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Cancer Biostatistics Monthly Seminar

December 7, 2023 @ 12:00 pm - 1:00 pm UTC

Hongkai Ji, PhD Cancer Biostatistics Image

A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

Dr. Hongkai Ji, PhD


Associate Chair

Director of the Graduate Program

Department of Biostatistics

Bloomberg School of Public Health

Johns Hopkins University  



Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.  


Join Zoom Meeting here

Meeting ID: 895 1762 3227

Passcode: 5f74neBi


This group meets monthly from Noon – 1 p.m. The meeting agenda includes a presentation, programmatic announcements, and updates from Cancer Center program leaders.


December 7, 2023
12:00 pm - 1:00 pm UTC
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