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Updated: Feb 7, 2026

Transcriptome Analysis of Single Cells
Published on: April 25, 2011
Fusion gene discovery in single cells from high throughput long read single cell transcriptomes
Cheng-Kai Shiau1,2, Hsiao-Yun Lin1,2, Timothy Pan1,2,3
1Department of Biochemistry and Molecular Genetics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA 60611.
Abstract:
High throughput long-read single cell RNA sequencing allows for fusion gene discovery in thousands of cells in parallel, which is however constrained by the lack of robust computational tools. Here, we develop LongFUSE that employs the XOR logic operation and stringent filtering criteria for the accurate detection of cell-specific fusion genes and their splicing isoforms. LongFUSE outperforms existing tools in both simulation and real data, demonstrating high accuracy and robustness.
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