Publications 2005

Attard, A., Gout, L., Ross, S., Parlange, F., Cattolico, L., Balesdent, M.H. and Rouxel, T.
 « Truncated and RIP-degenerated copies of the LTR retrotransposon Pholy are clustered in a pericentrorneric region of the Leptosphaeria maculans genome »
 Fungal Genetics and Biology. 2005. 42, 30-41.

Billotte, N., Marseillac, N., Risterucci, A.M., Adon, B., Brottier, P., Baurens, F.C., Singh, R., Herran, A., Asmady, H., Billot, C., Amblard, P., Durand-Gasselin, T., Courtois, B., Asmono, D., Cheah, S.C., Rohde, W., Ritter, E. and Charrier, A.
 « Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.) »
 Theoretical and Applied Genetics. 2005. 110, 754-765.

Boyer, F., Morgat, A., Labarre, L., Pothier, J. and Viari, A.
 « Syntons, metabolons and interactons : an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data »
 Bioinformatics. 2005. 21, 4209-4215.

Chantret, N., Salse, J., Sabot, F., Rahman, S., Bellec, A., Laubin, B., Dubois, I., Dossat, C., Sourdille, P., Joudrier, P., Gautier, M.F., Cattolico, L., Beckert, M., Aubourg, S., Weissenbach, J., Caboche, M., Bernard, M., Leroy, P. and Chalhoub, B.
 « Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and aegilops) »
 Plant Cell. 2005. 17, 1033-1045.

Chouari, R., Le Paslier, D., Daegelen, P., Ginestet, P., Weissenbach, J. and Sghir, A.
 « Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester »
 Environmental Microbiology. 2005. 7, 1104-1115.

Chouari, R., Le Paslier, D., Dauga, C., Daegelen, P., Weissenbach, J. and Sghir, A.
 « Novel major bacterial candidate division within a municipal anaerobic sludge digester »
 Applied and Environmental Microbiology. 2005. 71, 2145-2153.

Cirpus, I.E.Y., de Been, M., Op den Camp, H.J.M., Strous, M., Le Paslier, D., Kuenen, G.J. and Jetten, M.S.M. 
 « A new soluble 10 kDa monoheme cytochrome c-552 from the anammox bacterium Candidatus Kuenenia stuttgartiensis  »
 Fems Microbiology Letters. 2005. 252, 273-278.

Cruveiller, S., Le Saux, J., Vallenet, D., Lajus, A., Bocs, S. and Medigue, C.
 « MICheck : a web tool for fast checking of syntactic annotations of bacterial genomes »
 Nucleic Acids Research. 2005. 33, W471-W479.

Daims, H., LePaslier, D., Spieck, E. and Wagner, M. 
 « Ecophysiology and genomics of nitrite-oxidizing bacteria important for wastewater treatment »
 Journal of Biotechnology. 2005. 118, S163-S163. [Congrès]

Dauga, C., Dore, J. and Sghir, A.
 « Expanding the known diversity and environmental distribution of cultured and uncultured bacteria »
 M S-Medecine Sciences. 2005. 21, 290-296.

Edvardsen, R.B., Seo, H.C., Jensen, M.F., Mialon, A., Mikhaleva, J., Bjordal, M., Cartry, J., Reinhardt, R., Weissenbach, J., Wincker, P. and Chourrout, D.
 « Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica  »
 Current Biology. 2005. 15, R12-R13.

Eiglmeier, K., Wincker, P., Cattolico, L., Anthouard, V., Holm, I., Eckenberg, R., Quesneville, H., Jaillon, O., Collins, F.H., Weissenbach, J., Brey, P.T. and Roth, C.W.
 « Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation »
 Insect Biochemistry and Molecular Biology. 2005. 35, 799-814.

Esnault, Y., Jaillon, O., Aury, J.M., Weissenbach, J. and Crollius, H.R.
 «  Tetraodon, fish in the genomic model »
 Biofutur. 2005. 24-28.

Espagne, E., Douris, V., Lalmanach, G., Provost, B., Cattolico, L., Lesobre, J., Kurata, S., Iatrou, K., Drezen, J.M. and Huguet, E.
 « A virus essential for insect host-parasite interactions encodes cystatins »
 Journal of Virology. 2005. 79, 9765-9776.

Fischer, C., Bouneau, L., Coutanceau, J.P., Weissenbach, J., Ozouf-Costaz, C. and Volff, J.N.
 « Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis  »
 Cytogenetic and Genome Research. 2005. 110, 522-536.

Gomez, S.M., Eiglmeier, K., Segurens, B., Dehoux, P., Couloux, A., Scarpelli, C., Wincker, P., Weissenbach, J., Brey, P.T. and Roth, C.W.
 « Pilot Anopheles gambiae full-length cDNA study : sequencing and initial characterization of 35,575 clones »
 Genome Biology. 2005. 6, 11.

International Rice Genome Sequencing Project : Matsumoto, T., Wu, J.Z., Kanamori, H., Katayose, Y., Fujisawa, M., Namiki, N., Mizuno, H., Yamamoto, K., Antonio, B.A., Baba, T., Sakata, K., Nagamura, Y., Aoki, H., Arikawa, K., Arita, K., Bito, T., Chiden, Y., Fujitsuka, N., Fukunaka, R., Hamada, M., Harada, C., Hayashi, A., Hijishita, S., Honda, M., Hosokawa, S., Ichikawa, Y., Idonuma, A., Iijima, M., Ikeda, M., Ikeno, M., Ito, K., Ito, S., Ito, T., Ito, Y., Ito, Y., Iwabuchi, A., Kamiya, K., Karasawa, W., Kurita, K., Katagiri, S., Kikuta, A., Kobayashi, H., Kobayashi, N., Machita, K., Maehara, T., Masukawa, M., Mizubayashi, T., Mukai, Y., Nagasaki, H., Nagata, Y., Naito, S., Nakashima, M., Nakama, Y., Nakamichi, Y., Nakamura, M., Meguro, A., Negishi, M., Ohta, I., Ohta, T., Okamoto, M., Ono, N., Saji, S., Sakaguchi, M., Sakai, K., Shibata, M., Shimokawa, T., Song, J.Y., Takazaki, Y., Terasawa, K., Tsugane, M., Tsuji, K., Ueda, S., Waki, K., Yamagata, H., Yamamoto, M., Yamamoto, S., Yamane, H., Yoshiki, S., Yoshihara, R., Yukawa, K., Zhong, H.S., Yano, M., Sasaki, T., Yuan, Q.P., Shu, O.T., Liu, J., Jones, K.M., Gansberger, K., Moffat, K., Hill, J., Bera, J., Fadrosh, D., Jin, S.H., Johri, S., Kim, M., Overton, L., Reardon, M., Tsitrin, T., Vuong, H., Weaver, B., Ciecko, A., Tallon, L., Jackson, J., Pai, G., Van Aken, S., Utterback, T., Reidmuller, S., Feldblyum, T., Hsiao, J., Zismann, V., Iobst, S., de Vazeille, A.R., Buell, C.R., Ying, K., Li, Y., Lu, T.T., Huang, Y.C., Zhao, Q., Feng, Q., Zhang, L., Zhu, J.J., Weng, Q.J., Mu, J., Lu, Y.Q., Fan, D.L., Liu, Y.L., Guan, J.P., Zhang, Y.J., Yu, S.L., Liu, X.H., Zhang, Y., Hong, G.F., Han, B., Choisne, N., Demange, N., Orjeda, G., Samain, S., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., D’Hont, A., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Yu, Y., Kim, H.R., Rambo, T., Currie, J., Collura, K., Luo, M.Z., Yang, T.J., Ammiraju, J.S.S., Engler, F., Soderlund, C., Wing, R.A., Palmer, L.E., de la Bastide, M., Spiegel, L., Nascimento, L., Zutavern, T., O’Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Balija, V., McCombie, W.R., Chow, T.Y., Chen, H.H., Chung, M.C., Chen, C.S., Shaw, J.F., Wu, H.P., Hsiao, K.J., Chao, Y.T., Chu, M.K., Cheng, C.H., Hour, A.L., Lee, P.F., Lin, S.J., Lin, Y.C., Liou, J.Y., Liu, S.M., Hsing, Y.I., Raghuvanshi, S., Mohanty, A., Bharti, A.K., Gaur, A., Gupta, V., Kumar, D., Ravi, V., Vij, S., Kapur, A., Khurana, P., Khurana, P., Khurana, J.P., Tyagi, A.K., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S., Dixit, A., Pal, A.K., Ghazi, I.A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Batra, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Messing, J., Nelson, A.B., Fuks, G., Kavchok, S., Keizer, G., Llaca, E.L.V., Song, R.T., Tanyolac, B., Young, S., Il, K.H., Hahn, J.H., Sangsakoo, G., Vanavichit, A., de Mattos, L.A.T., Zimmer, P.D., Malone, G., Dellagostin, O., de Oliveira, A.C., Bevan, M., Bancroft, I., Minx, P., Cordum, H., Wilson, R., Cheng, Z.K., Jin, W.W., Jiang, J.M., Leong, S.A., Iwama, H., Gojobori, T., Itoh, T., Niimura, Y., Fujii, Y., Habara, T., Sakai, H., Sato, Y., Wilson, G., Kumar, K., McCouch, S., Juretic, N., Hoen, D., Wright, S., Bruskiewich, R., Bureau, T., Miyao, A., Hirochika, H., Nishikawa, T., Kadowaki, K. and Sugiura, M. 
 « The map-based sequence of the rice genome »
 Nature. 2005. 436, 793-800.

Medigue, C.
 « Annotating bacterial genomes »
 Biofutur. 2005. 23-27.

Medigue, C., Krin, E., Pascal, G., Barbe, V., Bernsel, A., Bertin, P.N., Cheung, F., Cruveiller, S., D’Amico, S., Duilio, A., Fang, G., Feller, G., Ho, C., Mangenot, S., Marino, G., Nilsson, J., Parrilli, E., Rocha, E.P.C., Rouy, Z., Sekowska, A., Tutino, M.L., Vallenet, D., von Heijne, G. and Danchin, A. -« Coping with cold : The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125  »
 Genome Research. 2005. 15, 1325-1335.

Neuveglise, C., Chalvet, F., Wincker, P., Gaillardin, C. and Casaregola, S.
 « Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings »
 Eukaryotic Cell. 2005. 4, 615-624.

Pascal, G., Medigue, C. and Danchin, A.
  « Universal biases in protein composition of model prokaryotes » Proteins-Structure Function and Bioinformatics. 2005. 60, 27-35.

Raible, F., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., Ferrier, D., Benes, V., de Jong, P., Weissenbach, J., Bork, P. and Arendt, D.
 « Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii  »
 Science. 2005. 310, 1325-1326.

Roest Crollius, H. and Weissenbach, J.
 « Fish genomics and biology »
 Genome Research. 2005. 15, 1675-1682.

Siroy, A., Molle, V., Lemaitre-Guillier, C., Vallenet, D., Pestel-Caron, M., Cozzone, A.J., Jouenne, T. and De, E.
 « Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii  »
 Antimicrobial Agents and Chemotherapy. 2005. 49, 4876-4883.

Smit, M.A., Tordoir, X., Gyapay, G., Cockett, N.E., Georges, M. and Charlier, C.
 « BEGAIN : A novel imprinted gene that generates paternally expressed transcripts in a tissue- and promoter-specific manner in sheep »
 Mammalian Genome. 2005. 16, 801-814.

Talla, E., Anthouard, V., Bouchier, C., Frangeul, L. and Dujon, B.
 « The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans  »
 Febs Letters. 2005. 579, 30-40.

The Rice Chromosomes 11 and 12 Sequencing Consortia : Choisne, N., Demange, N., Orjeda, G., Samain, S., D’Hont, A., Cattolico, L., Pelletier, E., Couloux, A., Segurens, B., Wincker, P., Scarpelli, C., Weissenbach, J., Salanoubat, M., Quetier, F., Singh, N.K., Mohapatra, T., Sharma, T.R., Gaikwad, K., Singh, A., Dalal, V., Srivastava, S.K., Dixit, A., Pal, A.K., Ghazi, I.A., Yadav, M., Pandit, A., Bhargava, A., Sureshbabu, K., Dixit, R., Singh, H., Swain, S.C., Pal, S., Ragiba, M., Singh, P.K., Singhal, V., Mendiratta, S.D., Batra, K., Raghuvanshi, S., Mohanty, A., Bharti, A.K., Gaur, A., Gupta, V., Kumar, D., Vydianathan, R., Vij, S., Kapur, A., Khurana, P., Sharma, S., Khurana, P., Khurana, J.P., Tyagi, A.K., Yuan, Q.P., Ouyang, S., Liu, J., Zhu, W., Wang, A.H., Lin, H.N., Hamilton, J., Haas, B., Wortman, J., Jones, K.M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S.H., Johri, S., Reardon, M., Vuong, H., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A.R., Salzberg, S.L., White, O., Fraser, C., Buell, C.R., Yu, Y., Rambo, T., Currie, J., Collura, K., Kim, H.R., Stum, D., Wang, W.M., Kudrna, D., Mueller, C., Wing, R.A., Kramer, M., Spiegel, L., Nascimento, L., Preston, R., Zutavern, T., Palmer, L., O’Shaughnessy, A., Dike, S., McCombie, W.R., Messing, J., Du, C., Fuks, G., Linton, E., Tanyolac, B., Wu, J.Z., Namiki, N., Mizuno, H., Matsumoto, T., Sasaki, T., Jin, W.W. and Jiang, J.M. 
 « The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications »
 Bmc Biology. 2005. 3, 18.

Viaud, M., Legeai, F., Pradier, J.M., Brygoo, Y., Bitton, F., Weissenbach, J., Brunet-Simon, A., Duclert, A., Fillinger, S., Fortini, D., Gioti, A., Giraud, C., Halary, S., Lebrun, I., Le Pecheur, P., Samson, D. and Levis, C.
 « Expressed sequence tags from the phytopathogenic fungus Botrytis cinerea  »
 European Journal of Plant Pathology. 2005. 111, 139-146.

Zivanovic, Y., Wincker, P., Vacherie, B., Bolotin-Fukuhara, M. and Fukuhara, H.
 « Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis  »
 Fems Yeast Research. 2005. 5, 315-322.