ArticleNucleic acids research2022
FusionGDB 2.0: fusion gene annotation updates aided by deep learning.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 50 citations in OpenAlex.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Anchored random reverse primer sequencing for quantitative detection of novel gene fusions.Nature biomedical engineering · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- FusionTarget: Computational framework for drug repurposing against modeled fusion protein structures from genomic breakpoints.iScience · 2026Article
- FuDiCo: Gene Fusion-Initiated Path Propagation for Disease Comorbidity Prediction.Current issues in molecular biology · 2026Article
- Fusion-positive rhabdomyosarcoma oncofusions share a common interactome.Nature communications · 2026Article
- EXaCT-2: an augmented and customizable oncology-focused whole exome sequencing platform.NPJ precision oncology · 2026Article
- Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment.Genome medicine · 2026Article
- The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer.iScience · 2026Article
- Detection of Chimeric RNAs from RNA-Seq Data with ChiTaRS 8.0: Insights for Liquid Biopsy and Drug Target Identification.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Case Report: Novel ASAP1::BRAF fusion in a young adult with low-grade temporal lobe glioma.Frontiers in oncology · 2026Article
- Systematic evaluation of long- and short-read RNA-seq for human peripheral blood.NAR molecular medicine · 2026Article
- Fusions4U: a resource of validated and annotated gene fusions in 328 cancer cell lines.BMC cancer · 2025Article
- Regulatory Mechanisms and Functional Roles of Readthrough Transcripts in Tumorigenesis.International journal of molecular sciences · 2025Review
- Epidermal Growth Factor Receptor Aberrations Identified by Next-Generation Sequencing in Patients with Metastatic Cancers.Cancer research and treatment · 2025Article
- Computation strategies and clinical applications in neoantigen discovery towards precision cancer immunotherapy.Biomarker research · 2025Review
- Predicting Protein Function in the AI and Big Data Era.Biochemistry · 2025Review
- KinaseFusionDB: an integrative knowledge of kinase fusion proteins in multi-scales.Briefings in bioinformatics · 2025Article
- Single-cell multi-omics elucidates the role of RPS27-RPS24 fusion gene in osteosarcoma chemoresistance and metabolic regulation.Cell death discovery · 2025Article
- FusionPub, a therapeutic landscape of human fusion genes.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human genomic features across five cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of the protein feature retention of individual fusion partner genes in the protein level. Among ∼102k fusion genes, about 15k kept their ORF as In-frames, which is two times compared to the previous version, FusionGDB. FusionGDB 2.0 will be used as the reference knowledgebase of fusion gene annotations. FusionGDB 2.0 provides eight categories of annotations and it will be helpful for diverse human genomic studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.