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2010
items
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http://www.edyp.fr/web/wp-content/plugins/zotpress/
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Ferro, M., Brugiere, S., Salvi, D., Seigneurin-Berny, D., Court, M., Moyet, L., Ramus, C., Miras, S., Mellal, M., Le Gall, S., Kieffer-Jaquinod, S., Bruley, C., Garin, J., Joyard, J., Masselon, C., & Rolland, N. (2010). AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics, 9(6), 1063–1084. https://doi.org/10.1074/mcp.M900325-MCP200
Joyard, J., Ferro, M., Masselon, C., Seigneurin-Berny, D., Salvi, D., Garin, J., & Rolland, N. (2010). Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism. Progress in Lipid Research, 49(2), 128–158. https://doi.org/10.1016/j.plipres.2009.10.003
Mischak, H., Kolch, W., Aivaliotis, M., Bouyssié, D., Court, M., Dihazi, H., Dihazi, G. H., Franke, J., Garin, J., Gonzalez de Peredo, A., Iphöfer, A., Jänsch, L., Lacroix, C., Makridakis, M., Masselon, C., Metzger, J., Monsarrat, B., Mrug, M., Norling, M., … Vlahou, A. (2010). Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics. Clinical Applications, 4(4), 464–478. https://doi.org/10.1002/prca.200900189
Dos Santos, A., Court, M., Thiers, V., Sar, S., Guettier, C., Samuel, D., Bréchot, C., Garin, J., Demaugre, F., & Masselon, C. D. (2010). Identification of cellular targets in human intrahepatic cholangiocarcinoma using laser microdissection and accurate mass and time tag proteomics. Molecular & Cellular Proteomics: MCP, 9(9), 1991–2004. https://doi.org/10.1074/mcp.M110.000026
Moné, Y., Gourbal, B., Duval, D., Du Pasquier, L., Kieffer-Jaquinod, S., & Mitta, G. (2010). A large repertoire of parasite epitopes matched by a large repertoire of host immune receptors in an invertebrate host/parasite model. PLoS Neglected Tropical Diseases, 4(9). https://doi.org/10.1371/journal.pntd.0000813
Graindorge, M., Giustini, C., Jacomin, A. C., Kraut, A., Curien, G., & Matringe, M. (2010). Identification of a plant gene encoding glutamate/aspartate-prephenate aminotransferase: the last homeless enzyme of aromatic amino acids biosynthesis. FEBS Letters, 584(20), 4357–4360. https://doi.org/10.1016/j.febslet.2010.09.037
