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 931 to 960 publications on 1402 in total

Efficient learning of Bayesian network classifiers:An extension to the TAN classifie

A. Carvalho, A. Oliveira, M.-F. Sagot

20th Australian Joint Conference on Artificial Intelligence . 4830 : 16-25

DOI: 10.1007/978-3-540-76928-6_4

Conference paper

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The solution space of sorting by reversals

Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007) . 4463 : 293-304

DOI: 10.1007/978-3-540-72031-7_27

Conference paper

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Evolution under Reversals: Parsimony and Conservation of Common Intervals

Y. Diekmann, M.-F. Sagot, Eric Tannier

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 4 : 301-309

Journal article

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Regulation of expression following nutritional stresses in the reduced genome of Buchnera aphidicola, "Is there any life left?

Yvan Rahbé, H. Charles, J. Vinuelas, N. Reymond, Federica Calevro, J.M. Fayard...

Seminarios del Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE) - Univ. Valencia (ESP) . : 1-1

Conference paper

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Metabolic network visualization eliminating node redundance and preserving metabolic pathways

Romain Bourqui, L. Cottret, Vincent Lacroix, D. Auber, P. Mary, M.-F. Sagot...

BMC Biology . 1 - n°29 : 1-19

DOI: 10.1186/1752-0509-1-29

Journal article

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Advances on sorting by reversals

Eric Tannier, A. Bergeron, M.-F. Sagot

Discrete Applied Mathematics . 155 : 881-888

Journal article

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Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene

S. Mignard, J.-P. Flandrois

Journal of Medical Microbiology . 56 ( 8 ) : 1033-1041

DOI: 10.1099/jmm.0.47105-0

Journal article

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In vitro detection of the enzymatic activity of folate-dependent tRNA(U54 C5)methyltransferase

J. Urbonavicius, Céline Brochier-Armanet, S. Skouloubris, H. Myllykallio, H. Grosjean

Methods in Enzymology . 25 : 103-19

Journal article

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In vitro detection of the enzymatic activity of folate-dependent tRNA (Uracil-54,-C5)-methyltransferase: evolutionary implications.

Jaunius Urbonavicius, Céline Brochier-Armanet, Stéphane Skouloubris, Hannu Myllykallio, Henri Grosjean

Methods in Enzymology . 425 : 103-19

DOI: 10.1016/S0076-6879(07)25004-9

Journal article

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Comparative RNomics and modomics in mollicutes: prediction of gene function and evolutionary implications

V. de Crécy-Lagard, C. Marck, Céline Brochier-Armanet, H. Grosjean

IUBMB Life . 59 : 634-58

Journal article

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Grinding up wheat: A massive loss of nucleotide diversity since domestication

Annabelle Haudry, Alberto Cenci, C. Ravel, Thomas Bataillon, Dominique Brunel, C. Poncet...

Molecular Biology and Evolution . 24 ( 7 ) : 1506-1517

DOI: 10.1093/molbev/msm077

Journal article

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A General Comparison of Relaxed Molecular Clock Models

Thomas Lepage, David Bryant, Herve Philippe, Nicolas Lartillot

Molecular Biology and Evolution . 24 ( 12 ) : 2669-2680

DOI: 10.1093/molbev/msm193

Journal article

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Exploring Fast Computational Strategies for Probabilistic Phylogenetic analysis

Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot

Systematic Biology . 56 : 711-726

DOI: 10.1080/10635150701611258

Journal article

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Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues

E. Lerat, M. Sémon

Gene . 396 : 303-311

Journal article

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Horizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms

Saliou Fall, Anne Mercier, Franck Bertolla, Alexandra Calteau, Laurent Gueguen, Guy Perrière...

PLoS ONE . 2 ( 10 ) : e1055-e1066

DOI: 10.1371/journal.pone.0001055

Journal article

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MareyMap: an R-based tool with graphical interface for estimating recombination rates

C. Rezvoy, D. Charif, Laurent Guéguen, Gabriel Marais

Bioinformatics . 23 : 2188-2189

Journal article

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Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

Nicolas Galtier, L. Duret

Trends in Genetics . 23 ( 6 ) : 273-277

DOI: 10.1016/j.tig.2007.03.011

Journal article

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Unexpected observations after mapping LongSAGE tags to the human genome.

Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon

BMC Bioinformatics . 8 : 154

DOI: 10.1186/1471-2105-8-154

Journal article

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Repetition-free longest common subsequence

S.S. Adi, M.D.V. Braga, C.G. Fernandes, C.E. Ferreira, F.V. Martinez, M.-F. Sagot...

IV Latin-American Algorithms, Graphs and Optimization Symposium (LAGOS) . 30 : 243-248

DOI: 10.1016/j.endm.2008.01.042

Conference paper

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The maximum agreement forest problem: Approximation algorithms and computational experiments

E. Rodrigues, M.-F. Sagot, Y. Wakabayashi

Theoretical Computer Science . 374 : 91-110

Journal article

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Enumerating precursor sets of target metabolites in a metabolic network

L. Cottret, P.V. Milreu, Vicente Acuna, A. Marchetti-Spaccamela, F. Viduani Martinez, M.F. Sagot...

8th Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 233-244

Conference paper

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Recherche de précurseurs dans un réseau métabolique

L. Cottret, Vicente Acuna, H. Charles, M.F. Sagot

Réseaux d'interaction : analyse, modélisation et simulation (RIAMS) . : 1-1

Conference paper

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All Maximal Pairs in Step-Leap Representation of Melodic Sequences

Emilios Cambouropoulos, Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot

Information Sciences . 177 ( 9 ) : 1954-1962

DOI: 10.1016/j.ins.2006.11.012

Journal article

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SymBioCyc: Metabolic data on endosymbiotic, parasitic and free bacteria

L. Cottret, H. Charles, M.F. Sagot

Integrative Post-Genomics - IPG'07 . : 1-1

Conference paper

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Integrating transcription factor binding site information with gene expression datasets

I.B. Jeffery, S.F. Madden, P.A. Mcgettigan, G. Perrière, A.C. Culhane, D.G. Higgins

Bioinformatics . 23 : 298-305

Journal article

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Identification de motifs dans les réseaux métaboliques

Vincent Lacroix

Thesis

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An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro.

Arnaud Hecker, Nicolas Leulliot, Danièle Gadelle, Marc Graille, Anthony Justome, Pierre Dorlet...

Nucleic Acids Research . 35 ( 18 ) : 6042-51

DOI: 10.1093/nar/gkm554

Journal article

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Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1

Nicolas Chomont, Hakim Hocini, Gérard Grésenguet, Céline Brochier-Armanet, Hicham Bouhlal, Laurent Andréoletti...

AIDS. Official journal of the international AIDS Society . 21 : 153--162

DOI: 10.1097/QAD.0b013e328011f94b

Journal article

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Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure

Elie Desmond-Le Quéméner, Céline Brochier-Armanet, Simonetta Gribaldo

BMC Evolutionary Biology . 7 : 53-70

DOI: 10.1186/1471-2148-7-106

Journal article

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Grinding up wheat: a massive loss of nucleotide diversity since domestication

A. Haudry, A. Cenci, C. Ravel, T. Bataillon, D. Brunel, C. Poncet...

Molecular Biology and Evolution . 24 : 1506-1517

Journal article

see the publication