Bruley, C., Dupierris, V., Salvi, D., Rolland, N., & Ferro, M. (2012). AT_CHLORO: A Chloroplast Protein Database Dedicated to Sub-Plastidial Localization. Front Plant Sci, 3, 205. https://doi.org/10.3389/fpls.2012.00205

Tardif, M., Atteia, A., Specht, M., Cogne, G., Rolland, N., Brugière, S., Hippler, M., Ferro, M., Bruley, C., Peltier, G., Vallon, O., & Cournac, L. (2012). PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Molecular Biology and Evolution, 29(12), 3625–3639. https://doi.org/10.1093/molbev/mss178

Ivaldi, C., Martin, B. R., Kieffer-Jaquinod, S., Chapel, A., Levade, T., Garin, J., & Journet, A. (2012). Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23. PloS One, 7(5), e37187. https://doi.org/10.1371/journal.pone.0037187

Forestier, A., Sarrazy, F., Caillat, S., Vandenbrouck, Y., & Sauvaigo, S. (2012). Functional DNA repair signature of cancer cell lines exposed to a set of cytotoxic anticancer drugs using a multiplexed enzymatic repair assay on biochip. PloS One, 7(12), e51754. https://doi.org/10.1371/journal.pone.0051754

Filhol, O., Ciais, D., Lajaunie, C., Charbonnier, P., Foveau, N., Vert, J.-P., & Vandenbrouck, Y. (2012). DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes. PloS One, 7(10), e48057. https://doi.org/10.1371/journal.pone.0048057

Destercke, S., & Burger, T. (2012). Revisiting the Notion of Conflicting Belief Functions. In Belief Functions: Theory and Applications (pp. 153–160). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29461-7_18

Burger, T., & Destercke, S. (2012). Random Generation of Mass Functions: A Short Howto. In Belief Functions: Theory and Applications (pp. 145–152). Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29461-7_17

Journet, A., Klein, G., Brugière, S., Vandenbrouck, Y., Chapel, A., Kieffer, S., Bruley, C., Masselon, C., & Aubry, L. (2012). Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry. Proteomics, 12(2), 241–245. https://doi.org/10.1002/pmic.201100313

Govin, J., Gaucher, J., Ferro, M., Debernardi, A., Garin, J., Khochbin, S., & Rousseaux, S. (2012). Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome. Molecular Human Reproduction, 18(1), 1–13. https://doi.org/10.1093/molehr/gar063

Tarrago, L., Kieffer-Jaquinod, S., Lamant, T., Marcellin, M. N., Garin, J. R. M., Rouhier, N., & Rey, P. (2012). Affinity chromatography: a valuable strategy to isolate substrates of methionine sulfoxide reductases? Antioxidants & Redox Signaling, 16(1), 79–84. https://doi.org/10.1089/ars.2011.4153

Greco, A., Arata, L., Soler, E., Gaume, X., Couté, Y., Hacot, S., Callé, A., Monier, K., Epstein, A. L., Sanchez, J.-C., Bouvet, P., & Diaz, J.-J. (2012). Nucleolin interacts with US11 protein of herpes simplex virus 1 and is involved in its trafficking. Journal of Virology, 86(3), 1449–1457. https://doi.org/10.1128/JVI.06194-11

Huillet, C., Adrait, A., Lebert, D., Picard, G., Trauchessec, M., Louwagie, M., Dupuis, A., Hittinger, L., Ghaleh, B., Le Corvoisier, P., Jaquinod, M., Garin, J., Bruley, C., & Brun, V. (2012). Accurate quantification of cardiovascular biomarkers in serum using Protein Standard Absolute Quantification (PSAQ^TM) and selected reaction monitoring. Molecular & Cellular Proteomics: MCP, 11(2), M111.008235. https://doi.org/10.1074/mcp.M111.008235

Lupo, J., Conti, A., Sueur, C., Coly, P.-A., Couté, Y., Hunziker, W., Burmeister, W. P., Germi, R., Manet, E., Gruffat, H., Morand, P., & Boyer, V. (2012). Identification of new interacting partners of the shuttling protein ubinuclein (Ubn-1). Experimental Cell Research, 318(5), 509–520. https://doi.org/10.1016/j.yexcr.2011.12.020

Jaquinod, M., Trauchessec, M., Huillet, C., Louwagie, M., Lebert, D., Picard, G., Adrait, A., Dupuis, A., Garin, J., Brun, V., & Bruley, C. (2012). Mass spectrometry-based absolute protein quantification: PSAQ^TM strategy makes use of “noncanonical” proteotypic peptides. Proteomics, 12(8), 1217–1221. https://doi.org/10.1002/pmic.201100538

Paik, Y.-K., Omenn, G. S., Uhlen, M., Hanash, S., Marko-Varga, G., Aebersold, R., Bairoch, A., Yamamoto, T., Legrain, P., Lee, H.-J., Na, K., Jeong, S.-K., He, F., Binz, P.-A., Nishimura, T., Keown, P., Baker, M. S., Yoo, J. S., Garin, J., … Hancock, W. S. (2012). Standard guidelines for the chromosome-centric human proteome project. Journal of Proteome Research, 11(4), 2005–2013. https://doi.org/10.1021/pr200824a

Kurowska, M., Goudin, N., Nehme, N. T., Court, M., Garin, J., Fischer, A., de Saint Basile, G., & Ménasché, G. (2012). Terminal transport of lytic granules to the immune synapse is mediated by the kinesin-1/Slp3/Rab27a complex. Blood, 119(17), 3879–3889. https://doi.org/10.1182/blood-2011-09-382556

Wade, A., Thomas, C., Kalmar, B., Terenzio, M., Garin, J., Greensmith, L., & Schiavo, G. (2012). Activated leukocyte cell adhesion molecule modulates neurotrophin signaling. Journal of Neurochemistry, 121(4), 575–586. https://doi.org/10.1111/j.1471-4159.2012.07658.x

Huang, Y., Yoon, S. H., Heron, S. R., Masselon, C. D., Edgar, J. S., Tureček, F., & Goodlett, D. R. (2012). Surface acoustic wave nebulization produces ions with lower internal energy than electrospray ionization. Journal of the American Society for Mass Spectrometry, 23(6), 1062–1070. https://doi.org/10.1007/s13361-012-0352-8

Adrait, A., Lebert, D., Trauchessec, M., Dupuis, A., Louwagie, M., Masselon, C., Jaquinod, M., Chevalier, B., Vandenesch, F., Garin, J., Bruley, C., & Brun, V. (2012). Development of a Protein Standard Absolute Quantification (PSAQ^TM) assay for the quantification of Staphylococcus aureus enterotoxin A in serum. Journal of Proteomics, 75(10), 3041–3049. https://doi.org/10.1016/j.jprot.2011.11.031

Mininno, M., Brugière, S., Pautre, V., Gilgen, A., Ma, S., Ferro, M., Tardif, M., Alban, C., & Ravanel, S. (2012). Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as lysine-methylated proteins in plants. The Journal of Biological Chemistry, 287(25), 21034–21044. https://doi.org/10.1074/jbc.M112.359976

Merle, N., Féraud, O., Gilquin, B., Hubstenberger, A., Kieffer-Jacquinot, S., Assard, N., Bennaceur-Griscelli, A., Honnorat, J., & Baudier, J. (2012). ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A. Mitochondrion, 12(4), 441–448. https://doi.org/10.1016/j.mito.2012.05.005

Xie, L. X., Ozeir, M., Tang, J. Y., Chen, J. Y., Jaquinod, S.-K., Fontecave, M., Clarke, C. F., & Pierrel, F. (2012). Overexpression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the coenzyme Q6 biosynthetic pathway. The Journal of Biological Chemistry, 287(28), 23571–23581. https://doi.org/10.1074/jbc.M112.360354

Louwagie, M., Kieffer-Jaquinod, S., Dupierris, V., Couté, Y., Bruley, C., Garin, J., Dupuis, A., Jaquinod, M., & Brun, V. (2012). Introducing AAA-MS, a rapid and sensitive method for amino acid analysis using isotope dilution and high-resolution mass spectrometry. Journal of Proteome Research, 11(7), 3929–3936. https://doi.org/10.1021/pr3003326

Schvartz, D., Couté, Y., Brunner, Y., Wollheim, C. B., & Sanchez, J.-C. (2012). Modulation of neuronal pentraxin 1 expression in rat pancreatic β-cells submitted to chronic glucotoxic stress. Molecular & Cellular Proteomics: MCP, 11(8), 244–254. https://doi.org/10.1074/mcp.M112.018051

Schvartz, D., Brunner, Y., Couté, Y., Foti, M., Wollheim, C. B., & Sanchez, J.-C. (2012). Improved characterization of the insulin secretory granule proteomes. Journal of Proteomics, 75(15), 4620–4631. https://doi.org/10.1016/j.jprot.2012.04.023

Yoon, S. H., Huang, Y., Edgar, J. S., Ting, Y. S., Heron, S. R., Kao, Y., Li, Y., Masselon, C. D., Ernst, R. K., & Goodlett, D. R. (2012). Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis. Analytical Chemistry, 84(15), 6530–6537. https://doi.org/10.1021/ac300807p

Courty, N., Burger, T., & Marteau, P.-F. (2012). Geodesic Analysis on the Gaussian RKHS Hypersphere. Machine Learning and Knowledge Discovery in Databases, 299–313. https://doi.org/10.1007/978-3-642-33460-3_25

Picard, G., Lebert, D., Louwagie, M., Adrait, A., Huillet, C., Vandenesch, F., Bruley, C., Garin, J., Jaquinod, M., & Brun, V. (2012). PSAQ^TM standards for accurate MS-based quantification of proteins: from the concept to biomedical applications. Journal of Mass Spectrometry: JMS, 47(10), 1353–1363. https://doi.org/10.1002/jms.3106

Ozeir, M. O., Xie, L. X., Chehade, M. H., Tang, J. Y., Jacquinod, S.-K., Fontecave, M., Pierrel, F., & Clarke, C. F. (2012). In vivo accumulation of coenzyme Q biosynthetic intermediates and aminated analogs in the yeast Saccharomyces cerevisiae. BBA - Bioenergetics, 1817, S92–S92. https://doi.org/10.1016/j.bbabio.2012.06.249

Tarasova, I. A., Perlova, T. Y., Pridatchenko, M. L., Goloborod’ko, A. A., Levitsky, L. I., Evreinov, V. V., Guryca, V., Masselon, C. D., Gorshkov, A. V., & Gorshkov, M. V. (2012). Inversion of chromatographic elution orders of peptides and its importance for proteomics. Journal of Analytical Chemistry, 67(13), 1014–1025. https://doi.org/10.1134/S1061934812130102

Jézégou, A., Llinares, E., Anne, C., Kieffer-Jaquinod, S., O’Regan, S., Aupetit, J., Chabli, A., Sagné, C., Debacker, C., Chadefaux-Vekemans, B., Journet, A., André, B., & Gasnier, B. (2012). Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy. Proceedings of the National Academy of Sciences of the United States of America, 109(50), E3434-3443. https://doi.org/10.1073/pnas.1211198109