Ghent University Academic Bibliography

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doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Fabricio De Almeida Silva (UGent) and Yves Van de Peer (UGent)

(2025) BIOINFORMATICS. 41(2).
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ELLIPSIS : robust quantification of splicing in scRNA-seq

Marie Van Hecke (UGent) , Niko Beerenwinkel, Thibault Lootens (UGent) , Jan Fostier (UGent) , Robrecht Raedt (UGent) and Kathleen Marchal (UGent)

(2025) BIOINFORMATICS. 41(2).
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BioArchLinux : community-driven fresh reproducible software repository for life sciences

Guoyi Zhang, Pekka Ristola, Han Su, Bipin Kumar, Boyu Zhang, Yujin Hu, Michael G. Elliot, Viktor Drobot, Jie Zhu, Jens Staal (UGent) , et al.

(2025) BIOINFORMATICS. 41(3).
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wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Hengchi Chen (UGent) , Arthur Zwaenepoel and Yves Van de Peer (UGent)

(2024) BIOINFORMATICS. 40(5).
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Uncertainty-aware single-cell annotation with a hierarchical reject option

Lauren Theunissen (UGent) , Thomas Mortier (UGent) , Yvan Saeys (UGent) and Willem Waegeman (UGent)

(2024) BIOINFORMATICS. 40(3).
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GeNNius: an ultrafast drug-target interaction inference method based on graph neural networks

Uxia Veleiro, Jesus de la Fuente, Guillermo Serrano, Marija Pizurica (UGent) , Mikel Casals, Antonio Pineda-Lucena, Silve Vicent, Idoia Ochoa, Olivier Gevaert and Mikel Hernaez

(2024) BIOINFORMATICS. 40(1).
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Scywalker : scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing

Peter De Rijk, Tijs Watzeels, Fahri Küçükali, Jasper Van Dongen, Júlia Faura, Patrick Willems (UGent) , Lara De Deyn, Lena Duchateau, Carolin Seyfferth (UGent) , Thomas Eekhout (UGent) , et al.

(2024) BIOINFORMATICS. 40(9).
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Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools

Artuur Couckuyt (UGent) , Benjamin Rombaut (UGent) , Yvan Saeys (UGent) and Sofie Van Gassen (UGent)

(2024) BIOINFORMATICS. 40(4).
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ECCB2024 : the 23rd European Conference on Computational Biology

Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, et al.

(2024) BIOINFORMATICS. 40(Supplement 2). p.ii1-ii3
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Mutate and observe : utilizing deep neural networks to investigate the impact of mutations on translation initiation

Utku Özbulak (UGent) , Hyun Jung Lee (UGent) , Jasper Zuallaert (UGent) , Wesley De Neve (UGent) , Stephen Depuydt (UGent) and Joris Vankerschaver (UGent)

(2023) BIOINFORMATICS. 39(6).

Academic Bibliography

doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

ELLIPSIS : robust quantification of splicing in scRNA-seq

BioArchLinux : community-driven fresh reproducible software repository for life sciences

wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Uncertainty-aware single-cell annotation with a hierarchical reject option

GeNNius: an ultrafast drug-target interaction inference method based on graph neural networks

Scywalker : scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing

Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools

ECCB2024 : the 23rd European Conference on Computational Biology

Mutate and observe : utilizing deep neural networks to investigate the impact of mutations on translation initiation

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