Faculty profile
Travis Gagie
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Research
Latest papers
Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.
NAR genomics and bioinformatics · 2026
Movi 2: fast and space-efficient queries on pangenomes.
Bioinformatics (Oxford, England) · 2026
Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes".
Bioinformatics (Oxford, England) · 2026
Latest funding
- $12,500
Compact Data Structures for Computational Genomics
NSERC · 2020 · Principal investigator
- $170,000
Compact Data Structures for Computational Genomics
NSERC · 2020 · Principal investigator
39 publications.
Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.
Kafaie S, Naseri S, Mahoney DBJ, Gagie T, Beiko RG, Maguire F
Movi 2: fast and space-efficient queries on pangenomes.
Zakeri M, Brown NK, Gagie T, Langmead B
Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes".
Alanko JN, Slizovskiy IB, Lokshtanov D, Gagie T, Noyes NR, Boucher C
Suffixient Arrays: A New Efficient Suffix Array Compression Technique.
Cenzato D, Depuydt L, Gagie T, Kim SH, Manzini G, Olivares F, Prezza N
Prefix-free parsing for merging big BWTs.
Díaz-Domínguez D, Gagie T, Guerrini V, Langmead B, Lipták Z, Manzini G, Masillo F, Shivakumar V
KeBaB: k-mer based breaking for finding long MEMs.
Brown NK, Depuydt L, Zakeri M, Alhadi A, Allam N, Begleiter D, Kabilan Karpagavalli NB, Khajjayam SS, Wahed H, Gagie T, Langmead B
Run-length compressed metagenomic read classification with SMEM-finding and tagging.
Depuydt L, Ahmed OY, Fostier J, Langmead B, Gagie T
Columba: fast approximate pattern matching with optimized search schemes.
Renders L, Depuydt L, Gagie T, Fostier J
b-move: faster lossless approximate pattern matching in a run-length compressed index.
Depuydt L, Renders L, Van de Vyver S, Veys L, Gagie T, Fostier J
Efficient Grammar Compression via RLZ-based RePair.
Varki R, Gagie T, Boucher C
Compact Data Structures for Computational Genomics
Principal investigators: Gagie, Travis
Compact Data Structures for Computational Genomics
Principal investigators: Gagie, Travis
Keywords: compact data structures; data compression; genomic databases; pan-genome references; pattern matching; read alignment
From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.
Frequent collaborators
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