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 1201 to 1230 publications on 1402 in total
A mathematical model describing the thermal virus inactivation
Vaccine . 19 : 3575-3582
Journal article
see the publicationComparaison de séquences d`éléments transposables et de gènes d`hôtes chez cinq espèces : A. Thaliana C. Elegans D. Melanogaster H. Sapiens S. Cerevisiae
incollection . -- : 347-354
Journal article
see the publicationSmall-subunit rRNA genotyping of rhizobia nodulating Australian Acacia spp.
Applied and Environmental Microbiology . 67 ( 1 ) : 396-402
Journal article
see the publicationFitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals
Journal of Antimicrobial Chemotherapy . 47 ( 3 ) : 277-283
DOI: 10.1093/jac/47.3.277
Journal article
see the publicationGene flow in a facultative apomictic poacea the savanna grass Hyparrhenia diplandra
Genetics . 156 : 823-831
Journal article
see the publicationSelective sweep near the In(2L)t inversion breakpoint in an African population of Drosophila melanogaster
Genetical Research . 76 : 149-158
Journal article
see the publicationIdentification and molecular analysis of BANP
Gene . 253 ( 2 ) : 189-196
Journal article
see the publicationEuGene an eurocaryotic gene finder that combines several sources of evidence
Journées ouvertes biologie informatique mathématiques .
Conference paper
see the publicationtRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
Trends in Genetics . 16 : 287-289
Journal article
see the publicationHOBACGEN: database system for comparative genomics in bacteria
Genome Research . 10 : 379-385
DOI: 10.1101/gr.10.3.379
Journal article
see the publicationThe covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact
Molecular Biology and Evolution . 17 : 1620-1625
Journal article
see the publicationNature and structure of human genes that generate retropseudogenes
Genome Research . 10 : 672-678
Journal article
see the publicationDeterminants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate
Molecular Biology and Evolution . 17 : 68-74
Journal article
see the publicationUse of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera
Journal of General Virology . 81 : 2949-2958
Journal article
see the publicationInfering regulatory elements from a whole genome. An application to the analysis of genome of $\itemize{Helicobacter Pylori}$ $\sigma_{80}$ family of promoter signals
Journal of Molecular Biology . 297 ( 1 ) : 335-353
Journal article
see the publicationInferring regulatory elements from a whole genome. An application to the analysis of the genome of Helicobacter pylori sigma 80 family of promoter signals
Journal of Molecular Biology . 297 : 335-353
Journal article
see the publicationAlgorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification
Journal of Computational Biology . 7 : 345-360
Journal article
see the publicationThe Enhanced Microbial Genomes Library
Nucleic Acids Research . 27 : 63-65
Journal article
see the publicationEMGLib: the enhanced microbial genomes library (update 2000)
Nucleic Acids Research . 28 ( 1 ) : 68-71
DOI: 10.1093/nar/28.1.68
Journal article
see the publicationPhylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990)
Journal of Eukaryotic Microbiology . 47 ( 3 ) : 288-293
Journal article
see the publicationCodon usage and the origin of P elements
Molecular Biology and Evolution . 17 : 467-468
Journal article
see the publicationTransposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans
Genetics . 156 : 1661-1669
Journal article
see the publicationChromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family
AIDS Research and Human Retroviruses . 16 : 731-740
Journal article
see the publicationMultiple alignments for structural functional or phylogenetic analyses of homologous sequences
incollection . -- : 51-76
Journal article
see the publicationSequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain
Marine Biotechnology . 2 : 419-428
Journal article
see the publicationThe evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome
Trends in Genetics . 16 ( 12 ) : 529-533
Journal article
see the publicationAbsence of translationally selected synonymous codon usage bias in Helicobacter pylori.
Microbiology . 146 ( Pt 4) : 851-60
Journal article
see the publicationMolecular Systematics of sponges (Porifera)
Hydrobiologia . 420 ( 1 ) : 15-27
Journal article
see the publicationA nonhyperthermophilic common ancestor to extant life forms
Science . 283 ( 5399 ) : 220-221
Journal article
see the publication