Research Explorer

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Researcher

Lore Depuydt

Publications & Research Data

Awards & Distinctions

13 Results

2025

Advancing practical pan-genomics with compressed indexing

Lore DepuydtJan FostierTravis Gagie

b-move : faster lossless approximate pattern matching in a run-length compressed index

Lore DepuydtLuca RendersSimon Van de VyverLennart VeysTravis GagieJan Fostier

A1 Journal Article in ALGORITHMS FOR MOLECULAR BIOLOGY

Columba: fast approximate pattern matching with optimized search schemes

Luca RendersLore DepuydtTravis GagieJan Fostier

U Journal Article in BIOINFORMATICS

KeBaB : k-mer Based Breaking for Finding Long MEMs

Nathaniel K. BrownLore DepuydtMohsen ZakeriAnas AlhadiNour AllamDove BegleiterNithin Bharathi Kabilan KarpagavalliSuchith Sridhar KhajjayamHamza WahedTravis Gagie et al.

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

Lore DepuydtOmar Y. AhmedJan FostierBen LangmeadTravis Gagie

U Journal Article in ISCIENCE

Search schemes for approximate pattern matching : an overview

Lore DepuydtJan FostierSimon GottliebGregory KucherovKnut ReinertLuca Renders

Bookchapter in The Expanding World of Compressed Data : A Festschrift for Giovanni Manzini's 60th Birthday

2024

Automated design of efficient search schemes for lossless approximate pattern matching

Luca RendersLore DepuydtSven RahmannJan Fostier

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

Lore DepuydtLuca RendersSimon Van de VyverLennart VeysT. GagieJan Fostier

Faster maximal exact matches with lazy LCP evaluation

Adrián GogaLore DepuydtNathaniel K. BrownJan FostierTravis GagieGonzalo Navarro

Lossless approximate pattern matching : automated design of efficient search schemes

Luca RendersLore DepuydtSven RahmannJan Fostier

A1 Journal Article in JOURNAL OF COMPUTATIONAL BIOLOGY

2023

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

Lore DepuydtLuca RendersThomas AbeelJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

2022

Approximate pattern matching using search schemes and in-text verification

Luca RendersLore DepuydtJan Fostier

Approximate pattern matching using search schemes and in-text verification

Luca RendersLore DepuydtJan Fostier