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Bastien Cazaux
Researcher at University of Helsinki
Publications - 41
Citations - 341
Bastien Cazaux is an academic researcher from University of Helsinki. The author has contributed to research in topics: Time complexity & Superstring theory. The author has an hindex of 8, co-authored 38 publications receiving 259 citations. Previous affiliations of Bastien Cazaux include University of Montpellier.
Papers
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Journal ArticleDOI
Read mapping on de Bruijn graphs
TL;DR: A formal definition of mapping on a de Bruijn graph is proposed, the problem complexity turns out to be NP-complete, and a practical solution is provided combining efficiency with an improved mapping capacity compared to assembly-based mapping even for complex eukaryotic data.
Journal ArticleDOI
Read Mapping on de Bruijn graph
TL;DR: Greedy Graph MAPping (GGMAP) as discussed by the authors is a pipeline to map reads on branching paths of the graph, for which a heuristic algorithm called BGREAT (de Bruijn Graph REAd mapping Tool) is designed.
Book ChapterDOI
From Indexing Data Structures to de Bruijn Graphs
TL;DR: Here, the relationship between suffix trees/arrays and dBGs is formalised, and linear time algorithms for constructing the full or contracted dBGs are exhibited.
Journal ArticleDOI
Reverse engineering of compact suffix trees and links
Bastien Cazaux,Eric Rivals +1 more
TL;DR: This work investigates the Reverse Engineering problem on ST with links and introduces a new suffix tree characterisation that makes up a valuable step towards a better understanding of suffix tree combinatorics.
Journal ArticleDOI
Finding all maximal perfect haplotype blocks in linear time.
TL;DR: Two algorithms are given that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows–Wheeler Transform, that is very efficient also in practice.