GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 901 to 930 publications on 1243 in total

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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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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

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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

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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

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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

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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

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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

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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

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The Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny

E. Belle, L. Duret, N. Galtier, A. Eyre-Walker

Journal of Molecular Evolution . 58 : 653-660

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

C. Keime, F. Damiola, Dominique Mouchiroud, L. Duret, Olivier Gandrillon

BMC Bioinformatics . 5 : 1-12

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ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

N. Reymond, H. Charles, L. Duret, Federica Calevro, G. Beslon, J.-M. Fayard

Bioinformatics . 20 : 271-273

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Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

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Efficient Extraction of Structured Motifs Using Box-links

A. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

International Symposium on String Processing and Information Retrieval : SPIRE . 3246 : 267-268

DOI: 10.1007/978-3-540-30213-1_37

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A first approach to finding common motifs with Gaps

Costas S. Iliopoulos, James Mchugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot

Prague Stringology Conference 2004 . : 88-97

Conference paper

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A parallel algorithm for the extraction of structured motifs

A. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

ACM Symposium on Applied Computing . -- : 147-153

Conference paper

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