Author

Sean Kennedy

Institut PasteurORCID 0000-0002-3932-8922Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:benchmarking· 3 Assay:metagenomics· 3 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Christiane BouchieriD· 2 shared Dimitri DesvillechabroliD· 2 shared Thomas CokelaeriD· 2 shared Agnes Baud· 1 shared Alec M. ChiuiD· 1 shared Amine GhozlaneiD· 1 shared Anne‐Sophie AlvareziD· 1 shared Antoine AuvergneiD· 1 shared

Activity by Year

2016-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 7 mutual co-author links

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2 shared papersBioinformatics

Christiane BouchierORCID

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Author profile →

6 papers

Recent·Most cited

Competitive advantage of hypervirulent Group B Streptococcus for neonatal colonization revealed by metagenomic analysis of gut microbiota

Anne‐Sophie Alvarez, Florian Plaza Oñate, Gérald Touak, Sean Kennedy, François Goffinet, Céline Plainvert, Laurent Mandelbrot, Stanislav Dusko Ehrlich, Claire Poyart, Asmaa Tazi

The paper identifies GBS CC17's competitive advantage over non-CC17 GBS in neonatal gut colonization through metagenomic analysis and in vitro experiments.

bioRxiv · Jun 19, 2026 · PreprintMicrobiology

Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples

Agnes Baud, Sean Kennedy

The paper introduces Moonbase, a pipeline for building targeted metagenomic databases to improve taxonomic detection and quantification, showing improved species precision and statistical power in microbial community analysis.

Microorganisms · Jan 10, 2024Peer-reviewedBioinformatics

A multivariate outcome test of covariance

Christophe Boetto, Arthur Frouin, Léo Henches, Antoine Auvergne, Yuka Suzuki, Étienne Patin, Marius Bredon, Alec M. Chiu, Sriram Sankararaman, Noah Zaitlen, Sean Kennedy, Lluís Quintana‐Murci, Darragh Duffy, Harry Sokol, Hugues Aschard

The paper introduces MANOCCA, a method to test the effect of predictors on the covariance matrix of multivariate outcomes, showing it outperforms existing methods in simulations and identifies significant associations in real data.

bioRxiv · Sep 20, 2023 · PreprintBioinformatics

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

Stevenn Volant, Pierre Lechat, Perrine Woringer, Laurence Motreff, Pascal Campagne, Christophe Malabat, Sean Kennedy, Amine Ghozlane

SHAMAN provides a web tool for metataxonomic analysis, integrating data processing, statistical modeling, and visualization for non-expert users.

BMC Bioinformatics · Aug 10, 2020Peer-reviewedBioinformatics

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer

Sequanix provides a graphical interface for Snakemake workflows to make them more accessible to a broader audience.

Bioinformatics · Jan 18, 2018Peer-reviewedBioinformatics

Detection and characterization of low and high genome coverage regions using an efficient running median and a double threshold approach.

Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer

The paper introduces a method to detect and characterize low and high coverage regions in genomes using a running median and double threshold approach.

bioRxiv · Dec 8, 2016 · PreprintBioinformatics