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DTSTART;TZID=America/Los_Angeles:20210212T110000
DTEND;TZID=America/Los_Angeles:20210212T113000
DTSTAMP:20260518T075331
CREATED:20210204T152332Z
LAST-MODIFIED:20210226T200938Z
UID:16453-1613127600-1613129400@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Nicolas Rochette (Campbell-Staton)
DESCRIPTION:TITLE: Cis-regulatory divergence between highland and lowland deer mice populations highlight the essential role of pleiotropic genes for high-altitude adaptation. \nABSTRACT: Variation in gene expression regulation contributes extensively to phenotypic diversity within and between species and plays a major role in complex trait evolution. However\, the characterization of the genetic basis of regulatory variation is complicated by the inter-dependencies between the expressions of all genes. A promising approach to circumvent this issue is to measure gene-wise allelic imbalance (also known as allele-specific expression) as it intrinsically emphasizes cis-regulatory effects. Here\, we demonstrate the power of the allelic imbalance approach and use it to investigate the cis-regulatory landscape of local adaptation to high altitude in the deer mouse (Peromyscus maniculatus). We find evidence that freely segregating regulatory alleles are ubiquitous in wild populations. Then\, we detect strong cis-regulatory differentiation between highland and lowland populations in a small set of genes\, which comprises known adaptations as well as new candidates and underlines the role of integrative genes to explain the broad range of organismal changes observed in high altitude populations.
URL:https://qcb.ucla.edu/event/qcbio-research-seminars-nicolas-rochette-campbell-staton/
LOCATION:ZOOM\, CA\, United States
CATEGORIES:Research Seminars
ATTACH;FMTTYPE=image/jpeg:https://wp-misc.lifesci.ucla.edu/qcb/wp-content/uploads/sites/14/2021/02/Nicolas-Rochette.jpg
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DTSTART;TZID=America/Los_Angeles:20210212T113000
DTEND;TZID=America/Los_Angeles:20210212T120000
DTSTAMP:20260518T075331
CREATED:20210112T233425Z
LAST-MODIFIED:20210215T163620Z
UID:15816-1613129400-1613131200@qcb.ucla.edu
SUMMARY:QCBio Research Seminar: Kexin Li (Li JJ)
DESCRIPTION:TITLE: “scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling.” \nABSTRACT: Single-cell RNA sequencing (scRNA-seq) captures whole transcriptome information of individual cells. While scRNA-seq measures thousands of genes\, researchers are often interested in only dozens to hundreds of genes for a closer study. Then a question is how to select those informative genes from scRNA-seq data. Moreover\, single-cell targeted gene profiling technologies are gaining popularity for their low costs\, high sensitivity\, and extra (e.g.\, spatial) information; however\, they typically can only measure up to a few hundred genes. Then another challenging question is how to select genes for targeted gene profiling based on existing scRNA-seq data. Here we develop the single-cell Projective Non-negative Matrix Factorization (scPNMF) method to select informative genes from scRNA-seq data in an unsupervised way. Compared with existing gene selection methods\, scPNMF has two advantages. First\, its selected informative genes can better distinguish cell types. Second\, it enables the alignment of new targeted gene profiling data with reference data in a low-dimensional space to facilitate the prediction of cell types in the new data. Technically\, scPNMF modifies the PNMF algorithm for gene selection by changing the initialization and adding a basis selection step\, which selects informative bases to distinguish cell types. We demonstrate that scPNMF outperforms the state-of-the-art gene selection methods on diverse scRNA-seq datasets. Moreover\, we show that scPNMF can guide the design of targeted gene profiling experiments and cell-type annotation on targeted gene profiling data. \n\nhttps://qcb.ucla.edu/wp-content/uploads/sites/14/2021/01/Kexin-Li-edited.mp4
URL:https://qcb.ucla.edu/event/qcbio-research-seminar-kexin-li-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/14/2021/01/KexinLi.jpg
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