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X-WR-CALDESC:Events for Biomedical Mathematics Group
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DTSTART;TZID=Asia/Seoul:20210813T090000
DTEND;TZID=Asia/Seoul:20210813T100000
DTSTAMP:20260427T154932
CREATED:20210810T220000Z
LAST-MODIFIED:20210811T064522Z
UID:4837-1628845200-1628848800@www.ibs.re.kr
SUMMARY:TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data
DESCRIPTION:We will discuss about “TimeCycle: Topology Inspired MEthod for the Detection of Cycling Transcripts in Circadian Time-Series Data”\, Ness-Cohn and Braun\, Bioinformatics\, 2021 \nAbstract \nMotivation: The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics\, coupled with the significant implicatins of the circadian clock for human health\, has sparked an interest in circadian profiling studies to discover genes under circadian control.\nResult: We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series\, the method reconstructs the state space using time-delay embedding\, a data transformation technique from dynamical systems theory. In the embedded space\, Takens’ theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology\, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution\, cycling genes are identified. Results in both synthetic and biological data highlight TimeCycle’s ability to identify cycling genes across a range of sampling schemes\, number of replicates\, and missing data. Comparison to competing methods highlights their relative strengths\, providing guidance as to the optimal choice of cycling detection method.\nAvailability: A fully documented open-source R package implementing TimeCycle is available at: https://nesscoder.github.io/TimeCycle/ .
URL:https://www.ibs.re.kr/bimag/event/2021-08-13-2/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
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