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 841 to 870 publications on 1402 in total
Silene as a model system in ecology and evolution
Heredity . 103 : 583-589
Journal article
see the publicationAcypiCyc (Acyrthosiphon pisum Cyc database) : a model database to visualize and study the metabolic network underlying the pea aphid-Buchnera symbiosis
6. International Symbiosis Society (ISS) Congress .
Conference paper
see the publicationAcypiCyc (Acyrthosiphon pisumCyc database) and CycADS (CycAnnotation Database System) : moving from genome sequence annotation to metabolic network analyses
8. International Symposium on Aphids (8 ISA 2009) .
Conference paper
see the publicationAcypiCyc (Acyrthosiphon pisumCyc database) and CycADS (CycAnnotation Database System) : moving from genome sequence annotation to metabolic network analyses
Réseau Français de Biologie Adaptative des Pucerons .
Conference paper
see the publicationCycADS: an annotation management system for the development and update of BioCyc metabolic network databases
1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE .
Conference paper
see the publicationDifferential retention of metabolic genes following whole-genome duplication
Molecular Biology and Evolution . 26 ( 5 ) : 1067-1072
Journal article
see the publicationDatabases of Homologous Gene Families for Comparative Genomics
BMC Bioinformatics . 10 (Suppl.6) :S3 : 13
Journal article
see the publicationA new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
BMC Bioinformatics . 9 ( 1 ) : 460
Journal article
see the publicationEvolution of the mitochondrial ribosomal proteome
16th Annual Meeting of the Society of Molecular Biology and Evolution (SMBE'08) .
Poster
see the publicationDynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.
Human Mutation . 29 ( 10 ) : 1171-80
DOI: 10.1002/humu.20757
Journal article
see the publicationTranscription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes
Molecular Biology and Evolution . 26 ( 1 ) : 131-142
Journal article
see the publicationSex-specific genetic structure and social organization in Central Asia: insights from a multi-locus study.
PLoS Genetics . 4 ( 9 ) : e1000200
Journal article
see the publicationAncient bacteria liked it hot
Nature . 451 : 635-636
DOI: 10.1038/451635a
Journal article
see the publicationISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis.
Molecular and Cellular Proteomics . 7 : epub ahead of print
Journal article
see the publicationTranslational control of intron splicing in eukaryotes
Nature . 451 ( 7176 ) : 359-362
DOI: 10.1038/nature06495
Journal article
see the publicationBiased Gene Conversion and its Impact on Human Genome Evolution
incollection . -- : 273-277
Journal article
see the publicationEnumerating precursor sets of target metabolites in a metabolic network
WABI 2008 - 8th International Workshop on Algorithms in Bioinformatics . 5251 : 233-244
Conference paper
see the publicationEvolution des organismes bactériens
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 12 diapos
Conference paper
see the publicationBenchmarking RNA secondary structure comparison algorithms
Actes des Journées Ouvertes de Biologie, Informatique et Mathématiques . : 67-68
Conference paper
see the publicationA small trip in the untranquil world of genomes a survey on the detection and analysis of genome rearrangement breakpoints
Theoretical Computer Science . 395 : 171-192
Journal article
see the publicationExploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution
IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 3 ) : 348-356
DOI: 10.1109/TCBB.2008.16
Journal article
see the publicationBenchmarking RNA secondary structure comparison algorithms
Proc. JOBIM . : 67-68
Journal article
see the publicationDevelopment of the Acyrthosiphon pisum Cyc database (ApsCyc) : from genome sequence to metabolic network analyses
Integrative Post-Genomics - IPG'08 .
Conference paper
see the publicationLes réseaux métaboliques et génétiques
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1
Conference paper
see the publicationCaractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum
Séminaire INRA AgroBI .
Conference paper
see the publicationAnnotation of metabolism genes : towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses
4. Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1" .
Poster
see the publicationModes and Cuts in Metabolic Networks:Complexity and Algorithms
BioSystems . 95 - n°1 : 51-60
Journal article
see the publicationPrecise detection of rearrangement breakpoints in mammalian chromosomes
: 26
Report
see the publicationTranscriptomique
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant" . : 1-1
Conference paper
see the publicationEfficient representation and P-value computation for high-order Markov motifs
Bioinformatics . 24 : i160-i166
Journal article
see the publication