ArticleBioinformatics (Oxford, England)2016
Gapped sequence alignment using artificial neural networks: application to the MHC class I system.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 654 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
654 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysis of the different subpeptidomes presented by the HLA class I molecules of the B7 supertype.Cellular immunology · 2023Pooled it
- A phase 3, randomized, double-blind, multicenter, placebo-controlled study of S-588410, a five-peptide cancer vaccine as an adjuvant therapy after curative resection in patients with esophageal squamous cell carcinoma.Esophagus : official journal of the Japan Esophageal Society · 2024Trial
- Design and in silico evaluation of PV-GNProtecta: an mRNA multi-epitope vaccine candidate against Puumala virus using immunoinformatics and structural analysis.Genomics & informatics · 2026Article
- SmartVax-Bp: An Immunoinformatic guided Multi-Epitope Vaccine Blueprint Against Burkholderia pseudomallei.Probiotics and antimicrobial proteins · 2026Article
- Reconstitution of glycan-driven MHC-I recycling reveals calreticulin as mediator between TAPBPR and tapasin.The EMBO journal · 2026Article
- Immuno-Informatics Design of Multi-Epitope Vaccine Candidate AgainstHealth science reports · 2026Article
- Ensembles ofbioRxiv : the preprint server for biology · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Cell type-specific expression and subcellular localization of the human insulin upstream open reading frame (INSU) protein in pancreatic β-cells.The Journal of biological chemistry · 2026Article
- Molecular classification identifies aggressive gastrointestinal stromal tumor subtype targetable by PARP inhibitors.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- Automating neoantigen selection for personalized cancer vaccine design.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Geospatial genetic evolution and phenotypic plasticity in triple-negative breast cancer.Genome medicine · 2026Article
- Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer.NPJ precision oncology · 2026Article
- Navigating luminal heterogeneity: etiology-based proteogenomic subtyping for targeted treatment strategies in breast cancer.Molecular cancer · 2026Article
- Immunoinformatics-Driven Identification of Conserved Multi-Epitope Vaccine Candidates from PDI Protein of Leishmania Donovani for Visceral Leishmaniasis.Cell biochemistry and biophysics · 2026Article
- TransBindpMHCI: a transformer-based model for pan-specific MHC-I peptide binding prediction.BMC bioinformatics · 2026Article
- Healthy donor T cell receptors expand functional neoantigen recognition beyond patient vaccination.Science advances · 2026Article
- The Effects of Past COVID-19 and Vaccination on Antibody Levels, Cellular Immunity, and Cytokine Production by Peripheral Blood Mononuclear Cells.Biomedicines · 2026Article
- Computational identification of conserved dengue virus envelope protein epitopes for vaccine design and immunodiagnostic platform.Scientific reports · 2026Article
594 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
motivationMany biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to peptides of length 8-11 amino acids. On this relatively simple system, we developed a sequence alignment method based on artificial neural networks that allows insertions and deletions in the alignment.
resultsWe show that prediction methods based on alignments that include insertions and deletions have significantly higher performance than methods trained on peptides of single lengths. Also, we illustrate how the location of deletions can aid the interpretation of the modes of binding of the peptide-MHC, as in the case of long peptides bulging out of the MHC groove or protruding at either terminus. Finally, we demonstrate that the method can learn the length profile of different MHC molecules, and quantified the reduction of the experimental effort required to identify potential epitopes using our prediction algorithm. AVAILABILITY AND IMPLEMENTATION: The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment is publicly available at: http://www.cbs.dtu.dk/services/NetMHC-4.0.
Indexed as
Identifiers
What OpenQuestion holds
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.