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dc.contributor.author
Garde, Christian
dc.contributor.author
Ramarathinam, Sri H.
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Jappe, Emma C.
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Nielsen, Morten
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Kringelum, Jens V.
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Trolle, Thomas
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dc.contributor.author
Purcell, Anthony W.
dc.date.available
2022-02-01T02:23:23Z
dc.date.issued
2019-05
dc.identifier.citation
Garde, Christian; Ramarathinam, Sri H.; Jappe, Emma C.; Nielsen, Morten; Kringelum, Jens V.; et al.; Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data; Springer; Immunogenetics; 71; 7; 5-2019; 445-454
dc.identifier.issn
0093-7711
dc.identifier.uri
http://hdl.handle.net/11336/151021
dc.description.abstract
Major histocompatibility complex (MHC) class II antigen presentation is a key component in eliciting a CD4+ T cell response. Precise prediction of peptide-MHC (pMHC) interactions has thus become a cornerstone in defining epitope candidates for rational vaccine design. Current pMHC prediction tools have, so far, primarily focused on inference from in vitro binding affinity. In the current study, we collate a large set of MHC class II eluted ligands generated by mass spectrometry to guide the prediction of MHC class II antigen presentation. We demonstrate that models developed on eluted ligands outperform those developed on pMHC binding affinity data. The predictive performance can be further enhanced by combining the eluted ligand and pMHC affinity data in a single prediction model. Furthermore, by including ligand data, the peptide length preference of MHC class II can be accurately learned by the prediction model. Finally, we demonstrate that our model significantly outperforms the current state-of-the-art prediction method, NetMHCIIpan, on an external dataset of eluted ligands and appears superior in identifying CD4+ T cell epitopes.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Springer
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dc.rights
info:eu-repo/semantics/restrictedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
CD4+ EPITOPE
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LIGAND PREDICTION
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MACHINE LEARNING
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MASS SPECTROMETRY
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MHC CLASS II
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PAN METHOD
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PEPTIDOMICS
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Otras Medicina Básica
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dc.subject.classification
Medicina Básica
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dc.subject.classification
CIENCIAS MÉDICAS Y DE LA SALUD
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dc.title
Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2020-11-20T18:10:18Z
dc.journal.volume
71
dc.journal.number
7
dc.journal.pagination
445-454
dc.journal.pais
Alemania
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dc.description.fil
Fil: Garde, Christian. Evaxion Biotech; Dinamarca
dc.description.fil
Fil: Ramarathinam, Sri H.. Monash University; Australia
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Fil: Jappe, Emma C.. Evaxion Biotech; Dinamarca. Technical University of Denmark; Dinamarca
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Fil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina. Technical University of Denmark; Dinamarca
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Fil: Kringelum, Jens V.. Evaxion Biotech; Dinamarca
dc.description.fil
Fil: Trolle, Thomas. Evaxion Biotech; Dinamarca
dc.description.fil
Fil: Purcell, Anthony W.. Monash University; Australia
dc.journal.title
Immunogenetics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1007/s00251-019-01122-z
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs00251-019-01122-z
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