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:20210503T110000
DTEND;TZID=America/Los_Angeles:20210503T120000
DTSTAMP:20260518T031850
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:20260518T031850
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).\n\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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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:20260518T031851
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