Publications of 2006

Aury, J.M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B.M., Segurens, B., Daubin, V., Anthouard, V., Aiach, N., Arnaiz, O., Billaut, A., Beisson, J., Blanc, I., Bouhouche, K., Camara, F., Duharcourt, S., Guigo, R., Gogendeau, D., Katinka, M., Keller, A.M., Kissmehl, R., Klotz, C., Koll, F., Le Mouel, A., Lepere, G., Malinsky, S., Nowacki, M., Nowak, J.K., Plattner, H., Poulain, J., Ruiz, F., Serrano, V., Zagulski, M., Dessen, P., Betermier, M., Weissenbach, J., Scarpelli, C., Schachter, V., Sperling, L., Meyer, E., Cohen, J. and Wincker, P.
 “Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia ”
 Nature. 2006. 444, 171-178.

Bourdet, A., Ciaudo, C., Zakin, L., Elalouf, J.M., Rusniol, C., Weissenbach, J. and Avner, P.
 “A SAGE approach to identifying novel trans-acting factors involved in the X inactivation process”
 Cytogenetic and Genome Research. 2006. 113, 325-335.

Brunet, F.G., Crollius, H.R., Paris, M., Aury, J.M., Gibert, P., Jaillon, O., Laudet, V. and Robinson-Rechavi, M.
 “Gene loss and evolutionary rates following whole-genome duplication in teleost fishes”
 Molecular Biology and Evolution. 2006. 23, 1808-1816.

Cannon, S.B., Sterck, L., Rombauts, S., Sato, S., Cheung, F., Gouzy, J., Wang, X.H., Mudge, J., Vasdewani, J., Scheix, T., Spannagl, M., Monaghan, E., Nicholson, C., Humphray, S.J., Schoof, H., Mayer, K.F.X., Rogers, J., Quetier, F., Oldroyd, G.E., Debelle, F., Cook, D.R., Retzel, E.F., Roe, B.A., Town, C.D., Tabata, S., Van de Peer, Y. and Young, N.D.
 “Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes”
 Proceedings of the National Academy of Sciences of the United States of America. 2006. 103, 14959-14964.

Choulet, F., Aigle, B., Gallois, A., Mangenot, S., Gerbaud, C., Truong, C., Francou, F.X., Fourrier, C., Guerineau, M., Decaris, B., Barbe, V., Pernodet, J.L. and Leblond, P.
 “Evolution of the terminal regions of the streptomyces linear chromosome”
 Molecular Biology and Evolution. 2006. 23, 2361-2369.

Choulet, F., Gallois, A., Aigle, B., Mangenot, S., Gerbaud, C., Truong, C., Francou, F.X., Borges, F., Fourrier, C., Guerineau, M., Decaris, B., Barbe, V., Pernodet, J.L. and Leblond, P.
 “Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens ”
 Journal of Bacteriology. 2006. 188, 6599-6610.

Danchin, A., Fujiyama, A., Matsubara, K., Roberts, R., Sugano, S. and Weissenbach, J.
 “Re: Request from the International Advisory Committee to DDBJ/EMBL/GenBank”
 Journal of Medical Virology. 2006. 78, 995-995.

Drezen, J.M., Bezier, A., Lesobre, J., Huguet, E., Cattolico, L., Periquet, G. and Dupuy, C.
 “The few virus-like genes of Cotesia congregata bracovirus”
 Archives of Insect Biochemistry and Physiology. 2006. 61, 110-122.

Durand, P., Labarre, L., Meil, A., Divo, J.L., Vandenbrouck, Y., Viari, A. and Wojcik, J.
 “GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins”
 Bmc Bioinformatics. 2006. 7, 11.

Duret, L., Chureau, C., Samain, S., Weissenbach, J. and Avner, P.
 “The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene”
 Science. 2006. 312, 1653-1655.

Fournier, P.E., Vallenet, D., Barbe, V., Audic, S., Ogata, H., Poirel, L., Richet, H., Robert, C., Mangenot, S., Abergel, C., Nordmann, P., Weissenbach, J., Raoult, D. and Claverie, J.M.
 “Comparative genomics of multidrug resistance in Acinetobacter baumannii ”
 Plos Genetics. 2006. 2, 62-72.

Fuchs, J., Cruaud, C., Couloux, A. and Pasquet, E.
 “Complex biogeographic history of the cuckoo-shrikes and allies (Passeriformes: Campephagidae) revealed by mitochondrial and nuclear sequence data”
 Mol Phylogenet Evol. 2006.

Gout, L., Fudal, I., Kuhn, M.L., Blaise, F., Eckert, M., Cattolico, L., Balesdent, M.H. and Rouxel, T.
 “Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans ”
 Molecular Microbiology. 2006. 60, 67-80.

Lamoureux, D., Bernole, A., Le Clainche, I., Tual, S., Thareau, V., Paillard, S., Legeai, F., Dossat, C., Wincker, P., Oswald, M., Merdinoglu, D., Vignault, C., Delrot, S., Caboche, M., Chalhoub, B. and Adam-Blondon, A.F.
 “Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome”
 Theoretical and Applied Genetics. 2006. 113, 344-356.

Lebofsky, R., Heilig, R., Sonnleitner, M., Weissenbach, J. and Bensimon, A.
 “DNA replication origin interference increases the spacing between initiation events in human cells”
 Molecular Biology of the Cell. 2006. 17, 5337-5345.

Le Fur, S., Auffray, C., Letourneur, F., Cruaud, C., Le Stunff, C. and Bougnères, P.
 “Heterogeneity of class I INS VNTR allele association with insulin secretion in obese children”
 Physiol Genomics. 2006. 25, 480-484.

Louvel, H., Bommezzadri, S., Zidane, N., Boursaux-Eude, C., Creno, S., Magnier, A., Rouy, Z., Medigue, C., Saint Girons, I., Bouchier, C. and Picardeau, M.
 “Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp ”
 Journal of Bacteriology. 2006. 188, 7893-7904.

Marenda, M., Barbe, V., Gourgues, G., Mangenot, S., Sagne, E. and Citti, C.
 “A new integrative conjugative element occurs in Mycoplasma agalactiae as chromosomal and free circular forms”
 Journal of Bacteriology. 2006. 188, 4137-4141.

Marlétaz, F., Martin, E., Perez, Y., Papillon, D., Caubit, X., Lowe, C., Freeman, B., Fasano, L., Dossat, C., Wincker, P., Weissenbach, J. and Le Parco, Y.
  “Chaetognath phylogenomics: a protostome with deuterostome-like development”
 Curr Biol. 2006. 16, R577-578.

Muller, D., Simeonova, D., Riegel, P., Mangenot, S., Koechler, S., Lièvremont, D., Bertin, P. and Lett, M.
 “ Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium”
 Int J Syst Evol Microbiol. 2006. 56, 1765-1769.

Pascal, G., Medigue, C. and Danchin, A.
 “Persistent biases in the amino acid composition of prokaryotic proteins”
 Bioessays. 2006. 28, 726-738.

Perez, J.O., Dambier, D., Ollitrault, P., D’Eeckenbrugge, G.C., Brottier, P., Froelicher, Y. and Risterucci, A.M.
 “Microsatellite markers in Carica papaya L.: isolation, characterization and transferability to Vasconcellea species”
 Molecular Ecology Notes. 2006. 6, 212-217.

Quetier, F., Salanoubat, M. and Weissenbach, J.
 “Sequence of the nuclear genoms of the plants”
 Biofutur. 2006. 27-32.

Sabater-Munoz, B., Legeai, F., Rispe, C., Bonhomme, J., Dearden, P., Dossat, C., Duclert, A., Gauthier, J.P., Ducray, D.G., Hunter, W., Dang, P., Kambhampati, S., Martinez-Torres, D., Cortes, T., Moya, A., Nakabachi, A., Philippe, C., Prunier-Leterme, N., Rahbe, Y., Simon, J.C., Stern, D.L., Wincker, P. and Tagu, D.
 “Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)”
 Genome Biology. 2006. 7, 11.

Sanlaville, D., Etchevers, H.C., Gonzales, M., Martinovic, J., Clement-Ziza, M., Delezoide, A.L., Aubry, M.C., Pelet, A., Chemouny, S., Cruaud, C., Audollent, S., Esculpavit, C., Goudefroye, G., Ozilou, C., Fredouille, C., Joye, N., Morichon-Delvallez, N., Dumez, Y., Weissenbach, J., Munnich, A., Amiel, J., Encha-Razavi, F., Lyonnet, S., Vekemans, M. and Attie-Bitach, T.
 “Phenotypic spectrum of CHARGE syndrome in fetuses with CHD7 truncating mutations correlates with expression during human development”
 Journal of Medical Genetics. 2006. 43, 211-217.

Smidtas, S., Schachter, V. and Kepes, F.
 “The adaptive filter of the yeast galactose pathway”
 Journal of Theoretical Biology. 2006. 242, 372-381.

Smidtas, S., Yartseva, A., Schachter, V. and Kepes, F.
 “Model of interactions in biology and application to heterogeneous network in yeast”
 Comptes Rendus Biologies. 2006. 329, 945-952.

Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M.W., Horn, M., Daims, H., Bartol-Mavel, D., Wincker, P., Barbe, V., Fonknechten, N., Vallenet, D., Segurens, B., Schenowitz-Truong, C., Medigue, C., Collingro, A., Snel, B., Dutilh, B.E., Op den Camp, H.J.M., van der Drift, C., Cirpus, I., van de Pas-Schoonen, K.T., Harhangi, H.R., van Niftrik, L., Schmid, M., Keltjens, J., van de Vossenberg, J., Kartal, B., Meier, H., Frishman, D., Huynen, M.A., Mewes, H.W., Weissenbach, J., Jetten, M.S.M., Wagner, M. and Le Paslier, D.
 “Deciphering the evolution and metabolism of an anammox bacterium from a community genome”
 Nature. 2006. 440, 790-794.

Tarrade, A., Fassier, C., Charvin, D., Charvin, D., Vitte, J., Peris, L., Thorel, A., Mouisel, E., Fonknechten, N., Roblot, N., Seilhean, D., Dierich, A., Hauw, J.J. and Melki, J.
 “A mutation of spastin is responsible for swellings and impairment of transport in a region of axon characterized by changes in microtubule composition”
 Human Molecular Genetics. 2006. 15, 3544-3558.

Thill, G., Castelli, V., Pallud, S., Salanoubat, M., Wincker, P., de la Grange, P., Auboeuf, D., Schachter, V. and Weissenbach, J.
 “ASEtrap: A biological method for speeding up the exploration of spliceomes”
 Genome Research. 2006. 16, 776-786.

Turlin, E., Pascal, G., Rousselle, J.C., Lenormand, P., Ngo, S., Danchin, A. and Derzelle, S.
 “Proteome analysis of the phenotypic variation process in Photorhabdus luminescens ”
 Proteomics. 2006. 6, 2705-2725.

Vallenet, D., Labarre, L., Rouy, Z., Barbe, V., Bocs, S., Cruveiller, S., Lajus, A., Pascal, G., Scarpelli, C. and Medigue, C.
 “MaGe: a microbial genome annotation system supported by synteny results”
 Nucleic Acids Research. 2006. 34, 53-65.

van de Guchte, M., Penaud, S., Grimaldi, C., Barbe, V., Bryson, K., Nicolas, P., Robert, C., Oztas, S., Mangenot, S., Couloux, A., Loux, V., Dervyn, R., Bossy, R., Bolotin, A., Batto, J.M., Walunas, T., Gibrat, J.F., Bessieres, P., Weissenbach, J., Ehrlich, S.D. and Maguin, E.
 “The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution, Proceedings of the National”
 Academy of Sciences of the United States of America. 2006. 103, 9274-9279.

Vodovar, N., Vallenet, D., Cruveiller, S., Rouy, Z., Barbe, V., Acosta, C., Cattolico, L., Jubin, C., Lajus, A., Segurens, B., Vacherie, B., Wincker, P., Weissenbach, J., Lemaitre, B., Medigue, C. and Boccard, F.
 “Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila ”
 Nature Biotechnology. 2006. 24, 673-679.