
Chercheur en biologie computationnelle, évolution, liens sciences-sociétés, permaculture
Recherches :
- Thèses de Alexandre Laverré (avec Anouk Necsulea), Théo Tricou (avec Damien de Vienne), Hugo Menet (avec Vincent Daubin)
- Action exploratoire "Community Garden Book" (équipe projet Inria Beagle)
- Fabrique des Questions Simples, laboratoire incubateur de recherches dans l'anthropocène
Enseignements :
- Cours M1 bioinformatique MADG
- Cours Ethique (Master et Doctorat), Video 1 et Video 2, Intégrité Scientifique Partie 1, Partie 2, Partie 3
- Atelier Sciences Environnements Sociétés
Responsabilités - Animations :
- Membre du comité scientifique de la Plateforme Resetis
- Membre du comité scientifique de la boutique des sciences
- Co-fondateur de Peer Community in Mathematical and Computational Biology
Publications
Display of 1 to 30 publications on 112 in total
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Bioinformatics . : 1-3
Journal article
see the publicationGhost lineages highly influence the interpretation of introgression tests
Systematic Biology . : 1-39
Journal article
see the publicationSeaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
Multiple Sequence Alignment . 2231 : 241-260
Book chapter
see the publicationAncestral Genome Organization as a Diagnosis Tool for Phylogenomics
Phylogenetics in the Genomic Era . : 2.5:1--2.5:19
Book chapter
see the publicationTreerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Journal article
see the publicationEvolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
BMC Biology . 18 ( 1 ) : 1-20
Journal article
see the publicationGene tree reconciliation including transfers with replacement is NP-hard and FPT
Journal of Combinatorial Optimization . 38 ( 2 ) : 502–544
Journal article
see the publicationGene tree species tree reconciliation with gene conversion
Journal of Mathematical Biology . 78 ( 6 ) : 1981–2014
Journal article
see the publicationZombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages
Bioinformatics .
Journal article
see the publicationQuand les branches de l’arbre du vivant s’entremêlent
Pour la science .
Journal article
see the publicationRecPhyloXML: a format for reconciled gene trees
Bioinformatics . 34 ( 21 ) : 3646-3652
Journal article
see the publicationPhylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes
BMC Genomics . 19 ( S2 ) : 1-15
Journal article
see the publicationGene transfers can date the tree of life
Nature Ecology & Evolution . 2 ( 5 ) : 904-909
Journal article
see the publicationComparative Methods for Reconstructing Ancient Genome Organization
Comparative Genomics: Methods and Protocols . : 343 - 362
Book chapter
see the publicationMaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
DOI: 10.1101/127548
Other publication
see the publicationAlgorithms for computing the double cut and join distance on both gene order and intergenic sizes
Algorithms for Molecular Biology . 12 : 16 (11 pages)
Journal article
see the publicationResolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Bioinformatics . 33 ( 7 ) : 980-987
Journal article
see the publicationDeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies
Genome Biology and Evolution . 9 ( 5 ) : 1312-1319
DOI: 10.1093/gbe/evx069
Journal article
see the publicationIn silico experimental evolution provides independent and challenging benchmarks for comparative genomics
Journées ouvertes Biologie Informatique Mathématiques . : 79-82
Conference paper
see the publicationEfficient gene tree correction guided by genome evolution
PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)
Journal article
see the publicationComparative Genomics on Artificial Life
Computability in Europe . 9709 : 35-44
Conference paper
see the publicationGenome Rearrangements on both Gene Order and Intergenic Regions
WABI 2016 . 9838 : 162-173
Conference paper
see the publicationBreaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
Genome Biology and Evolution . 8 ( 5 ) : 1427-1439
DOI: 10.1093/gbe/evw083
Journal article
see the publication