Publications

Publications 2021

Takata-Tsuji, F., Chounlamountri, N., Do, L.-D., Philippot, C., Novion Ducassou, J., Couté, Y., Ben Achour, S., Honnorat, J., Place, C., & Pascual, O. (2021). Microglia modulate gliotransmission through the regulation of VAMP2 proteins in astrocytes. Glia, 69(1), 61–72. https://doi.org/10.1002/glia.23884
Adrait, A., Dumonceau, J.-M., Delhaye, M., Annessi-Ramseyer, I., Frossard, J.-L., Couté, Y., & Farina, A. (2021). Liquid Biopsy of Bile based on Targeted Mass Spectrometry for the Diagnosis of Malignant Biliary Strictures. Clinical and Translational Science, 14(1), 148–152. https://doi.org/10.1111/cts.12890
van Lis, R., Couté, Y., Brugière, S., Tourasse, N. J., Laurent, B., Nitschke, W., Vallon, O., & Atteia, A. (2021). Phylogenetic and functional diversity of aldehyde-alcohol dehydrogenases in microalgae. Plant Molecular Biology. https://doi.org/10.1007/s11103-020-01105-9
Felix, J., Siebert, C., Ducassou, J. N., Nigou, J., Garcia, P. S., Fraudeau, A., Huard, K., Mas, C., Brochier-Armanet, C., Couté, Y., Gutsche, I., & Renesto, P. (2021). Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance. Scientific Reports, 11(1), 972. https://doi.org/10.1038/s41598-020-79611-5
Trauchessec, M., Hesse, A. M., Kraut, A., Berard, Y., Herment, L., Fortin, T., Bruley, C., Ferro, M., & Manin, C. (2021). An innovative standard for LC-MS-based HCP-profiling and accurate quantity assessment: Application to batch consistency in viral vaccine samples. Proteomics, e2000152. https://doi.org/10.1002/pmic.202000152
Rayapuram, N., Jarad, M., Alhoraibi, H. M., Bigeard, J., Abulfaraj, A. A., Völz, R., Mariappan, K. G., Almeida-Trapp, M., Schlöffel, M., Lastrucci, E., Bonhomme, L., Gust, A. A., Mithöfer, A., Arold, S. T., Pflieger, D., & Hirt, H. (2021). Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity. Proceedings of the National Academy of Sciences of the United States of America, 118(3). https://doi.org/10.1073/pnas.2004670118
Gilquin, B., Cubizolles, M., Den Dulk, R., Revol-Cavalier, F., Alessio, M., Goujon, C.-E., Echampard, C., Arrizabalaga, G., Adrait, A., Louwagie, M., Laurent, P., Navarro, F. P., Couté, Y., Cosnier, M.-L., & Brun, V. (2021). PepS: An Innovative Microfluidic Device for Bedside Whole Blood Processing before Plasma Proteomics Analyses. Analytical Chemistry, 93(2), 683–690. https://doi.org/10.1021/acs.analchem.0c02270
Kerjouan, A., Boyault, C., Oddou, C., Hiriart-Bryant, E., Grichine, A., Kraut, A., Pezet, M., Balland, M., Faurobert, E., Bonnet, I., Coute, Y., Fourcade, B., Albiges-Rizo, C., & Destaing, O. (2021). Control of SRC molecular dynamics encodes distinct cytoskeletal responses by specifying signaling pathway usage. Journal of Cell Science, 134(2). https://doi.org/10.1242/jcs.254599
Vellino, S., Oddou, C., Rivier, P., Boyault, C., Hiriart-Bryant, E., Kraut, A., Martin, R., Coute, Y., Knölker, H.-J., Valverde, M. A., Albigès-Rizo, C., & Destaing, O. (2021). Cross-talk between the calcium channel TRPV4 and reactive oxygen species interlocks adhesive and degradative functions of invadosomes. Journal of Cell Biology, 220(2), e201910079. https://doi.org/10.1083/jcb.201910079
Borges, H., Hesse, A.-M., Kraut, A., Couté, Y., Brun, V., & Burger, T. (2021). Well Plate Maker: A user-friendly randomized block design application to limit batch effects in largescale biomedical studies. Bioinformatics (Oxford, England). https://doi.org/10.1093/bioinformatics/btab065
Permiakova, O., Guibert, R., Kraut, A., Fortin, T., Hesse, A.-M., & Burger, T. (2021). CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis. BMC Bioinformatics, 22(1), 68. https://doi.org/10.1186/s12859-021-03969-0
Härrer, D., Windhorst, C., Böhner, N., Novion Ducassou, J., Couté, Y., & Gescher, J. (2021). Production of acetoin from renewable resources under heterotrophic and mixotrophic conditions. Bioresource Technology, 124866. https://doi.org/10.1016/j.biortech.2021.124866
Curien, G., Lyska, D., Guglielmino, E., Westhoff, P., Janetzko, J., Tardif, M., Hallopeau, C., Brugière, S., Dal Bo, D., Decelle, J., Gallet, B., Falconet, D., Carone, M., Remacle, C., Ferro, M., Weber, A. P. M., & Finazzi, G. (2021). Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism. The New Phytologist. https://doi.org/10.1111/nph.17359
Hseiky, A., Crespo, M., Kieffer-Jaquinod, S., Fenaille, F., & Pflieger, D. (2021). Small Mass but Strong Information: Diagnostic Ions Provide Crucial Clues to Correctly Identify Histone Lysine Modifications. Proteomes, 9(2). https://doi.org/10.3390/proteomes9020018
Montillet, J.-L., Rondet, D., Brugière, S., Henri, P., Rumeau, D., Reichheld, J.-P., Couté, Y., Leonhardt, N., & Rey, P. (2021). Plastidial and cytosolic thiol reductases participate in the control of stomatal functioning. Plant, Cell & Environment, 44(5), 1417–1435. https://doi.org/10.1111/pce.14013
Chiari, L., Carpentier, P., Kieffer-Jaquinod, S., Gogny, A., Perard, J., Ravanel, S., Cobessi, D., Ménage, S., Dumas, R., & Hamelin, O. (2021). LEAFY protein crystals with a honeycomb structure as a platform for selective preparation of outstanding stable bio-hybrid materials. Nanoscale. https://doi.org/10.1039/d1nr00268f
Postic, G., Andreani, J., Marcoux, J., Reys, V., Guerois, R., Rey, J., Mouton-Barbosa, E., Vandenbrouck, Y., Cianferani, S., Burlet-Schiltz, O., Labesse, G., & Tufféry, P. (2021). Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab332
Pallavicini, G., Gai, M., Iegiani, G., Berto, G. E., Adrait, A., Couté, Y., & Cunto, F. D. (2021). Goldberg-Shprintzen syndrome protein KIF1BP is a CITK interactor implicated in cytokinesis. Journal of Cell Science, jcs.250902. https://doi.org/10.1242/jcs.250902
Schmid, F., Novion Ducassou, J., Couté, Y., & Gescher, J. (2021). Developing Rhodobacter sphaeroides for cathodic biopolymer production. Bioresource Technology, 125340. https://doi.org/10.1016/j.biortech.2021.125340
Edel, M., Sturm, G., Sturm-Richter, K., Wagner, M., Ducassou, J. N., Couté, Y., Horn, H., & Gescher, J. (2021). Extracellular riboflavin induces anaerobic biofilm formation in Shewanella oneidensis. Biotechnology for Biofuels, 14(1), 130. https://doi.org/10.1186/s13068-021-01981-3
Alfaro, J. A., Bohländer, P., Dai, M., Filius, M., Howard, C. J., van Kooten, X. F., Ohayon, S., Pomorski, A., Schmid, S., Aksimentiev, A., Anslyn, E. V., Bedran, G., Cao, C., Chinappi, M., Coyaud, E., Dekker, C., Dittmar, G., Drachman, N., Eelkema, R., … Joo, C. (2021). The emerging landscape of single-molecule protein sequencing technologies. Nature Methods, 18(6), 604–617. https://doi.org/10.1038/s41592-021-01143-1
Humbert, P., Brennan, M. Á., De Lima, J., Brion, R., Adrait, A., Charrier, C., Brulin, B., Trichet, V., Couté, Y., Blanchard, F., & Layrolle, P. (2021). Apoptotic mesenchymal stromal cells support osteoclastogenesis while inhibiting multinucleated giant cells formation in vitro. Scientific Reports, 11(1), 12144. https://doi.org/10.1038/s41598-021-91258-4
Pipier, A., Devaux, A., Lavergne, T., Adrait, A., Couté, Y., Britton, S., Calsou, P., Riou, J. F., Defrancq, E., & Gomez, D. (2021). Constrained G4 structures unveil topology specificity of known and new G4 binding proteins. Scientific Reports, 11(1), 13469. https://doi.org/10.1038/s41598-021-92806-8
Combes, F., Loux, V., & Vandenbrouck, Y. (2021). GO Enrichment Analysis for Differential Proteomics Using ProteoRE. In D. Cecconi (Ed.), Proteomics Data Analysis (Vol. 2361, pp. 179–196). Springer US. https://doi.org/10.1007/978-1-0716-1641-3_11
Gloaguen, P., Vandenbrouck, Y., Joyard, J., & Curien, G. (2021). ChloroKB, a cell metabolism reconstruction of the model plant Arabidopsis thaliana. Comptes Rendus. Biologies, 344(2), 157–163. https://doi.org/10.5802/crbiol.49
Clement, K., Reynaud, A., Defoort, M., Vysotskyi, B., Fortin, T., Lai, S.-H., Çumaku, V., Dominguez-Medina, S., Hentz, S., & Masselon, C. (2021). Requirements and attributes of nano-resonator mass spectrometry for the analysis of intact viral particles. Analytical and Bioanalytical Chemistry. https://doi.org/10.1007/s00216-021-03511-4
Notaro, A., Couté, Y., Belmudes, L., Laugieri, M. E., Salis, A., Damonte, G., Molinaro, A., Tonetti, M., Abergel, C., & De Castro, C. (2021). Expanding the occurrence of polysaccharides to the viral world: the case of Mimivirus. Angewandte Chemie International Edition, anie.202106671. https://doi.org/10.1002/anie.202106671
Farhat, D. C., Bowler, M. W., Communie, G., Pontier, D., Belmudes, L., Mas, C., Corrao, C., Couté, Y., Bougdour, A., Lagrange, T., Hakimi, M., & Swale, C. (2021). A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma. ELife, 10, e68312. https://doi.org/10.7554/eLife.68312
Do, L.-D., Moritz, C. P., Muñiz-Castrillo, S., Pinto, A.-L., Tholance, Y., Brugiere, S., Couté, Y., Stoevesandt, O., Taussig, M. J., Rogemond, V., Vogrig, A., Joubert, B., Ferraud, K., Camdessanché, J.-P., Antoine, J.-C., & Honnorat, J. (2021). Argonaute Autoantibodies as Biomarkers in Autoimmune Neurologic Diseases. Neurology - Neuroimmunology Neuroinflammation, 8(5), e1032. https://doi.org/10.1212/NXI.0000000000001032
Fortin, T., Vysotskyi, B., Defoort, M., Reynaud, A., Lai, S.-H., Dominguez-Medina, S., Clement, K., Cumaku, V., Hentz, S., & Masselon, C. (2021). A nonlinear model for nano-electro mechanical mass sensing signals processing. IEEE Sensors Journal, 1–1. https://doi.org/10.1109/JSEN.2021.3103713
Permiakova, O., & Burger, T. (2021). Sketched Stochastic Dictionary Learning for large‐scale data and application to high‐throughput mass spectrometry. Statistical Analysis and Data Mining: The ASA Data Science Journal, sam.11542. https://doi.org/10.1002/sam.11542
Pailleux, F., Maes, P., Jaquinod, M., Barthelon, J., Darnaud, M., Lacoste, C., Vandenbrouck, Y., Gilquin, B., Louwagie, M., Hesse, A.-M., Kraut, A., Garin, J., Leroy, V., Zarski, J.-P., Bruley, C., Couté, Y., Samuel, D., Ichai, P., Faivre, J., & Brun, V. (2021). Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury. International Journal of Molecular Sciences, 22(20), 11071. https://doi.org/10.3390/ijms222011071
Deutsch, E. W., Omenn, G. S., Sun, Z., Maes, M., Pernemalm, M., Palaniappan, K. K., Letunica, N., Vandenbrouck, Y., Brun, V., Tao, S., Yu, X., Geyer, P. E., Ignjatovic, V., Moritz, R. L., & Schwenk, J. M. (2021). Advances and Utility of the Human Plasma Proteome. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.1c00657
Jalabert, A., Reininger, L., Berger, E., Coute, Y., Meugnier, E., Forterre, A., Errazuriz-Cerda, E., Geloen, A., Aouadi, M., Bouzakri, K., Rieusset, J., & Rome, S. (2021). Profiling of ob/ob mice skeletal muscle exosome-like vesicles demonstrates combined action of miRNAs, proteins and lipids to modulate lipid homeostasis in recipient cells. Scientific Reports, 11(1), 21626. https://doi.org/10.1038/s41598-021-00983-3
Ropers, D., Couté, Y., Faure, L., Ferré, S., Labourdette, D., Shabani, A., Trouilh, L., Vasseur, P., Corre, G., Ferro, M., Teste, M.-A., Geiselmann, J., & de Jong, H. (2021). Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.1c00115
Häge, S., Büscher, N., Pakulska, V., Hahn, F., Adrait, A., Krauter, S., Borst, E. M., Schlötzer-Schrehardt, U., Couté, Y., Plachter, B., & Marschall, M. (2021). The Complex Regulatory Role of Cytomegalovirus Nuclear Egress Protein pUL50 in the Production of Infectious Virus. Cells, 10(11), 3119. https://doi.org/10.3390/cells10113119
Capizzi, M., Carpentier, R., Denarier, E., Adrait, A., Kassem, R., Mapelli, M., Couté, Y., & Humbert, S. (2021). Developmental defects in Huntington’s disease show that axonal growth and microtubule reorganization require NUMA1. Neuron, S0896627321008631. https://doi.org/10.1016/j.neuron.2021.10.033
Bouroumeau, A., Bussot, L., Hamaidia, S., Garcìa-Sandoval, A., Bergan-Dahl, A., Betton-Fraisse, P., Duley, S., Fournier, C., Aucagne, R., Adrait, A., Couté, Y., McLeer, A., Col, E., David-Boudet, L., Raskovalova, T., Jacob, M.-C., Vettier, C., Chevalier, S., Carras, S., … Emadali, A. (2021). CYCLON and NPM1 Cooperate within an Oncogenic Network Predictive of R-CHOP Response in DLBCL. Cancers, 13(23), 5900. https://doi.org/10.3390/cancers13235900