Author

Bernard De Baets C

Ghent UniversityORCID 0000-0002-3876-620XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:database / resource· 2 Approach:machine learning (classical)· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Approach:large language model· 1

Frequent Co-Authors

Michiel StockiD· 3 shared Tapio PahikkalaiD· 2 shared Willem WaegemaniD· 2 shared Yves BriersiD· 2 shared Alexandre BoulayiD· 1 shared Antti AirolaiD· 1 shared Bjorn CrieliD· 1 shared Clovis GalieziD· 1 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Michiel StockORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery

Alexandre Boulay, Victor Németh, Bjorn Criel, Michiel Stock, Bernard De Baets C, Clovis Galiez, Elsa Rousseau, Yves Briers, Roberto Vázquez

PhaLP 2.0 enhances a phage lysin database by integrating metagenomic data and introducing SUBLYME, a machine learning tool that identifies and classifies lysins with high accuracy.

Database · Jan 1, 2026Peer-reviewedBioinformatics

DepoScope: accurate phage depolymerase annotation and domain delineation using large language models

Robby Concha-Eloko, Michiel Stock, Bernard De Baets C, Yves Briers, Rafael Sanjuán, Pilar Domingo‐Calap, Dimitri Boeckaerts

DepoScope uses large language models to accurately annotate phage depolymerases and their domains, improving detection through sequence and amino-acid level predictions.

PLoS Computational Biology · Aug 5, 2024Peer-reviewedBioinformatics

A Comparison of Embedding Aggregation Strategies in Drug-Target Interaction Prediction

Dimitrios Iliadis, Bernard De Baets C, Tapio Pahikkala, Willem Waegeman

This study compares three embedding aggregation strategies for drug-target interaction prediction using benchmark datasets, showing when each strategy is most effective.

BMC Bioinformatics · Feb 6, 2024Peer-reviewedBioinformatics

Algebraic Shortcuts for Leave-One-Out Cross-Validation in Supervised Network Inference

Michiel Stock, Tapio Pahikkala, Antti Airola, Willem Waegeman, Bernard De Baets C

The paper introduces algebraic shortcuts for leave-one-out cross-validation to evaluate kernel-based network inference methods efficiently.

Briefings in Bioinformatics · Sep 10, 2018Peer-reviewedSystems Biology