Stat Colloquium: Dr. Indranil Mukhopadhyay
University of Nebraska-Lincoln
Location
Mathematics/Psychology : 401
Date & Time
April 11, 2025, 11:00 am – 12:00 pm
Description
Title: PseudoGA: an efficient Pseudotime reconstruction method using
single cell RNA-seq data
Abstract: Dynamic regulation of gene expression is
often governed by progression through transient cell states. Bulk RNA-seq
analysis only detects average change in expression levels and is unable to
identify this dynamics. Single cell RNA-seq (scRNA-seq) presents an
unprecedented opportunity that helps in placing cells on a hypothetical time
trajectory that reflects gradual transition of their transcriptomes. This
continuum trajectory (pseudotime) may reveal the developmental pathway that
provides information on dynamic transcriptomic changes. Existing approaches
heavily depend on reducing huge dimension to very low dimensional subspaces and
may lead to loss of information. We propose PseudoGA, a genetic algorithm based
approach to order cells assuming gene expressions vary according to a smooth
curve along the pseudotime trajectory. Our method shows higher accuracy in
simulated and real datasets. Generality of the assumption behind PseudoGA and
no dependence on dimensionality reduction technique make it a robust choice for
pseudotime estimation from scRNA-seq data. We use resampling technique while
applying PseudoGA to a large scRNA-seq data. PseudoGA is adaptable to parallel
computing. I shall also discuss some possible downstream analysis once
pseudotime is constructed.
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