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Updated: May 15, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

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Published on: August 4, 2016

FUSIM: a software tool for simulating fusion transcripts.

Andrew E Bruno1, Jeffrey C Miecznikowski, Maochun Qin

  • 1Department of Biostatistics, SUNY at Buffalo, Buffalo, NY 14214, USA. aebruno2@buffalo.edu

BMC Bioinformatics
|January 18, 2013
PubMed
Summary
This summary is machine-generated.

Simulating gene fusions is crucial for advancing cancer research tools. FUSIM (FUsion SIMulator) software generates fusion transcripts to test and improve computational methods for discovering these cancer-associated genetic alterations.

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Last Updated: May 15, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Gene fusions, resulting from chromosomal aberrations, produce fusion transcripts critical in cancer development.
  • High-throughput transcriptome sequencing enables computational discovery of novel fusion genes.
  • Accurate simulation of fusion transcripts is vital for validating and enhancing these discovery tools.

Purpose of the Study:

  • To develop a computational tool for simulating fusion transcripts.
  • To provide a method for generating datasets of fusion transcripts for benchmarking.

Main Methods:

  • Development of FUSIM (FUsion SIMulator) software.
  • Implementation of simulation for various fusion-generating events: inter-chromosome translocations, trans-splicing, complex rearrangements, and transcriptional read-through.

Main Results:

  • FUSIM software enables the simulation of fusion transcripts.
  • The tool supports simulation of diverse mechanisms leading to gene fusions.
  • Generated datasets can be used for testing and benchmarking.

Conclusions:

  • FUSIM facilitates the creation of fusion transcript datasets.
  • This capability aids in testing and benchmarking computational tools for fusion gene discovery.