Transformers meets neoantigen detection: a systematic literature review
Open accessAbstract
Cancer immunology offers a new alternative to traditional cancer treatments, such as radiotherapy and chemotherapy. One notable alternative is the development of personalized vaccines based on cancer neoantigens. Moreover, Transformers are considered a revolutionary development in artificial intelligence with a significant impact on natural language processing (NLP) tasks and have been utilized in proteomics studies in recent years. In this context, we conducted a systematic literature review to investigate how Transformers are applied in each stage of the neoantigen detection process. Additionally, we mapped current pipelines and examined the results of clinical trials involving cancer vaccines.
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Cites
Evolutionary-scale prediction of atomic level protein structure with a language model
Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,523 · see citing works
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning
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A universal SNP and small-indel variant caller using deep neural networks
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Evaluating Protein Transfer Learning with TAPE
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- Authors
- Machaca, V., Goyzueta, V., Cruz, M. G., Sejje, E., Pilco, L. M., López, J., & Túpac, Y.
- Affiliations
- 27840 Universidad La Salle , Arequipa , Perú
- Universidad La Salle (PE)
- Universidad Católica San Pablo (PE)
- Universidad Nacional de San Agustin de Arequipa (PE)
- Fuerza Aérea del Perú , Arequipa , Perú
- 187038 Universidad Católica San Pablo , Arequipa , Perú
- ORCID
- Venue
- Journal of Integrative Bioinformatics
- Publisher
- Walter de Gruyter GmbH
- Published
- 2024-06-01
- Volume
- 21
- Issue
- 2
- ISSN
- 1432-4385 (ISSN-L)
- 1613-4516
- PMC
- PMC11377031
- OpenAlex
- W4400337122
- Cited by
- 5
- References
- 5
- Citations by year
- 2026: 4 · 2025: 1
- FWCI
- 0.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- De La Salle University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Keywords
- transformer models, neoantigens, personalized cancer vaccines, cancer immunotherapy, proteomics, natural language processing
- MeSH terms
- Antigens, Neoplasm, Artificial Intelligence, Humans, Natural Language Processing, Neoplasms, Cancer Vaccines
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