ArticleGenome biology2023
BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 20 citations in OpenAlex.
- pXg: Comprehensive and Reliable Identification of MHC-I Antigens Using De Novo Peptide Sequencing and Immunotranscriptomic Datasets.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Invas: an inversion-aware method for transcriptome assembly.Nature communications · 2026Article
- Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors.Molecular & cellular proteomics : MCP · 2026Article
- Next-generation neoantigen mRNA vaccines: Immuno-engineering strategies for precision cancer immunotherapy.Cellular oncology (Dordrecht, Netherlands) · 2026Review
- PepQueryMHC: rapid and comprehensive tumor antigen prioritization from immunopeptidomics data.Genome biology · 2025Article
- HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer.Journal for immunotherapy of cancer · 2025Article
- Tumor antigens preferentially derive from unmutated genomic sequences in melanoma and non-small cell lung cancer.Nature cancer · 2025Article
- Immunopeptidomics-guided discovery and characterization of neoantigens for personalized cancer immunotherapy.Science advances · 2025Article
- Interferon-α promotes HLA-B-restricted presentation of conventional and alternative antigens in human pancreatic β-cells.Nature communications · 2025Article
- Endogenous retroelements in hematological malignancies: From epigenetic dysregulation to therapeutic targeting.American journal of hematology · 2025Review
- Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies.Human vaccines & immunotherapeutics · 2024Review
- MHC-I-presented non-canonical antigens expand the cancer immunotherapy targets in acute myeloid leukemia.Scientific data · 2024Article
- Immunogenicity of Non-Mutated Ovarian Cancer-Specific Antigens.Current oncology (Toronto, Ont.) · 2024Article
- Autophagy degrades immunogenic endogenous retroelements induced by 5-azacytidine in acute myeloid leukemia.Leukemia · 2024Article
- Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy.Experimental hematology & oncology · 2024Review
- Activation of human endogenous retroviruses and its physiological consequences.Nature reviews. Molecular cell biology · 2024Review
- Breast cancer immunopeptidomes contain numerous shared tumor antigens.The Journal of clinical investigation · 2024Article
- Exploring HERV-K (HML-2) Influence in Cancer and Prospects for Therapeutic Interventions.International journal of molecular sciences · 2023Review
- BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens.Genome biology · 2023Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 2 countries.
Funding
Abstract
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens' RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
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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.