Ghent University Academic Bibliography

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Benchmarking DNA barcode decoding strategies under high error rates

Franco Alexander Poma Soto (UGent) , Hanne Van Droogenbroeck (UGent) , Brecht Soulliaert (UGent) , Maya Giridhar, Jürgen Behr, Hamed Sabzalipoor, Mark Somoza, Pieter Mestdagh (UGent) and Jo Vandesompele (UGent)

(2026) BMC BIOINFORMATICS.
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Direct construction of sparse suffix arrays with Libsais

Simon Van de Vyver (UGent) , Tibo Vande Moortele (UGent) , Peter Dawyndt (UGent) , Bart Mesuere (UGent) and Pieter Verschaffelt (UGent)

(2025) BMC BIOINFORMATICS. 26(1).
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Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning

Espoir Kabanga (UGent) , Seonil Jee, Soeun Yun, Stephen Depuydt, Arnout Van Messem and Wesley De Neve (UGent)

(2025) BMC BIOINFORMATICS. 26(1).
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Solu : a cloud platform for real-time genomic pathogen surveillance

Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega Sanz (UGent) , Jacob L. Steenwyk and Samuel Sihvonen

(2025) BMC BIOINFORMATICS. 26(1).
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A comparison of embedding aggregation strategies in drug-target interaction prediction

Dimitrios Iliadis (UGent) , Bernard De Baets (UGent) , Tapio Pahikkala and Willem Waegeman (UGent)

(2024) BMC BIOINFORMATICS. 25(1).
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Assessing the reliability of point mutation as data augmentation for deep learning with genomic data

Hyunjung Lee, Utku Özbulak (UGent) , Homin Park, Stephen Depuydt (UGent) , Wesley De Neve (UGent) and Joris Vankerschaver (UGent)

(2024) BMC BIOINFORMATICS. 25(1).
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Pan-genome de Bruijn graph using the bidirectional FM-index

Lore Depuydt (UGent) , Luca Renders (UGent) , Thomas Abeel (UGent) and Jan Fostier (UGent)

(2023) BMC BIOINFORMATICS. 24(1).
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CamPype : an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

Irene Ortega Sanz (UGent) , José A. Barbero-Aparicio, Antonio Canepa-Oneto, Jordi Rovira and Beatriz Melero

(2023) BMC BIOINFORMATICS. 24(1).
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CRISPR-Cas-Docker : web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins

Homin Park, Jong Bum Won, Yunseol Park, Esla Timothy Anzaku (UGent) , Joris Vankerschaver (UGent) , Arnout Van Messem (UGent) , Wesley De Neve (UGent) and Hyunjin Shim (UGent)

(2023) BMC BIOINFORMATICS. 24(1).
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VariantscanR : an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

Fréderique Boeykens (UGent) , Sofie Bhatti (UGent) , Luc Peelman (UGent) and Bart Broeckx (UGent)

(2023) BMC BIOINFORMATICS. 24(1).

Academic Bibliography

Benchmarking DNA barcode decoding strategies under high error rates

Direct construction of sparse suffix arrays with Libsais

Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning

Solu : a cloud platform for real-time genomic pathogen surveillance

A comparison of embedding aggregation strategies in drug-target interaction prediction

Assessing the reliability of point mutation as data augmentation for deep learning with genomic data

Pan-genome de Bruijn graph using the bidirectional FM-index

CamPype : an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

CRISPR-Cas-Docker : web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins

VariantscanR : an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

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