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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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DTSTART:20210314T100000
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220202T120000
DTEND;TZID=America/Los_Angeles:20220202T123000
DTSTAMP:20260517T200720
CREATED:20211216T231745Z
LAST-MODIFIED:20220202T224019Z
UID:20174-1643803200-1643805000@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Xinzhou Ge (Li JJ)\, Postdoc in Statistics
DESCRIPTION:TITLE: “P-value-free solution to fix exaggerated false positives by popular differential expression methods.” \nABSTRACT: We report a surprising phenomenon that popular bioinformatics methods for identifying differentially expressed genes (DEG) between two conditions have unexpectedly high false discovery rates (FDRs) on large-sample-size RNA-seq datasets. Failed FDR control is likely due to the invalid p-values which rely on unrealistic assumptions. To address this issue\, we use a general statistical framework Clipper to control the FDR in DEG analysis without relying on p-values. \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/12/Xinzhou-Ge-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-xinzhou-ge-li-jj-postdoc-in-statistics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/12/Xinzhou-Ge.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220207T160000
DTEND;TZID=America/Los_Angeles:20220207T170000
DTSTAMP:20260517T200720
CREATED:20220103T173705Z
LAST-MODIFIED:20220103T174530Z
UID:20359-1644249600-1644253200@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Dana Pe'er\, PhD\, Chair\, Computational and Systems Biology Program\, Sloan Kettering Institute
DESCRIPTION:TITLE: “Cellular plasticity in Cancer.” \nHosted by Jason Ernst.
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-dana-peer-phd-chair-computational-and-systems-biology-program-sloan-kettering-institute/
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/14/2022/01/5.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220209T120000
DTEND;TZID=America/Los_Angeles:20220209T123000
DTSTAMP:20260517T200720
CREATED:20211207T223237Z
LAST-MODIFIED:20220209T224539Z
UID:20086-1644408000-1644409800@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Apeksha Singh (Hoffmann)\, Graduate Student in Biomathematics
DESCRIPTION:TITLE: “Characterizing distinct cell states based on stimulus-response dynamics.” \nABSTRACT: Macrophages show remarkable functional pleiotropy that is dependent on microenvironmental context.  Prior studies have characterized how polarizing cytokines alter epigenetic or signaling mechanisms\, but how they affect specific macrophage functions has not been characterized systematically.  One hallmark function of macrophages is to mount immune-threat appropriate responses\, in part via the signaling dynamics of transcription factor NFκB.  Here\, we measured single-cell nuclear NFκB trajectories in macrophages polarized into 6 states and stimulated with 8 different stimuli resulting in a vast dataset.  Linear Discriminant Analysis revealed how NFκB signaling codons compose the immune threat level of stimuli\, placing polarization states along a linear continuum between the M1/M2 dichotomy.  Machine learning classification revealed losses of stimulus distinguishability with polarization\, which reflect a switch from sentinel to effector functions.  However\, the stimulus response dynamics and discrimination patterns did not fit the M1/M2 continuum.  Instead\, our analysis suggests macrophage functional niches within a multi-dimensional polarization landscape.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/12/Apeksha-Singh-Edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-apeksha-singh-hoffmann-graduate-student-in-biomathematics/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/png:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/12/Apeksha-Singh-1.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220209T123000
DTEND;TZID=America/Los_Angeles:20220209T130000
DTSTAMP:20260517T200720
CREATED:20211209T230759Z
LAST-MODIFIED:20220209T224043Z
UID:20138-1644409800-1644411600@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Richard Law (Park)\, Graduate Student in Chemical and Biomolecular Engineering
DESCRIPTION:TITLE: “Quantitative flux analysis reveals redistribution of glycolytic pathways in dynamic nutrient environments.” \nABSTRACT: Optimal operation of metabolic fluxes is critical for an organism to be evolutionarily competitive. Textbook glycolysis is a conserved pathway that optimally utilizes carbohydrates for growth. However\, it is unclear why some organisms simultaneously possess the parallel Entner-Doudoroff (ED) pathway\, which has a lower bioenergetic yield. By integrating stable isotope tracing\, mass spectrometry\, and mathematical modeling\, we measure fluxes of these pathways in near-real time. Here\, we identify the benefits of the ED pathway under transitory environments. We utilized these tools for flux analysis to study central carbon metabolism in dynamic nutrient conditions. Specifically\, we hypothesized that parallel pathways enable cells to rapidly upshift their overall glycolytic flux to benefit growth in response to sudden nutrient availability. Our studies revealed that parallel yet specialized pathways enable dynamic redistribution of metabolic fluxes that are linked to rapid changes in metabolism and broader biological phenotypes.\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/12/Richard-Law-Edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-richard-law-park-graduate-student-in-chemical-and-biomolecular-engineering/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/12/Richard-Law-.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220214T160000
DTEND;TZID=America/Los_Angeles:20220214T170000
DTSTAMP:20260517T200720
CREATED:20220103T173906Z
LAST-MODIFIED:20220103T173906Z
UID:20364-1644854400-1644858000@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Leila Jamal\, PhD\, Genetic Counselor and Bioethicist\, Associate Director for Cancer Genomics\, National Cancer Institute and the Johns Hopkins Bloomberg School of Public Health
DESCRIPTION:TITLE: “Walking the line between progress and paternalism in genetic counseling.” \nHosted by Christina Palmer.
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-leila-jamal-phd-genetic-counselor-and-bioethicist-associate-director-for-cancer-genomics-national-cancer-institute-and-the-johns-hopkins-bloomberg-sch/
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/14/2022/01/6.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220223T120000
DTEND;TZID=America/Los_Angeles:20220223T123000
DTSTAMP:20260517T200720
CREATED:20211207T223900Z
LAST-MODIFIED:20220223T222057Z
UID:20094-1645617600-1645619400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Matthew Heffel (Luo)\, Graduate Student in Bioinformatics
DESCRIPTION:TITLE: “Multimodal Single-Cell Epigenomic Sequencing of the Developing Human Cerebral Cortex.” \nABSTRACT: Single cell epigenomic technologies allow the measurement of unique molecular signatures within cells\, however cell type complexity remains highly enigmatic. Emerging methods have enabled multiple modalities of epigenomic sequencing to be gathered from the same cell. Single-nucleus methyl-3C sequencing (sn-m3C-seq) delivers the capacity to capture chromatin conformation and DNA methylation information of 5’-methylcytosines with single cell fidelity. Developing neurons accumulate significant DNA methylation at non-CG sites (mCH)\, adjust patterns of CG methylation (mCG)\, and endure rearrangements of chromatin domains. These patterns of mCH\, mCG\, and chromatin interactions are specific to neuronal subtypes. We collected prefrontal cortex samples from 13 individuals at several developmental time stamps divided into four major age groups\, second trimester (2T)\, third trimester (3T)\, infant\, and adult. Applying sn-m3C-seq to our data of >29\,000 cells we identify 27 adult cell types and their developmental trajectories from five 2T cell types. The methylation features allow for intricate\, deeply specific cell type annotations and while the 3C modality highlights less specific cell types\, it can pick up forward trajectory signals that methylation either does not or that resolve as a single heterogeneous cell type in methylation; We observe developing glial progenitor cells identified in 3C that cluster as radial glia in the methylation feature space alone. The temporal forward stepping of the 3C feature set further allows us to validate cell types in different sample age groups. The integration of single cell modalities in sn-m3C-seq allows for the highly robust cell type classification as well as strong downstream analysis of epigenetic divergences of developing cell lineages. \nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/12/Matthew-Heffel-edited.mp4\n 
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-matthew-heffel-luo-graduate-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/14/2021/12/Matthew-Heffel.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220223T123000
DTEND;TZID=America/Los_Angeles:20220223T130000
DTSTAMP:20260517T200720
CREATED:20211207T224209Z
LAST-MODIFIED:20220214T212656Z
UID:20099-1645619400-1645621200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Chenghao (Trevor) Zhu (Boutros)\, Postdoc in Human Genetics
DESCRIPTION:TITLE: “moPepGen: a fast custom database generator from multi-omics data for proteogenomics.” \nABSTRACT: Cancers are driven by genomic variants such as SNV (single nucleotide variants) and INDEL\, often accompanied by many transcriptional variants. Modern mass spectrometry based proteomics is able to identify and quantify peptides and proteins comprehensively\, however the variant-harboring peptides that are absent in canonical databases are largely under-studied. A common problem in custom database construction is the large number of combinations of variants to consider. Thus major proteogenomic studies often choose a strategy that only captures peptides harboring a single variant. Existing algorithms also suffer from limited sources of variation. We developed moPepGen (multi-omics peptide database generator) that aims at accelerating proteogenomic researching by generating custom peptide database from variety of genomic and transcriptional variants. MoPepGen uses a graph-based algorithm that achieves a linear time complexity in integrating variants in contrast to the exponential complexity of exhaust searching. MoPepGen integrates variants from a variety of sources including SNV\, indel\, transcription fusion\, alternative splicing\, RNA editing\, and circRNA. It is able to generate peptides harboring any combinations of variants on the single peptide. MoPepGen is also highly extensible for other types of genomic and transcriptional variants. \n 
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-chenghao-trevor-zhu-boutros-postdoc/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/12/Chenghao-Trevor-Zhu-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20220228T160000
DTEND;TZID=America/Los_Angeles:20220228T170000
DTSTAMP:20260517T200720
CREATED:20220103T174045Z
LAST-MODIFIED:20220103T174045Z
UID:20368-1646064000-1646067600@qcb.ucla.edu
SUMMARY:Bioinformatics/Human Genetics Seminar Series: Jason Moore\, PhD\, Founding Chair of the Department of Computational Biomedicine\, Cedars-Sinai
DESCRIPTION:TITLE: “Automated genetic analysis” \nHosted by Nandita Garud.
URL:https://qcb.ucla.edu/event/bioinformatics-human-genetics-seminar-series-jason-moore-phd-founding-chair-of-the-department-of-computational-biomedicine-cedars-sinai/
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/14/2022/01/7.jpg
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