Ghent University Academic Bibliography

PhD Thesis

Approximate sequence alignment using search schemes

Luca Renders (UGent)

(2025)

Journal Article
A1
open access

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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Automated design of efficient search schemes for lossless approximate pattern matching

Luca Renders (UGent) , Lore Depuydt (UGent) , Sven Rahmann and Jan Fostier (UGent)

(2024) RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB 2024. In Lecture Notes in Computer Science 14758. p.164-184

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Conference Paper
C1
open access

B-move : faster bidirectional character extensions in a run-length compressed index

Lore Depuydt (UGent) , Luca Renders (UGent) , Simon Van de Vyver (UGent) , Lennart Veys, T. Gagie and Jan Fostier (UGent)

(2024) 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). In Leibniz International Proceedings in Informatics (LIPIcs) 312. p.1-18

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Journal Article
A1
open access

Lossless approximate pattern matching : automated design of efficient search schemes

Luca Renders (UGent) , Lore Depuydt (UGent) , Sven Rahmann and Jan Fostier (UGent)

(2024) JOURNAL OF COMPUTATIONAL BIOLOGY. 31(10). p.975-989

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Conference Paper
P1
open access

Faster maximal exact matches with lazy LCP evaluation

Adrián Goga, Lore Depuydt (UGent) , Nathaniel K. Brown, Jan Fostier (UGent) , Travis Gagie and Gonzalo Navarro

(2024) 2024 Data Compression Conference (DCC). In IEEE Data Compression Conference p.123-132

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Journal Article
A1
open access

Improved node and arc multiplicity estimation in de Bruijn graphs using approximate inference in conditional random fields

Aranka Steyaert (UGent) , P. Audenaert (UGent) and Jan Fostier (UGent)

(2023) IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 20(3). p.1995-2006

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Journal Article
A1
open access

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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Journal Article
A1
open access

Oracle selection provides insight into how far off practice is from Utopia in plant breeding

David Vanavermaete, Steven Maenhout (UGent) , Jan Fostier (UGent) and Bernard De Baets (UGent)

(2023) FRONTIERS IN PLANT SCIENCE. 14.

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Conference Paper
C1
open access

Detecting translocation of DNA nanostructures through nanopores : first steps towards structural barcode readout

Pratima Upretee (UGent) , Sybren Santermans, Koen Martens, Juliette Gevers, Sanjin Marion, Wouter Van Den Bosch, Jan Fostier (UGent) and Nilesh Madhu (UGent)

(2023) 2023 31st European Signal Processing Conference (EUSIPCO). In European Signal Processing Conference p.1205-1209

Academic Bibliography

Approximate sequence alignment using search schemes

ELLIPSIS : robust quantification of splicing in scRNA-seq

Automated design of efficient search schemes for lossless approximate pattern matching

B-move : faster bidirectional character extensions in a run-length compressed index

Lossless approximate pattern matching : automated design of efficient search schemes

Faster maximal exact matches with lazy LCP evaluation

Improved node and arc multiplicity estimation in de Bruijn graphs using approximate inference in conditional random fields

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

Oracle selection provides insight into how far off practice is from Utopia in plant breeding

Detecting translocation of DNA nanostructures through nanopores : first steps towards structural barcode readout

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