Speaker: Silvia Liu, PhD
Assistant Professor in University of Pittsburgh Department of Pharmacology and Chemical Biology
About the Seminar
“Computational multi-omics integration: long-read, single-cell, and spatial transcriptomics”
Driven by rapid and promising technological breakthroughs, high-throughput multi-omics data are being generated at an unprecedented scale. These advances have transformed disease diagnosis and drug discovery, marking an important step toward precision medicine.
Long-read transcriptome sequencing (long-RNA-seq) has greatly advanced the study of isoform diversity by capturing full-length transcripts and enabling precise detection of transcriptome structural variations, including novel isoforms, alternative splicing events, and fusion transcripts. In the first project, I will introduce IFDlong, a computational tool for detecting isoforms and fusion transcripts from bulk or single-cell long-RNA-seq data. The software quantifies isoform expression using a novel expectation–maximization algorithm and subsequently profiles fusion transcripts. IFDlong demonstrates strong accuracy and robustness across diverse in-house and public datasets, spanning healthy tissues, cancer samples, cell lines, and multiple disease contexts. Isoform-level biomarkers identified by IFDlong have significant translational potential.
In the second project, we aim to develop a multi-omics integration framework that combines long-read, single-cell, and spatial transcriptomic data. Traditional strategies often depend on batch-effect correction methods, but these approaches risk either under- or over-normalizing heterogeneous datasets. Instead, we will integrate data using innovative combinations of p-values, effect sizes, or newly designed optimization functions. The proposed framework has already been applied to acute kidney injury datasets to identify fibroblast subtypes across time points, and to liver tumor datasets to dissect the heterogeneity of the tumor microenvironment. Overall, these developments offer a comprehensive framework for accurate isoform profiling and scalable multi-omics integration, with broad potential to accelerate precision medicine.
Event Details
- Date: January 12, 2026
- Time: 11:30 a.m. – 12:30 p.m.
- Location: BST3 6014