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 1051 to 1080 publications on 1408 in total

Natural history of the ERVWE 1 endogenous retroviral locus.

Bertrand Bonnaud, Jean Beliaeff, Olivier Bouton, Guy Oriol, Laurent Duret, François Mallet

Retrovirology . 2:57 : 1 - 7

DOI: 10.1186/1742-4692-2-57

Journal article

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Reaction motifs in metabolic networks

Vincent Lacroix, C.G. Fernandes, M.-F. Sagot

International Workshop on Algorithms in Bioinformatics (WABI) . 3692 : 178-191

DOI: 10.1007/11557067_15

Conference paper

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Perfect sorting by reversals

M.-F. Sagot, Eric Tannier

International Computing and Combinatorics Conference . 3595 : 42-51

DOI: 10.1007/11533719_7

Conference paper

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A new distance for high level RNA secondary structure comparison

Julien Allali, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 2 : 3--14

Journal article

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Bases of motifs for generating repeated patterns with wild cards

Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 2 : 40-50

DOI: 10.1109/TCBB.2005.5

Journal article

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Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière

Bioinformatics . 21 : 545-547

Journal article

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MADE4: an R package for multivariate analysis of gene expression data

A.C. Culhane, J. Thioulouse, G. Perrière, D.G. Higgins

Bioinformatics . 21 : 2789-2790

Journal article

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Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

A. Calteau, Manolo Gouy, G. Perrière

Journal of Molecular Evolution . 60 ( 5 ) : 557-65

DOI: 10.1007/s00239-004-0094-8

Journal article

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Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

F. Baty, M.P. Bihl, G. Perrière, A.C. Culhane, M.H. Brutsche

BMC Bioinformatics . 6 : 1-12

Journal article

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Type I Polyketide Synthases May Have Evolved Through Horizontal Gene Transfer

Aurélien Ginolhac, Cyrille Jarrin, Patrick Robe, Guy Perrière, Timothy M. Vogel, Pascal Simonet...

Journal of Molecular Evolution . ( 60 ) : 716-725

DOI: 10.1007/s00239-004-0161-1

Journal article

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In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant

A. Aouacheria, V. Navratil, W. Wen, M. Jiang, Dominique Mouchiroud, Christian Gautier...

Oncogene . 24 : 6133-6142

DOI: 10.1038/sj.onc.1208745

Journal article

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Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity

V. Huguet, Manolo Gouy, P. Normand, J.F. Zimpfer, M.P. Fernandez

Molecular Phylogenetics and Evolution . 34 ( 3 ) : 557-568

DOI: 10.1016/j.ympev.2004.11.018

Journal article

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Phylogeography and taxonomic status of Niphargus virei (subterranean amphipod).

T. Lefébure, Christophe Jean Douady, M. Gouy, P. Trontelj, J. Briolay, Janine Gibert

Proceedings on Symposium on World Subterranean Biodiversity . : 73-74

Conference paper

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Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes

H. Aurell, Pierre Farge, H. Meugnier, Manolo Gouy, F. Forey, G. Lina...

Applied and Environmental Microbiology . 71 : 282-289

DOI: 10.1128/AEM.71.1.282-289.2005

Journal article

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De la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques

B. Lamy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Annales de Biologie Clinique . 63 : 493-502

Journal article

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Site Interdependence Attributed to Tertiary Structure in Amino Acid Sequence Evolution

N. Rodrigue, Nicolas Lartillot, D. Bryant, H. Philippe

Gene . 347 ( 2 ) : 207-217

DOI: 10.1016/j.gene.2004.12.011

Journal article

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A bunch of fun-guys: the whole-genome view of yeast evolution

H. Ochman, Vincent Daubin, E. Lerat

Trends in Genetics . 21 : 1-3

Journal article

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Examining bacterial species under the specter of gene transfer and exchange

H. Ochman, E. Lerat, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 102 : 6595-6599

Journal article

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Quantitative prediction for two-dimensional bacterial genomic displays

Jean-François Mercier, Gary W. Slater, Bénédicte Lafay

Joint 15th IUPAB and 5th EBSA International Biophysics Congress .

Conference paper

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Intron size and exon evolution in Drosophila

Gabriel Marais, P. Nouvellet, P.D. Keightley, B. Charlesworth

Genetics . 170 : 481-485

Journal article

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A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants

M. Nicolas, Gabriel Marais, V. Hykelova, B. Janousek, V. Laporte, B. Vyskot...

PLoS Biology . 3 : 0047-0056

Journal article

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A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants.

Michael Nicolas, Gabriel Marais, Vladka Hykelova, Bohuslav Janousek, Valérie Laporte, Boris Vyskot...

PLoS Biology . 3 : 0001-0010

DOI: 10.1371/journal.pbio.0030004

Journal article

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Steps in the evolution of heteromorphic sex chromosomes

D. Charlesworth, B. Charlesworth, Gabriel Marais

Heredity . 95 : 118-128

Journal article

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A first approach to finding common motifs with gaps,

Costas Iliopoulos, J. Mchugh, Pierre Peterlongo, Nadia Pisanti, W. Rytter, Marie-France Sagot

International Journal of Foundations of Computer Science . 16 ( 6 ) : 1145--1155

Journal article

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Molecular polymorphism in Drosophila melanogaster and D. simulans: what have we learned from recent studies?

Sylvain Mousset, N. Derome

Genetica . 120 : 79-86

Journal article

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The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae

J.F. Baines, A. Das, Sylvain Mousset, W. Stephan

Genetics . 168 : 1987-1998

Journal article

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A test of neutrality and constant population size based on the mismatch distribution

Sylvain Mousset, N. Derome, M. Veuille

Molecular Biology and Evolution . 21 : 724-731

Journal article

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Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon

BMC Bioinformatics . 5 : 143

DOI: 10.1186/1471-2105-5-143

Journal article

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The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology

Frédéric Mallet, O. Bouton, S. Prudhomme, V. Cheynet, G. Oriol, B. Bonnaud...

Proceedings of the National Academy of Sciences of the United States of America . 101 : 1731-1736

Journal article

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Evidence that functional transcription units cover at least half of the human genome

M. Sémon, L. Duret

Trends in Genetics . 20 : 229-232

Journal article

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