ASA Connect

Dear Colleagues,

The ASA Philadelphia chapter is delighted to organize a webinar talk on integrating transcriptomics and lineage information for differentiation trajectory inference in single cell studies. The webinar will be on Thursday, Dec 11 from 11:00am to 12:00pm Eastern Time. The talk will be given by Dr. Juan Xie, a research associate in the Department of Epidemiology and Public Health at the University of Maryland, Baltimore.

Register for free using the following link. After registering, you will receive a confirmation email containing information about joining the meeting. 

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Abstract: 

Single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (scTCR-seq) provide complementary information for studying T cell differentiation: scRNA-seq captures functional phenotypes, while scTCR-seq encodes clonal lineage. Traditional trajectory inference methods rely solely on transcriptomics and may obscure clonal-level heterogeneity. I will present LRT, a computational framework that integrates scRNA-seq and scTCR-seq to reveal clonal differentiation trajectory heterogeneity. LRT first constructs global trajectories from transcriptomic profiles, then incorporates TCR sequence and phenotypic information to identify clonotype clusters exhibiting distinct differentiation biasedness. The framework provides a full analysis workflow-including preprocessing, clonotype clustering, trajectory biasedness evaluation, and clonotype cluster characterization-and is implemented as an R package with two interactive Shiny apps. Applications to viral infection datasets demonstrate that LRT uncovers biologically meaningful clonal substructures that cannot be detected from scRNA-seq alone.

Short Bio:

Juan Xie, PhD is a research associate in the Department of Epidemiology and Public Health at the University of Maryland, Baltimore. Her research focuses on statistical and computational methods for single cell and spatial omics data, with application to cancer immunology. She received her PhD in Biostatistics from The Ohio State University in 2025.

Thanks and wishing everyone a wonderful Thanksgiving!