Academic Bibliography

Search 200 years of publications by Ghent University researchers.

ir. Lore Depuydt

Faculty of Engineering and Architecture > Department of Information technology

ORCID iD: 0000-0001-8517-0479

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- Journal Article
- A1
- open access
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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- Journal Article
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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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KeBaB : k-mer Based Breaking for Finding Long MEMs

Nathaniel K. Brown, Lore Depuydt (UGent) , Mohsen Zakeri, Anas Alhadi, Nour Allam, Dove Begleiter, Nithin Bharathi Kabilan Karpagavalli, Suchith Sridhar Khajjayam, Hamza Wahed, Travis Gagie, et al.

(2025) STRING PROCESSING AND INFORMATION RETRIEVAL, SPIRE 2025. In Lecture Notes in Computer Science 16073. p.10-17
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- PhD Thesis
Advancing practical pan-genomics with compressed indexing

Lore Depuydt (UGent)

(2025)
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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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- Journal Article
- A1
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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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- Journal Article
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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
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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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- Conference Paper
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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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- Conference Paper
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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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