ArticleBioinformatics advances2022
NeoSplice: a bioinformatics method for prediction of splice variant neoantigens.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 38 citations in OpenAlex.
- Advances and challenges of splicing prediction with AI.Nature genetics · 2026Review
- pVACtools v6: A comprehensive suite for neoantigen prediction, visualization, and therapy design.ArXiv · 2026Article
- Neoantigen Targeting as a Novel Approach for Therapy-Resistant Tumors.Molecular diagnosis & therapy · 2026Review
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- In vivo CAR-T therapy: from molecular design to precision delivery.Journal of nanobiotechnology · 2026Review
- iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.Genome biology · 2026Article
- ImmunoPepper: extracting personalized peptides from complex splicing graphs.Bioinformatics (Oxford, England) · 2026Article
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Targeting splicing-derived neoantigens for precision cancer immunotherapy.Frontiers in immunology · 2026Review
- Alternative splicing: from tumorigenesis to neoantigen-mediated cancer immunotherapy.Biomarker research · 2025Review
- NovumRNA: Accurate prediction of non-canonical tumor antigens from RNA sequencing data.iScience · 2025Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- Advancements and challenges in personalized neoantigen-based cancer vaccines.Oncology reviews · 2025Review
- CAR-T therapy for neuroendocrine neoplasms: a review of molecular targets and clinical translation.Frontiers in immunology · 2025Review
- Identifying Strong Neoantigen MHC-I/II Binding Candidates for Targeted Immunotherapy with SINE.International journal of molecular sciences · 2024Article
- DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data.Computational and structural biotechnology journal · 2024Article
- SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors.Cancer research communications · 2024Article
- Quantifying tumor specificity using Bayesian probabilistic modeling for drug and immunotherapeutic target discovery.Cell reports methods · 2024Article
- Comprehensive profiling of cancer neoantigens from aberrant RNA splicing.Journal for immunotherapy of cancer · 2024Article
- Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates.Bioinformatics advances · 2024Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Motivation: Splice variant neoantigens are a potential source of tumor-specific antigen (TSA) that are shared between patients in a variety of cancers, including acute myeloid leukemia. Current tools for genomic prediction of splice variant neoantigens demonstrate promise. However, many tools have not been well validated with simulated and/or wet lab approaches, with no studies published that have presented a targeted immunopeptidome mass spectrometry approach designed specifically for identification of predicted splice variant neoantigens. Results: In this study, we describe NeoSplice, a novel computational method for splice variant neoantigen prediction based on (i) prediction of tumor-specific k-mers from RNA-seq data, (ii) alignment of differentially expressed k-mers to the splice graph and (iii) inference of the variant transcript with MHC binding prediction. NeoSplice demonstrates high sensitivity and precision (>80% on average across all splice variant classes) through Availability and implementation: https://github.com/Benjamin-Vincent-Lab/NeoSplice. Supplementary information: Supplementary data are available at
Identifiers
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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.