Publications 2020

Lezzerini, M., Penzo, M., O’Donohue, M.-F., Marques Dos Santos Vieira, C., Saby, M., Elfrink, H. L., Diets, I. J., Hesse, A.-M., Couté, Y., Gastou, M., Nin-Velez, A., Nikkels, P. G. J., Olson, A. N., Zonneveld-Huijssoon, E., Jongmans, M. C. J., Zhang, G., van Weeghel, M., Houtkooper, R. H., Wlodarski, M. W., … MacInnes, A. W. (2020). Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism. Nucleic Acids Research, 48(2), 770–787. https://doi.org/10.1093/nar/gkz1042
Sokolovska, N., Permiakova, O., Forslund, S. K., & Zucker, J.-D. (2020). Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(1), 358–364. https://doi.org/10.1109/TCBB.2018.2879504
van Lis, R., Brugière, S., Baffert, C., Couté, Y., Nitschke, W., & Atteia, A. (2020). Hybrid cluster proteins in a photosynthetic microalga. The FEBS Journal, 287(4), 721–735. https://doi.org/10.1111/febs.15025
Lacombe, M., Jaquinod, M., Belmudes, L., Couté, Y., Ramus, C., Combes, F., Burger, T., Mintz, E., Barthelon, J., Leroy, V., Poujois, A., Lachaux, A., Woimant, F., & Brun, V. (2020). Comprehensive and comparative exploration of the Atp7b−/− mouse plasma proteome. Metallomics, 12(2), 249–258. https://doi.org/10.1039/c9mt00225a
Jeudy, S., Bertaux, L., Alempic, J.-M., Lartigue, A., Legendre, M., Belmudes, L., Santini, S., Philippe, N., Beucher, L., Biondi, E. G., Juul, S., Turner, D. J., Couté, Y., Claverie, J.-M., & Abergel, C. (2020). Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world. The ISME Journal, 14(3), 727–739. https://doi.org/10.1038/s41396-019-0565-y
Farhat, D. C., Swale, C., Dard, C., Cannella, D., Ortet, P., Barakat, M., Sindikubwabo, F., Belmudes, L., De Bock, P.-J., Couté, Y., Bougdour, A., & Hakimi, M.-A. (2020). A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nature Microbiology, 5(4), 570–583. https://doi.org/10.1038/s41564-020-0674-4
Van Gool, A., Corrales, F., Čolović, M., Krstić, D., Oliver-Martos, B., Martínez-Cáceres, E., Jakasa, I., Gajski, G., Brun, V., Kyriacou, K., Burzynska-Pedziwiatr, I., Wozniak, L. A., Nierkens, S., Pascual García, C., Katrlik, J., Bojic-Trbojevic, Z., Vacek, J., Llorente, A., Antohe, F., … Sammar, M. (2020). Analytical techniques for multiplex analysis of protein biomarkers. Expert Review of Proteomics, 17(4), 257–273. https://doi.org/10.1080/14789450.2020.1763174
Bouyssié, D., Hesse, A.-M., Mouton-Barbosa, E., Rompais, M., Macron, C., Carapito, C., Gonzalez de Peredo, A., Couté, Y., Dupierris, V., Burel, A., Menetrey, J.-P., Kalaitzakis, A., Poisat, J., Romdhani, A., Burlet-Schiltz, O., Cianférani, S., Garin, J., & Bruley, C. (2020). Proline: an efficient and user-friendly software suite for large-scale proteomics. Bioinformatics, 36(10), 3148–3155. https://doi.org/10.1093/bioinformatics/btaa118
Crespo, M., Damont, A., Blanco, M., Lastrucci, E., Kennani, S. E., Ialy-Radio, C., Khattabi, L. E., Terrier, S., Louwagie, M., Kieffer-Jaquinod, S., Hesse, A.-M., Bruley, C., Chantalat, S., Govin, J., Fenaille, F., Battail, C., Cocquet, J., & Pflieger, D. (2020). Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes. Nucleic Acids Research, 48(8), 4115–4138. https://doi.org/10.1093/nar/gkaa163
Began, J., Cordier, B., Březinová, J., Delisle, J., Hexnerová, R., Srb, P., Rampírová, P., Kožíšek, M., Baudet, M., Couté, Y., Galinier, A., Veverka, V., Doan, T., & Strisovsky, K. (2020). Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease. The EMBO Journal, 39(10). https://doi.org/10.15252/embj.2019102935
Couté, Y., Kraut, A., Zimmermann, C., Büscher, N., Hesse, A.-M., Bruley, C., De Andrea, M., Wangen, C., Hahn, F., Marschall, M., & Plachter, B. (2020). Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus. Microorganisms, 8(6), 820. https://doi.org/10.3390/microorganisms8060820
Kloehn, J., Oppenheim, R. D., Siddiqui, G., De Bock, P.-J., Kumar Dogga, S., Coute, Y., Hakimi, M.-A., Creek, D. J., & Soldati-Favre, D. (2020). Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii. BMC Biology, 18(1), 67. https://doi.org/10.1186/s12915-020-00791-7
Monestier, M., Pujol, A. M., Lamboux, A., Cuillel, M., Pignot-Paintrand, I., Cassio, D., Charbonnier, P., Um, K., Harel, A., Bohic, S., Gateau, C., Balter, V., Brun, V., Delangle, P., & Mintz, E. (2020). A liver-targeting Cu( i ) chelator relocates Cu in hepatocytes and promotes Cu excretion in a murine model of Wilson’s disease. Metallomics, 12(6), 1000–1008. https://doi.org/10.1039/d0mt00069h
Parry, G., Provart, N. J., Brady, S. M., Uzilday, B., & Multinational Arabidopsis Steering Committee. (2020). Current status of the multinational Arabidopsis community. Plant Direct, 4(7), e00248. https://doi.org/10.1002/pld3.248
Locard‐Paulet, M., Voisinne, G., Froment, C., Goncalves Menoita, M., Ounoughene, Y., Girard, L., Gregoire, C., Mori, D., Martinez, M., Luche, H., Garin, J., Malissen, M., Burlet‐Schiltz, O., Malissen, B., Gonzalez De Peredo, A., & Roncagalli, R. (2020). LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN 2 as a regulator of effector functions. Molecular Systems Biology, 16(7), e9524. https://doi.org/10.15252/msb.20209524
Postic, G., Marcoux, J., Reys, V., Andreani, J., Vandenbrouck, Y., Bousquet, M.-P., Mouton-Barbosa, E., Cianférani, S., Burlet-Schiltz, O., Guerois, R., Labesse, G., & Tufféry, P. (2020). Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. Journal of Proteome Research, 19(7), 2807–2820. https://doi.org/10.1021/acs.jproteome.0c00066
Sansa, M., Defoort, M., Brenac, A., Hermouet, M., Banniard, L., Fafin, A., Gely, M., Masselon, C., Favero, I., Jourdan, G., & Hentz, S. (2020). Optomechanical mass spectrometry. Nature Communications, 11(1), 3781. https://doi.org/10.1038/s41467-020-17592-9
Hahn, F., Niesar, A., Wangen, C., Wild, M., Grau, B., Herrmann, L., Capci, A., Adrait, A., Couté, Y., Tsogoeva, S. B., & Marschall, M. (2020). Target verification of artesunate-related antiviral drugs: Assessing the role of mitochondrial and regulatory proteins by click chemistry and fluorescence labeling. Antiviral Research, 180, 104861. https://doi.org/10.1016/j.antiviral.2020.104861
Roblin, C., Chiumento, S., Bornet, O., Nouailler, M., Müller, C. S., Jeannot, K., Basset, C., Kieffer-Jaquinod, S., Couté, Y., Torelli, S., Le Pape, L., Schünemann, V., Olleik, H., De La Villeon, B., Sockeel, P., Di Pasquale, E., Nicoletti, C., Vidal, N., Poljak, L., … Duarte, V. (2020). The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties. Proceedings of the National Academy of Sciences, 117(32), 19168–19177. https://doi.org/10.1073/pnas.2004045117
Nguyen, M. V. C., Courtier, A., Adrait, A., Defendi, F., Couté, Y., Baillet, A., Guigue, L., Gottenberg, J.-E., Dumestre-Pérard, C., Brun, V., & Gaudin, P. (2020). Fetuin-A and thyroxin binding globulin predict rituximab response in rheumatoid arthritis patients with insufficient response to anti-TNFα. Clinical Rheumatology, 39(9), 2553–2562. https://doi.org/10.1007/s10067-020-05030-6
Sentausa, E., Basso, P., Berry, A., Adrait, A., Bellement, G., Couté, Y., Lory, S., Elsen, S., & Attrée, I. (2020). Insertion sequences drive the emergence of a highly adapted human pathogen. Microbial Genomics, 6(9). https://doi.org/10.1099/mgen.0.000265
Di Giovanni, D., Lepetit, D., Guinet, B., Bennetot, B., Boulesteix, M., Couté, Y., Bouchez, O., Ravallec, M., & Varaldi, J. (2020). A Behavior-Manipulating Virus Relative as a Source of Adaptive Genes for Drosophila Parasitoids. Molecular Biology and Evolution, 37(10), 2791–2807. https://doi.org/10.1093/molbev/msaa030
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., Van Eyk, J. E., Uhlén, M., Lindskog, C., Chan, D. W., Bairoch, A., Waddington, J. C., Justice, J. L., LaBaer, J., Rodriguez, H., … Baker, M. S. (2020). A high-stringency blueprint of the human proteome. Nature Communications, 11(1), 5301. https://doi.org/10.1038/s41467-020-19045-9
Lamboux, A., Couchonnal-Bedoya, E., Guillaud, O., Laurencin, C., Lion-François, L., Belmalih, A., Mintz, E., Brun, V., Bost, M., Lachaux, A., & Balter, V. (2020). The blood copper isotopic composition is a prognostic indicator of the hepatic injury in Wilson disease. Metallomics, 12(11), 1781–1790. https://doi.org/10.1039/d0mt00167h
Chabrolles, H., Auclair, H., Vegna, S., Lahlali, T., Pons, C., Michelet, M., Couté, Y., Belmudes, L., Chadeuf, G., Kim, Y., Di Bernardo, A., Jalaguier, P., Cosset, F.-L., Fusil, F., Rivoire, M., Arnold, L. D., Lopatin, U., Combet, C., Zoulim, F., … Salvetti, A. (2020). Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production. PLoS Pathogens, 16(11), e1008593. https://doi.org/10.1371/journal.ppat.1008593
Couté, Y., Bruley, C., & Burger, T. (2020). Beyond Target–Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Analytical Chemistry, 92(22), 14898–14906. https://doi.org/10.1021/acs.analchem.0c00328
Dia, M., Gomez, L., Thibault, H., Tessier, N., Leon, C., Chouabe, C., Ducreux, S., Gallo-Bona, N., Tubbs, E., Bendridi, N., Chanon, S., Leray, A., Belmudes, L., Couté, Y., Kurdi, M., Ovize, M., Rieusset, J., & Paillard, M. (2020). Reduced reticulum–mitochondria Ca2+ transfer is an early and reversible trigger of mitochondrial dysfunctions in diabetic cardiomyopathy. Basic Research in Cardiology, 115(6), 74. https://doi.org/10.1007/s00395-020-00835-7
Ngo, T.-D., Perdu, C., Jneid, B., Ragno, M., Novion Ducassou, J., Kraut, A., Couté, Y., Stopford, C., Attrée, I., Rietsch, A., & Faudry, E. (2020). The PopN Gate-keeper Complex Acts on the ATPase PscN to Regulate the T3SS Secretion Switch from Early to Middle Substrates in Pseudomonas aeruginosa. Journal of Molecular Biology, 432(24), 166690. https://doi.org/10.1016/j.jmb.2020.10.024
Del Corpo, D., Fullone, M. R., Miele, R., Lafond, M., Pontiggia, D., Grisel, S., Kieffer‐Jaquinod, S., Giardina, T., Bellincampi, D., & Lionetti, V. (2020). AtPME17 is a functional Arabidopsis thaliana pectin methylesterase regulated by its PRO region that triggers PME activity in the resistance to Botrytis cinerea. Molecular Plant Pathology, 21(12), 1620–1633. https://doi.org/10.1111/mpp.13002
Vandenbrouck, Y., Pineau, C., & Lane, L. (2020). The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology. Journal of Proteome Research, 19(12), 4782–4794. https://doi.org/10.1021/acs.jproteome.0c00516