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X-WR-CALNAME:Institute for Quantitative and Computational Biosciences
X-ORIGINAL-URL:https://qcb.ucla.edu
X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231207T120000
DTEND;TZID=America/Los_Angeles:20231207T143000
DTSTAMP:20260616T002523
CREATED:20231120T165356Z
LAST-MODIFIED:20231120T195105Z
UID:26038-1701950400-1701959400@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: MINI SYMPOSIUM - Emily Maciejewski (Ernst)\, Grad Student\, Computer Science - Chenlu Di (Lohmueller)\, Postdoc\, Ecology & Evolutionary Biology -  Qingyang Wang (Li JJ)\, Grad Student\, Statistics - Alex Bermudez (Lin)\, Grad Student\, Bioengineering
DESCRIPTION:12pm: Emily Maciejewski (Ernst)\, Grad Student\, Computer Science \nTITLE:  “Cross-species and tissue imputation of species-level DNA methylation samples” \nABSTRACT: DNA methylation data is highly informative to study a variety of aspects of mammalian biology. The availability of such data for many mammals at conserved sites was recently vastly enhanced by the development and large-scale application of the mammalian methylation array. For instance\, we consider here 13\,245 samples profiled on this array representing 348 species and 59 tissues from 746 species-tissue combinations. While having some coverage of many different species and tissue types\, this data only captures 3.6% of potential species-tissue combinations. We thus developed CMImpute (Cross-species Methylation Imputation) which uses a Conditional Variational Autoencoder to impute DNA methylation of non-profiled species-tissue combinations. In cross-validation\, we show that CMImpute yields high correlation with held-out observed values\, outperforming multiple baselines. We then train a model on all the data to impute 19\,786 new species-tissue combinations. We expect CMImpute and our imputed data resource will be useful for DNA methylation analyses across mammalian species. \n  \n12:30pm: Chenlu Di (Lohmueller)\, Postdoc\, Ecology & Evolutionary Biology \nTITLE: “Inference of fitness effects of mutations in noncoding regions of the human genome” \nABSTRACT: TBD \n  \n1:30pm: Qingyang Wang (Li JJ)\, Grad Student\, Statistics \nTITLE “Review of computational methods for estimating cell potency from single-cell RNA-seq data” \nABSTRACT: In single-cell RNA sequencing (scRNA-seq) data analysis\, a critical challenge is to infer hidden dynamic cellular processes from measured static cell snapshots. To tackle this challenge\, many computational methods have been developed from distinct perspectives. Besides the common perspectives of inferring trajectories (or pseudotime) and RNA velocity\, another important perspective is to estimate the differentiation potential of cells\, which is commonly referred to as “cell potency.” In this review\, we provide a comprehensive summary of 11 computational methods that estimate cell potency from scRNA-seq data under different assumptions\, some of which are even conceptually contradictory. We divide these methods into three categories: mean-based\, entropy-based\, and correlation-based methods\, depending on how a method summarizes gene expression levels of a cell or cell type into a potency measure. Our review focuses on the key similarities and differences of the methods within each category and between the categories\, providing a high-level intuition of each method. Moreover\, we use a unified set of mathematical notations to detail the 11 methods’ methodologies and summarize their usage complexities\, including the number of ad-hoc parameters\, the number of required inputs\, and the existence of discrepancies between the method description in publications and the method implementation in software packages. Realizing the conceptual contradictions of existing methods and the difficulty of fair benchmarking without single-cell-level ground truths\, we conclude that accurate estimation of cell potency from scRNA-seq data remains an open challenge. \n  \n2:00pm: Alex Bermudez (Lin)\, Grad Student\, Bioengineering \nTITLE: “TCell Morphology Impacts Chromatin States During Crowding” \nABSTRACT: Variability is an inherent characteristic of all biological systems\, exemplified by the diverse shapes\, sizes\, and gene expression profiles of cells comprising tissues. Despite its ubiquity\, our understanding of how such a phenotypic heterogeneity plays a role in regulating cell biology remains incomplete. In this talk\, I will discuss how cell shape heterogeneity arises and its impacts on chromatin organization of each cell during epithelial crowding\, a canonical process where cells proliferate until a densely packed monolayer forms. Our findings suggest that cell morphological heterogeneity is not mere noise\, but a crucial factor driving chromatin state and gene expression\, directing tissue development and remodeling.
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-mini-symposium-emily-maciejewski-ernst-grad-student-computer-science-chenlu-di-lohmueller-postdoc-ecology-evolutionary-biology-qingyang-wang-l/
LOCATION:Boyer Hall 130
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=application/pdf:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/11/Mini-Symposium-12723-1.pdf
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231204T120000
DTEND;TZID=America/Los_Angeles:20231204T130000
DTSTAMP:20260616T002523
CREATED:20231017T092149Z
LAST-MODIFIED:20231017T092236Z
UID:25854-1701691200-1701694800@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Monday\, December 4\, 2023  Graciela Gonzalez-Hernandez\, PhD\, Vice Chair of Research and Education\, Department of Computational Biomedicine\, Cedars-Sinai Medical Center
DESCRIPTION:TITLE: “ChatGPT for Clinical Informatics: what can LLMs do now for Health AI?” \nHosted by William Hsu for Medical Informatics \n 
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-monday-december-4-2023-graciela-gonzalez-hernandez-phd-vice-chair-of-research-and-education-department-of-computational-biomedicine-cedars/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture6.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231201T133000
DTEND;TZID=America/Los_Angeles:20231201T140000
DTSTAMP:20260616T002523
CREATED:20231018T093230Z
LAST-MODIFIED:20231201T221917Z
UID:25893-1701437400-1701439200@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Samir Akre (Bui)\, Graduate Student in Medical Informatics
DESCRIPTION:TITLE: “Detection of Symptoms of Depression Using Data From the iPhone and Apple Watch.” \nABSTRACT: Digital health data from consumer wearable devices and smartphones have the potential to improve our understanding of mental illness. However\, in conditions like depression\, there is not yet a consistent uniform measurement tool whose result can be reliably used as a gold standard measure of depression severity. This work seeks to specify what symptoms and dimensions of depression can be detected using vitals\, activity\, and sleep monitored by consumer wearable devices. Machine learning models are fit to digital health data and used to detect responses to individual questions from self-reports as well as summary scores. Data is analyzed from an ongoing study with data from the Apple Watch\, iPhone\, and validated self-reports. The digital health data investigated was found to detect depression severity and specific symptoms like poor appetite\, aspects of anhedonia\, and sleep timings (ROC AUC 0.63 to 0.72). \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Samir-Akre.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-samir-akre-bui-graduate-student-in-medical-informatics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Akre-Samir-AMIA2022_crop.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231201T130000
DTEND;TZID=America/Los_Angeles:20231201T133000
DTSTAMP:20260616T002523
CREATED:20231030T181641Z
LAST-MODIFIED:20231201T222154Z
UID:25976-1701435600-1701437400@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Kaija Gahm (Pinter-Wollman)\, Graduate Student in Ecology & Evolutionary Biology
DESCRIPTION:TITLE: “An updated movement path randomization method to distinguish social and spatial drivers of animal interactions.” \nABSTRACT: Studying the spatial-social interface requires tools that distinguish between social and spatial drivers of interactions. Testing hypotheses regarding the factors determining animal interactions often involves comparing observed interactions with reference or ’null’ models. One approach to constructing reference models that account for spatial drivers of social interactions is randomizing animal movement paths to decouple their spatial and social phenotypes while maintaining environmental effects on movements. Here we propose a new randomization approach. Using agent-based simulations\, we explore the utility of the new approach for different types of animal movements and compare its performance to existing approaches. We show that our method provides reference models that are more similar to the original tracking data\, while still distinguishing between social and spatial drivers. Furthermore\, the new approach results in fewer false-positives than other approaches\, especially when animals do not return to the same place each night but change movement foci\, either locally or directionally. Finally\, we show that interactions among GPStracked griffon vultures (Gyps fulvus) emerge from social attraction rather than from their movement patterns alone. We conclude by highlighting the biological situations in which the new method might be most suitable for testing hypotheses about the underlying causes of social interactions. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Kaija-Gahm.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-kaija-gahm-pinter-wollman-graduate-student-in-ecology-evolutionary-biology/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Kaija_Headshot_Final-3.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231129T133000
DTEND;TZID=America/Los_Angeles:20231129T140000
DTSTAMP:20260616T002523
CREATED:20231116T191717Z
LAST-MODIFIED:20231130T154218Z
UID:26027-1701264600-1701266400@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Christy Lee (Li JJ)\, Graduate Student in Statistics and Data Science
DESCRIPTION:TITLE: “scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters.” \nABSTRACT: Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding(t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however\, it is well known that t-SNE and UMAP’s 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge\, we present a statistical method\, scDEED\, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding\, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover\, by minimizing the number of dubious cell embeddings\, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Christy-Lee.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-christy-lee-li-jj-graduate-student-in-statistics-and-data-science/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/11/Christy_Lee_profile.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231129T130000
DTEND;TZID=America/Los_Angeles:20231129T133000
DTSTAMP:20260616T002523
CREATED:20231113T160845Z
LAST-MODIFIED:20231130T153643Z
UID:26015-1701262800-1701264600@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Matthew Soldano (Pellegrini)\, Staff Research Associate\, Institute for Genomics and Proteomics at DGSOM
DESCRIPTION:TITLE: “A Non-Invasive Epigenetic Measure of Inflammation.” \nABSTRACT: Existing epigenetic phenotype tests often lack mechanistic explanations of the observed correlations between specific methylation sites and phenotypes. This raises the crucial question: are these correlations primarily a result of marginal correlations\, or do they stem from plausible biological mechanisms? To delve deeper into this question\, we conducted a Targeted Epigenome Association Study focusing on CpG sites associated with aging\, metabolism\, and obesity. Our study leveraged a clinical investigation on fitness\, encompassing comprehensive measurements of phenotypes\, traditional biomarkers linked to metabolism\, obesity\, and fitness\, as well as extensive profiling of hundreds of metabolites and proteins. Additionally\, we had access to buccal swabs for targeted bisulfite sequencing. Our analysis discovered eight CpG sites exhibiting robust associations with the complement system\, alongside indicators of adiposity and epithelial cell ratio found in the buccal swab samples. These sites reside within the region of the peptidoglycan recognition 1 gene promoter\, a protein that senses inflammatory processes. This discovery sheds light on the intricate interplay between epigenetic markers with oral and systemic inflammation pathways.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Matthew-Soldano.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-matthew-soldano-pellegrini-graduate-student-institute-for-genomics-and-proteomics-at-dgsom/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/11/Matthew-Soldano.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231127T120000
DTEND;TZID=America/Los_Angeles:20231127T130000
DTSTAMP:20260616T002523
CREATED:20231017T091350Z
LAST-MODIFIED:20231017T091350Z
UID:25845-1701086400-1701090000@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Qunhua Li\, PhD\, Associate Professor\, Department of Statistics\, The Pennsylvania State University
DESCRIPTION:TITLE: “TBD” \nHosted by Jingyi Jessica Li for Bioinformatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-qunhua-li-phd-associate-professor-department-of-statistics-the-pennsylvania-state-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture5.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231117T133000
DTEND;TZID=America/Los_Angeles:20231117T140000
DTSTAMP:20260616T002523
CREATED:20231107T155230Z
LAST-MODIFIED:20231118T002605Z
UID:25997-1700227800-1700229600@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Michael Cheng (Yang)\, Graduate Student in Bioinformatics
DESCRIPTION:TITLE: “scGRNdb: A Cell Type Gene Regulatory Network Atlas for Human and Mouse.” \nABSTRACT: Gene regulatory networks (GRNs) elucidate the complex regulatory landscape in cells and tissues\, making them powerful tools for understanding mechanisms in disease pathophysiology and identifying therapeutic targets. The advent of single cell RNA-sequencing (scRNAseq) enables a more granular study of disease mechanisms using cell type-specific GRNs\, but most existing GRN methods are not optimized for scRNAseq and robust network resources are scarce. We recently developed SCING\, which improves GRN performance on scRNAseq and spatial transcriptomics data compared to existing methods. Here we present scGRNdb: a GRN atlas of 1\,000+ SCING GRNs for cell types across 12 human and mouse single cell data atlases. Functional annotation of these networks revealed subnetworks that recapitulate known cell type specific pathways and gene mechanisms for neurological and cardiovascular diseases. Furthermore\, we will host scGRNdb and GRN analysis tools on a public web server to facilitate single cell research and biomedical discovery. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Michael-Cheng-111723.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-michael-cheng-yang-graduate-student-in-bioinformatics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/11/michaelcheng_headshot.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231117T130000
DTEND;TZID=America/Los_Angeles:20231117T133000
DTSTAMP:20260616T002523
CREATED:20231026T193016Z
LAST-MODIFIED:20231026T193016Z
UID:25962-1700226000-1700227800@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Mao Tian (Boutros)\, Junior Bioinformatician in JCCC Cancer Data Science
DESCRIPTION:TITLE: “Characterization of Genomics Landscape and Natural History of Anaplastic Thyroid Cancer using High Depth WGS and Subclonal Reconstruction.” \nABSTRACT: Anaplastic thyroid cancer (ATC) is among the most lethal cancer types\, with a median survival rate of approximately 12 weeks. ATC is resistant to both chemo- and radiotherapy\, a characteristic attributed to its surrounding tissues and rapid progression. Although ATC is less common than other thyroid cancers\, such as papillary thyroid carcinoma (PTC) and differentiated thyroid carcinoma (DTC)\, it frequently co-occurs with both PTC and DTC. In this study\, we assembled a 108-sample cohort consisting of 46 ATC patients and 5 thyroid cancer cell lines. We conducted high-depth (x90) whole genome sequencing on ATC samples\, as well as on adjacent PTC or DTC tissues\, and included blood controls when available. Our analysis identified both germline and somatic variants in ATC\, revealing a moderate mutation burden compared to C-type tumors and a higher incidence of recurrent SNVs and CNVs than in PTC or DTC. Notably\, ATC samples exhibited more active mutational signatures\, such as SBS2 and SBS13\, than DTC or PTC samples. Additionally\, we employed subclonal reconstruction to model the natural history of ATC in relation to cooccurring DTC and PTC.
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-mao-tian-boutros-junior-bioinformatician-in-jccc-cancer-data-science/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/MaoTian_Headshot_2019.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231113T120000
DTEND;TZID=America/Los_Angeles:20231113T130000
DTSTAMP:20260616T002523
CREATED:20231017T091008Z
LAST-MODIFIED:20231017T091500Z
UID:25841-1699876800-1699880400@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Haiyuan Yu\, PhD\, Tisch University Professor\, Deparment of Computational Biology\, Cornell University
DESCRIPTION:TITLE: “TBD” \nHosted by Grace Xiao for Bioinformatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-haiyuan-yu-phd-tisch-university-professor-deparment-of-computational-biology-cornell-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture4.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231108T160000
DTEND;TZID=America/Los_Angeles:20231108T170000
DTSTAMP:20260616T002523
CREATED:20231024T101808Z
LAST-MODIFIED:20231024T101808Z
UID:25927-1699459200-1699462800@qcb.ucla.edu
SUMMARY:Special Seminar: Sara Monaco\, Managing Editor\, European Molecular Biology Organization (EMBO)
DESCRIPTION:TITLE: “The new culture of preprint peer-review”
URL:https://qcb.ucla.edu/event/special-seminar-sara-monaco-managing-editor-european-molecular-biology-organization-embo/
LOCATION:Boyer Hall 130
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Sara-Monico.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231108T133000
DTEND;TZID=America/Los_Angeles:20231108T140000
DTSTAMP:20260616T002523
CREATED:20231018T092214Z
LAST-MODIFIED:20231102T152047Z
UID:25889-1699450200-1699452000@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Xiaolu Guo (Hoffmann)\, Postdoc in Microbiology\, Immunology & Molecular Genetics
DESCRIPTION:TITLE: “Modeling the heterogenous NFκB dynamics of single immune cells.” \nABSTRACT: Macrophages function as immune sentinel cells\, initiating appropriate and specialized immune responses to a great variety of pathogens.  The transcription factor NFκB controls macrophage gene expression responses\, and its temporal dynamics enable stimulus-specificity of these responses.  Using a fluorescent reporter mouse our laboratory recently generated large amounts of single-cell NFκB dynamic data and identified dynamic features\, termed ‘signaling codons’\, that convey information to the nucleus about stimulus identity and dose.  Here\, we aimed to recapitulate the stimulus-specific but highly cell-to-cell heterogeneous NFκB dynamics with a mathematical model of the signaling network.  The parameters that are subject to biological variation provide the potential to account for the heterogeneity in observed stimulus responses.  We estimated parameter distributions using the Stochastic Approximation Expectation Maximization (SAEM) approach and then fit the individual cell data using Bayesian maximum a posteriori (MAP) estimation.  Visual inspection revealed an excellent fit with the data.  To quantitatively evaluate the fitting performance\, we compared the experimental and predicted distributions of NFκB signaling codons.  Further\, we identified biochemical reactions that may account for the cellular heterogeneity in NFκB dynamics.  We verified that the stimulus-specificity of the virtual macrophage NFκB responses was consistent with their live-cell counterparts\, as assessed by mutual information and machine learning classification. Additionally\, the mathematical model allowed us extend experimental dose response studies\, revealing the doses that maximize information. Furthermore\, the virtual NFκB macrophages enabled the exploration of individual cell responses to different ligands. Leveraging this capability\, we made predictions regarding combinatorial ligands\, that were then experimentally tested. Discrepancies between the experimental results and model predictions led to the identification of a competition mechanism between CpG and PolyIC for endosome trafficking\, resulting in non-integrative responses behavior. Our results establish a mathematical modeling tool that may be used to study the molecular determinants of response specificity and dynamical coding in immune sentinel cells at the single cell level.
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-xiaolu-guo-hoffmann-postdoc-in-microbiology-immunology-molecular-genetics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Xiaolu.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231108T130000
DTEND;TZID=America/Los_Angeles:20231108T133000
DTSTAMP:20260616T002523
CREATED:20231102T151931Z
LAST-MODIFIED:20231108T223740Z
UID:25982-1699448400-1699450200@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Jonatan Hervoso (Xiao)\, Graduate Student in Bioinformatics
DESCRIPTION:TITLE: “Splicing-specific transcriptome-wide association uncovers novel genetic mechanisms for Schizophrenia.” \nABSTRACT: Recent studies have highlighted the essential role of RNA splicing\, a key mechanism of alternative RNA processing\, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits\, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders\, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless\, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with GWAS to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-seq datasets\, BrainGVEX and CommonMind (CMC)\, revealing 137 and 88 trait-associated exons (in 84 and 67 genes)\, respectively.  Enriched biological functions in the associated gene sets converged on neuronal function and development\, immune cell activation\, cellular transport\, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein (RBP) binding sites\, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level\, identifying putative causal 36 genes and 48 exons for SCZ. We highlight VPS45 and APOPT1\, where splicing of specific exons was associated with disease risk\, eluding detection by conventional gene expression analysis. Collectively\, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ\, providing a valuable approach for future investigations in this area. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/11/Jonatan-Hervoso.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-jonatan-hervoso-xiao-graduate-student-in-bioinformatics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/11/Hervoso.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231106T120000
DTEND;TZID=America/Los_Angeles:20231106T130000
DTSTAMP:20260616T002523
CREATED:20231017T090714Z
LAST-MODIFIED:20231017T091610Z
UID:25837-1699272000-1699275600@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Monica Munoz-Torres\, PhD\, Associate Professor\, Department of Biomedical Informatics\, University of Arizona
DESCRIPTION:TITLE: “TBD” \nHosted by William Hsu for Medical Informatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-monica-munoz-torres-phd-associate-professor-department-of-biomedical-informatics-university-of-arizona/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture3.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231103T133000
DTEND;TZID=America/Los_Angeles:20231103T140000
DTSTAMP:20260616T002523
CREATED:20231027T181948Z
LAST-MODIFIED:20231103T210314Z
UID:25967-1699018200-1699020000@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Alexis Weber (de la Torre-Ubieta and Geschwind)\, Graduate Student in Human Genetics
DESCRIPTION:TITLE: “Defining molecular dysregulation in Down Syndrome neocortex and neural progenitor cells.” \nABSTRACT: Down syndrome (DS) is the most common form of genetic\, intellectual disability\, which occurs 1 in 700 newborns and presents in patients as cognitive deficits\, particularly diminished in learning\, memory\, and language development.1\,2\,3 DS symptoms result from impaired cortical development\, which is demonstrated\, in contrast to neurotypical (NTD) brains\, by postnatally reduced whole brain weight\, volume and surface area\, lower numbers of progenitors\, excitatory neurons and oligodendrocytes\, increased numbers of astrocytes\, interneurons and microglia\, and altered neuronal morphology\, maturation\, and migration.3–10 These DS neuropathologies result through some means from the triplication of human chromosome 21 (hsa21) or trisomy 21 (T21). However\, the way in which T21 confers DS pathology and inhibits cortical development remains unclear. I hypothesize that increased hsa21 gene dosage alters global gene expression in neural progenitors\, changing neural cell fate specification and differentiation. By single nuclei Multiome sequencing\, T21 neocortices demonstrate a disproportionate increase in progenitors\, interneurons and oligodendrocyte precursor cells and decrease in excitatory neurons\, contrast to neurotypical (NT) donors. Furthermore\, T21 neocortices show cell-specific differential expression of critical neurodevelopmental genes and transcription factors. These data support potential\, cell-specific mechanisms of gene dysregulation during T21 neurodevelopment. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Alexis-Weber.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-alexis-weber-de-la-torre-ubieta-and-geschwind-graduate-student-in-human-genetics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Alexis-Weber.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231103T130000
DTEND;TZID=America/Los_Angeles:20231103T133000
DTSTAMP:20260616T002523
CREATED:20231019T182813Z
LAST-MODIFIED:20231103T205708Z
UID:25904-1699016400-1699018200@qcb.ucla.edu
SUMMARY:Research-in-Progress (RIP) Seminar: Amantha O'Keeffe (Park)\, Graduate Student in Chemical and Biomolecular Engineering
DESCRIPTION:TITLE: “Quantification of Absolute Metabolite Concentrations in T cells by Shotgun Metabolomics.” \nABSTRACT: Quantitative understanding of immunometabolism underlies improving immune functions and developing successful immunotherapies. Kinetic and thermodynamic laws rely on absolute\, not relative\, metabolite concentrations to map metabolism. However\, until now\, comprehensive absolute metabolite quantification has been inaccessible due to the need for iterative analytical procedures involving internal standards. Here we developed a simple technique to facilitate absolute metabolite quantitation. Shotgun metabolomics leverages the known absolute metabolite concentrations of model systems and 13C labeling to distinguish metabolites from two different cell types in a single extraction sample. We cultured T cells in unlabeled media and E. coli or epithelial cells in 13C-labeled media and extracted their metabolites simultaneously. Using LC-MS and known concentrations of 13C-labeled metabolites as internal standards\, we quantified ~80 metabolites en masse in human T cells. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/10/Samantha-OKeeffe.mp4
URL:https://qcb.ucla.edu/event/research-in-progress-rip-seminar-amantha-okeeffe-park-graduate-student-in-chemical-and-biomolecular-engineering/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/samantha.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231030T120000
DTEND;TZID=America/Los_Angeles:20231030T130000
DTSTAMP:20260616T002523
CREATED:20231017T090117Z
LAST-MODIFIED:20231017T091657Z
UID:25831-1698667200-1698670800@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Stefen Canzar\, PhD\, Associate Professor of Computer Science and Engineering\, Pennsylvania State University
DESCRIPTION:TITLE: “Algorithms or experiments? How to improve transcriptome analysis” \nHosted Jingyi Jessica Li for Bioinformatics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-stefen-canzar-phd-associate-professor-of-computer-science-and-engineering-pennsylvania-state-university/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture2.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20231023T120000
DTEND;TZID=America/Los_Angeles:20231023T130000
DTSTAMP:20260616T002523
CREATED:20231017T085001Z
LAST-MODIFIED:20231017T091737Z
UID:25821-1698062400-1698066000@qcb.ucla.edu
SUMMARY:Frontiers in Computational Biosciences Seminar Series: Seth Bordenstein\, PhD\, Director\, One Health Microbiome Center\, Huck Endowed Chair in Microbiome Sciences\, The Pennsylvania State University
DESCRIPTION:TITLE: “human microbiome variation across ethnicity and race” \nHosted by Nandita Garud for Genetics & Genomics
URL:https://qcb.ucla.edu/event/frontiers-in-computational-biosciences-seminar-series-seth-bordenstein-phd/
LOCATION:Boyer 159\, 611 Charles E. Young Dr. E.\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:QCBio Seminar Series
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/10/Picture1.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230724T110000
DTEND;TZID=America/Los_Angeles:20230724T120000
DTSTAMP:20260616T002523
CREATED:20230719T153531Z
LAST-MODIFIED:20230719T153531Z
UID:24891-1690196400-1690200000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Andras Gyorgy\, Assistant Professor of Electrical Engineering and Bioengineering - NYU Abu Dhabi
DESCRIPTION:TITLE: “Inducible plasmid copy number control and a blueprint for a synthetic genetic feedback optimizer” \nABSTRACT: The ability to control gene expression has been paradigm shifting for all areas of biological research\, especially for synthetic biology. This talk will focus on two recent advancements in gene expression control. First\, TULIP (TUnable Ligand Inducible Plasmid) is presented: a self-contained plasmid with inducible copy number control\, designed for portability across various Escherichia coli strains commonly used for cloning\, protein expression\, and metabolic engineering. As demonstrated through multiple application examples\, flexible plasmid copy number control via TULIP accelerates the design and optimization of gene circuits\, enables efficient probing of metabolic burden\, and facilitates the prototyping and recycling of modules in different genetic contexts. Second\, the blueprint of a genetic feedback module is presented to optimize a broadly defined performance metric by adjusting the production and decay rate of a set of regulator species. The optimizer can be implemented by combining available synthetic biology parts and components\, and it can be readily integrated with existing pathways and genetically encoded biosensors to ensure its successful deployment in a variety of settings when relying on mass action kinetics-based dynamics and parameter values typical in Escherichia coli.
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-andras-gyorgy-assistant-professor-of-electrical-engineering-and-bioengineering-nyu-abu-dhabi/
LOCATION:Boyer Hall 130
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/07/Andras-Gyorgy-7.24.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230721T160000
DTEND;TZID=America/Los_Angeles:20230721T170000
DTSTAMP:20260616T002523
CREATED:20230719T152504Z
LAST-MODIFIED:20230719T152504Z
UID:24886-1689955200-1689958800@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Jimmy Hu\, Assistant Professor in the Division of Oral Biology & Medicine at the UCLA School of Dentistry
DESCRIPTION:TITLE: “Building a tooth from transcriptome to tissue morphogenesis” \nABSTRACT: During craniofacial development\, the oral epithelium begins as a morphologically homogeneous tissue that gives rise to locally complex structures\, including the teeth\, salivary glands\, and taste buds. How the epithelium is initially patterned and later shaped to generate diverse organ and cell types remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations\, we mapped the transcriptional landscape of embryonic day (E) 12 mouse mandibular epithelia at single cell resolution. Our analysis identified key transcription factors and gene regulatory networks that define different epithelial cell types. By examining the spatiotemporal patterning process along the oral-aboral axis\, our results inform a model where the dental field is progressively confined to its position by the formation of the aboral epithelium anteriorly and the non-dental oral epithelium posteriorly. As dental suprabasal cells are enriched with genes related to actomyosin-based motility\, we next studied mutant embryos lacking non-muscle myosin II to explore the roles of cellular forces during tooth morphogenesis. We found that myosin II is critical for maintaining cell-cell adhesion and for efficient cellular movement that drives dental epithelial invagination. Together\, our results describe the transcriptional regulation during oral epithelial patterning and unveil an actomyosin-based mechanism that promotes tooth invagination.
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-jimmy-hu-assistant-professor-in-the-division-of-oral-biology-medicine-at-the-ucla-school-of-dentistry/
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/14/2023/07/Jimmy-Hu.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230714T160000
DTEND;TZID=America/Los_Angeles:20230714T170000
DTSTAMP:20260616T002523
CREATED:20230711T184053Z
LAST-MODIFIED:20230711T184148Z
UID:24861-1689350400-1689354000@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Xianghong Jasmine Zhou\, Professor\, Pathology and Laboratory Medicine at UCLA
DESCRIPTION:TITLE: “Liquid Biopsies for Precision Oncology.” \nABSTRACT: Liquid biopsies are new diagnostic approaches to profile molecular features of solid tumors by blood\, saliva\, urine\, and other body fluids. Such approaches offer non-invasive options in early cancer detection\, tumor sampling\, continuous monitoring\, and designing personalized therapeutic options. Therefore\, liquid biopsies have the potential to transform the field of clinical oncology. Recently\, cell-free DNA analysis from a simple blood draw received enormous attention for its promise in these applications. In this talk\, we will discuss several novel computational and experimental technologies on using cell-free DNA for the detection and monitoring of cancer and other diseases.
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-xianghong-jasmine-zhou-professor-pathology-and-laboratory-medicine-at-ucla/
LOCATION:Boyer Hall 159
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/07/Jasmine_round-3.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230707T160000
DTEND;TZID=America/Los_Angeles:20230707T170000
DTSTAMP:20260616T002523
CREATED:20230627T234736Z
LAST-MODIFIED:20230627T234745Z
UID:24835-1688745600-1688749200@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Xia Yang\, Professor\, Integrative Biology and Physiology Molecular and Medical Pharmacology at UCLA
DESCRIPTION:TITLE: “Single Cell Multiomics Integration to Understand Complex Diseases.” \nABSTRACT: Recent advances in single cell multiomics technologies such as single cell RNA-seq\, single cell ATAC-seq\, and spatial transcriptomics have brought enormous opportunities that enable our understanding of the molecular underpinnings of pathophysiology at a single cell or cell type resolution. However\, integrative analysis across single cell multiomics domains has proven challenging.  I will introduce our recent efforts in single cell multiomics integration and gene regulatory network modeling\, present computational tools to carry out these analyses\, and showcase application examples in studies of various complex diseases. \n 
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-xia-yang-professor-integrative-biology-and-physiology-molecular-and-medical-pharmacology-at-ucla/
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/14/2023/06/Xia-Yang-Ph.D..jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230630T160000
DTEND;TZID=America/Los_Angeles:20230630T170000
DTSTAMP:20260616T002523
CREATED:20230627T234352Z
LAST-MODIFIED:20230627T234352Z
UID:24831-1688140800-1688144400@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Eric Deeds\, Associate Professor\, Integrative Biology & Physiology - Vice Chair\, Life Sciences Core at UCLA
DESCRIPTION:TITLE: “A lack of distinct cellular identities in scRNA-seq data: revisiting Waddington’s landscape.” \nABSTRACT: Single-cell RNA sequencing is revolutionizing our understanding of development\, differentiation and disease. Analysis of this data is often challenging\, however\, and tasks like clustering cells to uncover distinct cellular identities sometimes yields results that fail to align with existing biological knowledge. We analyzed publicly available data where the cell identity for each cell is known a priori\, and found that cells of very different types and lineages do not occupy distinct regions of gene expression space. Rather\, cells from different lineages overlap extensively with one another\, significantly complicating attempts to recover distinct identities within the data. Indeed\, our analysis of available epigenetic data for a wide variety of tissues and organisms revealed these data are not consistent with the predictions of Waddington’s landscape\, suggesting a need to revisit our picture of gene expression changes during differentiation and development. \n 
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-eric-deeds-associate-professor-integrative-biology-physiology-vice-chair-life-sciences-core-at-ucla/
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/14/2023/06/eric-deeds.jpeg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230623T163000
DTEND;TZID=America/Los_Angeles:20230623T170000
DTSTAMP:20260616T002523
CREATED:20230621T151413Z
LAST-MODIFIED:20230627T233954Z
UID:24821-1687537800-1687539600@qcb.ucla.edu
SUMMARY:BIG Summer Research Seminar: Brunilda Balliu\, Assistant Professor in the Departments of Pathology & Laboratory Medicine and Computational Medicine at UCLA
DESCRIPTION:TITLE: “FastGxC: a statistical framework for mapping context-specific regulatory variants using bulk and single-cell RNA-seq data.” \nABSTRACT: Recent studies suggest that context-specific eQTLs underlie genetic risk factors for complex diseases. However\, methods for identifying them are still nascent\, limiting their comprehensive characterization and downstream interpretation of disease-associated variants. In this talk\, I will introduce FastGxC\, a method to efficiently and powerfully map context-specific eQTLs by leveraging the correlation structure of bulk multi-tissue and single-cell RNA-seq studies. We applied FastGxC to simulated and real bulk and single-cell RNA-Seq data sets and show that FastGxC is orders of magnitude more powerful and computationally efficient than existing eQTL mapping approaches\, making previously yearlong computations possible in minutes. In addition\, FastGxC provides a three-fold increase in precision to identify relevant tissues and cell types for GWAS variants than standard eQTL mapping approaches. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/06/Brunilda-Balliu-62323.mp4
URL:https://qcb.ucla.edu/event/big-summer-research-seminar-brunilda-balliu-assistant-professor-in-the-departments-of-pathology-laboratory-medicine-and-computational-medicine-at-ucla/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/06/Brunilda-Balliu-PhD-11r5x7.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230517T173000
DTEND;TZID=America/Los_Angeles:20230517T183000
DTSTAMP:20260616T002523
CREATED:20241215T202645Z
LAST-MODIFIED:20241215T202645Z
UID:27307-1684344600-1684348200@qcb.ucla.edu
SUMMARY:Webinar: Digital Immune Twins: The Future of Healthcare?
DESCRIPTION:
URL:https://qcb.ucla.edu/event/webinar-digital-immune-twins-the-future-of-healthcare/
LOCATION:Webinar
CATEGORIES:Webinar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230517T173000
DTEND;TZID=America/Los_Angeles:20230517T183000
DTSTAMP:20260616T002523
CREATED:20230414T183313Z
LAST-MODIFIED:20241215T203316Z
UID:24702-1684344600-1684348200@qcb.ucla.edu
SUMMARY:QCBio Special Virtual Event: "Digital Immune Twins: The Future of Healthcare?"
DESCRIPTION:Join us for an illuminating conversation with: \nAlexander Hoffmann\, Director\, Institute for Quantitative & Computational Biosciences\, Thomas M. Asher Professor of Microbiology\, UCLA Microbiology\, Immunology & Molecular Genetics \nElaine F. Reed\, Daljit S. and Elaine Sarkaria Endowed Chair in Diagnostic Medicine\, Professor\, Pathology and Laboratory Medicine\, Director\, UCLA Immunogenetics Center \nAaron Meyer\, Assistant Professor\, Bioengineering \nWith introductory remarks by \nTracy Johnson\, Keith and Cecilia Terasaki Presidential Endowed Chair\, Professor\, Molecular\, Cell & Developmental Biology\, Dean of Life Sciences\, UCLA College
URL:https://qcb.ucla.edu/event/qcbio-special-virtual-event-digital-immune-twins-the-future-of-healthcare/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Webinar
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/04/Screen-Shot-2023-04-14-at-11.32.53-AM.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230425T133000
DTEND;TZID=America/Los_Angeles:20230427T163000
DTSTAMP:20260616T002523
CREATED:20191212T192953Z
LAST-MODIFIED:20230403T171544Z
UID:10808-1682429400-1682613000@qcb.ucla.edu
SUMMARY:W23: Advanced Cytoscape
DESCRIPTION:The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources\, and the role of interaction data in the interpretation of large scale datasets. Highly encourage: Students should working knowledge of python scripting.
URL:https://qcb.ucla.edu/event/w22-advanced-cytoscape/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230411T120000
DTEND;TZID=America/Los_Angeles:20230411T130000
DTSTAMP:20260616T002523
CREATED:20250212T154812Z
LAST-MODIFIED:20250212T160540Z
UID:27565-1681214400-1681218000@qcb.ucla.edu
SUMMARY:Academic Jobs - Postdoc Career Development Series
DESCRIPTION:
URL:https://qcb.ucla.edu/event/academic-jobs-postdoc-career-development-series/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Workshop
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2025/02/2023-Postdoc-Career-Development-Seminars-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230324T123000
DTEND;TZID=America/Los_Angeles:20230324T130000
DTSTAMP:20260616T002523
CREATED:20230319T153305Z
LAST-MODIFIED:20230327T174010Z
UID:24633-1679661000-1679662800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Nicholas Wang (Boutros)\, Grad Student\, Bioinformatics
DESCRIPTION:TITLE: “Germline structural variants shape prostate cancer clinical and molecular evolution.” \nABSTRACT: Inherited genetic variation profoundly influences cancer risk and outcome. While the impact of germline single nucleotide polymorphisms has been well-studied in several cancer types\, the effects of germline structural variants (gSVs) on cancer biology and clinical outcomes is largely unknown. From our cohort of 300 men with localized\, intermediate risk prostate cancer\, we identified 6\,003 gSVs present in at least 3% of patients\, with 48 associated with recurrent somatic alterations or clinical outcome. Of these\, ~50% associated with expression of nearby genes or intersected with exons or regulatory regions. Using external cohorts\, we validated three gSVs that were strongly associated with poor clinical outcomes\, including an inversion at chr14q24.1 present in ~20% of patients. Notably\, a strong synergistic effect on outcome was observed in patients with somatic TP53 alterations or high genomic instability\, defining a new aggressive prostate cancer subtype with chr14INV as a novel\, recurrent biomarker. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Nicholas-Wang-32423.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-nicholas-wang-boutros-grad-student-bioinformatics-p/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/Nicholas-Wang.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20230324T120000
DTEND;TZID=America/Los_Angeles:20230324T123000
DTSTAMP:20260616T002523
CREATED:20230307T193641Z
LAST-MODIFIED:20230327T173940Z
UID:24514-1679659200-1679661000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Dongyuan Song (Li JJ)\, Grad Student\, Bioinformatics IDP
DESCRIPTION:TITLE: “ClusterDE: a post-clustering differentially expressed (DE) gene identification method robust to false-positive inflation caused by double-dipping” \nABSTRACT: In typical single-cell RNA-seq data analysis\, first\, a clustering algorithm is applied to cluster cells; then\, a statistical method is used to identify the differentially expressed (DE) genes between the cell clusters. However\, this common procedure uses the same data twice\,  an issue known as “double dipping”: the same gene expression data are used to define cell clusters and DE genes\, leading to false-positive DE genes even when the cell clusters are spurious. To overcome this challenge\, we propose ClusterDE\, a post-clustering DE method for controlling the false discovery rate (FDR) regardless of clustering quality. The core idea of ClusterDE is to generate in silico negative control data with only one cluster\, which can be used in contrast to real data for evaluating the whole clustering+DE procedure. Using comprehensive simulation and real data analysis\, we show that ClusterDE can not only has solid FDR control but also finds cell-type marker genes that are biologically meaningful. ClusterDE is fast\, transparent\, and adaptive to a wide range of clustering methods and statistical tests. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2023/03/Dongyuan-Song-32423.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-dongyuan-song-li-jj-grad-student-bioinformatics-idp/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2023/03/UCLA.jpg
END:VEVENT
END:VCALENDAR