Academic Bibliography

Search 200 years of publications by Ghent University researchers.

prof. dr. ir. Jan Fostier

Faculty of Engineering and Architecture > Department of Information technology

ORCID iD: 0000-0002-9994-8269

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- Journal Article
- A1
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Run-length compressed metagenomic read classification with SMEM-finding and tagging

Lore Depuydt (UGent) , Omar Y. Ahmed, Jan Fostier (UGent) , Ben Langmead and Travis Gagie

(2025) ISCIENCE. 28(12).
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Columba : fast approximate pattern matching with optimized search schemes

Luca Renders (UGent) , Lore Depuydt (UGent) , Travis Gagie and Jan Fostier (UGent)

(2025) BIOINFORMATICS. 41(12).
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- Book Chapter
- open access
Search schemes for approximate pattern matching : an overview

Lore Depuydt (UGent) , Jan Fostier (UGent) , Simon Gottlieb, Gregory Kucherov, Knut Reinert and Luca Renders (UGent)

(2025) The Expanding World of Compressed Data : A Festschrift for Giovanni Manzini's 60th Birthday. In Open Access Series in Informatics (OASIcs) 131.
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b-move : faster lossless approximate pattern matching in a run-length compressed index

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

(2025) ALGORITHMS FOR MOLECULAR BIOLOGY. 20(1).
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Methods for single-biomolecule translocation event detection from nanopore current signal : a review

Pratima Upretee (UGent) , Wouter Botermans, Koen Martens, Sanjin Marion, Jan Fostier (UGent) and Nilesh Madhu (UGent)

(2025) IEEE SENSORS JOURNAL. 25(9). p.14505-14521
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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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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
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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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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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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