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 en video (Master et Doctorat), Video 1 et Video 2, Intégrité Scientifique Partie 1, Partie 2, Partie 3
- Cours Ethique en diapos
- 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 et éditeur de Peer Community in Mathematical and Computational Biology
Publications
Display of 31 to 60 publications on 121 in total
Resolution 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 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 publicationNucleotide, gene and genome evolution : a score to bind them all
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationDating with transfers
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationGenome Rearrangements on both Gene Order and Intergenic Regions
WABI 2016 . 9838 : 162-173
Conference paper
see the publicationFrancisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?
Microbial Cell . 3 ( 11 ) : 576-578
Journal article
see the publicationComment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationAncestral Reconstruction: Theory and Practice
Encyclopedia of Evolutionary Biology . : 70–77
Book chapter
see the publicationComparative Genomics on Artificial Life
Computability in Europe . 9709 : 35-44
Conference paper
see the publicationEfficient gene tree correction guided by genome evolution
PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)
Journal article
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 publicationSorting Signed Permutations by Reversal (Reversal Sequence)
Encyclopedia of Algorithms . 978-1-4939-2863-7 : 2028-2032
Book chapter
see the publicationGenome rearrangements with indels in intergenes restrict the scenario space
BMC Bioinformatics . 17 ( Suppl 14 ) : 426 (7 pages)
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 publicationReconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence
BMC Genomics . 16 ( Suppl 10 ) : S9
Journal article
see the publicationThe inference of gene trees with species trees
Systematic Biology . 64 ( 1 ) : e42-e62
Journal article
see the publicationMoments of genome evolution by Double Cut-and-Join
BMC Bioinformatics . 16 ( Suppl 14 ) : S7
Journal article
see the publicationKaryotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops
Genome Biology and Evolution . 7 ( 3 ) : 735-749
DOI: 10.1093/gbe/evv014
Journal article
see the publicationFoundations of Coding: Compression, Encryption, Error-Correction
978-1-118-88144-6 : 376
Book
see the publicationAncestral gene synteny reconstruction improves extant species scaffolding
BMC Genomics . 16 ( Suppl 10 ) : S11
Journal article
see the publicationProbabilistic modeling of the evolution of gene synteny within reconciled phylogenies
BMC Bioinformatics . 16 ( Suppl 14 ) : S5
Journal article
see the publicationGenome-scale phylogenetic analysis finds extensive gene transfer among fungi
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)
Journal article
see the publicationCounting and sampling SCJ small parsimony solutions
Theoretical Computer Science . 552 : 83-98
Journal article
see the publicationThéorie des Codes : compression, cryptage, correction, 2e edition
9782100599110 : 384
Book
see the publicationLateral Gene Transfer from the Dead.
Systematic Biology . 62 ( 3 ) : 386-397
Journal article
see the publicationLateral gene transfer, rearrangement, reconciliation
BMC Bioinformatics . 14 ( Suppl 15 ) : S4
Journal article
see the publicationGene tree correction guided by orthology
BMC Bioinformatics . 14 ( Suppl 15 ) : S5
Journal article
see the publication