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 1171 to 1200 publications on 1402 in total

Current methods of gene prediction their strengths and weaknesses

C. Mathé, M.-F. Sagot, Thomas Schiex, P. Rouzé

Nucleic Acids Research . 30 : 4103-4117

2002

Journal article

see the publication

Occurrence probability of structured motifs in random sequences

S. Robin, J.J. Daudin, H. Richard, M.-F. Sagot, S. Schbath

Journal of Computational Biology . 9 ( 6 ) : 761-773

DOI: 10.1089/10665270260518254

2002

Journal article

see the publication

A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, J. Thioulouse, G. Perrière, X. Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

DOI: 10.1099/00207713-52-2-573

2002

Journal article

see the publication

A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, Jean Thioulouse, Guy Perrière, Xavier Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

2002

Journal article

see the publication

NUREBASE: database of nuclear hormone receptors

J. Duarte, G. Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 30 : 364-368

2002

Journal article

see the publication

Automatic RNA secondary structure prediction with a comparative approach

F. Tahi, Manolo Gouy, M. Regnier

Journal of Computational Chemistry . 26 ( 5 ) : 521-530

DOI: 10.1016/S0097-8485(02)00012-8

2002

Journal article

see the publication

Functional and evolutionary analysis of a eukaryotic parasitic genome

Christian Vivarès, Manolo Gouy, F. Thomarat, G. Metenier

Current Opinion in Microbiology . 5 : 499-505

DOI: 10.1016/S1369-5274(02)00356-9

2002

Journal article

see the publication

Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

F. Baty, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Applied and Environmental Microbiology . 68 : 5816-5825

2002

Journal article

see the publication

The relative abundance of dinucleotides in transposable elements in five species

E. Lerat, P. Capy, C. Biémont

Molecular Biology and Evolution . 19 : 964-967

2002

Journal article

see the publication

Codon usage by transposable elements and their host genes in five species

E. Lerat, P. Capy, C. Biémont

Journal of Molecular Evolution . 54 : 625-637

2002

Journal article

see the publication

Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes

Gabriel Marais, G. Piganeau

Molecular Biology and Evolution . 19 : 1399-1406

2002

Journal article

see the publication

Haplotype tests using coalescent simulations conditional on the number of segregating sites

F. Depaulis, Sylvain Mousset, M. Veuille

Molecular Biology and Evolution . 18 : 1136-1138

2001

Journal article

see the publication

Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

L. Duret

incollection . -- : 287-289

2001

Journal article

see the publication

Why do genes have introns? Recombination might add a new piece to the puzzle

L. Duret

Trends in Genetics . 17 : 172-175

2001

Journal article

see the publication

Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification

Laurent Marsan, Marie-France Sagot

Journal of Computational Biology . 7 ( 1 ) : 345-360

2001

Journal article

see the publication

Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

C. Lavire, D. Louis, G. Perrière, J. Briolay, P. Normand, B. Cournoyer

FEMS Microbiology Letters . 197 : 111-116

DOI: 10.1111/j.1574-6968.2001.tb10591.x

2001

Journal article

see the publication

Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

O. Pierrugues, C. Brutesco, J. Oshiro, Manolo Gouy, Y. Deveaux, G.M. Carman...

Journal of Biological Chemistry . 276 ( 23 ) : 20300-20308

DOI: 10.1074/jbc.M009726200

2001

Journal article

see the publication

Spatial Modeling of Nitrifier Microhabitats in Soil

G. Grundmann, A. Dechesne, F. Bartoli, Jean-Pierre Flandrois, J. Chassé, R. Kizungu

Soil Science Society of America Journal . 65 ( 6 ) : 1709

DOI: 10.2136/sssaj2001.1709

2001

Journal article

see the publication

Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Emmanuelle Lerat

2001

Thesis

see the publication

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Gabriel Marais, Dominique Mouchiroud, L. Duret

Proceedings of the National Academy of Sciences of the United States of America . 98 : 5688-5692

2001

Journal article

see the publication

Determinants of CpG islands: expression in early embryo and isochore structure

L. Ponger, L. Duret, Dominique Mouchiroud

Genome Research . 11 : 1854-1860

2001

Journal article

see the publication

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

Gabriel Marais, L. Duret

Journal of Molecular Evolution . 52 : 275-280

2001

Journal article

see the publication

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

N. Galtier, G. Piganeau, Dominique Mouchiroud, L. Duret

Genetics . 159 : 907-911

2001

Journal article

see the publication

Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication

P. Frendo, M.J. Jimenez, C. Mathieu, L. Duret, D. Gallesi, G. van de Sype...

Plant Physiology . 126 : 1706-1715

2001

Journal article

see the publication

The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

L. Duret, L.D. Hurst

Molecular Biology and Evolution . 18 : 757-762

2001

Journal article

see the publication

Some approximation results for the maximum agreement forest problem

E. M. Rodrigues, Marie-France Sagot, Y. Wakabayashi

Approximation, Randomization and Combinatorial Optimization: Algorithms and Techniques (APPROX RANDOM 2001) . 2129 : 159-169

2001

Conference paper

see the publication

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Stéphane Guindon, G. Perrière

Molecular Biology and Evolution . 18 ( 9 ) : 1838-1840

DOI: 10.1093/oxfordjournals.molbev.a003972

2001

Journal article

see the publication

Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis

A. Aouacheria, Estelle Arnaud, S. Venet, P. Lalle, M. Gouy, D. Rigal...

Oncogene . 20 : 5846-5855

DOI: 10.1038/sj.onc.1204740

2001

Journal article

see the publication

Molecular evidence for the existence of two species of Marteilia in Europe

F. Le Roux, G. Lorenzo, P. Peyret, C. Audemard, A. Figueras, C. Vivares...

Journal of Eukaryotic Microbiology . 48 ( 4 ) : 449-454

DOI: 10.1111/j.1550-7408.2001.tb00178.x

2001

Journal article

see the publication

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

M.D. Katinka, S. Duprat, E. Cornillot, G. Metenier, F. Thomarat, G. Prensier...

Nature . 414 : 450-453

DOI: 10.1038/35106579

2001

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Current methods of gene prediction their strengths and weaknesses

Occurrence probability of structured motifs in random sequences

A mathematical method for determining genome divergence and species delineation using AFLP

A mathematical method for determining genome divergence and species delineation using AFLP

NUREBASE: database of nuclear hormone receptors

Automatic RNA secondary structure prediction with a comparative approach

Functional and evolutionary analysis of a eukaryotic parasitic genome

Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

The relative abundance of dinucleotides in transposable elements in five species

Codon usage by transposable elements and their host genes in five species

Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes

Haplotype tests using coalescent simulations conditional on the number of segregating sites

Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

Why do genes have introns? Recombination might add a new piece to the puzzle

Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification

Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

Spatial Modeling of Nitrifier Microhabitats in Soil

Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Determinants of CpG islands: expression in early embryo and isochore structure

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication

The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

Some approximation results for the maximum agreement forest problem

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis

Molecular evidence for the existence of two species of Marteilia in Europe

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi