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. https://doi.org/10.1007/978-1-4939-9164-8_15
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. https://doi.org/10.1007/978-1-4939-9164-8_9
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. https://doi.org/10.3389/fmicb.2019.00430
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. https://doi.org/10.1007/978-1-4939-9164-8_18
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. https://doi.org/10.1007/978-1-4939-9639-1_1
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. https://doi.org/10.1080/22221751.2019.1615848
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. https://doi.org/10.1021/acs.jproteome.8b00516
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. https://doi.org/10.1016/j.dci.2018.12.001
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. https://doi.org/10.1074/jbc.RA118.007049
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. https://doi.org/10.1002/2211-5463.12627
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. https://doi.org/10.1038/s41564-019-0431-8
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. https://doi.org/10.1074/mcp.RA118.000988
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. https://doi.org/10.1016/j.jprot.2019.103441
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. https://doi.org/10.1186/s12864-019-5431-9
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. https://doi.org/10.1016/j.molcel.2018.12.020
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. https://doi.org/10.1016/j.algal.2019.101415
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. https://doi.org/10.1007/s12311-018-0987-5
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. https://doi.org/10.1016/j.chembiol.2018.12.001
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. https://doi.org/10.1126/sciadv.aav3235
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. https://doi.org/10.1016/j.gene.2018.12.037
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. https://doi.org/10.1126/sciadv.aaw9969
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. https://doi.org/10.3390/jcm8101544
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. https://doi.org/10.1002/hep.30655
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. https://doi.org/10.3389/fcell.2019.00222
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. https://doi.org/10.1016/j.jcis.2019.06.071
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. https://doi.org/10.1002/pmic.201800489
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. https://doi.org/10.1104/pp.19.00912
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. https://doi.org/10.1093/nar/gkz880
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. https://doi.org/10.1021/acs.jproteome.9b00542