GECO Evolutionary and Computational Genomics
The main goal of the GECO department is to foster integration and synergies between theoretical and methodological research relevant for the analysis of genomes (computational genomics) and empirical analysis of genomic and multi-omic data (evolutionary and functional genomics). The department is structured in two teams, BAOBAB and BPGE:
BAOBAB is deeply rooted in computer science. Its strengths are in algorithms, models, and mathematical analysis of graphs and networks, with applications to transcriptomics and metabolic networks.
BPGE is oriented towards bioinformatics, phylogenetics and evolutionary genomics. Its research projects cover a broad range of subjects, such as methodological developments for phylogenetic inference, their applications to the reconstruction of the evolutionary history of bacteria and archaea, the role of mobile genetic elements in the evolution of bacteria and of antibioresistance, or the role of recombination, of genomic rearrangements and of transposable elements in the evolution of eukaryotic genomes.
As detailed on their pages, the research conducted in both teams integrates deep and long-ranging theoretical and methodological (algorithmic and computational) developments with data analysis driven by empirical questions. This integration is bi-directional: methodological developments are guided by empirical questions and then used in empirical applications, while theoretical modeling helps clarify the conceptual basis of subsequent empirical analyses.
Publications
Display of 211 to 240 publications on 1378 in total
An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
Genome Research . 30 ( 2 ) : 164-172
Journal article
see the publicationThe wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication
Genome Biology . 21 ( 1 ) : 223
Journal article
see the publicationAn Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice
Genes . 11 ( 9 ) : 1046
Journal article
see the publicationEvolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates
eLife . 9
DOI: 10.7554/eLife.63650
Journal article
see the publicationSex differences in adult lifespan and aging rates of mortality across wild mammals
Proceedings of the National Academy of Sciences of the United States of America . 117 ( 15 ) : 8546-8553
Journal article
see the publicationA Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
Journal of Clinical Microbiology . 58 ( 6 ) : 1128
DOI: 10.1128/JCM.00060-20
Journal article
see the publicationEvidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Genes . 11 ( 7 ) : 787
Journal article
see the publicationY chromosome makes fruit flies die younger
Peer Community In Evolutionary Biology . : 100105
Other publication
see the publicationPopulation genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest
Evolutionary Applications . 13 : 442-457
DOI: 10.1111/eva.12881
Journal article
see the publicationCapybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
Bioinformatics . 36 ( 14 ) : 4197-4199
Journal article
see the publicationAlgorithms for the quantitative Lock/Key model of cytoplasmic incompatibility
Algorithms for Molecular Biology . : 1-16
Journal article
see the publicationFrom conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria
PLoS ONE . 15 ( 4 ) : e0231839
Journal article
see the publicationIsotopic systematics point to wild origin of mummified birds in Ancient Egypt
Scientific Reports . 10 ( 1 )
Journal article
see the publicationThe Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France
Journal of Archaeological Science: Reports . 34 : 102595
Journal article
see the publicationMetapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards
eLife . 9
DOI: 10.7554/eLife.54795
Journal article
see the publicationDickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)
International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514
Journal article
see the publicationδ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?
Journal of African Earth Sciences . 162 : 103702
Journal article
see the publicationClinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene
PLoS ONE . 15 ( 7 ) : e0235655
Journal article
see the publicationFitting diversification models on undated or partially dated trees
Peer Community In Evolutionary Biology . : 100088
Other publication
see the publicationStudying genetic antagonisms as drivers of genome evolution
Peer Community In Evolutionary Biology .
Journal article
see the publicationSyndrome de Klinefelter, rôle du chromosome Y dans l’espérance de vie humaine ?
36ème Congrès de la Société Française d'Endocrinologie (SFE Marseille 2020) . 81 ( 4 ) : 194
Conference paper
see the publicationMindfulness-Based Programs Improve Psychological Flexibility, Mental Health, Well-Being, and Time Management in Academics
European Journal of Investigation in Health, Psychology and Education . 10 ( 4 ) : 1035-1050
Journal article
see the publicationBedrock radioactivity influences the rate and spectrum of mutation
eLife . 9 : e56830
DOI: 10.7554/eLife.56830
Journal article
see the publicationKey role of chromosomal mobile genetic elements transferring by conjugation in the dissemination of antimicrobial resistance in Streptococcus suis
8th symposium on Antimicrobial Resistance in Animal and Environment .
Conference paper
see the publicationThe ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus.
8th symposium on Antimicrobial Resistance in Animal and Environment .
Conference paper
see the publicationThe ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus
4th International Workshop on Streptococcus suis .
Poster
see the publicationNaturally radioactive environments influence the rate and spectrum of mutation
Annual conference of the Society for Molecular Biology and Evolution .
Poster
see the publicationDevelopment of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions
Journée scientifique de la FR BioEnviS .
Poster
see the publicationKey role of chromosomal mobile genetic elements transferred by conjugation in the dissemination of antimicrobial resistance in S. suis
4th International Workshop on Streptococcus suis .
Conference paper
see the publicationDevelopment of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions
Auvergne Rhône-Alpes Regional Workshop on Microbiome .
Poster
see the publication