-0800 TZNAME:PST DTSTART:20211107T090000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:-0800 TZOFFSETTO:-0700 TZNAME:PDT DTSTART:20220313T100000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0700 TZOFFSETTO:-0800 TZNAME:PST DTSTART:20221106T090000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210521T113000 DTEND;TZID=America/Los_Angeles:20210521T120000 DTSTAMP:20260518T064611 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.\n\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:20260518T064611 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:20260518T064611 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:20260518T064611 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 BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210604T110000 DTEND;TZID=America/Los_Angeles:20210604T113000 DTSTAMP:20260518T064611 CREATED:20210327T144110Z LAST-MODIFIED:20210528T150155Z UID:17682-1622804400-1622806200@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Amelia Palermo (Graeber) DESCRIPTION:TITLE: “Metabolic dependencies of ecDNA and HSR focal amplification modes and plasticity.” \nABSTRACT: The focal amplification (FA) of genes that support the uncontrolled growth and proliferation of cells (i.e.\, oncogenes) on homogeneous chromosomal staining regions (HSRs\, chromosomal) ans extrachromosomal DNA (ecDNA) is a hallmark of resistant cancers. However\, it remains an open question whether oncogene FA is affected by cellular metabolism and by the composition of the tumor microenvironment. This is important because cancers carrying oncogene focal amplifications\, particularly on ecDNA\, can evolve fast\, and are highly malignant and difficult to treat. In this context\, our group recently observed high plasticity of ecDNA+/HSR+ BRAF amplification upon combined BRAF plus MEK inhibitor (i.e.\, vemurafenib plus selumetinib) escalation in an in-house model of resistant melanoma. We profiled this in vitro model by metabolomics and lipidomics analysis\, revealing that both FA- vs FA+\, and ecDNA+ vs HSR+ cells are characterized by extensive metabolism reprogramming and substantial changes in lipid composition. Ultimately\, our observations support the hypothesis that oncogene focal amplification on ecDNA and HSRs can be modulated by leveraging unique metabolic vulnerabilities. URL:https://qcb.ucla.edu/event/qcbio-research-seminar-amelia-palermo-graeber/ 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/Amelia-Palermo.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210604T113000 DTEND;TZID=America/Los_Angeles:20210604T120000 DTSTAMP:20260518T064611 CREATED:20210528T004803Z LAST-MODIFIED:20210604T195111Z UID:18220-1622806200-1622808000@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Nan (Miles) Xi (Li JJ) DESCRIPTION:TITLE: “DoubletCollection: An R package that integrates cutting-edge computational doublet-detection methods.”\nABSTRACT: The existence of doublets is a key confounder in single-cell RNA sequencing (scRNA-seq) data analysis. There are several computational methods for detecting doublets from scRNA-seq data.\nWe develop an R package DoubletCollection to integrate the installation and execution of those methods. DoubletCollection also provides a unified interface to perform and visualize downstream analysis after doublet detection.\nIn this talk\, we will introduce a protocol of using DoubletCollection to benchmark doublet-detection methods. This protocol can automatically accommodate new doublet-detection methods and datasets in the fast-growing scRNA-seq field.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/05/Nan-Miles-Xi-edited.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-nan-miles-xi-li-jj-2/ 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/Nan-Miles-Xi.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210702T140000 DTEND;TZID=America/Los_Angeles:20210702T143000 DTSTAMP:20260518T064611 CREATED:20210630T133436Z LAST-MODIFIED:20210720T145203Z UID:18304-1625234400-1625236200@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: Jingyi Jessica Li DESCRIPTION:TITLE: “Applications of generalized additive models and copulas to single-cell RNAseq computational method development: PseudotimeDE and scDesign2” \nABSTRACT:\nPart 1: PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data \nTo investigate molecular mechanisms underlying cell state changes\, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. However\, existing methods do not account for pseudotime inference uncertainty\, and they have either ill-posed p-values or restrictive models. Here we propose PseudotimeDE\, a DE gene identification method that adapts to various pseudotime inference methods\, accounts for pseudotime inference uncertainty\, and outputs well-calibrated p-values. Comprehensive simulations and real-data applications verify that PseudotimeDE outperforms existing methods in false discovery rate control and power. \nPart 2: scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured \nA pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators\, but existing simulators cannot simultaneously achieve three goals: preserving genes\, capturing gene correlations\, and generating any number of cells with varying sequencing depths. To fill this gap\, we propose scDesign2\, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular\, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/06/Jessica-Li-7.2.21-edited.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-jingyi-jessica-li/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/06/7.2.21-Jessica-Li.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210709T140000 DTEND;TZID=America/Los_Angeles:20210709T143000 DTSTAMP:20260518T064611 CREATED:20210630T133900Z LAST-MODIFIED:20210630T133904Z UID:18309-1625839200-1625841000@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: Paivi Pajukanta DESCRIPTION:TITLE: “Integrating single cell omics and deep phenotype data to discover genes underlying cardiometabolic disorders” \nABSTRACT: Obesity predisposes to cardiometabolic disorders (CMDs)\, such as type 2 diabetes\, multiple dyslipidemias\, and non-alcoholic fatty liver disease (NAFLD). We are interested in how cell-type level gene expression contributes to CMDs and impacts cross talk between cardiometabolic tissues. We hypothesized that obesity-induced inflammatory changes in adipose tissue alter the cell-type composition and key functions of this obesity responsive tissue\, which drives ectopic deposition of fat into the liver. To this end\, we have generated adipose and liver single nucleus RNA-seq reference data sets\, and leveraged the cell-type markers identified in these reference data sets to decompose cell-type proportions in bulk adipose tissue and liver RNA-seq cohorts. This decomposition has allowed us to identify which adipose tissue and liver cell-types are associated with human CMDs. Moving forward\, our goal is to discover genetic and biological mechanisms underlying CMDs at the single cell resolution. URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-paivi-pajukanta/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/06/paivi-copy.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210716T140000 DTEND;TZID=America/Los_Angeles:20210716T143000 DTSTAMP:20260518T064611 CREATED:20210709T221802Z LAST-MODIFIED:20210720T145037Z UID:18333-1626444000-1626445800@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: Hilary Coller DESCRIPTION:TITLE: “Is there a Quiescence Histone Code?” \nABSTRACT: Many of the cells in our bodies are quiescent\, that is\, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance\, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing\, stem cell maintenance\, and immunological responses. Histone modifications have been shown to play a role in chromatin packing and accessibility\, nucleosome mobility\, gene expression\, and chromosome arrangement. We have been testing the role of the H4K20me3 mark as a regulator of quiescence in cultured cells and in mice. Our data implicate this histone mark in chromatin compaction\, cell proliferation\, chromosome positioning\, expression of critical cell cycle regulatory proteins\, and mouse growth during development. Moving forward\, our goal is to test whether H4K20me3 is part of a histone code that ensures proper chromosome compaction and positioning to establish and maintain a quiescent state. URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-hilary-coller/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/07/7.16.21-Hilary-Coller-V2.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210724T140000 DTEND;TZID=America/Los_Angeles:20210724T143000 DTSTAMP:20260518T064611 CREATED:20210720T144701Z LAST-MODIFIED:20210726T170612Z UID:18460-1627135200-1627137000@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: Harold Pimentel DESCRIPTION:TITLE: “Model driven design and analysis of quantitative phenotype screens” \nABSTRACT: Increasingly\, CRISPR screens are coupled with flow cytometry (FACS) to sort cells and quantify the \nimpact of genetic perturbations on a continuous phenotype. While FACS provides much more \nquantitative information than simple survival screens\, it introduces a number of experimental and \nstatistical challenges. Furthermore\, as experimentalists push these screens in limited primary cells \nor in vivo\, they lack principled guidelines on how experimental parameters including multiplicity of \ninfection\, guide RNA coverage\, or FACS bin cutoffs affect statistical power. We present models for \nboth experimental design and inference of gene regulation in these screens. We show that \ncommonly used parameters are far from optimal and screens can be performed with a 20 times \nreduction in cells at comparable accuracy. Our inference procedure models biological replicates\, \ninfers the latent protein distribution\, and infers experimental parameters. Together these analyses \nprovide a holistic framework for designing and analyzing highly parallel FACS screens. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/07/Harold-Pimentel-edited.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-harold-pimentel/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/07/7.23.21-Harold-Pimentel.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210730T140000 DTEND;TZID=America/Los_Angeles:20210730T143000 DTSTAMP:20260518T064611 CREATED:20210720T144936Z LAST-MODIFIED:20210730T223229Z UID:18464-1627653600-1627655400@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: David Wong DESCRIPTION:TITLE: “Salivary exRNA for Gastric Cancer Detection” \nABSTRACT: Biomarkers are needed for non-invasive early detection of gastric cancer (GC). We investigated whether salivary extracellular RNA (exRNA) biomarkers can be used as an efficient and economical clinical evaluation tool for GC. Unstimulated whole saliva samples were prospectively collected from 294 subjects (163 GC and 131 non-GC controls) who underwent endoscopic evaluation at the Samsung Medical Center in Korea. The salivary transcriptomes of 63 GC and 31 non-GC controls were profiled\, and mRNA biomarker candidates were verified with RT-qPCR. In parallel\, microRNA biomarkers were profiled and verified with saliva samples from 10 GC and 10 controls. Candidate biomarkers were validated with RT-qPCR in an independent cohort of 100/100 saliva samples from GC and non-GC patients. Validated individual markers were configured into a best performance panel. We identified 30 mRNA and 15 miRNA candidates whose expression pattern associated with the presence of gastric cancer. Among them\, 12 mRNA and 6 miRNA candidates were verified with the discovery cohort by RT-qPCR and further validated with the independent cohort (n=200). The configured biomarker panel consisted of 3 mRNAs (SPINK7\, PPL and SEMA4B) and 2 miRNAs (miR-140-5p and miR-301a)\, which were all significantly down-regulated in GC group\, yielded an AUC of 0.81 (95%CI\, 0.72-0.89). When combined with demographic factors\, the performance of the panel reached an AUC of 0.87 (95%CI\, 0.80-0.93). We have discovered and validated a panel of salivary exRNA biomarkers with credible clinical performance for the detection of GC. Our study demonstrates the credential of salivary exRNA biomarker as a potential screening and risk-assessing tool for GC. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/07/David-Wong-edited.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-david-wong/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/07/7.30.21-David-Wong.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210806T140000 DTEND;TZID=America/Los_Angeles:20210806T143000 DTSTAMP:20260518T064611 CREATED:20210726T165209Z LAST-MODIFIED:20210809T140637Z UID:18492-1628258400-1628260200@qcb.ucla.edu SUMMARY:QCBio Research Seminar in collaboration with B.I.G. Summer: Valerie Arboleda DESCRIPTION:TITLE: “From Bench to Vending Machine: Development and Deployment of Novel Diagnostic testing for SARS-CoV-2 using Genomic Technology” \nABSTRACT: Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity\, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here\, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay\, which we named SwabSeq\, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives\, and that reduces the requirements for automation\, purification and sample-to-sample normalization. We used SwabSeq to perform 80\,000 tests\, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests\, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/07/Valerie-Arboleda-edited.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-in-collaboration-with-b-i-g-summer-valerie-arboleda2/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/07/8.6.21-Valerie-Arboleda.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20210927T110000 DTEND;TZID=America/Los_Angeles:20210927T120000 DTSTAMP:20260518T064611 CREATED:20210916T150045Z LAST-MODIFIED:20210916T155236Z UID:18816-1632740400-1632744000@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Karen Mohlke\, Professor\, Genetics\, School of Medicine\, UNC-Chapel Hill DESCRIPTION:“Genetic and environmental effects on chromatin accessibility at cardiometabolic trait loci” \nHosted by Paivi Pajukanta URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-karen-mohlke-professor-genetics-school-of-medicine-unc-chapel-hill/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Mohlke.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211004T110000 DTEND;TZID=America/Los_Angeles:20211004T120000 DTSTAMP:20260518T064611 CREATED:20210916T150436Z LAST-MODIFIED:20210916T155209Z UID:18822-1633345200-1633348800@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Abigail Bigham\, Associate Professor\, Anthropology\, UCLA DESCRIPTION:“Omic insights into Andean high-altitude adaptation” \nHosted by Jason Ernst URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-abigail-bigham-associate-professor-anthropology-ucla/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Bigham.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211011T110000 DTEND;TZID=America/Los_Angeles:20211011T120000 DTSTAMP:20260518T064611 CREATED:20210916T150622Z LAST-MODIFIED:20210916T155139Z UID:18826-1633950000-1633953600@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Maria C. Avila Arcos\, Assistant Professor\, Internat. Laboratory for Human Genome Research\, Universidad Nacional Autonoma de Mexico DESCRIPTION:“The genetic legacy of the trans-atlantic slave trade into New Spain” \nHosted by Kirk Lohmueller URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-maria-c-avila-arcos-assistant-professor-internat-laboratory-for-human-genome-research-universidad-nacional-autonoma-de-mexico/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Arcos.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211018T110000 DTEND;TZID=America/Los_Angeles:20211018T120000 DTSTAMP:20260518T064611 CREATED:20210916T150832Z LAST-MODIFIED:20210916T150832Z UID:18830-1634554800-1634558400@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Doug Speed\, Professor\, Center for Quantitative Genetics and Genomics\, Aarhus University DESCRIPTION:“New methods for analyzing genome-wide association study data\, including improved tools for computing polygenic risk\nscores” \nHosted by Maria Izabel Cavassim URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-doug-speed-professor-center-for-quantitative-genetics-and-genomics-aarhus-university/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Speed.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211025T110000 DTEND;TZID=America/Los_Angeles:20211025T120000 DTSTAMP:20260518T064611 CREATED:20210916T151712Z LAST-MODIFIED:20211022T164227Z UID:18835-1635159600-1635163200@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Fabian Theis\, Head of the Institute of Computational Biology at Gelmholtz Munich\, Professor\, Technical University of Munich DESCRIPTION:TITLE: “Learning cellular state and dynamics in single cell genomics” \nHosted by Jessica Li URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-fabian-theis-phd-head-of-the-institute-of-computational-biology-at-gelmholtz-munich-professor-technical-university-of-munich/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/THEIS.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211027T120000 DTEND;TZID=America/Los_Angeles:20211027T123000 DTSTAMP:20260518T064611 CREATED:20211017T155101Z LAST-MODIFIED:20211029T185848Z UID:19702-1635336000-1635337800@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Giovanni Quinones Valdez (Xiao)\, Grad student in Bioengineering DESCRIPTION:TITLE: “scAllele\, a versatile tool for the detection and analysis of variants in scRNA-seq.” \nABSTRACT: Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene\, transcript\, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles\, and it remains challenging to extract nucleotide variants and isoform-specific information. Here\, we present scAllele\, an integrative approach that detects single nucleotide variants\, insertions\, deletions\, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. The read-specific variant calls by scAllele enables allele-specific splicing analysis. Applied to a lung cancer scRNA-seq data set\, scAllele identified variants with strong allelic linkage to alternative splicing\, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/10/Giovanni-Valdez.mp4\n  URL:https://qcb.ucla.edu/event/qcbio-research-seminar-giovanni-quinones-valdez-xiao-grad-student-in-bioinformatics/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Giovanni-Quinones-valdez.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211027T123000 DTEND;TZID=America/Los_Angeles:20211027T130000 DTSTAMP:20260518T064611 CREATED:20211018T180755Z LAST-MODIFIED:20211029T190003Z UID:19713-1635337800-1635339600@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Ulzee An (Sankararaman)\, Grad student in Computer Science DESCRIPTION:TITLE: “AutoComplete: Deep Learning-based Phenotype Imputation” \nABSTRACT: Health data has become increasingly available\, vast in scale\, and highly missing. For many downstream applications\, the ability to accurately impute missing features in health records may tap into additional analytical power which would be unrealized otherwise. While existing imputation methods are applicable\, many fall short in one or more aspects of being reliable or scalable in the domain of massive\, highly incomplete\, and heterogenous population-scale data. We propose AutoComplete\, a deep learning-based imputation method that extends with ease to incomplete datasets with millions of entries and handles heterogeneous data of continuous and categorical format. In imputing phenotypes for a collection of half-million individuals from the UK Biobank\, AutoComplete significantly improved imputation accuracy for several phenotypes in comparison to best-performing low-rank factorization and deep learning methods. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/10/Ulzee-An.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-ulzee-an-sankararaman-grad-student-in-computer-science/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Ulzee-An.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211101T110000 DTEND;TZID=America/Los_Angeles:20211101T120000 DTSTAMP:20260518T064611 CREATED:20210916T153500Z LAST-MODIFIED:20210916T155008Z UID:18839-1635764400-1635768000@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Anya Prince\, Associate Professor of Law\, Genetic Cluster\, University of Iowa College of Law DESCRIPTION:“Regulating Insurer Use of Genetic Information” \nHosted by Christina Palmer URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-anya-prince-jd-associate-professor-of-law-genetic-cluster-university-of-iowa-college-of-law/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Prince.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211103T120000 DTEND;TZID=America/Los_Angeles:20211103T123000 DTSTAMP:20260518T064611 CREATED:20211019T215840Z LAST-MODIFIED:20211020T213535Z UID:19723-1635940800-1635942600@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Alexander Markowitz (Boutros)\, Postdoc in Human Genetics DESCRIPTION:TITLE: “A pan-cancer multi-omic analysis of tumor proliferation.” \nABSTRACT: The underlying mechanisms of dysregulated cellular proliferation in cancer remain unclear; however\, it is hypothesized that specific mutations\, mutational signatures\, evolutionary trajectories and other global (epi)genomic features may be linked to differing rates of proliferation. In this presentation\, I will showcase a landscape analysis of cellular proliferation across primary cancers and cell lines using genome\, transcriptome and proteome data from 11\,597 primary tumors and 1\,804 cell lines across six major consortia.  The approach is to develop computational pipelines that will take in next-generation sequenced\, multi-omic datasets from an expanding source of consortia\, apply rigorous statistical methods to test multiple hypotheses on the global\, functional and pharmacogenomics of tumor proliferation and output detailed integration analyses on the underlying genomics of tumor proliferation.  By evaluating proliferation at these molecular levels\, key insights will be yielded including expansive new resources on the variation of proliferation rate across and within cancer types. \nFor lunch at 12:30pm with the speaker\, please RSVP at qcboffice@lifesci.ucla.edu URL:https://qcb.ucla.edu/event/qcbio-research-seminar-alexander-markowitz-boutros-postdoc-in-human-genetics/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/IMG_0679.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211103T130000 DTEND;TZID=America/Los_Angeles:20211103T133000 DTSTAMP:20260518T064611 CREATED:20211020T212859Z LAST-MODIFIED:20211105T032035Z UID:19760-1635944400-1635946200@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Ricky Wolff (Garud)\, Graduate Student in Ecology & Evolutionary Biology DESCRIPTION:TITLE: “Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome.” \nABSTRACT: The human gut microbiome is a complex community that harbors substantial ecological diversity at the species level\, as well as at the strain level within species. In healthy hosts\, species abundance fluctuations in the microbiome community are thought to be stable\, and these fluctuations can be described by macroecological laws. However\, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves\, exhibiting stability and following the macroecological relationships known to hold at the species level\, or whether strains have different dynamics\, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. In this study\, we sought to characterize the typical strain-level dynamics of the healthy human gut microbiome on timescales ranging from days to years. We show that genetic diversity within almost all species is stationary\, tending towards a long-term typical value within hosts over time scales of several years\, despite fluctuations on shorter timescales. Moreover\, the abundance fluctuations of strains can be sufficiently described by a stochastic logistic model (SLM) – a model used to describe abundance fluctuations among species around a fixed carrying capacity – in the vast majority of cases\, suggesting that strains are dynamically stable. Lastly\, we find that strain abundances follow the same macroecological laws known to hold at the species level. Together\, our results suggest that macroecological properties of the human gut microbiome\, including its stability\, emerge at the level of strains. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/10/Ricky-Wolff.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-ricky-wolff-garud-graduate-student-in-ecology-evolutionary-biology/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Ricky-Wolff.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211108T110000 DTEND;TZID=America/Los_Angeles:20211108T120000 DTSTAMP:20260518T064611 CREATED:20210916T153730Z LAST-MODIFIED:20210916T154942Z UID:18843-1636369200-1636372800@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Eimear Kenny\, Founding Director\, Institute for Genomic Health\, Mount Sinai School of Medicine DESCRIPTION:“Population genetics in an era of genomic health” \nHosted by Christa Caggiano URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-eimear-kenny-phd-founding-director-institute-for-genomic-health-mount-sinai-school-of-medicine/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Kenny.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211110T120000 DTEND;TZID=America/Los_Angeles:20211110T123000 DTSTAMP:20260518T064611 CREATED:20211027T205511Z LAST-MODIFIED:20211027T205554Z UID:19913-1636545600-1636547400@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Mariana Harris Heredia (Garud)\, Grad student in Biomathematics DESCRIPTION:TITLE: “Differences in the Signatures of Selection Between the Autosomes and the X Chromosome in Drosophila melanogaster.” \nABSTRACT: Sex chromosomes in Drosophila are found in a hemizygous state in males. Thus\, deleterious mutations may be purged more rapidly on the X chromosome than on the autosomes. This purging can result in less available standing variation that can seed adaptation on the X chromosome. Here\, we investigate how differences in the recessivity of alleles on the X chromosome versus autosomes impact the mode and tempo of adaptation. Specifically\, we test the hypothesis that hard sweeps\, in which a single adaptive mutation rises to high frequency\, are more common on the X chromosome\, while soft sweeps\, in which multiple haplotypes rise to high frequency simultaneously\, are more common on the autosomes. We analyze D. melanogaster genomic data from two populations\, North Carolina\, and Zambia\, and find evidence that suggests that indeed\, hard sweeps are more prevalent on the X chromosome and soft sweeps are more common on the autosomes. \nFor lunch at 12:30pm with the speaker\, please RSVP at qcboffice@lifesci.ucla.edu URL:https://qcb.ucla.edu/event/qcbio-research-seminar-mariana-harris-heredia-garud-grad-student-in-biomathematics/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Mariana-Harris-Heredia.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211110T130000 DTEND;TZID=America/Los_Angeles:20211110T133000 DTSTAMP:20260518T064611 CREATED:20211026T011133Z LAST-MODIFIED:20211027T205757Z UID:19880-1636549200-1636551000@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Guo Xiaohui (Pinter-Wollman)\, Postdoc in Ecology & Evolutionary Biology DESCRIPTION:TITLE: “Decoding alarm signal propagation of seed-harvester ants\, Pogonomyrmex californicus.” \nABSTRACT: Alarm signal propagation through social-insect colonies provides an empirically tractable context for analyzing information flow through a natural system\, with useful insights for network dynamics in other social groups\, including human social networks. Here\, I develop a methodological approach to track alarm spread within the group of harvester ants\, Pogonomyrmex californicus. I alarmed initial 3 individuals and tracked subsequent signal transmission through the group. Because there was no actual threat\, the alarm was false\, allowing us to assess amplification and adaptive damping of collective alarm response. I trained a Random-Forest machine learning regression model to quantify alarm behavior of individual workers from multiple movement features associated with alarm behavior in this species. This approach provides reliable continuous assessments of an individual’s behavioral state at much finer temporal scales and more consistently than can be achieved visually. I combined the ML alarm state assessments with proximity data from tracking software (ABCTracker) to construct a propagation network of alarm spread. Using this system\, alarm propagation can be manipulated and assessed to ask and answer a wide range of questions on information and misinformation flow in social networks. \nFor lunch at 12:30pm with the speaker\, please RSVP at qcboffice@lifesci.ucla.edu URL:https://qcb.ucla.edu/event/qcbio-research-seminar-guo-xiaohui-pinter-wollman-postdoc-in-ecology-evolutionary-biology/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Guo-Xiaohui.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211115T110000 DTEND;TZID=America/Los_Angeles:20211115T120000 DTSTAMP:20260518T064611 CREATED:20210916T153920Z LAST-MODIFIED:20210916T154921Z UID:18847-1636974000-1636977600@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Erick Matsen\, Professor\, Public Health Sciences Division\, Associate Program Head of Herbold Computational Biology Program\, Fred Hutchinson Cancer Center DESCRIPTION:“Towards Bayesian phylogenetics via systematic search and gradient ascent” \nHosted by Sriram Sankararaman URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-erick-matsen-phd-professor-public-health-sciences-division-associate-program-head-of-herbold-computational-biology-program-fred-hutchinson-cancer-cent/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Matsen.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211117T120000 DTEND;TZID=America/Los_Angeles:20211117T123000 DTSTAMP:20260518T064611 CREATED:20211005T013231Z LAST-MODIFIED:20211117T223513Z UID:19200-1637150400-1637152200@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Chloe Yap (Gandal)\, Visiting Graduate Student\, University of Queensland DESCRIPTION:TITLE: “Restricted diet drives autism gut-microbiome associations\, and other tales from the Australian Autism Biobank” \nABSTRACT: The Australian Autism Biobank (AAB) is an initiative of the Autism CRC – the first national\, cooperative research effort focused on autism across the lifespan. The AAB recruited a total of ~2\,500 autistic children\, family members\, and unrelated undiagnosed children\, and couples deep phenotypic information with multi-omic datasets (SNP genotyping\, stool metagenomics\, DNA methylation\, metabolomics\, WGS). One particularly controversial area in the field has been the potential causal contribution of the gut microbiome to autism. I will present results from one of the largest metagenomics study of the autism stool microbiome to date (n=246\, including 99 children diagnosed with autism). We propose a model whereby microbiome changes in autistic children may reflect consequences of behaviour and dietary preferences\, and we caution against undue emphasis on the microbiome having an upstream role in autism. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/10/Chloe-Yap.mp4\n  URL:https://qcb.ucla.edu/event/qcbio-research-seminar-chloe-yap-visiting-graduate-student-university-of-queensland/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/10/Chloe-Yap.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211117T130000 DTEND;TZID=America/Los_Angeles:20211117T133000 DTSTAMP:20260518T064611 CREATED:20210930T174023Z LAST-MODIFIED:20211117T223438Z UID:19185-1637154000-1637155800@qcb.ucla.edu SUMMARY:QCBio Research Seminar: Paheli Desai-Chowdhry (Savage)\, Grad student in Biomathematics DESCRIPTION:TITLE: “Asymmetric Branching Scale Factors as Features in Neuronal Cell-Type Classification” \nABSTRACT: Neurons are connected by complex branching processes – axons and dendrites – that process information for organisms to respond to their environment. Classifying neurons according to differences in structure or function is a fundamental piece of neuroscience. In previous work\, we constructed a biophysical theory that establishes a correspondence between neuron structure and function as mediated by principles such as time or power minimization\, using undetermined Lagrange multipliers to predict scaling ratios for axon and dendrite sizes across branching levels. Here\, we relax the assumption of symmetrical branching in the model to determine asymmetric branching powers that differ across different cell types due to functional tradeoffs. Furthermore\, we use scale factors related to asymmetric branching as features in machine learning classification to distinguish between different cell types. We find significant distinctions in the asymmetric scaling ratios between Purkinje cells and motoneurons. The performance of these classification methods gives us important insights into the correspondence between structure and function across different cell types. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/09/Paheli-Desai-Chowdhri.mp4 URL:https://qcb.ucla.edu/event/qcbio-research-seminar-paheli-desai-chowdhry-savage-grad-student-in-biomathematics/ LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Paheli-Desai-Chowdhry.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211122T110000 DTEND;TZID=America/Los_Angeles:20211122T120000 DTSTAMP:20260518T064611 CREATED:20210916T154109Z LAST-MODIFIED:20210916T154109Z UID:18851-1637578800-1637582400@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Katie Peichel\, Head of the Division Evolutionary Ecology\, University of Bern DESCRIPTION:“The role of chromosome evolution in adaptation and speciation in stickleback fish” \nHosted by Kirk Lohmueller URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-katie-peichel-head-of-the-division-evolutionary-ecology-university-of-bern/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Peichel.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=America/Los_Angeles:20211129T110000 DTEND;TZID=America/Los_Angeles:20211129T120000 DTSTAMP:20260518T064611 CREATED:20210916T154748Z LAST-MODIFIED:20210916T154748Z UID:18855-1638183600-1638187200@qcb.ucla.edu SUMMARY:Bioinformatics/Human Genetics Seminar Series: Stephen Piccolo\, Associate Professor\, Biology\, Member of Simmons Center for Cancer Research\, Brigham Young University DESCRIPTION:TITLE: “TBD” \nHosted by Sarah Spendlove URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-stephen-piccolo-associate-professor-biology-member-of-simmons-center-for-cancer-research-brigham-young-university/ LOCATION:ZOOM\, CA\, United States CATEGORIES:Research Seminars ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/09/Piccolo.jpg END:VEVENT END:VCALENDAR