Publications 2019

Wieczorek, S., Combes, F., Borges, H., & Burger, T. (2019). Protein-Level Statistical Analysis of Quantitative Label-Free Proteomics Data with ProStaR. Methods in Molecular Biology (Clifton, N.J.), 1959, 225–246.
Kraut, A., Louwagie, M., Bruley, C., Masselon, C., Couté, Y., Brun, V., & Hesse, A.-M. (2019). Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry. Methods in Molecular Biology (Clifton, N.J.), 1959, 129–150.
Legendre, M., Alempic, J.-M., Philippe, N., Lartigue, A., Jeudy, S., Poirot, O., Ta, N. T., Nin, S., Couté, Y., Abergel, C., & Claverie, J.-M. (2019). Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes. Frontiers in Microbiology, 10, 430.
Nguyen, L., Brun, V., Combes, F., Loux, V., & Vandenbrouck, Y. (2019). Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework. Methods in Molecular Biology (Clifton, N.J.), 1959, 275–289.
Louwagie, M., Kieffer-Jaquinod, S., & Brun, V. (2019). Ultrasensitive Quantification of Recombinant Proteins Using AAA-MS. Methods in Molecular Biology (Clifton, N.J.), 2030, 1–10.
Siebert, C., Lindgren, H., Ferré, S., Villers, C., Boisset, S., Perard, J., Sjöstedt, A., Maurin, M., Brochier-Armanet, C., Couté, Y., & Renesto, P. (2019). Francisella tularensis: FupA mutation contributes to fluoroquinolone resistance by increasing vesicle secretion and biofilm formation. Emerging Microbes & Infections, 8(1), 808–822.
Borges, H., Guibert, R., Permiakova, O., & Burger, T. (2019). Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra. Journal of Proteome Research, 18(1), 571–573.
Pinaud, S., Portet, A., Allienne, J.-F., Belmudes, L., Saint-Beat, C., Arancibia, N., Galinier, R., Du Pasquier, L., Duval, D., & Gourbal, B. (2019). Molecular characterisation of immunological memory following homologous or heterologous challenges in the schistosomiasis vector snail, Biomphalaria glabrata. Developmental and Comparative Immunology, 92, 238–252.
Steingruber, M., Keller, L., Socher, E., Ferre, S., Hesse, A.-M., Couté, Y., Hahn, F., Büscher, N., Plachter, B., Sticht, H., & Marschall, M. (2019). Cyclins B1, T1, and H differ in their molecular mode of interaction with cytomegalovirus protein kinase pUL97. The Journal of Biological Chemistry, 294(15), 6188–6203.
Azevedo, J., Picart, C., Dureau, L., Pontier, D., Jaquinod-Kieffer, S., Hakimi, M.-A., & Lagrange, T. (2019). UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis. FEBS Open Bio, 9(5), 973–985.
Braun, L., Brenier-Pinchart, M.-P., Hammoudi, P.-M., Cannella, D., Kieffer-Jaquinod, S., Vollaire, J., Josserand, V., Touquet, B., Couté, Y., Tardieux, I., Bougdour, A., & Hakimi, M.-A. (2019). The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2. Nature Microbiology, 4(7), 1208–1220.
Bouchnak, I., Brugière, S., Moyet, L., Le Gall, S., Salvi, D., Kuntz, M., Tardif, M., & Rolland, N. (2019). Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity. Molecular & Cellular Proteomics: MCP, 18(7), 1285–1306.
Wieczorek, S., Giai Gianetto, Q., & Burger, T. (2019). Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses. Journal of Proteomics, 207, 103441.
Guillot, L., Delage, L., Viari, A., Vandenbrouck, Y., Com, E., Ritter, A., Lavigne, R., Marie, D., Peterlongo, P., Potin, P., & Pineau, C. (2019). Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics, 20(1), 56.
Wei, J., Kishton, R. J., Angel, M., Conn, C. S., Dalla-Venezia, N., Marcel, V., Vincent, A., Catez, F., Ferré, S., Ayadi, L., Marchand, V., Dersh, D., Gibbs, J. S., Ivanov, I. P., Fridlyand, N., Couté, Y., Diaz, J.-J., Qian, S.-B., Staudt, L. M., … Yewdell, J. W. (2019). Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance. Molecular Cell, 73(6), 1162-1173.e5.
Lupette, J., Jaussaud, A., Seddiki, K., Morabito, C., Brugière, S., Schaller, H., Kuntz, M., Putaux, J.-L., Jouneau, P.-H., Rébeillé, F., Falconet, D., Couté, Y., Jouhet, J., Tardif, M., Salvaing, J., & Maréchal, E. (2019). The architecture of lipid droplets in the diatom Phaeodactylum tricornutum. Algal Research, 38, 101415.
Do, L. D., Gupton, S. L., Tanji, K., Bastien, J., Brugière, S., Couté, Y., Quadrio, I., Rogemond, V., Fabien, N., Desestret, V., & Honnorat, J. (2019). TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration. Cerebellum (London, England), 18(2), 245–254.
Hajj Chehade, M., Pelosi, L., Fyfe, C. D., Loiseau, L., Rascalou, B., Brugière, S., Kazemzadeh, K., Vo, C.-D.-T., Ciccone, L., Aussel, L., Couté, Y., Fontecave, M., Barras, F., Lombard, M., & Pierrel, F. (2019). A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone. Cell Chemical Biology, 26(4), 482-492.e7.
Sonego, M., Pellarin, I., Costa, A., Vinciguerra, G. L. R., Coan, M., Kraut, A., D’Andrea, S., Dall’Acqua, A., Castillo-Tong, D. C., Califano, D., Losito, S., Spizzo, R., Couté, Y., Vecchione, A., Belletti, B., Schiappacassi, M., & Baldassarre, G. (2019). USP1 links platinum resistance to cancer cell dissemination by regulating Snail stability. Science Advances, 5(5), eaav3235.
Bhalla, P., Vernekar, D. V., Gilquin, B., Couté, Y., & Bhargava, P. (2019). Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II. Gene, 702, 205–214.
Chiumento, S., Roblin, C., Kieffer-Jaquinod, S., Tachon, S., Leprètre, C., Basset, C., Aditiyarini, D., Olleik, H., Nicoletti, C., Bornet, O., Iranzo, O., Maresca, M., Hardré, R., Fons, M., Giardina, T., Devillard, E., Guerlesquin, F., Couté, Y., Atta, M., … Duarte, V. (2019). Ruminococcin C, a promising antibiotic produced by a human gut symbiont. Science Advances, 5(9), eaaw9969.
Darrieutort-Laffite, C., Arnolfo, P., Garraud, T., Adrait, A., Couté, Y., Louarn, G., Trichet, V., Layrolle, P., Le Goff, B., & Blanchard, F. (2019). Rotator Cuff Tenocytes Differentiate into Hypertrophic Chondrocyte-Like Cells to Produce Calcium Deposits in an Alkaline Phosphatase-Dependent Manner. Journal of Clinical Medicine, 8(10), 1544.
Desroches-Castan, A., Tillet, E., Ricard, N., Ouarné, M., Mallet, C., Belmudes, L., Couté, Y., Boillot, O., Scoazec, J.-Y., Bailly, S., & Feige, J.-J. (2019). Bone Morphogenetic Protein 9 Is a Paracrine Factor Controlling Liver Sinusoidal Endothelial Cell Fenestration and Protecting Against Hepatic Fibrosis. Hepatology (Baltimore, Md.), 70(4), 1392–1408.
Chapelle, J., Sorokina, O., McLean, C., Salemme, V., Alfieri, A., Angelini, C., Morellato, A., Adrait, A., Menna, E., Matteoli, M., Couté, Y., Ala, U., Turco, E., Defilippi, P., & Armstrong, J. D. (2019). Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons. Frontiers in Cell and Developmental Biology, 7, 222.
Moulin, M., Mossou, E., Signor, L., Kieffer-Jaquinod, S., Kwaambwa, H. M., Nermark, F., Gutfreund, P., Mitchell, E. P., Haertlein, M., Forsyth, V. T., & Rennie, A. R. (2019). Towards a molecular understanding of the water purification properties of Moringa seed proteins. Journal of Colloid and Interface Science, 554, 296–304.
Vandenbrouck, Y., Christiany, D., Combes, F., Loux, V., & Brun, V. (2019). Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer. PROTEOMICS, 19(21–22), 1800489.
Dell’Aglio, E., Giustini, C., Kraut, A., Couté, Y., Costa, A., Decros, G., Gibon, Y., Mazars, C., Matringe, M., Finazzi, G., & Curien, G. (2019). Identification of the Arabidopsis Calmodulin-Dependent NAD + Kinase That Sustains the Elicitor-Induced Oxidative Burst. Plant Physiology, 181(4), 1449–1458.
Beurton, F., Stempor, P., Caron, M., Appert, A., Dong, Y., Chen, R. A., Cluet, D., Couté, Y., Herbette, M., Huang, N., Polveche, H., Spichty, M., Bedet, C., Ahringer, J., & Palladino, F. (2019). Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. Nucleic Acids Research, 47(21), 11164–11180.
Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., Paik, Y.-K., Weintraub, S. T., Vandenbrouck, Y., & Omenn, G. S. (2019). Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. Journal of Proteome Research, 18(12), 4108–4116.