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Andreas Kloetgen

dblp:91/11251 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2021
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › immunoinformatics
epitope prediction
0.512021
EpitopeVec: linear epitope prediction using deep protein sequence embeddings · Bioinform. 2021
Bioinformatics and computational biology › immunoinformatics › epitope prediction
linear b-cell epitope prediction
0.512021
EpitopeVec: linear epitope prediction using deep protein sequence embeddings · Bioinform. 2021
Bioinformatics and computational biology › protein analysis › protein bioinformatics › protein representation learning
protein language model embedding
0.112021
EpitopeVec: linear epitope prediction using deep protein sequence embeddings · Bioinform. 2021
Bioinformatics and computational biology › protein analysis › protein bioinformatics
protein representation learning
0.112021
EpitopeVec: linear epitope prediction using deep protein sequence embeddings · Bioinform. 2021

Methods — techniques the papers use, named apart from their topics

residue property encoding · 0.5protein language model · 0.5antigenicity scale · 0.5
YearPublicationVenuePosition
2021 EpitopeVec: linear epitope prediction using deep protein sequence embeddings
abstract
MOTIVATION: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51-53%. RESULTS: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance. AVAILABILITY AND IMPLEMENTATION: The software is available at https://github.com/hzi-bifo/epitope-prediction. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Akash Bahai, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy
Bioinform.4