BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Institute for Quantitative and Computational Biosciences - ECPv6.16.2//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
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
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:20210702T140000
DTEND;TZID=America/Los_Angeles:20210702T143000
DTSTAMP:20260518T032337
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. \n\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
END:VCALENDAR