GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

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 901 to 930 publications on 1408 in total

A multiple layer model to compare RNA secondary structures

Julien Allali, Marie-France Sagot

Software: Practice and Experience . 38 ( 8 ) : 775-792

DOI: 10.1002/spe.846

Journal article

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Indexing gapped-factors using a tree

Pierre Peterlongo, Julien Allali, Marie-France Sagot

International Journal of Foundations of Computer Science . 19 ( 1 ) : 71-87

DOI: 10.1142/S0129054108005541

Journal article

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Lossless filter for multiple repetitions with Hamming distance

Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira Do Lago, Marie-France Sagot

Journal of Discrete Algorithms . 6 ( 3 ) : 497-509

DOI: 10.1016/j.jda.2007.03.003

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

BMC Bioinformatics . 9 ( 1 ) : 286

DOI: 10.1186/1471-2105-9-286

Journal article

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Development of the Acyrthosiphon pisum Cyc database (ApsCyc): from genome sequence to metabolic network analyses

A. Vellozo, Stefano Colella, L. Cottret, G. Febvay, Federica Calevro, Yvan Rahbé...

Integrative Post-Genomics - IPG'08 . : 1-1

Conference paper

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Annotation of metabolism genes: towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses

Stefano Colella, A. Vellozo, L. Cottret, G. Febvay, Federica Calevro, Yvan Rahbé...

4th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1" . : 1-1

Conference paper

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Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN

Perrine Portier, Denis Costechareyre, Daniel Muller, David Chapulliot, Christine Oger, Guy Perrière...

7. Colloque national du Bureau des Ressources Génétiques . 7

Conference paper

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Automatic Identification of Large Collections of Protein-Coding or rRNA Sequences

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy

Biochimie . 90 ( 4 ) : 609-614

DOI: 10.1016/j.biochi.2007.08.006

Journal article

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Bioinformatics in the complete genome sequence era

G. Perrière

Biochimie . 90 : 553-554

Journal article

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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

Journal article

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A seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees

S. Mignard, Jean-Pierre Flandrois

International Journal of Systematic and Evolutionary Microbiology . 58(part 6) : 1432-1441

Journal article

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Exact Transcriptome Reconstruction from Short Sequence Reads

Vincent Lacroix, M. Sammeth, R. Guigo, A. Bergeron

International Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 50-63

DOI: 10.1007/978-3-540-87361-7_5

Conference paper

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Identification de motifs dans les réseaux métaboliques : définitions algorithmes et application au métabolisme d’Escherichia coli

Vincent Lacroix

Edilivre . 978-2-35607-642-7

Book

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Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

Journal article

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A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.

Céline Brochier-Armanet, Simonetta Gribaldo, Patrick Forterre

Biol Direct . 3 : 54

DOI: 10.1186/1745-6150-3-54

Journal article

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Les Archaea : évolution et diversité du troisième domaine du vivant

Simonetta Gribaldo, Patrick Forterre, Céline Brochier-Armanet

Bulletin - Société Française de Microbiologie . 23 ( 3 ) : 137-145

Journal article

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Metagenome Annotation Using a Distributed Grid of Undergraduate Students

P. Hingamp, Céline Brochier-Armanet, E. Talla, D. Gautheret, D. Thieffry, C. Herrmann

PLoS Biology . 6 : 239-241

Journal article

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Mating system and recombination affect molecular evolution in four Triticeae species

A. Haudry, A. Cenci, C. Guilhaumon, E. Paux, S. Poirier, S. Santoni...

Genetics Research . 90 : 97-109

Journal article

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Full molecular characterization of a simian immunodeficiency virus, SIVwrcpbt from Temminck's red colobus (Piliocolobus badius temminckii) from Abuko Nature Reserve, The Gambia

Sabrina Locatelli, Bénédicte Lafay, Florian Liegeois, Nelson Ting, Eric Delaporte, Martine Peeters

Virology . 376 ( 1 ) : 90-100

DOI: 10.1016/j.virol.2008.01.049

Journal article

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Prevalence and genetic diversity of simian immunodeficiency virus infection in wild-living red colobus monkeys (Piliocolobus badius badius) from the Taï forest, Côte d'Ivoire SIVwrc in wild-living western red colobus monkeys.

Sabrina Locatelli, Florian Liegeois, Bénédicte Lafay, Amy D Roeder, Michael W Bruford, Pierre Formenty...

Infection, Genetics and Evolution . 8 ( 1 ) : 1-14

DOI: 10.1016/j.meegid.2007.08.004

Journal article

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A Site- and Time-Heterogeneous Model of Amino Acid Replacement

Samuel Blanquart, Nicolas Lartillot

Molecular Biology and Evolution . 25 ( 5 ) : 842-858

DOI: 10.1093/molbev/msn018

Journal article

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Additional molecular support for the new chordate phylogeny.

Frédéric Delsuc, Georgia Tsagkogeorga, Nicolas Lartillot, Herve Philippe

Genesis - The Journal of Genetics and Development . 46 ( 11 ) : 592-604

DOI: 10.1002/dvg.20450

Journal article

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Mating system and recombination affect molecular evolution in four Triticeae species

A. A. Haudry, A. A. Cenci, C C Guilhaumon, Etienne Paux, S. S. Poirier, S. S. Santoni...

Genetics Research . 90 ( 1 ) : 97-109

DOI: 10.1017/S0016672307009032

Journal article

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Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy

Nature . 456 ( 7224 ) : 942-945

DOI: 10.1038/nature07393

Journal article

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Analyse et exploitation de la diversité génétique des polykétides synthases de type I dans l'ADN metagénomique d'un sol

Aurélien Ginolhac, Sandrine Demanèche, Cyrille Jarrin, Patrick Robe, Fabrice Lefevre, Renaud Nalin...

7ème colloque national "Ressources génétiques" . : 201-213

Conference paper

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Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia

Gabriel Marais, M. Nicolas, R. Bergero, P. Chambrier, E. Kejnovsky, F. Monéger...

Current Biology . 18 : 545-549

Journal article

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Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia

Gabriel Marais, Michael Nicolas, R. Bergero, Pierre Chambrier, E. Keinovsky, Françoise Moneger...

Current Biology . 18 ( 7 ) : 545-549

Journal article

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Genome-wide studies highlight indirect links between human replication origins and gene regulation.

Jean-Charles Cadoret, Françoise Meisch, Vahideh Hassan-Zadeh, Isabelle Luyten, Claire Guillet, L. Duret...

Proceedings of the National Academy of Sciences of the United States of America . 105 ( 41 ) : 15837-42

DOI: 10.1073/pnas.0805208105

Journal article

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Evolution of the proteome of mitochondrial ribosomes: a clue for the eukaryotic tree?

Elie Desmond-Le Quéméner, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Journées Ouvertes Biologie Informatique et Mathématiques JOBIM .

Poster

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