PAPPSO

Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. (2024-08-02) Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. J. Proteome Res., 8 (23) 3353-3366

US Patent & Trademark Office, 2017-05-02 : Becker C, Bern M, Kil YJ, Kim MT, Zhang B. Interactive analysis of mass spectrometry data. Protein Metrics Inc. (San Carlos, CA), 9640376 B1 (14/306020)

This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising an extracted mass chromatogram (XIC), an MS1 spectrum and an MS2 spectrum, all simultaneously representing a user-selected peptide. Another aspect provides a user interactive display simultaneously presenting paired spectra (XIC, MS1 and/or MS2) for a variant peptide and its corresponding wildtype counterpart.

US Patent & Trademark Office, 2014-11-27 : Bruce JE, Chavez J, Weisbrod C. Real-time analysis for cross-linked peptides. University of Washington (Seattle, WA), 9612246 B2 (14/283902)

Disclosed herein are methods for large-scale, high-throughput identification of protein-protein interactions and the topologies thereof under physiologically relevant conditions. In one aspect, the disclosure provides methods for identifying one or a plurality of interacting peptides within a biological system comprising obtaining a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker, cleaving the PIR crosslinker to produce released peptides and cleaved reporter ions, and analyzing the population of released peptides to identify interacting peptides. Also disclosed are methods for identifying candidate drug compounds, as well as methods of data processing and visualization of protein-protein interactions.

World Intellectual Property Organization, 2021-01-28 : Rautou PE, Boulanger-Robert C, Poisson J. Use of myeloperoxidase inhibitors for the treatment of cardiovascular diseases in patients suffering from myeloproliferative neoplasms. INSERM, APHP, Université de Paris, WO/2021/013942 (PCT/EP2020/070827)

Arterial cardiovascular events, i.e. the leading cause of death in patients with JAK2 V617F myeloproliferative neoplasms (MPN), are poorly understood. The inventors demonstrated that Jak2 V617F mice display a strong increase in arterial contraction with disturbed endothelial nitric oxide pathway and increased endothelial oxidative stress. This augmented arterial contraction was reproduced by circulating microvesicles isolated from patients carrying JAK2 V617F and by microvesicles derived from JAK2 V617F erythrocytes. Using proteomics, the inventors identified a high expression of myeloperoxidase in microvesicles derived from JAK2 V617F erythrocytes that could account for this effect. To assess the role of myeloperoxidase in this effect, the inventors then directly inhibited myeloperoxidase in microvesicles derived from Jak2 V617F erythrocytes and observed that it completely reversed the increase in endothelial oxidative stress induced by microvesicles derived from Jak2 V617F .The results prompt the inventors to conclude that JAK2 V617F MPN induce a potent increase in arterial contraction with increased endothelial oxidative stress, mediated by erythrocytes microvesicles and that myeloperoxidase (MPO) inhibitors would be suitable for preventing cardiovascular diseases in patient suffering from MPN.

10.1021/acs.jproteome.4c01119 Balliau T, Frambourg A, Langella O, Martin ML, Zivy M, Blein-Nicolas M. (2025-06-06) MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information. J. Proteome Res., 6 (24) 2861-2873

10.1021/acs.jproteome.4c00966 Teschner D, Gomez-Zepeda D, Łącki MK, Kemmer T, Busch A, Tenzer S, Hildebrandt A. (2025) Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data. Journal of Proteome Research, 5 (24) 2358-2368

10.1038/s41556-019-0307-4 A M, Fung TS, Kettenbach AN, Chakrabarti R, Higgs HN. (2019) A complex containing lysine-acetylated actin inhibits the formin INF2. Nature Cell Biology, 5 (21) 592-602

10.1093/pcp/pcw086 Abadie C, Mainguet S, Davanture M, Hodges M, Zivy M, Tcherkez G. (2016) Concerted Changes in the Phosphoproteome and Metabolome Under Different CO2/O2 Gaseous Conditions in Arabidopsis Rosettes. Plant and Cell Physiology, 7 (57) 1544-1556

Aggarwal S, Yadav AK. (2016) Dissecting the iTRAQ Data Analysis. , () 277-291

10.1101/2021.04.10.439193 Ambjoern SM, Duxin JP, Hertz EPT, Nasa I, Duro J, Kruse T, Mendez BL, Rymarczyk B, Cressey LE, van Overeem Hansen T, Kettenbach A, Oestergaard VH, Lisby M, Nilsson J. (2021) A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination. bioRxiv, () 2021.04.10.439193

10.1038/s41467-021-26079-0 Ambjørn SM, Duxin JP, Hertz EPT, Nasa I, Duro J, Kruse T, Lopez-Mendez B, Rymarczyk B, Cressey LE, van Overeem Hansen T, Kettenbach AN, Oestergaard VH, Lisby M, Nilsson J. (2021) A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination. Nature Communications, 1 (12) 5748

10.3390/plants9050591 Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. (2020) Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. Plants, 5 (9) 591

10.1186/s12915-023-01576-4 Amhaz S, Boëda B, Chouchène M, Colasse S, Dingli F, Loew D, Henri J, Prunier C, Levy L. (2023) The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia. BMC Biology, 1 (21) 73

10.1101/2024.07.12.603247 Ashenafi M, Balliau T, Blein-Nicolas M, Turc O, Zivy M, Marchadier E. (2024) A moderate water deficit induces profound changes in the proteome of developing maize ovaries. bioRxiv, () 2024.07.12.603247

10.1016/j.celrep.2024.114797 Assendorp N, Fossati M, Libé-Philippot B, Christopoulou E, Depp M, Rapone R, Dingli F, Loew D, Vanderhaeghen P, Charrier C. (2024) CTNND2 moderates the pace of synaptic maturation and links human evolution to synaptic neoteny. Cell Reports, 10 (43) 114797

10.1101/2022.09.13.507776 Assendorp N, Fossati M, Libé-Philippot B, Christopoulou E, Depp M, Rapone R, Dingli F, Loew D, Vanderhaeghen P, Charrier C. (2022) CTNND2 regulation by the SRGAP2 protein family links human evolution to synaptic neoteny. bioRxiv, () 2022.09.13.507776

10.1016/j.chembiol.2019.09.002 Bakail M, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard MC, Courbeyrette R, Mann C, Thuret JY, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du MH, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. (2019) Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chemical Biology, 11 (26) 1573-1585.e10

10.3390/biom14101239 Balliau T, Ashenafi M, Blein-Nicolas M, Turc O, Zivy M, Marchadier E. (2024) A Moderate Water Deficit Induces Profound Changes in the Proteome of Developing Maize Ovaries. Biomolecules, 10 (14) 1239

10.3390/proteomes6010006 Balliau T, Blein-Nicolas M, Zivy M. (2018) Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes, 1 (6) 6

10.1021/acs.jproteome.4c01119 Balliau T, Frambourg A, Langella O, Martin ML, Zivy M, Blein-Nicolas M. (2025) MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information. Journal of Proteome Research, ()

10.1051/ocl/2020074 Balliau T, Duruflé H, Blanchet N, Blein-Nicolas M, Langlade NB, Zivy M. (2021) Proteomic data from leaves of twenty-four sunflower genotypes under water deficit. OCL, (28) 12

10.1101/2020.06.26.171066 Balliau T, Duruflé H, Blanchet N, Blein-Nicolas M, Langlade NB, Zivy M. (2020) Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit. bioRxiv, () 2020.06.26.171066

10.3389/fpls.2019.00832 Bancel E, Bonnot T, Davanture M, Alvarez D, Zivy M, Martre P, Déjean S, Ravel C. (2019) Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. Frontiers in Plant Science, (10) 832

10.1038/s41556-020-0462-7 Barucci G, Cornes E, Singh M, Li B, Ugolini M, Samolygo A, Didier C, Dingli F, Loew D, Quarato P, Cecere G. (2020) Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants. Nature Cell Biology, 2 (22) 235-245

10.1107/s1600577517002478 Baud A, Aymé L, Gonnet F, Salard I, Gohon Y, Jolivet P, Brodolin K, Da Silva P, Giuliani A, Sclavi B, Chardot T, Mercère P, Roblin P, Daniel R. (2017) SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline. Journal of Synchrotron Radiation, 3 (24) 576-585

10.3390/ijms23137059 Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. (2022) Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. International Journal of Molecular Sciences, 13 (23) 7059

10.3389/fmicb.2021.616050 Bednarz B, Millan-Oropeza A, Kotowska M, Świat M, Haro JJQ, Henry C, Pawlik K. (2021) Coelimycin Synthesis Activatory Proteins Are Key Regulators of Specialized Metabolism and Precursor Flux in Streptomyces coelicolor A3(2). Frontiers in Microbiology, (12) 616050

10.1016/j.jaci.2020.03.020 Bekhouche B, Tourville A, Ravichandran Y, Tacine R, Abrami L, Dussiot M, Khau-Dancasius A, Boccara O, Khirat M, Mangeney M, Dingli F, Loew D, Boëda B, Jordan P, Molina TJ, Bellon N, Fraitag S, Hadj-Rabia S, Blanche S, Puel A, Etienne-Manneville S, van der Goot FG, Cherfils J, Hermine O, Casanova JL, Bodemer C, Smahi A, Delon J. (2020) A toxic palmitoylation of Cdc42 enhances NF-κB signaling and drives a severe autoinflammatory syndrome. Journal of Allergy and Clinical Immunology, 5 (146) 1201-1204.e8

10.1074/mcp.m116.060087 Bellati J, Champeyroux C, Hem S, Rofidal V, Krouk G, Maurel C, Santoni V. (2016) Novel Aquaporin Regulatory Mechanisms Revealed by Interactomics*. Molecular & Cellular Proteomics, 11 (15) 3473-3487

10.1104/pp.19.00086 Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat JP, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S. (2019) Modeling Protein Destiny in Developing Fruit. Plant Physiology, 3 (180) 1709-1724

10.1016/j.jprot.2018.10.003 Belouah I, Blein-Nicolas M, Balliau T, Gibon Y, Zivy M, Colombié S. (2018) Peptide filtering differently affects the performances of XIC-based quantification methods. Journal of Proteomics, (193) 131-141

10.1016/j.dib.2019.105015 Belouah I, Bénard C, Denton A, Blein-Nicolas M, Balliau T, Teyssier E, Gallusci P, Bouchez O, Usadel B, Zivy M, Gibon Y, Colombié S. (2019) Transcriptomic and proteomic data in developing tomato fruit. Data in Brief, (28) 105015

10.1101/2023.05.11.540411 Berg P, Popescu G. (2023) Baldur: Bayesian hierarchical modeling for label-free proteomics exploiting gamma dependent mean-variance trends. bioRxiv, () 2023.05.11.540411

10.1016/j.mcpro.2023.100658 Berg P, Popescu G. (2023) Baldur: Bayesian Hierarchical Modeling for Label-Free Proteomics with Gamma Regressing Mean-Variance Trends. Molecular & Cellular Proteomics, 12 (22) 100658

10.1371/journal.pone.0232425 Berrazaga I, Bourlieu-Lacanal C, Laleg K, Jardin J, Briard-Bion V, Dupont D, Walrand S, Micard V. (2020) Effect of protein aggregation in wheat-legume mixed pasta diets on their in vitro digestion kinetics in comparison to “rapid” and “slow” animal proteins. PLOS ONE, 5 (15) e0232425

10.1371/journal.pgen.1010618 Bidnenko V, Nicolas P, Guérin C, Dérozier S, Chastanet A, Dairou J, Redko-Hamel Y, Jules M, Bidnenko E. (2023) Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase. PLOS Genetics, 2 (19) e1010618

10.1038/s41598-017-15253-4 Bizzotto S, Uzquiano A, Dingli F, Ershov D, Houllier A, Arras G, Richards M, Loew D, Minc N, Croquelois A, Houdusse A, Francis F. (2017) Eml1 loss impairs apical progenitor spindle length and soma shape in the developing cerebral cortex. Scientific Reports, 1 (7) 17308

10.1074/mcp.m115.048058 Blein-Nicolas M, Albertin W, da Silva T, Valot B, Balliau T, Masneuf-Pomarède I, Bely M, Marullo P, Sicard D, Dillmann C, de Vienne D, Zivy M. (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast* [S]. Molecular & Cellular Proteomics, 8 (14) 2056-2071

10.1101/636514 Blein-Nicolas M, Negro SS, Balliau T, Welcker C, Bosquet LC, Nicolas SD, Charcosset A, Zivy M. (2019) A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize. bioRxiv, () 636514

10.1101/gr.255224.119 Blein-Nicolas M, Negro SS, Balliau T, Welcker C, Cabrera-Bosquet L, Nicolas SD, Charcosset A, Zivy M. (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Research, 11 (30) 1593-1604

10.1016/j.bbapap.2016.02.019 Blein-Nicolas M, Zivy M. (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 8 (1864) 883-895

10.1002/pmic.201100660 Blein‐Nicolas M, Xu H, de Vienne D, Giraud C, Huet S, Zivy M. (2012) Including shared peptides for estimating protein abundances: A significant improvement for quantitative proteomics. PROTEOMICS, 18 (12) 2797-2801

10.3389/fimmu.2016.00589 Boesch AW, Osei-Owusu NY, Crowley AR, Chu TH, Chan YN, Weiner JA, Bharadwaj P, Hards R, Adamo ME, Gerber SA, Cocklin SL, Schmitz JE, Miles AR, Eckman JW, Belli AJ, Reimann KA, Ackerman ME. (2016) Biophysical and Functional Characterization of Rhesus Macaque IgG Subclasses. Frontiers in Immunology, (7) 589

10.1093/jxb/eru268 Boex-Fontvieille E, Davanture M, Jossier M, Zivy M, Hodges M, Tcherkez G. (2014) Photosynthetic activity influences cellulose biosynthesis and phosphorylation of proteins involved therein in Arabidopsis leaves. Journal Of Experimental Botany, 17 (65) 4997-5010

10.1371/journal.pone.0070692 Boex-Fontvieille E, Daventure M, Jossier M, Zivy M, Hodges M, Tcherkez G. (2013) Photosynthetic Control of Arabidopsis Leaf Cytoplasmic Translation Initiation by Protein Phosphorylation. PLoS ONE, 7 (8) e70692

10.1074/mcp.m111.015867 Bonhomme L, Valot B, Tardieu F, Zivy M. (2012) Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated With Rapid Growth Adjustment in Maize Leaves*. Molecular & Cellular Proteomics, 10 (11) 957-972

10.1101/2023.12.12.571308 Bonnifet T, Sinnassamy S, Massiani-Beaudoin O, Mailly P, Monnet H, Loew D, Lombard B, Servant N, Joshi RL, Fuchs J. (2023) Steady-state neuron-predominant LINE-1 encoded ORF1p protein and LINE-1 RNA increase with aging in the mouse and human brain. bioRxiv, () 2023.12.12.571308

10.1111/tpj.13615 Bonnot T, Bancel E, Alvarez D, Davanture M, Boudet J, Pailloux M, Zivy M, Ravel C, Martre P. (2017) Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum. The Plant Journal, 5 (91) 894-910

10.1101/2024.03.13.582463 Bonnot T, Henriet C, Aimé D, Kreplak J, Térézol M, Balliau T, Ourry A, Zivy M, Vernoud V, Gallardo K. (2024) Molecular signatures and associated regulators of the pea leaf response to sulfur deficiency and water deficit as revealed by multi-omics analyses. bioRxiv, () 2024.03.13.582463

10.5802/crchim.272 Bouguechtouli C, Ghouil R, Alik A, Dingli F, Loew D, Theillet FX. (2025) Structural characterization of stem cell factors Oct4, Sox2, Nanog and Esrrb disordered domains, and a method to detect phospho-dependent binding partners. Comptes Rendus. Chimie, S3 (26) 1-19

10.1038/s41596-021-00604-3 Brauer BL, Wiredu K, Mitchell S, Moorhead GB, Gerber SA, Kettenbach AN. (2021) Affinity-based profiling of endogenous phosphoprotein phosphatases by mass spectrometry. Nature Protocols, 10 (16) 4919-4943

10.1021/acs.jproteome.2c00465 Brauer BL, Wiredu K, Gerber SA, Kettenbach AN. (2022) Evaluation of Quantification and Normalization Strategies for Phosphoprotein Phosphatase Affinity Proteomics: Application to Breast Cancer Signaling. Journal of Proteome Research, 1 (22) 47-61

10.15252/msb.20209569 Bryant JM, Baumgarten S, Dingli F, Loew D, Sinha A, Claës A, Preiser PR, Dedon PC, Scherf A. (2020) Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite. Molecular Systems Biology, 8 (16) msb209569

10.3389/fmicb.2021.793136 Canon F, Briard-Bion V, Jardin J, Thierry A, Gagnaire V. (2022) Positive Interactions Between Lactic Acid Bacteria Could Be Mediated by Peptides Containing Branched-Chain Amino Acids. Frontiers in Microbiology, (12) 793136

10.1038/s41420-020-00365-0 Castoldi F, Humeau J, Martins I, Lachkar S, Loew D, Dingli F, Durand S, Enot D, Bossut N, Chery A, Aprahamian F, Demont Y, Opolon P, Signolle N, Sauvat A, Semeraro M, Bezu L, Baracco EE, Vacchelli E, Pol JG, Lévesque S, Bloy N, Sica V, Maiuri MC, Kroemer G, Pietrocola F. (2020) Autophagy-mediated metabolic effects of aspirin. Cell Death Discovery, 1 (6) 129

10.3168/jds.2011-5233 Cebo C, Lopez C, Henry C, Beauvallet C, Ménard O, Bevilacqua C, Bouvier F, Caillat H, Martin P. (2012) Goat αs1-casein genotype affects milk fat globule physicochemical properties and the composition of the milk fat globule membrane. Journal of Dairy Science, 11 (95) 6215-6229

10.21203/rs.3.rs-87655/v1 Cecere G, Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Procaccia S. (2020) Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis. Research Square, ()

10.3390/beverages9030081 Chasseriaud L, Albertin W, Blein-Nicolas M, Balliau T, Zivy M, Coulon J, Bely M. (2023) Physical Contact between Torulaspora delbrueckii and Saccharomyces cerevisiae Alters Cell Growth and Molecular Interactions in Grape Must. Beverages, 3 (9) 81

10.1104/pp.19.00338 Chauffour F, Bailly M, Perreau F, Cueff G, Suzuki H, Collet B, Frey A, Clément G, Soubigou-Taconnat L, Balliau T, Krieger-Liszkay A, Rajjou L, Marion-Poll A. (2019) Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. Plant Physiology, 2 (180) 1198-1218

10.1016/j.foodres.2023.112883 Chauvet L, Ménard O, Le Gouar Y, Henry G, Jardin J, Hennetier M, Croguennec T, Van Audenhaege M, Dupont D, Lemaire M, Le Huërou-Luron I, Deglaire A. (2023) Protein ingredient quality of infant formulas impacts their structure and kinetics of proteolysis under in vitro dynamic digestion. Food Research International, (169) 112883

10.1016/j.celrep.2019.10.063 Chavez JD, Keller A, Zhou B, Tian R, Bruce JE. (2019) Cellular Interactome Dynamics during Paclitaxel Treatment. Cell Reports, 8 (29) 2371-2383.e5

10.1016/j.chembiol.2016.05.012 Chavez JD, Schweppe DK, Eng JK, Bruce JE. (2016) In Vivo Conformational Dynamics of Hsp90 and Its Interactors. Cell Chemical Biology, 6 (23) 716-726

10.1038/ncomms8928 Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE. (2015) Quantitative interactome analysis reveals a chemoresistant edgotype. Nature Communications, 1 (6) 7928

10.1074/mcp.m114.038075 Chaze T, Guillot A, Valot B, Langella O, Chamot-Rooke J, Di Guilmi AM, Trieu-Cuot P, Dramsi S, Mistou MY. (2014) O-Glycosylation of the N-terminal Region of the Serine-rich Adhesin Srr1 of Streptococcus agalactiae Explored by Mass Spectrometry*. Molecular & Cellular Proteomics, 9 (13) 2168-2182

10.1016/j.tibs.2018.09.003 Chen ZA, Rappsilber J. (2018) Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry. Trends in Biochemical Sciences, 11 (43) 908-920

10.1038/s41596-018-0089-3 Chen ZA, Rappsilber J. (2018) Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes. Nature Protocols, 1 (14) 171-201

10.1074/jbc.m117.798744 Chouchani ET, James AM, Methner C, Pell VR, Prime TA, Erickson BK, Forkink M, Lau GY, Bright TP, Menger KE, Fearnley IM, Krieg T, Murphy MP. (2017) Identification and quantification of protein S-nitrosation by nitrite in the mouse heart during ischemia. Journal of Biological Chemistry, 35 (292) 14486-14495

10.1101/2023.01.27.525863 Cocozza F, Martin-Jaular L, Lippens L, Di Cicco A, Arribas YA, Dingli F, Richard M, Merle L, Poullet P, Loew D, Lévy D, Hendrix A, Kassiotis G, Joliot A, Tkach M, Théry C. (2023) Extracellular vesicles and co-isolated endogenous retroviruses differently affect dendritic cells. bioRxiv, () 2023.01.27.525863

10.15252/embj.2023113590 Cocozza F, Martin‐Jaular L, Lippens L, Di Cicco A, Arribas YA, Ansart N, Dingli F, Richard M, Merle L, San Roman MJ, Poullet P, Loew D, Lévy D, Hendrix A, Kassiotis G, Joliot A, Tkach M, Théry C. (2023) Extracellular vesicles and co‐isolated endogenous retroviruses from murine cancer cells differentially affect dendritic cells. The EMBO Journal, 24 (42) e113590

10.3389/fchem.2018.00095 Coelho C, Julien P, Nikolantonaki M, Noret L, Magne M, Ballester J, Gougeon RD. (2018) Molecular and Macromolecular Changes in Bottle-Aged White Wines Reflect Oxidative Evolution–Impact of Must Clarification and Bottle Closure. Frontiers in Chemistry, (6) 95

10.1101/2022.12.31.522373 Coly PM, Chatterjee S, Mezine F, Jekmek CE, Devue C, Nipoti T, Corona ML, Dingli F, Loew D, van Niel G, Boulanger CM. (2023) Atheroprone shear stress stimulates noxious endothelial extracellular vesicle uptake by MCAM and PECAM-1 cell adhesion molecules. bioRxiv, () 2022.12.31.522373

10.1002/jev2.12414 Coly PM, Chatterjee S, Mezine F, Jekmek CE, Devue C, Nipoti T, Mazlan S, Corona ML, Dingli F, Loew D, van Niel G, Loyer X, Boulanger CM. (2024) Low fluid shear stress stimulates the uptake of noxious endothelial extracellular vesicles via MCAM and PECAM‐1 cell adhesion molecules. Journal of Extracellular Vesicles, 10 (13) e12414

10.1101/2020.06.26.163105 Cordon-Obras C, Barcons-Simon A, Scheidig-Benatar C, Claës A, Sabatet V, Loew D, Scherf A. (2020) An exon DNA element modulates heterochromatin spreading in the master regulator for sexual commitment in malaria parasites. bioRxiv, () 2020.06.26.163105

10.1016/j.foodchem.2021.130747 Cosson A, Oliveira Correia L, Descamps N, Saint-Eve A, Souchon I. (2021) Identification and characterization of the main peptides in pea protein isolates using ultra high-performance liquid chromatography coupled with mass spectrometry and bioinformatics tools. Food Chemistry, (367) 130747

10.1021/acs.jproteome.7b00205 Courcelles M, Coulombe-Huntington J, Cossette Émilie, Gingras AC, Thibault P, Tyers M. (2017) CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization. Journal of Proteome Research, 7 (16) 2645-2652

10.1016/j.foodchem.2018.12.086 Deglaire A, Oliveira SD, Jardin J, Briard-Bion V, Kroell F, Emily M, Ménard O, Bourlieu C, Dupont D. (2018) Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage. Food Chemistry, (281) 294-303

10.1002/elps.201500573 Deglaire A, De Oliveira SC, Jardin J, Briard-Bion V, Emily M, Ménard O, Bourlieu C, Dupont D. (2016) Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic term newborn digestion. ELECTROPHORESIS, 13 (37) 1839-1850

10.1016/j.yexmp.2014.03.004 Desjardin C, Chat S, Gilles M, Legendre R, Riviere J, Mata X, Balliau T, Esquerré D, Cribiu EP, Betch JM, Schibler L. (2014) Involvement of mitochondrial dysfunction and ER-stress in the physiopathology of equine osteochondritis dissecans (OCD). Experimental and Molecular Pathology, 3 (96) 328-338

10.26508/lsa.202201577 Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. (2022) Discovery of RUF6 ncRNA–interacting proteins involved in P. falciparum immune evasion. Life Science Alliance, 1 (6) e202201577

10.1101/2023.07.18.549525 Diffendall G, Claës A, Barcons-Simon A, , Dingli F, Santos M, Loew D, Claessens A, Scherf A. (2023) RNA polymerase III is involved in regulating Plasmodium falciparum virulence. bioRxiv, () 2023.07.18.549525

10.7554/elife.95879 Diffendall G, Claes A, Barcons-Simon A, Nyarko P, Dingli F, Santos MM, Loew D, Claessens A, Scherf A. (2024) RNA polymerase III is involved in regulating Plasmodium falciparum virulence. eLife, (13) rp95879

10.7554/elife.95879.3 Diffendall G, Claes A, Barcons-Simon A, Nyarko P, Dingli F, Santos MM, Loew D, Claessens A, Scherf A. (2024) RNA polymerase III is involved in regulating Plasmodium falciparum virulence. eLife, (13)

10.3389/fpls.2016.01611 Dobrenel T, Mancera-Martínez E, Forzani C, Azzopardi M, Davanture M, Moreau M, Schepetilnikov M, Chicher J, Langella O, Zivy M, Robaglia C, Ryabova LA, Hanson J, Meyer C. (2016) The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. Frontiers in Plant Science, (7) 1611

10.1038/s41586-020-1974-9 Dossin F, Pinheiro I, Żylicz JJ, Roensch J, Collombet S, Le Saux A, Chelmicki T, Attia M, Kapoor V, Zhan Y, Dingli F, Loew D, Mercher T, Dekker J, Heard E. (2020) SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature, 7795 (578) 455-460

10.3390/microorganisms8101621 Dubrulle G, Picot A, Madec S, Corre E, Pawtowski A, Baroncelli R, Zivy M, Balliau T, Le Floch G, Pensec F. (2020) Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis. Microorganisms, 10 (8) 1621

10.7554/elife.29303 Dumitru AMG, Rusin SF, Clark AEM, Kettenbach AN, Compton DA. (2017) Cyclin A/Cdk1 modulates Plk1 activity in prometaphase to regulate kinetochore-microtubule attachment stability. eLife, (6) e29303

Dumitru AMG, Compton DA. (2022) Identifying Cyclin A/Cdk1 Substrates in Mitosis in Human Cells. , () 175-182

10.1080/20013078.2017.1305677 Durcin M, Fleury A, Taillebois E, Hilairet G, Krupova Z, Henry C, Truchet S, Trötzmüller M, Köfeler H, Mabilleau G, Hue O, Andriantsitohaina R, Martin P, Le Lay S. (2017) Characterisation of adipocyte‐derived extracellular vesicle subtypes identifies distinct protein and lipid signatures for large and small extracellular vesicles. Journal of Extracellular Vesicles, 1 (6) 1305677

10.3390/cells9102249 Duruflé H, Ranocha P, Balliau T, Zivy M, Albenne C, Burlat V, Déjean S, Jamet E, Dunand C. (2020) An Integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations of Arabidopsis thaliana: A Focus on Cell Wall Changes. Cells, 10 (9) 2249

10.1016/j.plantsci.2017.07.015 Duruflé H, Hervé V, Ranocha P, Balliau T, Zivy M, Chourré J, San Clemente H, Burlat V, Albenne C, Déjean S, Jamet E, Dunand C. (2017) Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study. Plant Science, (263) 183-193

10.3390/biom13071110 Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. (2023) Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules, 7 (13) 1110

10.1016/j.dib.2019.104581 Duruflé H, Ranocha P, Balliau T, Dunand C, Jamet E. (2019) Transcriptomic and cell wall proteomic datasets of rosettes and floral stems from five Arabidopsis thaliana ecotypes grown at optimal or sub-optimal temperature. Data in Brief, (27) 104581

Désert A, Guitot K, Michaud A, Holoch D, Margueron R, Burlina F, Guianvarc’h D. (2022) Characterization of SET-Domain Histone Lysine Methyltransferase Substrates Using a Cofactor S-Adenosyl-l-Methionine Surrogate. , () 297-311

10.20944/preprints202412.1081.v1 Döring S, Weller MG, Reinders Y, Konthur Z, Jaeger C. (2024) Challenges and Insights in Absolute Quantification of Recombinant Therapeutic Antibodies by Mass Spectrometry: An Introductory Review. Preprints.org, () 202412.1081.v1

10.3390/antib14010003 Döring S, Weller MG, Reinders Y, Konthur Z, Jaeger C. (2025) Challenges and Insights in Absolute Quantification of Recombinant Therapeutic Antibodies by Mass Spectrometry: An Introductory Review. Antibodies, 1 (14) 3

10.1038/s42003-022-03049-w Estrada C, Mirabal-Ortega L, Méry L, Dingli F, Besse L, Messaoudi C, Loew D, Pouponnot C, Bertolotto C, Eychène A, Druillennec S. (2022) MITF activity is regulated by a direct interaction with RAF proteins in melanoma cells. Communications Biology, 1 (5) 101

10.3389/fpls.2021.644810 Fabre F, Urbach S, Roche S, Langin T, Bonhomme L. (2021) Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. Frontiers in Plant Science, (12) 644810

10.1111/pce.13549 Fabre F, Vignassa M, Urbach S, Langin T, Bonhomme L. (2019) Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism. Plant, Cell & Environment, 7 (42) 2291-2308

10.3389/fmicb.2019.02857 Fabre F, Bormann J, Urbach S, Roche S, Langin T, Bonhomme L. (2019) Unbalanced Roles of Fungal Aggressiveness and Host Cultivars in the Establishment of the Fusarium Head Blight in Bread Wheat. Frontiers in Microbiology, (10) 2857

10.1007/s11248-016-9943-7 Farré G, Perez-Fons L, Decourcelle M, Breitenbach J, Hem S, Zhu C, Capell T, Christou P, Fraser PD, Sandmann G. (2016) Metabolic engineering of astaxanthin biosynthesis in maize endosperm and characterization of a prototype high oil hybrid. Transgenic Research, 4 (25) 477-489

10.3389/fimmu.2023.1207545 Ferrant J, Pontis A, Zimmermann F, Dingli F, Poullet P, Loew D, Tarte K, Dumontet E. (2023) Phenotypic and proteomic analysis of plasma extracellular vesicles highlights them as potential biomarkers of primary Sjögren syndrome. Frontiers in Immunology, (14) 1207545

10.1073/pnas.1902922116 Ferrari ML, Malardé V, Grassart A, Salavessa L, Nigro G, Descorps-Declere S, Rohde JR, Schnupf P, Masson V, Arras G, Loew D, Sansonetti PJ, Sauvonnet N. (2019) Shigella promotes major alteration of gut epithelial physiology and tissue invasion by shutting off host intracellular transport. Proceedings of the National Academy of Sciences, 27 (116) 13582-13591

10.1038/s41589-020-0474-4 Forrester A, Rathjen SJ, Daniela Garcia-Castillo M, Bachert C, Couhert A, Tepshi L, Pichard S, Martinez J, Munier M, Sierocki R, Renard HF, Augusto Valades-Cruz C, Dingli F, Loew D, Lamaze C, Cintrat JC, Linstedt AD, Gillet D, Barbier J, Johannes L. (2020) Functional dissection of the retrograde Shiga toxin trafficking inhibitor Retro-2. Nature Chemical Biology, 3 (16) 327-336

10.3390/proteomes4030021 Francin-Allami M, Lollier V, Pavlovic M, San Clemente H, Rogniaux H, Jamet E, Guillon F, Larré C. (2016) Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach. Proteomes, 3 (4) 21

10.3389/fpls.2017.01984 Galland M, He D, Lounifi I, Arc E, Clément G, Balzergue S, Huguet S, Cueff G, Godin B, Collet B, Granier F, Morin H, Tran J, Valot B, Rajjou L. (2017) An Integrated “Multi-Omics” Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality. Frontiers in Plant Science, (8) 1984

10.1016/j.algal.2016.10.017 Garnier M, Bougaran G, Pavlovic M, Berard JB, Carrier G, Charrier A, Le Grand F, Lukomska E, Rouxel C, Schreiber N, Cadoret JP, Rogniaux H, Saint-Jean B. (2016) Use of a lipid rich strain reveals mechanisms of nitrogen limitation and carbon partitioning in the haptophyte Tisochrysis lutea. Algal Research, (20) 229-248

10.3389/fmicb.2019.02324 Gaucher F, Kponouglo K, Rabah H, Bonnassie S, Ossemond J, Pottier S, Jardin J, Briard-Bion V, Marchand P, Blanc P, Jeantet R, Jan G. (2019) Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying. Frontiers in Microbiology, (10) 2324

10.3390/plants12030526 Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Ouertani RN, Riahi J, de Oliveira AC, Abid G, Muhovski Y. (2023) Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley (Hordeum vulgare L.). Plants, 3 (12) 526

10.3390/plants11233287 Ghouili E, Abid G, Jebara M, Ouertani RN, de Oliveira AC, Ayed ME, Muhovski Y. (2022) Proteomic Analysis of Barley (Hordeum vulgare L.) Leaves in Response to Date Palm Waste Compost Application. Plants, 23 (11) 3287

Giai Gianetto Q. (2021) Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells. , () 267-302

10.1021/ac4021352 Gilmore JM, Milloy JA, Gerber SA. (2013) SILAC Surrogates: Rescue of Quantitative Information for Orphan Analytes in Spike-In SILAC Experiments. Analytical Chemistry, 22 (85) 10812-10819

10.1016/j.foodchem.2024.140886 Giribaldi M, Nebbia S, Briard-Bion V, Jardin J, Ménard O, Dupont D, Coscia A, Cresi F, Lamberti C, Cavallarin L, Deglaire A. (2024) Peptidomic profile of human milk as influenced by fortification with different protein sources: An in vitro dynamic digestion simulation. Food Chemistry, (462) 140886

10.1016/j.foodchem.2021.130998 Giribaldi M, Nebbia S, Briard-Bion V, Jardin J, Peila C, Coscia A, Dupont D, Cavallarin L, Deglaire A. (2021) Simulated dynamic digestion reveals different peptide releases from human milk processed by means of holder or high temperature-short time pasteurization. Food Chemistry, (369) 130998

10.48550/arxiv.2405.07772 Gornard S, Venon P, Lasfont F, Balliau T, Kaiser-Arnauld LMP, Mougel F. (2024) Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic. arXiv, ()

10.1186/s12864-024-10694-4 Gornard S, Venon P, Lasfont F, Balliau T, Kaiser L, Mougel F. (2024) Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic. BMC Genomics, 1 (25) 940

10.1101/2023.09.29.560133 Gutiérrez-Sanchez M, Zhang S, Gharsallah C, Lamotte S, Varet H, Rachel L, Dingli F, Loew D, Rotili D, Valente S, Mai A, Loiseau P, Pomel S, Jung M, Lecoeur H, Prina E, Späth GF. (2023) Inhibition of the macrophage demethylase LSD1 reverses Leishmania amazonensis-induced transcriptomic changes and causes a decrease in parasite load. bioRxiv, () 2023.09.29.560133

10.1093/jxb/erx482 Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C. (2018) Increases in activity of proteasome and papain-like cysteine protease in Arabidopsis autophagy mutants: back-up compensatory effect or cell-death promoting effect?. Journal of Experimental Botany, 6 (69) 1369-1385

10.1101/2023.05.14.540683 Hein JB, Nguyen HT, Garvanska DH, Nasa I, Feng Y, Mendez BL, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. (2023) Global substrate identification and high throughput in vitro dephosphorylation reactions uncover PP1 and PP2A-B55 specificity principles. bioRxiv, () 2023.05.14.540683

10.15252/msb.202311782 Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Mendez BL, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. (2023) Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Molecular Systems Biology, 12 (19) e11782

10.1093/jxb/eraa571 Henriet C, Balliau T, Aimé D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. (2021) Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. Journal of Experimental Botany, 7 (72) 2611-2626

10.3389/fmicb.2019.01329 Henry C, Haller L, Blein-Nicolas M, Zivy M, Canette A, Verbrugghe M, Mézange C, Boulay M, Gardan R, Samson S, Martin V, André-Leroux G, Monnet V. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Frontiers in Microbiology, (10) 1329

10.1038/s41598-019-41640-0 Hombach-Barrigah A, Bartsch K, Smirlis D, Rosenqvist H, MacDonald A, Dingli F, Loew D, Späth GF, Rachidi N, Wiese M, Clos J. (2019) Leishmania donovani 90 kD Heat Shock Protein – Impact of Phosphosites on Parasite Fitness, Infectivity and Casein Kinase Affinity. Scientific Reports, 1 (9) 5074

10.3389/fmicb.2018.02548 Huang S, Gaucher F, Cauty C, Jardin J, Le Loir Y, Jeantet R, Chen XD, Jan G. (2018) Growth in Hyper-Concentrated Sweet Whey Triggers Multi Stress Tolerance and Spray Drying Survival in Lactobacillus casei BL23: From the Molecular Basis to New Perspectives for Sustainable Probiotic Production. Frontiers in Microbiology, (9) 2548

10.1016/j.cub.2020.10.001 Itani OA, Zhong X, Tang X, Scott BA, Yan JY, Flibotte S, Lim Y, Hsieh AC, Bruce JE, Van Gilst M, Crowder CM. (2020) Coordinate Regulation of Ribosome and tRNA Biogenesis Controls Hypoxic Injury and Translation. Current Biology, 1 (31) 128-137.e5

10.1038/s42003-021-01693-2 Ivashenka A, Wunder C, Chambon V, Sandhoff R, Jennemann R, Dransart E, Podsypanina K, Lombard B, Loew D, Lamaze C, Poirier F, Gröne HJ, Johannes L, Shafaq-Zadah M. (2021) Glycolipid-dependent and lectin-driven transcytosis in mouse enterocytes. Communications Biology, 1 (4) 173

10.1093/jxb/erae417 James M, Masclaux-Daubresse C, Balliau T, Marmagne A, Chardon F, Trouverie J, Etienne P. (2024) Multi-scale phenotyping of senescence-related changes in roots of rapeseed in response to nitrate limitation. Journal of Experimental Botany, 2 (76) 312-330

10.1101/2024.04.03.587968 James M, Masclaux-Daubresse C, Balliau T, Marmagne A, Chardon F, Trouverie J, Etienne P. (2024) Multi-scale phenotyping of senescence-related changes in roots of Rapeseed in response to nitrogen deficiency. bioRxiv, () 2024.04.03.587968

10.1111/ppl.70287 James M, Masclaux‐Daubresse C, Goux D, Jing L, Etienne P, Trouverie J. (2025) The Taproot Acts as a Storage Organ During Rapeseed Vernalization. Physiologia Plantarum, 3 (177) e70287

10.1016/j.marpolbul.2024.117221 Jean N, James A, Balliau T, Martino C, Ghersy J, Savar V, Laabir M, Caruana AMN. (2024) Warming and polymetallic stress induce proteomic and physiological shifts in the neurotoxic Alexandrium pacificum as possible response to global changes. Marine Pollution Bulletin, Pt B (209) 117221

10.1016/j.jprot.2017.09.005 Jolivet P, Aymé L, Giuliani A, Wien F, Chardot T, Gohon Y. (2017) Structural proteomics: Topology and relative accessibility of plant lipid droplet associated proteins. Journal of Proteomics, (169) 87-98

10.1091/mbc.e22-01-0005 Kage F, Vicente-Manzanares M, McEwan BC, Kettenbach AN, Higgs HN. (2022) Myosin II proteins are required for organization of calcium-induced actin networks upstream of mitochondrial division. Molecular Biology of the Cell, 7 (33) ar63

10.1021/acs.jproteome.8b00703 Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE. (2018) Tools for 3D Interactome Visualization. Journal of Proteome Research, 2 (18) 753-758

10.1016/j.molcel.2024.10.045 Kelley JR, Dimitrova E, Maciuszek M, Nguyen HT, Szczurek AT, Hughes AL, Blackledge NP, Kettenbach AN, Klose RJ. (2024) The PNUTS phosphatase complex controls transcription pause release. Molecular Cell, 24 (84) 4843-4861.e8

10.1126/scisignal.aaq1441 Kettenbach AN, Schlosser KA, Lyons SP, Nasa I, Gui J, Adamo ME, Gerber SA. (2018) Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity. Science Signaling, 530 (11)

10.1016/j.jprot.2014.11.001 Kettenbach AN, Sano H, Keller SR, Lienhard GE, Gerber SA. (2014) SPECHT — Single-stage phosphopeptide enrichment and stable-isotope chemical tagging: Quantitative phosphoproteomics of insulin action in muscle. Journal of Proteomics, (114) 48-60

10.1101/557983 Kilani J, Davanture M, Zivy M, Fillinger S. (2019) Comparative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain loss of pathogenicity phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways. bioRxiv, () 557983

10.1016/j.jprot.2019.103580 Kilani J, Davanture M, Simon A, Zivy M, Fillinger S. (2019) Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways. Journal of Proteomics, (212) 103580

10.1039/c7mo00051k Kim M, Tagkopoulos I. (2018) Data integration and predictive modeling methods for multi-omics datasets. Molecular Omics, 1 (14) 8-25

10.1371/journal.ppat.1005672 Koeppen K, Hampton TH, Jarek M, Scharfe M, Gerber SA, Mielcarz DW, Demers EG, Dolben EL, Hammond JH, Hogan DA, Stanton BA. (2016) A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PLOS Pathogens, 6 (12) e1005672

10.1371/journal.pone.0211290 Koeppen K, Barnaby R, Jackson AA, Gerber SA, Hogan DA, Stanton BA. (2019) Tobramycin reduces key virulence determinants in the proteome of Pseudomonas aeruginosa outer membrane vesicles. PLOS ONE, 1 (14) e0211290

10.3389/fpls.2021.765846 Kolkas H, Balliau T, Chourré J, Zivy M, Canut H, Jamet E. (2022) The Cell Wall Proteome of Marchantia polymorpha Reveals Specificities Compared to Those of Flowering Plants. Frontiers in Plant Science, (12) 765846

10.1016/j.molcel.2023.09.023 Kovacs MT, Vallette M, Wiertsema P, Dingli F, Loew D, de Freitas Nader GP, Piel M, Ceccaldi R. (2023) DNA damage induces nuclear envelope rupture through ATR-mediated phosphorylation of lamin A/C. Molecular Cell, 20 (83) 3659-3668.e10

10.1073/pnas.1521230113 Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C. (2016) Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proceedings of the National Academy of Sciences, 8 (113) e968-e977

10.15252/embj.2019103695 Kruse T, Gnosa SP, Nasa I, Garvanska DH, Hein JB, Nguyen H, Samsøe‐Petersen J, Lopez‐Mendez B, Hertz EPT, Schwarz J, Pena HS, Nikodemus D, Kveiborg M, Kettenbach AN, Nilsson J. (2020) Mechanisms of site‐specific dephosphorylation and kinase opposition imposed by PP2A regulatory subunits. The EMBO Journal, 13 (39) embj2019103695

10.1101/2024.02.10.579793 Kruse T, Garvanska DH, Varga J, Garland W, McEwan B, Hein JB, Weisser MB, Puy IB, Chan CB, Parrila PS, Mendez BL, Arulanandam J, Schueler-Furman O, Jensen TH, Kettenbach A, Nilsson J. (2024) Substrate recognition principles for the PP2A-B55 protein phosphatase. bioRxiv, () 2024.02.10.579793

10.1126/sciadv.adp5491 Kruse T, Garvanska DH, Varga JK, Garland W, McEwan BC, Hein JB, Weisser MB, Benavides-Puy I, Chan CB, Sotelo-Parrilla P, Mendez BL, Jeyaprakash AA, Schueler-Furman O, Jensen TH, Kettenbach AN, Nilsson J. (2024) Substrate recognition principles for the PP2A-B55 protein phosphatase. Science Advances, 40 (10) eadp5491

10.1126/sciadv.aau6044 Kumar GS, Choy MS, Koveal DM, Lorinsky MK, Lyons SP, Kettenbach AN, Page R, Peti W. (2018) Identification of the substrate recruitment mechanism of the muscle glycogen protein phosphatase 1 holoenzyme. Science Advances, 11 (4) eaau6044

10.1016/j.mcpro.2021.100173 Laigle V, Dingli F, Amhaz S, Perron T, Chouchène M, Colasse S, Petit I, Poullet P, Loew D, Prunier C, Levy L. (2021) Quantitative Ubiquitylome Analysis Reveals the Specificity of RNF111/Arkadia E3 Ubiquitin Ligase for its Degradative Substrates SKI and SKIL/SnoN in TGF-β Signaling Pathway. Molecular & Cellular Proteomics, (20) 100173

10.1021/acs.jproteome.3c00732 Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. (2024) Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. Journal of Proteome Research, 8 (23) 3353-3366

10.1002/pmic.201200564 Langella O, Valot B, Jacob D, Balliau T, Flores R, Hoogland C, Joets J, Zivy M. (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. PROTEOMICS, 9 (13) 1457-1466

10.1021/acs.jproteome.6b00632 Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. (2016) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. Journal of Proteome Research, 2 (16) 494-503

10.1039/d3fo02693k Lavoisier A, Morzel M, Chevalier S, Henry G, Jardin J, Harel-Oger M, Garric G, Dupont D. (2023) In vitro digestion of two protein-rich dairy products in the ageing gastrointestinal tract. Food & Function, 20 (14) 9377-9390

10.1016/j.tjnut.2023.08.003 Le Guillou S, Ciobotaru C, Laubier J, Castille J, Aujean E, Hue-Beauvais C, Cherbuy C, Liuu S, Henry C, David A, Jaffrezic F, Laloë D, Charlier M, Alexandre-Gouabau MC, Le Provost F. (2023) Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth. The Journal of Nutrition, 10 (153) 2808-2826

10.3390/ijms21197400 Le Ribeuz H, Dumont F, Ruellou G, Lambert M, Balliau T, Quatredeniers M, Girerd B, Cohen-Kaminsky S, Mercier O, Yen-Nicolaÿ S, Humbert M, Montani D, Capuano V, Antigny F. (2020) Proteomic Analysis of KCNK3 Loss of Expression Identified Dysregulated Pathways in Pulmonary Vascular Cells. International Journal of Molecular Sciences, 19 (21) 7400

10.1038/s41598-022-21804-1 Leduc A, Le Guillou S, Bianchi L, Correia LO, Gelé M, Pires J, Martin P, Leroux C, Le Provost F, Boutinaud M. (2022) Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows. Scientific Reports, 1 (12) 18886

10.1016/j.jbc.2022.102379 Luciano AK, Korobkina ED, Lyons SP, Haley JA, Fluharty SM, Jung SM, Kettenbach AN, Guertin DA. (2022) Proximity labeling of endogenous RICTOR identifies mTOR complex 2 regulation by ADP ribosylation factor ARF1. Journal of Biological Chemistry, 10 (298) 102379

10.1093/jxb/eraa337 Luo J, Havé M, Clément G, Tellier F, Balliau T, Launay-Avon A, Guérard F, Zivy M, Masclaux-Daubresse C. (2020) Integrating multiple omics to identify common and specific molecular changes occurring in Arabidopsis under chronic nitrate and sulfate limitations. Journal of Experimental Botany, 20 (71) 6471-6490

10.1101/2022.12.02.518925 Luo J, Ranish J. (2022) Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes. bioRxiv, () 2022.12.02.518925

10.7554/elife.99809.3 Luo J, Ranish J. (2024) Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes. eLife, (13)

10.7554/elife.99809 Luo J, Ranish J. (2024) Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes.. eLife, (13)

10.1074/mcp.ra118.000822 Lyons SP, Jenkins NP, Nasa I, Choy MS, Adamo ME, Page R, Peti W, Moorhead GB, Kettenbach AN. (2018) A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans*. Molecular & Cellular Proteomics, 12 (17) i-2461

10.1101/2021.11.07.467570 Lyons SP, Greiner EC, Cressey LE, Adamo ME, Kettenbach AN. (2021) Regulation of PP2A, PP4, and PP6 holoenzyme assembly by carboxyl-terminal methylation. bioRxiv, () 2021.11.07.467570

10.1038/s41598-021-02456-z Lyons SP, Greiner EC, Cressey LE, Adamo ME, Kettenbach AN. (2021) Regulation of PP2A, PP4, and PP6 holoenzyme assembly by carboxyl-terminal methylation. Scientific Reports, 1 (11) 23031

10.1101/2023.09.12.557183 MacDonald E, Forrester A, Valades-Cruz CA, Madsen TD, Hetmanski JHR, Dransart E, Ng Y, Godbole R, Shp AA, Leconte L, Chambon V, Ghosh D, Pinet A, Bhatia D, Lombard B, Loew D, Larson MR, Leffler H, Lefeber DJ, Clausen H, Caswell P, Shafaq-Zadah M, Mayor S, Weigert R, Wunder C, Johannes L. (2023) Growth factor-induced desialylation for the fast control of endocytosis. bioRxiv, () 2023.09.12.557183

10.1038/s41556-025-01616-x MacDonald E, Forrester A, Valades-Cruz CA, Madsen TD, Hetmanski JHR, Dransart E, Ng Y, Godbole R, Shp AA, Leconte L, Chambon V, Ghosh D, Pinet A, Bhatia D, Lombard B, Loew D, Larsen MR, Leffler H, Lefeber DJ, Clausen H, Blangy A, Caswell P, Shafaq-Zadah M, Mayor S, Weigert R, Wunder C, Johannes L. (2025) Growth factor-triggered de-sialylation controls glycolipid-lectin-driven endocytosis. Nature Cell Biology, 3 (27) 449-463

10.1016/j.mcpro.2023.100614 Mariano NC, Rusin SF, Nasa I, Kettenbach AN. (2023) Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells. Molecular & Cellular Proteomics, 8 (22) 100614

10.1101/2020.10.27.323766 Mathieu M, Névo N, Jouve M, Valenzuela JI, Maurin M, Verweij F, Palmulli R, Lankar D, Dingli F, Loew D, Rubinstein E, Boncompain G, Perez F, Théry C. (2020) Specificities of exosome versus small ectosome secretion revealed by live intracellular tracking and synchronized extracellular vesicle release of CD9 and CD63. bioRxiv, () 2020.10.27.323766

10.1038/s41467-021-24384-2 Mathieu M, Névo N, Jouve M, Valenzuela JI, Maurin M, Verweij FJ, Palmulli R, Lankar D, Dingli F, Loew D, Rubinstein E, Boncompain G, Perez F, Théry C. (2021) Specificities of exosome versus small ectosome secretion revealed by live intracellular tracking of CD63 and CD9. Nature Communications, 1 (12) 4389

10.1021/acs.jproteome.5b00140 Mauriat M, Leplé JC, Claverol S, Bartholomé J, Negroni L, Richet N, Lalanne C, Bonneu M, Coutand C, Plomion C. (2015) Quantitative Proteomic and Phosphoproteomic Approaches for Deciphering the Signaling Pathway for Tension Wood Formation in Poplar. Journal of Proteome Research, 8 (14) 3188-3203

10.1101/2025.02.12.637884 Meeusen B, Ambjørn SM, Veis J, Riley RC, Vit G, Brauer BL, Møller MH, Greiner EC, Chan CB, Weisser MB, Garvanska DH, Zhu H, Davey NE, Kettenbach AN, Ogris E, Nilsson J. (2025) A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the catalytic metal ions. bioRxiv, () 2025.02.12.637884

10.3390/ijms21010239 Mehdi C, Virginie L, Audrey G, Axelle B, Colette L, Hélène R, Elisabeth J, Fabienne G, Mathilde FA. (2019) Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development. International Journal of Molecular Sciences, 1 (21) 239

10.1038/s41598-020-65087-w Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. (2020) Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Scientific Reports, 1 (10) 8492

10.1021/acs.jproteome.7b00163 Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. (2017) Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. Journal of Proteome Research, 7 (16) 2597-2613

10.20944/preprints202112.0212.v1 Millán-Oropeza A, Blein-Nicolas M, Monnet V, Zivy M, Henry C. (2021) Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Preprints.org, () 202112.0212.v1

10.3390/proteomes10010002 Millán-Oropeza A, Blein-Nicolas M, Monnet V, Zivy M, Henry C. (2022) Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes, 1 (10) 2

10.1016/j.envexpbot.2020.104062 Mirande-Ney C, Tcherkez G, Balliau T, Zivy M, Gilard F, Cui J, Ghashghaie J, Lamade E. (2020) Metabolic leaf responses to potassium availability in oil palm (Elaeis guineensis Jacq.) trees grown in the field. Environmental and Experimental Botany, (175) 104062

10.3390/biology14050525 Mouawad C, Awad MK, Rodrigues-Machado C, Henry C, Sanchis-Borja V, Chamy LE. (2025) High-Throughput Analysis of the Flagella FliK-Dependent Surfaceome and Secretome in Bacillus thuringiensis. Biology, 5 (14) 525

10.1083/jcb.201912061 Moulay G, Lainé J, Lemaître M, Nakamori M, Nishino I, Caillol G, Mamchaoui K, Julien L, Dingli F, Loew D, Bitoun M, Leterrier C, Furling D, Vassilopoulos S. (2020) Alternative splicing of clathrin heavy chain contributes to the switch from coated pits to plaques. Journal of Cell Biology, 9 (219) e201912061

10.1101/509133 Mu A, Fung TS, Kettenbach AN, Chakrabarti R, Higgs HN. (2018) A complex containing lysine-acetylated actin inhibits the formin INF2. bioRxiv, () 509133

10.1016/j.jprot.2020.103721 Müller F, Rappsilber J. (2020) A protocol for studying structural dynamics of proteins by quantitative crosslinking mass spectrometry and data-independent acquisition. Journal of Proteomics, (218) 103721

10.1101/693424 Müller S, Sindikubwabo F, Cañeque T, Lafon A, Versini A, Lombard B, Loew D, Durand A, Vallot C, Baulande S, Servant N, Rodriguez R. (2019) CD44 regulates epigenetic plasticity by mediating iron endocytosis. bioRxiv, () 693424

10.1126/scisignal.aai8669 Nasa I, Rusin SF, Kettenbach AN, Moorhead GB. (2018) Aurora B opposes PP1 function in mitosis by phosphorylating the conserved PP1-binding RVxF motif in PP1 regulatory proteins. Science Signaling, 530 (11)

10.1126/scisignal.aba7823 Nasa I, Cressey LE, Kruse T, Hertz EPT, Gui J, Graves LM, Nilsson J, Kettenbach AN. (2020) Quantitative kinase and phosphatase profiling reveal that CDK1 phosphorylates PP2Ac to promote mitotic entry. Science Signaling, 648 (13)

10.3389/fmars.2020.569560 Nef C, Henry C, Nicolau Élodie, Bérard JB, Hervé F, Caruana AMN, Kaas R, Mairet F, Garnier M. (2020) Cobalamin Scarcity Modifies Carbon Allocation and Impairs DMSP Production Through Methionine Metabolism in the Haptophyte Microalgae Tisochrysis lutea. Frontiers in Marine Science, (7) 569560

10.1007/s00018-020-03614-8 Nehlig A, Seiler C, Steblyanko Y, Dingli F, Arras G, Loew D, Welburn J, Prigent C, Barisic M, Nahmias C. (2020) Reciprocal regulation of Aurora kinase A and ATIP3 in the control of metaphase spindle length. Cellular and Molecular Life Sciences, 4 (78) 1765-1779

10.1038/s41598-023-49724-8 Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. (2023) Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Scientific Reports, 1 (13) 22785

10.15252/embj.2020104948 Ohnstad AE, Delgado JM, North BJ, Nasa I, Kettenbach AN, Schultz SW, Shoemaker CJ. (2020) Receptor‐mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy. The EMBO Journal, 24 (39) embj2020104948

10.1101/730242 Opalko HE, Nasa I, Kettenbach AN, Moseley JB. (2019) A mechanism for how Cdr1/Nim1 kinase promotes mitotic entry by inhibiting Wee1. bioRxiv, () 730242

10.1091/mbc.e19-08-0430 Opalko HE, Nasa I, Kettenbach AN, Moseley JB. (2019) A mechanism for how Cdr1/Nim1 kinase promotes mitotic entry by inhibiting Wee1. Molecular Biology of the Cell, 25 (30) 3015-3023

10.1016/j.celrep.2023.112456 Oudart M, Avila-Gutierrez K, Moch C, Dossi E, Milior G, Boulay AC, Gaudey M, Moulard J, Lombard B, Loew D, Bemelmans AP, Rouach N, Chapat C, Cohen-Salmon M. (2023) The ribosome-associated protein RACK1 represses Kir4.1 translation in astrocytes and influences neuronal activity. Cell Reports, 5 (42) 112456

10.1101/2022.07.16.500292 Oudart M, Avila-Gutierrez K, Moch C, Dossi E, Milior G, Boulay AC, Gaudey M, Moulard J, Lombard B, Loew D, Bemelmans AP, Rouach N, Chapat C, Cohen-Salmon M. (2022) Translational regulation by RACK1 in astrocytes represses KIR4.1 expression and regulates neuronal activity. bioRxiv, () 2022.07.16.500292

10.3390/foods9101415 Ozorio L, Mellinger-Silva C, Cabral LMC, Jardin J, Boudry G, Dupont D. (2020) The Influence of Peptidases in Intestinal Brush Border Membranes on the Absorption of Oligopeptides from Whey Protein Hydrolysate: An Ex Vivo Study Using an Ussing Chamber. Foods, 10 (9) 1415

10.1038/s41556-024-01432-9 Palmulli R, Couty M, Piontek MC, Ponnaiah M, Dingli F, Verweij FJ, Charrin S, Tantucci M, Sasidharan S, Rubinstein E, Kontush A, Loew D, Lhomme M, Roos WH, Raposo G, van Niel G. (2024) CD63 sorts cholesterol into endosomes for storage and distribution via exosomes. Nature Cell Biology, 7 (26) 1093-1109

10.1038/s41598-023-41951-3 Pasquereau-Kotula E, Nigro G, Dingli F, Loew D, Poullet P, Xu Y, Kopetz S, Davis J, Peduto L, Robbe-Masselot C, Sansonetti P, Trieu-Cuot P, Dramsi S. (2023) Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer. Scientific Reports, 1 (13) 14960

10.1101/2023.02.17.528913 Pasquereau-Kotula E, Nigro G, Dingli F, Loew D, Poullet P, Xu Y, Kopetz S, Davis J, Peduto L, Robbe-Masselot C, Sansonetti P, Trieu-Cuot P, Dramsi S. (2023) The oncogenic role of Streptococcus gallolyticus subsp. gallolyticus is linked to activation of multiple cancer-related signaling pathways. bioRxiv, () 2023.02.17.528913

10.1016/j.jbc.2024.107601 Perron T, Boissan M, Bièche I, Courtois L, Dingli F, Loew D, Chouchène M, Colasse S, Levy L, Prunier C. (2024) CYYR1 promotes the degradation of the E3 ubiquitin ligase WWP1 and is associated with favorable prognosis in breast cancer. Journal of Biological Chemistry, 9 (300) 107601

10.3390/foods11162429 Peslerbes M, Fellenberg A, Jardin J, Deglaire A, Ibáñez RA. (2022) Manufacture of Whey Protein Hydrolysates Using Plant Enzymes: Effect of Processing Conditions and Simulated Gastrointestinal Digestion on Angiotensin-I-Converting Enzyme (ACE) Inhibitory Activity. Foods, 16 (11) 2429

10.1038/s41598-022-26217-8 Petit I, Levy A, Estrach S, Féral CC, Trentin AG, Dingli F, Loew D, Qu J, Zhou H, Théry C, Prunier C, Aberdam D, Ferrigno O. (2022) Fibroblast growth factor-2 bound to specific dermal fibroblast-derived extracellular vesicles is protected from degradation. Scientific Reports, 1 (12) 22131

10.1074/mcp.m116.059394 Petrone A, Adamo ME, Cheng C, Kettenbach AN. (2016) Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics*. Molecular & Cellular Proteomics, 7 (15) 2448-2461

10.1038/s41467-024-47985-z Pichol-Thievend C, Anezo O, Pettiwala AM, Bourmeau G, Montagne R, Lyne AM, Guichet PO, Deshors P, Ballestín A, Blanchard B, Reveilles J, Ravi VM, Joseph K, Heiland DH, Julien B, Leboucher S, Besse L, Legoix P, Dingli F, Liva S, Loew D, Giani E, Ribecco V, Furumaya C, Marcos-Kovandzic L, Masliantsev K, Daubon T, Wang L, Diaz AA, Schnell O, Beck J, Servant N, Karayan-Tapon L, Cavalli FMG, Seano G. (2024) VC-resist glioblastoma cell state: vessel co-option as a key driver of chemoradiation resistance. Nature Communications, 1 (15) 3602

10.1101/2022.03.24.485623 Pinto MJ, Cottin L, Dingli F, Laigle V, Ribeiro LF, Triller A, Henderson FJ, Loew D, Fabre V, Bessis A. (2022) Microglial TNFα orchestrates brain phosphorylation during the sleep period and controls homeostatic sleep. bioRxiv, () 2022.03.24.485623

10.15252/embj.2022111485 Pinto MJ, Cottin L, Dingli F, Laigle V, Ribeiro LF, Triller A, Henderson F, Loew D, Fabre V, Bessis A. (2022) Microglial TNFα orchestrates protein phosphorylation in the cortex during the sleep period and controls homeostatic sleep. The EMBO Journal, 1 (42) embj2022111485

10.1101/2021.06.22.449387 Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. (2021) A combined test for feature selection on sparse metaproteomics data - an alternative to missing value imputation. bioRxiv, () 2021.06.22.449387

10.7717/peerj.13525 Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. (2022) A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation. PeerJ, (10) e13525

10.1172/jci124566 Poisson J, Tanguy M, Davy H, Camara F, Mdawar MBE, Kheloufi M, Dagher T, Devue C, Lasselin J, Plessier A, Merchant S, Blanc-Brude O, Souyri M, Mougenot N, Dingli F, Loew D, Hatem SN, James C, Villeval JL, Boulanger CM, Rautou PE. (2020) Erythrocyte-derived microvesicles induce arterial spasms in JAK2V617F myeloproliferative neoplasm. Journal of Clinical Investigation, 5 (130) 2630-2643

10.1126/sciadv.add9084 Priya A, Antoine-Bally S, Macé AS, Monteiro P, Sabatet V, Remy D, Dingli F, Loew D, Demetriades C, Gautreau AM, Chavrier P. (2023) Codependencies of mTORC1 signaling and endolysosomal actin structures. Science Advances, 37 (9) eadd9084

10.3389/fmicb.2019.00906 Proust L, Sourabié A, Pedersen M, Besançon I, Haudebourg E, Monnet V, Juillard V. (2019) Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus. Frontiers in Microbiology, (10) 906

10.1128/aem.01446-20 Proust L, Haudebourg E, Sourabié A, Pedersen M, Besançon I, Monnet V, Juillard V. (2020) Multi-omics Approach Reveals How Yeast Extract Peptides Shape Streptococcus thermophilus Metabolism. Applied and Environmental Microbiology, 22 (86) e01446-20

10.1101/2024.02.02.578547 Przybyla-Toscano J, Chetouhi C, Balliau T, Alban C, Bourguignon J, Ravanel S. (2024) Dynamics of the membrane- and cell wall-associated proteome of Arabidopsis thaliana roots in response to uranium stress. bioRxiv, () 2024.02.02.578547

10.1016/j.chemosphere.2024.143873 Przybyla-Toscano J, Chetouhi C, Pennera L, Boursiac Y, Galeone A, Devime F, Balliau T, Santoni V, Bourguignon J, Alban C, Ravanel S. (2024) New insights into uranium stress responses of Arabidopsis roots through membrane- and cell wall-associated proteome analysis. Chemosphere, (370) 143873

10.1101/2023.05.24.542041 Ramos R, Karaiskou A, Botuha C, Trichet M, Dingli F, Forté J, Lam F, Canette A, Chaumeton C, Salome M, Chenuel T, Bergonzi C, Meyer P, Bohic S, Loew D, Salmain M, Sobczak-Thépot J. (2023) Identification of the intracellular protein targets of a bio-active clickable half-sandwich iridium complex by chemical proteomics. bioRxiv, () 2023.05.24.542041

10.1021/acsagscitech.1c00264 Ramsey JS, Zhong X, Saha S, Chavez JD, Johnson R, Mahoney JE, Keller A, Moulton K, Mueller LA, Hall DG, MacCoss MJ, Bruce JE, Heck M. (2022) Quantitative Isotope-Labeled Cross-Linker Proteomics Reveals Developmental Variation in Protein Interactions and Post-Translational Modifications in Diaphorina citri, the Citrus Greening Insect Vector. ACS Agricultural Science & Technology, 3 (2) 486-500

10.1101/2021.11.09.467860 Ramsey JS, Zhong X, Saha S, Chavez JD, Johnson R, Mahoney JE, Keller A, Moulton K, Mueller LA, Hall DG, MacCoss MJ, Bruce JE, Heck M. (2021) Quantitative isotope-labeled crosslinker proteomics reveals developmental variation in protein interactions and posttranslational modifications in Diaphorina citri, the citrus greening insect vector. bioRxiv, () 2021.11.09.467860

10.1083/jcb.202004092 Ravichandran Y, Hänisch J, Murray K, Roca V, Dingli F, Loew D, Sabatet V, Boëda B, Stradal TE, Etienne-Manneville S. (2024) The distinct localization of CDC42 isoforms is responsible for their specific functions during migration. Journal of Cell Biology, 3 (223) e202004092

10.1101/2023.02.27.528078 Ravichandran Y, Hänisch J, Murray K, Roca V, Dingli F, Loew D, Sabatet V, Boëda B, Stradal T, Etienne-Manneville S. (2023) The functional specificity of CDC42 isoforms is caused by their distinct subcellular localization. bioRxiv, () 2023.02.27.528078

10.1021/pr401268v Rayapuram N, Bonhomme L, Bigeard J, Haddadou K, Przybylski C, Hirt H, Pflieger D. (2014) Identification of Novel PAMP-Triggered Phosphorylation and Dephosphorylation Events in Arabidopsis thaliana by Quantitative Phosphoproteomic Analysis. Journal of Proteome Research, 4 (13) 2137-2151

10.1074/mcp.ra117.000135 Rayapuram N, Bigeard J, Alhoraibi H, Bonhomme L, Hesse AM, Vinh J, Hirt H, Pflieger D. (2017) Quantitative Phosphoproteomic Analysis Reveals Shared and Specific Targets of Arabidopsis Mitogen-Activated Protein Kinases (MAPKs) MPK3, MPK4, and MPK6*. Molecular & Cellular Proteomics, 1 (17) 61-80

Renvoisé M, Bonhomme L, Davanture M, Zivy M, Lemaire C. (2017) Phosphoproteomic Analysis of Isolated Mitochondria in Yeast. , () 283-299

10.1016/j.jprot.2014.04.022 Renvoisé M, Bonhomme L, Davanture M, Valot B, Zivy M, Lemaire C. (2014) Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae. Journal of Proteomics, (106) 140-150

10.1101/2020.09.30.321497 Ribot J, Breton R, Calvo CF, Moulard J, Ezan P, Zapata J, Samama K, Bemelmans AP, Sabatet V, Dingli F, Loew D, Milleret C, Billuart P, Dallérac G, Rouach N. (2020) Astrocytes close the critical period for visual plasticity. bioRxiv, () 2020.09.30.321497

10.1126/science.abf5273 Ribot J, Breton R, Calvo CF, Moulard J, Ezan P, Zapata J, Samama K, Moreau M, Bemelmans AP, Sabatet V, Dingli F, Loew D, Milleret C, Billuart P, Dallérac G, Rouach N. (2021) Astrocytes close the mouse critical period for visual plasticity. Science, 6550 (373) 77-81

10.3390/cancers16050845 Romo BA, Karakyriakou B, Cressey L, Brauer BL, Yang H, Warren A, Johnson AL, Kettenbach AN, Miller TW. (2024) TRIM33 Is a Co-Regulator of Estrogen Receptor Alpha. Cancers, 5 (16) 845

10.2174/1389203722666210118160946 Rusconi F. (2021) Free Open Source Software for Protein and Peptide Mass Spectrometry-based Science. Current Protein & Peptide Science, 2 (22) 134-147

10.1021/acs.jproteome.9b00099 Rusconi F. (2019) mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability. Journal of Proteome Research, 5 (18) 2254-2259

10.3389/fcell.2017.00097 Rusin SF, Adamo ME, Kettenbach AN. (2017) Identification of Candidate Casein Kinase 2 Substrates in Mitosis by Quantitative Phosphoproteomics. Frontiers in Cell and Developmental Biology, (5) 97

10.1126/scisignal.aab3138 Rusin SF, Schlosser KA, Adamo ME, Kettenbach AN. (2015) Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells. Science Signaling, 398 (8) rs12

10.1111/tpj.16763 Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange‐Macherel MH, Macherel D. (2024) Multi‐scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy‐transducing organelles. The Plant Journal, 1 (119) 300-331

10.1074/mcp.o112.021907 Sandin M, Ali A, Hansson K, Månsson O, Andreasson E, Resjö S, Levander F. (2013) An Adaptive Alignment Algorithm for Quality-controlled Label-free LC-MS*. Molecular & Cellular Proteomics, 5 (12) 1407-1420

10.1016/j.bbapap.2013.03.026 Sandin M, Teleman J, Malmström J, Levander F. (2013) Data processing methods and quality control strategies for label-free LC–MS protein quantification. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1 (1844) 29-41

10.3389/fpls.2022.867263 Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. (2022) Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. Frontiers in Plant Science, (13) 867263

10.1101/2020.07.22.205203 Seetharaman S, Vianay B, Roca V, De Pascalis C, Boëda B, Dingli F, Loew D, Vassilopoulos S, Théry M, Etienne-Manneville S. (2020) Microtubules tune mechanosensitive cell responses. bioRxiv, () 2020.07.22.205203

10.1038/s41563-021-01108-x Seetharaman S, Vianay B, Roca V, Farrugia AJ, De Pascalis C, Boëda B, Dingli F, Loew D, Vassilopoulos S, Bershadsky A, Théry M, Etienne-Manneville S. (2021) Microtubules tune mechanosensitive cell responses. Nature Materials, 3 (21) 366-377

10.1101/2020.09.04.282863 Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Proccacia S, Cecere G. (2020) Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis. bioRxiv, () 2020.09.04.282863

10.1038/s41467-021-23615-w Singh M, Cornes E, Li B, Quarato P, Bourdon L, Dingli F, Loew D, Proccacia S, Cecere G. (2021) Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis. Nature Communications, 1 (12) 3492

10.3390/ijms21239162 Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. (2020) Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. International Journal of Molecular Sciences, 23 (21) 9162

10.20944/preprints201812.0129.v1 Smolikova G, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. (2018) Discovering Seed Proteome: Challenges and Perspectives. Preprints.org, ()

10.1038/s41586-023-06017-4 Solier S, Müller S, Cañeque T, Versini A, Mansart A, Sindikubwabo F, Baron L, Emam L, Gestraud P, Pantoș GD, Gandon V, Gaillet C, Wu TD, Dingli F, Loew D, Baulande S, Durand S, Sencio V, Robil C, Trottein F, Péricat D, Näser E, Cougoule C, Meunier E, Bègue AL, Salmon H, Manel N, Puisieux A, Watson S, Dawson MA, Servant N, Kroemer G, Annane D, Rodriguez R. (2023) A druggable copper-signalling pathway that drives inflammation. Nature, 7960 (617) 386-394

10.1038/s42003-024-07205-2 Song C, Zhang M, Kruse T, Møller MH, López-Méndez B, Zhang Y, Zhai Y, Wang Y, Lei T, Kettenbach AN, Nilsson J, Zhang G. (2024) Self-priming of Plk1 binding to BubR1 ensures accurate mitotic progression. Communications Biology, 1 (7) 1473

10.1371/journal.pone.0174060 Souza RFS, Jardin J, Cauty C, Rault L, Bouchard DS, Bermúdez-Humarán LG, Langella P, Monedero V, Seyffert N, Azevedo V, Le Loir Y, Even S. (2017) Contribution of sortase SrtA2 to Lactobacillus casei BL23 inhibition of Staphylococcus aureus internalization into bovine mammary epithelial cells. PLOS ONE, 3 (12) e0174060

10.1101/2023.12.12.570754 Tadi SK, Gesnik A, Frit P, Iehl F, Ropars V, Dingli F, Loew D, Calsou P, Callebaut I, Charbonnier JB, de Villartay JP. (2023) Ku-binding motifs in RAG2, XLF, PAXX and MRI support functional redundancy during V(D)J recombination. bioRxiv, () 2023.12.12.570754

10.1016/j.plaphy.2023.108213 Tarkowski Łukasz P, Clochard T, Blein-Nicolas M, Zivy M, Baillau T, Abadie C, Morère-Le Paven MC, Limami AM, Tcherkez G, Montrichard F. (2023) The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip. Plant Physiology and Biochemistry, (206) 108213

10.1038/s41598-020-64952-y Tartaglia NR, Nicolas A, Rodovalho VR, Luz BSR, Briard-Bion V, Krupova Z, Thierry A, Coste F, Burel A, Martin P, Jardin J, Azevedo V, Le Loir Y, Guédon E. (2020) Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome. Scientific Reports, 1 (10) 8467

10.1016/j.plantsci.2019.110352 Tcherkez G, Carroll A, Abadie C, Mainguet S, Davanture M, Zivy M. (2019) Protein synthesis increases with photosynthesis via the stimulation of translation initiation. Plant Science, New Phytol. 214 2017 (291) 110352

10.1128/aem.02061-19 Trunet C, Mtimet N, Mathot AG, Postollec F, Leguerinel I, Couvert O, Broussolle V, Carlin F, Coroller L. (2020) Suboptimal Bacillus licheniformis and Bacillus weihenstephanensis Spore Incubation Conditions Increase Heterogeneity of Spore Outgrowth Time. Applied and Environmental Microbiology, 6 (86) e02061-19

Truntzer C, Ducoroy P. (2016) Statistical Approach for Biomarker Discovery Using Label-Free LC-MS Data: An Overview. , () 177-201

10.1016/j.molcel.2019.08.029 Ueki Y, Kruse T, Weisser MB, Sundell GN, Larsen MSY, Mendez BL, Jenkins NP, Garvanska DH, Cressey L, Zhang G, Davey N, Montoya G, Ivarsson Y, Kettenbach AN, Nilsson J. (2019) A Consensus Binding Motif for the PP4 Protein Phosphatase. Molecular Cell, 6 (76) 953-964.e6

10.15252/embr.202052295 Ueki Y, Hadders MA, Weisser MB, Nasa I, Sotelo-Parrilla P, Cressey LE, Gupta T, Hertz EPT, Kruse T, Montoya G, Jeyaprakash AA, Kettenbach A, Lens SMA, Nilsson J. (2021) A highly conserved pocket on PP2A-B56 is required for hSgo1 binding and cohesion protection during mitosis. The EMBO Reports, 7 (22) embr202052295

10.21203/rs.3.rs-2591494/v1 Urrutia M, Blein-Nicolas M, Fernandez O, Bernillon S, Maucourt M, Deborde C, Balliau T, Rabier D, Bénard C, Prigent S, Quillere I, Jacob D, Gibon Y, Zivy M, Giauffret C, Hirel B, Moing A. (2023) Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids. Research Square, ()

10.1111/pce.13993 Urrutia M, Blein‐Nicolas M, Prigent S, Bernillon S, Deborde C, Balliau T, Maucourt M, Jacob D, Ballias P, Bénard C, Sellier H, Gibon Y, Giauffret C, Zivy M, Moing A. (2021) Maize metabolome and proteome responses to controlled cold stress partly mimic early‐sowing effects in the field and differ from those of Arabidopsis. Plant, Cell & Environment, 5 (44) 1504-1521

10.1016/j.celrep.2019.06.096 Uzquiano A, Cifuentes-Diaz C, Jabali A, Romero DM, Houllier A, Dingli F, Maillard C, Boland A, Deleuze JF, Loew D, Mancini GMS, Bahi-Buisson N, Ladewig J, Francis F. (2019) Mutations in the Heterotopia Gene Eml1/EML1 Severely Disrupt the Formation of Primary Cilia. Cell Reports, 6 (28) 1596-1611.e10

10.1002/prca.201700010 Valot B, Rognon B, Prenel A, Baraquin A, Knapp J, Anelli M, Richou C, Bresson‐Hadni S, Grenouillet F, Wang J, Vuitton DA, Gottstein B, Millon L. (2017) Screening of antigenic vesicular fluid proteins of Echinococcus multilocularis as potential viability biomarkers to monitor drug response in alveolar echinococcosis patients. PROTEOMICS – Clinical Applications, 11-12 (11)

10.1101/2021.01.21.427607 Vernekar DV, Reginato G, Adam C, Ranjha L, Dingli F, Marsolier MC, Loew D, Guérois R, Llorente B, Cejka P, Borde V. (2021) The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length. bioRxiv, () 2021.01.21.427607

10.1093/nar/gkab232 Vernekar DV, Reginato G, Adam C, Ranjha L, Dingli F, Marsolier MC, Loew D, Guérois R, Llorente B, Cejka P, Borde V. (2021) The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length. Nucleic Acids Research, 8 (49) 4522-4533

10.1101/380311 Verweij FJ, Revenu C, Arras G, Dingli F, Loew D, Follain G, Allio G, Goetz JG, Herbomel P, Del Bene F, Raposo G, van Niel G. (2018) Live tracking of inter-organ communication by endogenous exosomes in vivo. bioRxiv, () 380311

10.1016/j.devcel.2019.01.004 Verweij FJ, Revenu C, Arras G, Dingli F, Loew D, Pegtel DM, Follain G, Allio G, Goetz JG, Zimmermann P, Herbomel P, Del Bene F, Raposo G, van Niel G. (2019) Live Tracking of Inter-organ Communication by Endogenous Exosomes In Vivo. Developmental Cell, 4 (48) 573-589.e4

10.1016/j.molcel.2022.04.019 Vibert J, Saulnier O, Collin C, Petit F, Borgman KJE, Vigneau J, Gautier M, Zaidi S, Pierron G, Watson S, Gruel N, Hénon C, Postel-Vinay S, Deloger M, Raynal V, Baulande S, Laud-Duval K, Hill V, Grossetête S, Dingli F, Loew D, Torrejon J, Ayrault O, Orth MF, Grünewald TGP, Surdez D, Coulon A, Waterfall JJ, Delattre O. (2022) Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions. Molecular Cell, 13 (82) 2458-2471.e9

10.1101/2021.07.08.451586 Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez-Mendez B, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. (2021) Cellular toxicity of iHAP1 and DT-061 does not occur through PP2A-B56 targeting. bioRxiv, () 2021.07.08.451586

10.15252/embj.2022110611 Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. (2022) Chemogenetic profiling reveals PP2A‐independent cytotoxicity of proposed PP2A activators iHAP1 and DT‐061. The EMBO Journal, 14 (41) embj2022110611

10.1038/s41564-024-01609-w Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (2024) (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nature Microbiology, 3 (9) 647-656

10.7554/elife.55966 Wang X, Garvanska DH, Nasa I, Ueki Y, Zhang G, Kettenbach AN, Peti W, Nilsson J, Page R. (2020) A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment. eLife, (9) e55966

10.3390/ijms23169352 Wang X, Davanture M, Zivy M, Bailly C, Nambara E, Corbineau F. (2022) Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. International Journal of Molecular Sciences, 16 (23) 9352

10.1128/ec.00011-15 Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA. (2015) Analysis of the Candida albicans Phosphoproteome. Eukaryotic Cell, 5 (14) 474-485

10.1016/j.cbpa.2021.06.011 Wippel HH, Chavez JD, Tang X, Bruce JE. (2021) Quantitative interactome analysis with chemical cross-linking and mass spectrometry. Current Opinion in Chemical Biology, (66) 102076

10.1016/j.plantsci.2021.111121 Yip Delormel T, Avila-Ospina L, Davanture M, Zivy M, Lang J, Valentin N, Rayapuram N, Hirt H, Colcombet J, Boudsocq M. (2021) In vivo identification of putative CPK5 substrates in Arabidopsis thaliana. Plant Science, (314) 111121

10.1007/s00216-016-0023-x Yu P, Hahne H, Wilhelm M, Kuster B. (2016) Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics. Analytical and Bioanalytical Chemistry, 4 (409) 1049-1057

10.1083/jcb.201910132 Zagryazhskaya-Masson A, Monteiro P, Macé AS, Castagnino A, Ferrari R, Infante E, Duperray-Susini A, Dingli F, Lanyi A, Loew D, Génot E, Chavrier P. (2020) Intersection of TKS5 and FGD1/CDC42 signaling cascades directs the formation of invadopodia. Journal of Cell Biology, 9 (219) e201910132

10.3389/fpls.2022.832246 Zang L, Tarkowski Łukasz P, Paven MCML, Zivy M, Balliau T, Clochard T, Bahut M, Balzergue S, Pelletier S, Landès C, Limami AM, Montrichard F. (2022) The Nitrate Transporter MtNPF6.8 Is a Master Sensor of Nitrate Signal in the Primary Root Tip of Medicago truncatula. Frontiers in Plant Science, (13) 832246

10.1002/pmic.201200017 Zhang W, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H. (2012) LFQuant: A label‐free fast quantitative analysis tool for high‐resolution LC‐MS/MS proteomics data. PROTEOMICS, 23-24 (12) 3475-3484

10.1038/s41598-018-27900-5 Zhao Y, Zurawel AA, Jenkins NP, Duennwald ML, Cheng C, Kettenbach AN, Supattapone S. (2018) Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species. Scientific Reports, 1 (8) 9554

10.1021/acs.jproteome.6b00752 Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE. (2016) Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers. Journal of Proteome Research, 2 (16) 720-727

10.3390/microorganisms10091808 da Luz BSR, de Rezende Rodovalho V, Nicolas A, Chabelskaya S, Jardin J, Briard-Bion V, Le Loir Y, de Carvalho Azevedo VA, Guédon Éric. (2022) Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles. Microorganisms, 9 (10) 1808

10.1016/j.foodhyd.2021.106787 de Figueiredo Furtado G, Ménard O, Yu X, Ossemond J, Henry G, Jardin J, Briard-Bion V, Deglaire A, Hubinger MD, Dupont D. (2021) In vitro dynamic digestion of model infant formulae containing lactoferrin and medium chain triacylglycerols. Food Hydrocolloids, (118) 106787

10.1128/aem.02263-20 de Rezende Rodovalho V, da Luz BSR, Nicolas A, do Carmo FLR, Jardin J, Briard-Bion V, Jan G, Le Loir Y, de Carvalho Azevedo VA, Guédon E. (2020) Environmental Conditions Modulate the Protein Content and Immunomodulatory Activity of Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii. Applied and Environmental Microbiology, 4 (87) e02263-20

10.1016/j.mib.2012.04.003 van de Guchte M, Chaze T, Jan G, Mistou MY. (2012) Properties of probiotic bacteria explored by proteomic approaches. Current Opinion in Microbiology, 3 (15) 381-389

10.1016/j.cell.2018.11.041 Żylicz JJ, Bousard A, Žumer K, Dossin F, Mohammad E, da Rocha ST, Schwalb B, Syx L, Dingli F, Loew D, Cramer P, Heard E. (2018) The Implication of Early Chromatin Changes in X Chromosome Inactivation. Cell, 1-2 (176) 182-197.e23

10.1016/j.idairyj.2018.06.016 Almi-Sebbane D, Adt I, Degraeve P, Jardin J, Bettler E, Terreux R, Oulahal N, Mati A. (2018) Casesidin-like anti-bacterial peptides in peptic hydrolysate of camel milk β-casein. International Dairy Journal, (86) 49-56

10.3390/plants9050591 Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. (2020) Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. Plants, 5 (9) 591

10.1101/2024.07.12.603247 Ashenafi M, Balliau T, Blein-Nicolas M, Turc O, Zivy M, Marchadier E. (2024) A moderate water deficit induces profound changes in the proteome of developing maize ovaries. bioRxiv, () 2024.07.12.603247

Ayaz A, Kothandaraman N, Henkel R, Sikka SC. (2018) Chapter 21 Impact of Environmental Factors on the Genomics and Proteomics Landscapes of Male Infertility. , () 335-353

10.1111/tpj.16810 Bahammou D, Recorbet G, Cassim AM, Robert F, Balliau T, Van Delft P, Haddad Y, Mongrand S, Fouillen L, Simon‐Plas F. (2024) A combined lipidomic and proteomic profiling of Arabidopsis thaliana plasma membrane. The Plant Journal, 3 (119) 1570-1595

10.3390/biom14101239 Balliau T, Ashenafi M, Blein-Nicolas M, Turc O, Zivy M, Marchadier E. (2024) A Moderate Water Deficit Induces Profound Changes in the Proteome of Developing Maize Ovaries. Biomolecules, 10 (14) 1239

10.3390/proteomes6010006 Balliau T, Blein-Nicolas M, Zivy M. (2018) Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes, 1 (6) 6

10.1051/ocl/2020074 Balliau T, Duruflé H, Blanchet N, Blein-Nicolas M, Langlade NB, Zivy M. (2021) Proteomic data from leaves of twenty-four sunflower genotypes under water deficit. OCL, (28) 12

10.3389/fpls.2019.00832 Bancel E, Bonnot T, Davanture M, Alvarez D, Zivy M, Martre P, Déjean S, Ravel C. (2019) Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. Frontiers in Plant Science, (10) 832

10.1021/acs.jproteome.0c00669 Bassignani A, Plancade S, Berland M, Blein-Nicolas M, Guillot A, Chevret D, Moritz C, Huet S, Rizkalla S, Clément K, Doré J, Langella O, Juste C. (2021) Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets. Journal of Proteome Research, 3 (20) 1522-1534

10.1002/glia.24570 Baudouin L, Adès N, Kanté K, Bachelin C, Hmidan H, Deboux C, Panic R, Messaoud RB, Velut Y, Hamada S, Pionneau C, Duarte K, Poëa‐Guyon S, Barnier JV, Oumesmar BN, Bouslama‐Oueghlani L. (2024) Antagonistic actions of PAK1 and NF2/Merlin drive myelin membrane expansion in oligodendrocytes. Glia, 8 (72) 1518-1540

10.3390/ijms23137059 Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. (2022) Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. International Journal of Molecular Sciences, 13 (23) 7059

10.3389/fmicb.2021.616050 Bednarz B, Millan-Oropeza A, Kotowska M, Świat M, Haro JJQ, Henry C, Pawlik K. (2021) Coelimycin Synthesis Activatory Proteins Are Key Regulators of Specialized Metabolism and Precursor Flux in Streptomyces coelicolor A3(2). Frontiers in Microbiology, (12) 616050

10.1104/pp.19.00086 Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat JP, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S. (2019) Modeling Protein Destiny in Developing Fruit. Plant Physiology, 3 (180) 1709-1724

10.1016/j.jprot.2018.10.003 Belouah I, Blein-Nicolas M, Balliau T, Gibon Y, Zivy M, Colombié S. (2018) Peptide filtering differently affects the performances of XIC-based quantification methods. Journal of Proteomics, (193) 131-141

10.1016/j.dib.2019.105015 Belouah I, Bénard C, Denton A, Blein-Nicolas M, Balliau T, Teyssier E, Gallusci P, Bouchez O, Usadel B, Zivy M, Gibon Y, Colombié S. (2019) Transcriptomic and proteomic data in developing tomato fruit. Data in Brief, (28) 105015

10.1016/j.jinf.2021.09.023 Ben Salah E, Barrera C, Sakly W, Mosbahi S, Balliau T, Franche N, Gottstein B, Ben Youssef S, Mekki M, Babba H, Millon L. (2021) Novel biomarkers for the early prediction of pediatric cystic echinococcosis post-surgical outcomes. Journal of Infection, 1 (84) 87-93

10.1007/s10886-018-1002-9 Bichang’a G, Da Lage JL, Capdevielle-Dulac C, Zivy M, Balliau T, Sambai K, Le Ru B, Kaiser L, Juma G, Maina ENM, Calatayud PA. (2018) α-Amylase Mediates Host Acceptance in the Braconid Parasitoid Cotesia flavipes. Journal of Chemical Ecology, 11 (44) 1030-1039

10.1016/j.csbj.2022.01.018 Blakeley-Ruiz JA, Kleiner M. (2022) Considerations for constructing a protein sequence database for metaproteomics. Computational and Structural Biotechnology Journal, (20) 937-952

10.1101/gr.255224.119 Blein-Nicolas M, Negro SS, Balliau T, Welcker C, Cabrera-Bosquet L, Nicolas SD, Charcosset A, Zivy M. (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Research, 11 (30) 1593-1604

10.1101/2024.03.13.582463 Bonnot T, Henriet C, Aimé D, Kreplak J, Térézol M, Balliau T, Ourry A, Zivy M, Vernoud V, Gallardo K. (2024) Molecular signatures and associated regulators of the pea leaf response to sulfur deficiency and water deficit as revealed by multi-omics analyses. bioRxiv, () 2024.03.13.582463

10.1128/aem.01292-21 Boulay M, Metton C, Mézange C, Correia LO, Meylheuc T, Monnet V, Gardan R, Juillard V. (2021) Three Distinct Proteases Are Responsible for Overall Cell Surface Proteolysis in Streptococcus thermophilus. Applied and Environmental Microbiology, 23 (87) e01292-21

10.3389/fmicb.2021.793136 Canon F, Briard-Bion V, Jardin J, Thierry A, Gagnaire V. (2022) Positive Interactions Between Lactic Acid Bacteria Could Be Mediated by Peptides Containing Branched-Chain Amino Acids. Frontiers in Microbiology, (12) 793136

10.1128/aem.02210-20 Cazalé AC, Blanquet P, Henry C, Pouzet C, Bruand C, Meilhoc E. (2020) Tyrosine Nitration of Flagellins: a Response of Sinorhizobium meliloti to Nitrosative Stress. Applied and Environmental Microbiology, 1 (87) e02210-20

10.3390/beverages9030081 Chasseriaud L, Albertin W, Blein-Nicolas M, Balliau T, Zivy M, Coulon J, Bely M. (2023) Physical Contact between Torulaspora delbrueckii and Saccharomyces cerevisiae Alters Cell Growth and Molecular Interactions in Grape Must. Beverages, 3 (9) 81

10.1104/pp.19.00338 Chauffour F, Bailly M, Perreau F, Cueff G, Suzuki H, Collet B, Frey A, Clément G, Soubigou-Taconnat L, Balliau T, Krieger-Liszkay A, Rajjou L, Marion-Poll A. (2019) Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. Plant Physiology, 2 (180) 1198-1218

10.1016/j.foodres.2023.112883 Chauvet L, Ménard O, Le Gouar Y, Henry G, Jardin J, Hennetier M, Croguennec T, Van Audenhaege M, Dupont D, Lemaire M, Le Huërou-Luron I, Deglaire A. (2023) Protein ingredient quality of infant formulas impacts their structure and kinetics of proteolysis under in vitro dynamic digestion. Food Research International, (169) 112883

10.1002/pmic.201800286 Cherkaoui M, Geairon A, Lollier V, San Clemente H, Larré C, Rogniaux H, Jamet E, Guillon F, Francin‐Allami M. (2018) Cell Wall Proteome Investigation of Bread Wheat (Triticum Aestivum) Developing Grain in Endosperm and Outer Layers. PROTEOMICS, 23 (18) e1800286

10.1016/j.foodchem.2022.133624 Cherkaoui M, Tessier D, Lollier V, Larré C, Brossard C, Dijk W, Rogniaux H. (2022) High-resolution mass spectrometry unveils the molecular changes of ovalbumin induced by heating and their influence on IgE binding capacity. Food Chemistry, (395) 133624

10.1016/j.scitotenv.2020.136834 Chetouhi C, Masseret E, Satta CT, Balliau T, Laabir M, Jean N. (2020) Intraspecific variability in membrane proteome, cell growth, and morphometry of the invasive marine neurotoxic dinoflagellate Alexandrium pacificum grown in metal-contaminated conditions. Science of The Total Environment, (715) 136834

10.1016/j.foodchem.2021.130747 Cosson A, Oliveira Correia L, Descamps N, Saint-Eve A, Souchon I. (2021) Identification and characterization of the main peptides in pea protein isolates using ultra high-performance liquid chromatography coupled with mass spectrometry and bioinformatics tools. Food Chemistry, (367) 130747

10.1111/nph.15751 Cui J, Davanture M, Zivy M, Lamade E, Tcherkez G. (2019) Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm. New Phytologist, 1 (223) 310-322

10.1016/j.plantsci.2020.110628 Cui J, Lamade E, Tcherkez G. (2020) Potassium deficiency reconfigures sugar export and induces catecholamine accumulation in oil palm leaves. Plant Science, (300) 110628

10.1016/j.foodchem.2018.12.086 Deglaire A, Oliveira SD, Jardin J, Briard-Bion V, Kroell F, Emily M, Ménard O, Bourlieu C, Dupont D. (2018) Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage. Food Chemistry, (281) 294-303

10.1038/s41559-023-02241-3 Delogu F, Kunath BJ, Queirós PM, Halder R, Lebrun LA, Pope PB, May P, Widder S, Muller EEL, Wilmes P. (2023) Forecasting the dynamics of a complex microbial community using integrated meta-omics. Nature Ecology & Evolution, 1 (8) 32-44

10.1371/journal.pone.0241903 Doan THD, Yen-Nicolaÿ S, Bernet-Camard MF, Martin-Verstraete I, Péchiné S. (2020) Impact of subinhibitory concentrations of metronidazole on proteome of Clostridioides difficile strains with different levels of susceptibility. PLOS ONE, 11 (15) e0241903

10.1038/s41467-022-31421-1 Domenzain I, Sánchez B, Anton M, Kerkhoven EJ, Millán-Oropeza A, Henry C, Siewers V, Morrissey JP, Sonnenschein N, Nielsen J. (2022) Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. Nature Communications, 1 (13) 3766

10.1016/j.dib.2021.106818 Douché T, Valot B, Balliau T, San Clemente H, Zivy M, Jamet E. (2021) Cell wall proteomic datasets of stems and leaves of Brachypodium distachyon. Data in Brief, (35) 106818

10.3390/microorganisms8101621 Dubrulle G, Picot A, Madec S, Corre E, Pawtowski A, Baroncelli R, Zivy M, Balliau T, Le Floch G, Pensec F. (2020) Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis. Microorganisms, 10 (8) 1621

10.3390/cells9102249 Duruflé H, Ranocha P, Balliau T, Zivy M, Albenne C, Burlat V, Déjean S, Jamet E, Dunand C. (2020) An Integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations of Arabidopsis thaliana: A Focus on Cell Wall Changes. Cells, 10 (9) 2249

10.1016/j.plantsci.2017.07.015 Duruflé H, Hervé V, Ranocha P, Balliau T, Zivy M, Chourré J, San Clemente H, Burlat V, Albenne C, Déjean S, Jamet E, Dunand C. (2017) Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: An integrative study. Plant Science, (263) 183-193

10.3390/biom13071110 Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. (2023) Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules, 7 (13) 1110

10.1016/j.dib.2019.104581 Duruflé H, Ranocha P, Balliau T, Dunand C, Jamet E. (2019) Transcriptomic and cell wall proteomic datasets of rosettes and floral stems from five Arabidopsis thaliana ecotypes grown at optimal or sub-optimal temperature. Data in Brief, (27) 104581

10.1007/s12602-021-09808-1 El Mecherfi KE, Lupi R, Cherkaoui M, Albuquerque MAC, Todorov SD, Tranquet O, Klingebiel C, Rogniaux H, Denery-Papini S, Onno B, de Melo Franco BDG, Larré C. (2021) Fermentation of Gluten by Lactococcus lactis LLGKC18 Reduces its Antigenicity and Allergenicity. Probiotics and Antimicrobial Proteins, 5 (14) 779-791

10.3389/fpls.2021.644810 Fabre F, Urbach S, Roche S, Langin T, Bonhomme L. (2021) Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. Frontiers in Plant Science, (12) 644810

10.1111/pce.13549 Fabre F, Vignassa M, Urbach S, Langin T, Bonhomme L. (2019) Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism. Plant, Cell & Environment, 7 (42) 2291-2308

10.3389/fmicb.2019.02857 Fabre F, Bormann J, Urbach S, Roche S, Langin T, Bonhomme L. (2019) Unbalanced Roles of Fungal Aggressiveness and Host Cultivars in the Establishment of the Fusarium Head Blight in Bread Wheat. Frontiers in Microbiology, (10) 2857

10.1016/j.isci.2023.106056 Fernandes P, Loubens M, Marinach C, Coppée R, Baron L, Grand M, Andre TP, Hamada S, Langlois AC, Briquet S, Bun P, Silvie O. (2023) Plasmodium sporozoites require the protein B9 to invade hepatocytes. iScience, 2 (26) 106056

10.1016/j.ijbiomac.2024.134216 Freitas ADS, Barroso FAL, Campos GM, Américo MF, Viegas RCDS, Gomes GC, Vital KD, Fernandes SOA, Carvalho RDO, Jardin J, Miranda APGDS, Ferreira E, Martins FS, Laguna JG, Jan G, Azevedo V, de Jesus LCL. (2024) Exploring the anti-inflammatory effects of postbiotic proteins from Lactobacillus delbrueckii CIDCA 133 on inflammatory bowel disease model. International Journal of Biological Macromolecules, Pt 2 (277) 134216

10.3389/fnut.2022.888179 Gagnaire V, Lecomte X, Richoux R, Genay M, Jardin J, Briard-Bion V, Kerjean JR, Thierry A. (2022) Little Impact of NaCl Reduction in Swiss-Type Cheese. Frontiers in Nutrition, (9) 888179

10.1093/bib/bbab330 Galata V, Busi SB, Kunath BJ, de Nies L, Calusinska M, Halder R, May P, Wilmes P, Laczny CC. (2021) Functional meta-omics provide critical insights into long- and short-read assemblies. Briefings in Bioinformatics, 6 (22) bbab330

10.1002/jex2.103 Galio L, Bernet L, Rodriguez Y, Fourcault C, Dieudonné MN, Pinatel H, Henry C, Sérazin V, Fathallah K, Gagneux A, Krupova Z, Vialard F, Dos Santos E. (2023) The effect of obesity on uterine receptivity is mediated by endometrial extracellular vesicles that control human endometrial stromal cell decidualization and trophoblast invasion. Journal of Extracellular Biology, 7 (2) e103

10.1016/j.ijfoodmicro.2020.108574 Garnier L, Penland M, Thierry A, Maillard MB, Jardin J, Coton M, Leyva Salas M, Coton E, Valence F, Mounier J. (2020) Antifungal activity of fermented dairy ingredients: Identification of antifungal compounds. International Journal of Food Microbiology, (322) 108574

10.3389/fmicb.2019.02324 Gaucher F, Kponouglo K, Rabah H, Bonnassie S, Ossemond J, Pottier S, Jardin J, Briard-Bion V, Marchand P, Blanc P, Jeantet R, Jan G. (2019) Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying. Frontiers in Microbiology, (10) 2324

10.1371/journal.pone.0208160 Gaurivaud P, Ganter S, Villard A, Manso-Silvan L, Chevret D, Boulé C, Monnet V, Tardy F. (2018) Mycoplasmas are no exception to extracellular vesicles release: Revisiting old concepts. PLOS ONE, 11 (13) e0208160

10.3390/plants12030526 Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Ouertani RN, Riahi J, de Oliveira AC, Abid G, Muhovski Y. (2023) Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley (Hordeum vulgare L.). Plants, 3 (12) 526

10.1016/j.foodchem.2024.140886 Giribaldi M, Nebbia S, Briard-Bion V, Jardin J, Ménard O, Dupont D, Coscia A, Cresi F, Lamberti C, Cavallarin L, Deglaire A. (2024) Peptidomic profile of human milk as influenced by fortification with different protein sources: An in vitro dynamic digestion simulation. Food Chemistry, (462) 140886

10.1016/j.foodchem.2021.130998 Giribaldi M, Nebbia S, Briard-Bion V, Jardin J, Peila C, Coscia A, Dupont D, Cavallarin L, Deglaire A. (2021) Simulated dynamic digestion reveals different peptide releases from human milk processed by means of holder or high temperature-short time pasteurization. Food Chemistry, (369) 130998

10.48550/arxiv.2405.07772 Gornard S, Venon P, Lasfont F, Balliau T, Kaiser-Arnauld LMP, Mougel F. (2024) Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic. arXiv, ()

10.1186/s12864-024-10694-4 Gornard S, Venon P, Lasfont F, Balliau T, Kaiser L, Mougel F. (2024) Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic. BMC Genomics, 1 (25) 940

10.3389/fmicb.2017.01465 Guilbaud M, Bruzaud J, Bouffartigues E, Orange N, Guillot A, Aubert-Frambourg A, Monnet V, Herry JM, Chevalier S, Bellon-Fontaine MN. (2017) Proteomic Response of Pseudomonas aeruginosa PAO1 Adhering to Solid Surfaces. Frontiers in Microbiology, (8) 1465

10.3390/plants11243554 Guillou MC, Balliau T, Vergne E, Canut H, Chourré J, Herrera-León C, Ramos-Martín F, Ahmadi-Afzadi M, D’Amelio N, Ruelland E, Zivy M, Renou JP, Jamet E, Aubourg S. (2022) The PROSCOOP10 Gene Encodes Two Extracellular Hydroxylated Peptides and Impacts Flowering Time in Arabidopsis. Plants, 24 (11) 3554

10.3389/fimmu.2022.827712 Gérard C, Thébault M, Lamarthée B, Genet C, Cattin F, Brazdova A, Janikashvili N, Cladière C, Ciudad M, Ouandji S, Ghesquière T, Greigert H, Tinel C, Adotevi O, Saas P, Samson M, Audia S, Bonnotte B. (2022) Human Monocyte-Derived Suppressor Cell Supernatant Induces Immunoregulatory Effects and Mitigates xenoGvHD. Frontiers in Immunology, (13) 827712

10.1093/jxb/erx482 Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C. (2018) Increases in activity of proteasome and papain-like cysteine protease in Arabidopsis autophagy mutants: back-up compensatory effect or cell-death promoting effect?. Journal of Experimental Botany, 6 (69) 1369-1385

10.1093/jxb/eraa571 Henriet C, Balliau T, Aimé D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. (2021) Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. Journal of Experimental Botany, 7 (72) 2611-2626

10.3389/fmicb.2019.01329 Henry C, Haller L, Blein-Nicolas M, Zivy M, Canette A, Verbrugghe M, Mézange C, Boulay M, Gardan R, Samson S, Martin V, André-Leroux G, Monnet V. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Frontiers in Microbiology, (10) 1329

10.3390/cells11081340 Henry C, Bassignani A, Berland M, Langella O, Sokol H, Juste C. (2022) Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells, 8 (11) 1340

10.1111/mmi.14948 Hogrel G, Marino‐Puertas L, Laurent S, Ibrahim Z, Covès J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet‐d'Orval B, Basta T, Flament D, Franzetti B. (2022) Characterization of a small tRNA‐binding protein that interacts with the archaeal proteasome complex. Molecular Microbiology, 1-2 (118) 16-29

10.15252/embr.202152476 Hollenstein DM, Gérecová G, Romanov N, Ferrari J, Veis J, Janschitz M, Beyer R, Schüller C, Ogris E, Hartl M, Ammerer G, Reiter W. (2021) A phosphatase-centric mechanism drives stress signaling response. The EMBO Reports, 11 (22) embr202152476

10.3389/fmicb.2018.02548 Huang S, Gaucher F, Cauty C, Jardin J, Le Loir Y, Jeantet R, Chen XD, Jan G. (2018) Growth in Hyper-Concentrated Sweet Whey Triggers Multi Stress Tolerance and Spray Drying Survival in Lactobacillus casei BL23: From the Molecular Basis to New Perspectives for Sustainable Probiotic Production. Frontiers in Microbiology, (9) 2548

10.1093/jxb/erae417 James M, Masclaux-Daubresse C, Balliau T, Marmagne A, Chardon F, Trouverie J, Etienne P. (2024) Multi-scale phenotyping of senescence-related changes in roots of rapeseed in response to nitrate limitation. Journal of Experimental Botany, 2 (76) 312-330

10.1101/2024.04.03.587968 James M, Masclaux-Daubresse C, Balliau T, Marmagne A, Chardon F, Trouverie J, Etienne P. (2024) Multi-scale phenotyping of senescence-related changes in roots of Rapeseed in response to nitrogen deficiency. bioRxiv, () 2024.04.03.587968

10.1111/ppl.70287 James M, Masclaux‐Daubresse C, Goux D, Jing L, Etienne P, Trouverie J. (2025) The Taproot Acts as a Storage Organ During Rapeseed Vernalization. Physiologia Plantarum, 3 (177) e70287

10.1016/j.fm.2022.104042 Jan G, Tarnaud F, Rosa do Carmo FL, Illikoud N, Canon F, Jardin J, Briard-Bion V, Guyomarc'h F, Gagnaire V. (2022) The stressing life of Lactobacillus delbrueckii subsp. bulgaricus in soy milk. Food Microbiology, (106) 104042

10.1016/j.scitotenv.2021.151680 Jean N, Perié L, Dumont E, Bertheau L, Balliau T, Caruana AMN, Amzil Z, Laabir M, Masseret E. (2021) Metal stresses modify soluble proteomes and toxin profiles in two Mediterranean strains of the distributed dinoflagellate Alexandrium pacificum. Science of The Total Environment, (818) 151680

10.1016/j.marpolbul.2024.117221 Jean N, James A, Balliau T, Martino C, Ghersy J, Savar V, Laabir M, Caruana AMN. (2024) Warming and polymetallic stress induce proteomic and physiological shifts in the neurotoxic Alexandrium pacificum as possible response to global changes. Marine Pollution Bulletin, Pt B (209) 117221

10.1016/j.jprot.2017.09.005 Jolivet P, Aymé L, Giuliani A, Wien F, Chardot T, Gohon Y. (2017) Structural proteomics: Topology and relative accessibility of plant lipid droplet associated proteins. Journal of Proteomics, (169) 87-98

10.3168/jds.2018-15548 Jrad Z, El-Hatmi H, Adt I, Gouin S, Jardin J, Oussaief O, Dbara M, Arroum S, Khorchani T, Degraeve P, Oulahal N. (2019) Antilisterial activity of dromedary lactoferrin peptic hydrolysates. Journal of Dairy Science, 6 (102) 4844-4856

10.1021/acs.jafc.4c00468 Kasikci MB, Guilois-Dubois S, Billet K, Jardin J, Guyot S, Morzel M. (2024) Interactions between Salivary Proteins and Apple Polyphenols and the Fate of Complexes during Gastric Digestion. Journal of Agricultural and Food Chemistry, 16 (72) 9179-9189

10.1371/journal.pone.0177569 Kepplinger D, Takhar M, Sasaki M, Hollander Z, Smith D, McManus B, McMaster WR, Ng RT, Freue GVC. (2017) PGCA: An algorithm to link protein groups created from MS/MS data. PLOS ONE, 5 (12) e0177569

10.1016/j.jprot.2019.103580 Kilani J, Davanture M, Simon A, Zivy M, Fillinger S. (2019) Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways. Journal of Proteomics, (212) 103580

10.1142/s021972001740011x Kiseleva O, Poverennaya E, Shargunov A, Lisitsa A. (2018) Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night. Journal of Bioinformatics and Computational Biology, 01 (16) 1740011

10.3389/fpls.2021.765846 Kolkas H, Balliau T, Chourré J, Zivy M, Canut H, Jamet E. (2022) The Cell Wall Proteome of Marchantia polymorpha Reveals Specificities Compared to Those of Flowering Plants. Frontiers in Plant Science, (12) 765846

10.1016/j.idairyj.2024.106104 Krupova Z, Reyre M, Ye T, Gallier S, Martin P, Leroux C. (2025) Extracellular vesicles carrying significant amounts of microRNAs are present in goat milk powders. International Dairy Journal, (160) 106104

10.1021/acs.jproteome.3c00732 Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. (2024) Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. Journal of Proteome Research, 8 (23) 3353-3366

10.1021/jasms.0c00402 Langella O, Rusconi F. (2021) mineXpert2: Full-Depth Visualization and Exploration of MS n Mass Spectrometry Data. Journal of the American Society for Mass Spectrometry, 4 (32) 1138-1141

10.1039/d3fo02693k Lavoisier A, Morzel M, Chevalier S, Henry G, Jardin J, Harel-Oger M, Garric G, Dupont D. (2023) In vitro digestion of two protein-rich dairy products in the ageing gastrointestinal tract. Food & Function, 20 (14) 9377-9390

10.1016/j.tjnut.2023.08.003 Le Guillou S, Ciobotaru C, Laubier J, Castille J, Aujean E, Hue-Beauvais C, Cherbuy C, Liuu S, Henry C, David A, Jaffrezic F, Laloë D, Charlier M, Alexandre-Gouabau MC, Le Provost F. (2023) Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth. The Journal of Nutrition, 10 (153) 2808-2826

10.3390/ijms21197400 Le Ribeuz H, Dumont F, Ruellou G, Lambert M, Balliau T, Quatredeniers M, Girerd B, Cohen-Kaminsky S, Mercier O, Yen-Nicolaÿ S, Humbert M, Montani D, Capuano V, Antigny F. (2020) Proteomic Analysis of KCNK3 Loss of Expression Identified Dysregulated Pathways in Pulmonary Vascular Cells. International Journal of Molecular Sciences, 19 (21) 7400

10.3389/fphar.2022.993449 Lebeau RH, Mendez-David I, Kucynski-Noyau L, Henry C, Attali D, Plaze M, Colle R, Corruble E, Gardier AM, Gaillard R, Guilloux JP, David DJ. (2022) Peripheral proteomic changes after electroconvulsive seizures in a rodent model of non-response to chronic fluoxetine. Frontiers in Pharmacology, (13) 993449

10.1038/s41598-022-21804-1 Leduc A, Le Guillou S, Bianchi L, Correia LO, Gelé M, Pires J, Martin P, Leroux C, Le Provost F, Boutinaud M. (2022) Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows. Scientific Reports, 1 (12) 18886

10.3390/toxins14040249 Lefebvre D, Blanco-Valle K, Hennekinne JA, Simon S, Fenaille F, Becher F, Nia Y. (2022) Multiplex Detection of 24 Staphylococcal Enterotoxins in Culture Supernatant Using Liquid Chromatography Coupled to High-Resolution Mass Spectrometry. Toxins, 4 (14) 249

10.1186/s12859-019-2980-5 Li C, Li K, Li K, Lin F. (2019) MCtandem: an efficient tool for large-scale peptide identification on many integrated core (MIC) architecture. BMC Bioinformatics, 1 (20) 397

10.3390/ijms23010550 Malleck T, Fekraoui F, Bornard I, Henry C, Haudebourg E, Planchon S, Broussolle V. (2022) Insights into the Structure and Protein Composition of Moorella thermoacetica Spores Formed at Different Temperatures. International Journal of Molecular Sciences, 1 (23) 550

10.1021/acs.jproteome.7b00194 Martín-Campos T, Mylonas R, Masselot A, Waridel P, Petricevic T, Xenarios I, Quadroni M. (2017) MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications. Journal of Proteome Research, 8 (16) 3092-3101

10.1002/pmic.202400242 Marzano V, Mortera SL, Putignani L. (2024) Insights on Wet and Dry Workflows for Human Gut Metaproteomics. PROTEOMICS, () e202400242

10.3390/ijms21010239 Mehdi C, Virginie L, Audrey G, Axelle B, Colette L, Hélène R, Elisabeth J, Fabienne G, Mathilde FA. (2019) Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development. International Journal of Molecular Sciences, 1 (21) 239

10.3389/fncel.2017.00237 Mendez-David I, Boursier C, Domergue V, Colle R, Falissard B, Corruble E, Gardier AM, Guilloux JP, David DJ. (2017) Differential Peripheral Proteomic Biosignature of Fluoxetine Response in a Mouse Model of Anxiety/Depression. Frontiers in Cellular Neuroscience, (11) 237

10.1038/s41598-020-65087-w Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. (2020) Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Scientific Reports, 1 (10) 8492

10.1021/acs.jproteome.7b00163 Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. (2017) Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. Journal of Proteome Research, 7 (16) 2597-2613

10.20944/preprints202112.0212.v1 Millán-Oropeza A, Blein-Nicolas M, Monnet V, Zivy M, Henry C. (2021) Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Preprints.org, () 202112.0212.v1

10.3390/proteomes10010002 Millán-Oropeza A, Blein-Nicolas M, Monnet V, Zivy M, Henry C. (2022) Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes, 1 (10) 2

10.1016/j.envexpbot.2020.104062 Mirande-Ney C, Tcherkez G, Balliau T, Zivy M, Gilard F, Cui J, Ghashghaie J, Lamade E. (2020) Metabolic leaf responses to potassium availability in oil palm (Elaeis guineensis Jacq.) trees grown in the field. Environmental and Experimental Botany, (175) 104062

10.3390/biology14050525 Mouawad C, Awad MK, Rodrigues-Machado C, Henry C, Sanchis-Borja V, Chamy LE. (2025) High-Throughput Analysis of the Flagella FliK-Dependent Surfaceome and Secretome in Bacillus thuringiensis. Biology, 5 (14) 525

10.1038/s41598-023-49724-8 Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. (2023) Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Scientific Reports, 1 (13) 22785

10.1128/msystems.01237-20 Nicoud Q, Lamouche F, Chaumeret A, Balliau T, Le Bars R, Bourge M, Pierre F, Guérard F, Sallet E, Tuffigo S, Pierre O, Dessaux Y, Gilard F, Gakière B, Nagy I, Kereszt A, Zivy M, Mergaert P, Gourion B, Alunni B. (2021) Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems, 3 (6) 10.1128/msystems.01237-20

10.21203/rs.3.rs-1949552/v1 Onésime D, Vidal L, Thomas S, Henry C, Martin V, André G, Kubiak P, Minard P, Celinska E, Nicaud JM. (2022) A novel, unique four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica. Research Square, ()

10.1186/s12934-022-01925-y Onésime D, Vidal L, Thomas S, Henry C, Martin V, André G, Kubiak P, Minard P, Celinska E, Nicaud JM. (2022) A unique, newly discovered four-member protein family involved in extracellular fatty acid binding in Yarrowia lipolytica. Microbial Cell Factories, 1 (21) 200

10.3390/foods9101415 Ozorio L, Mellinger-Silva C, Cabral LMC, Jardin J, Boudry G, Dupont D. (2020) The Influence of Peptidases in Intestinal Brush Border Membranes on the Absorption of Oligopeptides from Whey Protein Hydrolysate: An Ex Vivo Study Using an Ussing Chamber. Foods, 10 (9) 1415

10.3390/foods11162429 Peslerbes M, Fellenberg A, Jardin J, Deglaire A, Ibáñez RA. (2022) Manufacture of Whey Protein Hydrolysates Using Plant Enzymes: Effect of Processing Conditions and Simulated Gastrointestinal Digestion on Angiotensin-I-Converting Enzyme (ACE) Inhibitory Activity. Foods, 16 (11) 2429

10.7717/peerj.13525 Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. (2022) A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation. PeerJ, (10) e13525

10.3389/fmicb.2019.00906 Proust L, Sourabié A, Pedersen M, Besançon I, Haudebourg E, Monnet V, Juillard V. (2019) Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus. Frontiers in Microbiology, (10) 906

10.1128/aem.01446-20 Proust L, Haudebourg E, Sourabié A, Pedersen M, Besançon I, Monnet V, Juillard V. (2020) Multi-omics Approach Reveals How Yeast Extract Peptides Shape Streptococcus thermophilus Metabolism. Applied and Environmental Microbiology, 22 (86) e01446-20

10.1101/2024.02.02.578547 Przybyla-Toscano J, Chetouhi C, Balliau T, Alban C, Bourguignon J, Ravanel S. (2024) Dynamics of the membrane- and cell wall-associated proteome of Arabidopsis thaliana roots in response to uranium stress. bioRxiv, () 2024.02.02.578547

10.1016/j.chemosphere.2024.143873 Przybyla-Toscano J, Chetouhi C, Pennera L, Boursiac Y, Galeone A, Devime F, Balliau T, Santoni V, Bourguignon J, Alban C, Ravanel S. (2024) New insights into uranium stress responses of Arabidopsis roots through membrane- and cell wall-associated proteome analysis. Chemosphere, (370) 143873

10.3390/ijms21218065 Rabani V, Lagoutte-Renosi J, Series J, Valot B, Xuereb JM, Davani S. (2020) Cholesterol-Rich Microdomains Contribute to PAR1 Signaling in Platelets Despite a Weak Localization of the Receptor in These Microdomains. International Journal of Molecular Sciences, 21 (21) 8065

10.1016/j.fgb.2021.103517 Recorbet G, Calabrese S, Balliau T, Zivy M, Wipf D, Boller T, Courty PE. (2021) Proteome adaptations under contrasting soil phosphate regimes of Rhizophagus irregularis engaged in a common mycorrhizal network. Fungal Genetics and Biology, (147) 103517

10.1093/jxb/erx355 Regente M, Pinedo M, San Clemente H, Balliau T, Jamet E, de la Canal L. (2017) Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth. Journal of Experimental Botany, 20 (68) 5485-5495

10.1016/j.molcel.2018.02.018 Repetto MV, Winters MJ, Bush A, Reiter W, Hollenstein DM, Ammerer G, Pryciak PM, Colman-Lerner A. (2018) CDK and MAPK Synergistically Regulate Signaling Dynamics via a Shared Multi-site Phosphorylation Region on the Scaffold Protein Ste5. Molecular Cell, 6 (69) 938-952.e6

10.1093/femsyr/foz088 Ridder M, Daran-Lapujade P, Pabst M. (2019) Shot-gun proteomics: why thousands of unidentified signals matter. FEMS Yeast Research, 1 (20) foz088

10.1016/j.jim.2017.07.012 Rouzet A, Reboux G, Dalphin JC, Gondouin A, De Vuyst P, Balliau T, Millon L, Valot B, Roussel S. (2017) An immunoproteomic approach revealed antigenic proteins enhancing serodiagnosis performance of bird fancier's lung. Journal of Immunological Methods, (450) 58-65

10.2174/1389203722666210118160946 Rusconi F. (2021) Free Open Source Software for Protein and Peptide Mass Spectrometry-based Science. Current Protein & Peptide Science, 2 (22) 134-147

10.1021/acs.jproteome.9b00099 Rusconi F. (2019) mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability. Journal of Proteome Research, 5 (18) 2254-2259

10.1111/tpj.16763 Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange‐Macherel MH, Macherel D. (2024) Multi‐scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy‐transducing organelles. The Plant Journal, 1 (119) 300-331

10.3389/fpls.2022.867263 Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. (2022) Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. Frontiers in Plant Science, (13) 867263

10.1021/acs.jproteome.1c00685 Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Van Den Bossche T. (2022) Pout2Prot: An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files. Journal of Proteome Research, 4 (21) 1175-1180

10.3389/fpls.2022.988709 Schilling M, Maia-Grondard A, Baltenweck R, Robert E, Hugueney P, Bertsch C, Farine S, Gelhaye E. (2022) Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches. Frontiers in Plant Science, (13) 988709

10.21203/rs.3.rs-3177442/v1 Silva TF, Glória RA, Sousa TJ, Americo MF, Freitas AS, Viana MVC, de Jesus LCL, Prado LCS, Daniel N, Ménard O, Cochet MF, Dupont D, Jardin J, Borges AD, Fernandes SOA, Cardoso VN, Brenig B, Ferreira E, Profeta R, Aburjaile FF, Carvalho RDO, Langella P, Loir YL, Cherbuy C, Jan G, Azevedo V, Guédon Éric. (2023) Comprehensive Probiogenomics Analysis of the Commensal Escherichia Coli CEC15 as a Potential Probiotic Strain. Research Square, ()

10.1111/1462-2920.16256 Smedile F, Foustoukos DI, Patwardhan S, Mullane K, Schlegel I, Adams MW, Schut GJ, Giovannelli D, Vetriani C. (2022) Adaptations to high pressure of Nautilia sp. strain PV‐1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep‐sea hydrothermal vent. Environmental Microbiology, 12 (24) 6164-6183

10.1371/journal.pone.0174060 Souza RFS, Jardin J, Cauty C, Rault L, Bouchard DS, Bermúdez-Humarán LG, Langella P, Monedero V, Seyffert N, Azevedo V, Le Loir Y, Even S. (2017) Contribution of sortase SrtA2 to Lactobacillus casei BL23 inhibition of Staphylococcus aureus internalization into bovine mammary epithelial cells. PLOS ONE, 3 (12) e0174060

10.1126/science.abm6380 Spaan AN, Neehus AL, Laplantine E, Staels F, Ogishi M, Seeleuthner Y, Rapaport F, Lacey KA, Van Nieuwenhove E, Chrabieh M, Hum D, Migaud M, Izmiryan A, Lorenzo L, Kochetkov T, Heesterbeek DAC, Bardoel BW, DuMont AL, Dobbs K, Chardonnet S, Heissel S, Baslan T, Zhang P, Yang R, Bogunovic D, Wunderink HF, Haas PJA, Molina H, Van Buggenhout G, Lyonnet S, Notarangelo LD, Seppänen MRJ, Weil R, Seminario G, Gomez-Tello H, Wouters C, Mesdaghi M, Shahrooei M, Bossuyt X, Sag E, Topaloglu R, Ozen S, Leavis HL, van Eijk MMJ, Bezrodnik L, Blancas Galicia L, Hovnanian A, Nassif A, Bader-Meunier B, Neven B, Meyts I, Schrijvers R, Puel A, Bustamante J, Aksentijevich I, Kastner DL, Torres VJ, Humblet-Baron S, Liston A, Abel L, Boisson B, Casanova JL. (2022) Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin. Science (New York, N.Y.), 6599 (376) eabm6380

10.1038/s42003-023-05574-8 Stander EA, Lehka B, Carqueijeiro I, Cuello C, Hansson FG, Jansen HJ, Dugé De Bernonville T, Birer Williams C, Vergès V, Lezin E, Lorensen MDBB, Dang TT, Oudin A, Lanoue A, Durand M, Giglioli-Guivarc’h N, Janfelt C, Papon N, Dirks RP, O’connor SE, Jensen MK, Besseau S, Courdavault V. (2023) The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids. Communications Biology, 1 (6) 1197

10.1016/j.foodchem.2024.140260 Suwareh O, Causeur D, Le Feunteun S, Jardin J, Briard-Bion V, Pezennec S, Nau F. (2024) Peptide bonds cleaved by pepsin are affected by the morphology of heat-induced ovalbumin aggregates. Food Chemistry, (458) 140260

10.1016/j.foodchem.2021.130098 Suwareh O, Causeur D, Jardin J, Briard-Bion V, Le Feunteun S, Pezennec S, Nau F. (2021) Statistical modeling of in vitro pepsin specificity. Food Chemistry, (362) 130098

10.1016/j.foodres.2024.114416 Suárez SE, Rabesona H, Ménard O, Jardin J, Anton M, Cristina Añón M. (2024) Dynamic digestion of a high protein beverage based on amaranth: Structural changes and antihypertensive activity. Food Research International, (187) 114416

10.1109/ispa/iucc.2017.00190 Tang J, Yang Y. (2017) Protein Quantitative Based on Simulated Annealing Algorithm. , () 1256-1260

10.1016/j.plaphy.2023.108213 Tarkowski Łukasz P, Clochard T, Blein-Nicolas M, Zivy M, Baillau T, Abadie C, Morère-Le Paven MC, Limami AM, Tcherkez G, Montrichard F. (2023) The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip. Plant Physiology and Biochemistry, (206) 108213

10.3389/fmicb.2020.549027 Tarnaud F, Gaucher F, do Carmo FLR, Illikoud N, Jardin J, Briard-Bion V, Guyomarc’h F, Gagnaire V, Jan G. (2020) Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA129 to Cow’s Milk Versus Soymilk Environments Modulates Its Stress Tolerance and Proteome. Frontiers in Microbiology, (11) 549027

10.1038/s41598-020-64952-y Tartaglia NR, Nicolas A, Rodovalho VR, Luz BSR, Briard-Bion V, Krupova Z, Thierry A, Coste F, Burel A, Martin P, Jardin J, Azevedo V, Le Loir Y, Guédon E. (2020) Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome. Scientific Reports, 1 (10) 8467

10.3389/fcimb.2018.00277 Tartaglia NR, Breyne K, Meyer E, Cauty C, Jardin J, Chrétien D, Dupont A, Demeyere K, Berkova N, Azevedo V, Guédon E, Le Loir Y. (2018) Staphylococcus aureus Extracellular Vesicles Elicit an Immunostimulatory Response in vivo on the Murine Mammary Gland. Frontiers in Cellular and Infection Microbiology, (8) 277

10.1016/j.plantsci.2019.110352 Tcherkez G, Carroll A, Abadie C, Mainguet S, Davanture M, Zivy M. (2019) Protein synthesis increases with photosynthesis via the stimulation of translation initiation. Plant Science, New Phytol. 214 2017 (291) 110352

10.21203/rs.3.rs-2591494/v1 Urrutia M, Blein-Nicolas M, Fernandez O, Bernillon S, Maucourt M, Deborde C, Balliau T, Rabier D, Bénard C, Prigent S, Quillere I, Jacob D, Gibon Y, Zivy M, Giauffret C, Hirel B, Moing A. (2023) Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids. Research Square, ()

10.1111/pce.13993 Urrutia M, Blein‐Nicolas M, Prigent S, Bernillon S, Deborde C, Balliau T, Maucourt M, Jacob D, Ballias P, Bénard C, Sellier H, Gibon Y, Giauffret C, Zivy M, Moing A. (2021) Maize metabolome and proteome responses to controlled cold stress partly mimic early‐sowing effects in the field and differ from those of Arabidopsis. Plant, Cell & Environment, 5 (44) 1504-1521

10.1002/prca.201700010 Valot B, Rognon B, Prenel A, Baraquin A, Knapp J, Anelli M, Richou C, Bresson‐Hadni S, Grenouillet F, Wang J, Vuitton DA, Gottstein B, Millon L. (2017) Screening of antigenic vesicular fluid proteins of Echinococcus multilocularis as potential viability biomarkers to monitor drug response in alveolar echinococcosis patients. PROTEOMICS – Clinical Applications, 11-12 (11)

10.1038/s41467-021-27542-8 Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen M, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. (2021) Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 1 (12) 7305

10.3390/proteomes5030019 Villegente M, Marmey P, Job C, Galland M, Cueff G, Godin B, Rajjou L, Balliau T, Zivy M, Fogliani B, Sarramegna-Burtet V, Job D. (2017) A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda. Proteomes, 3 (5) 19

10.1038/s41564-024-01609-w Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (2024) (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nature Microbiology, 3 (9) 647-656

10.1016/j.chembiol.2018.02.007 Wang PH, Khusnutdinova AN, Luo F, Xiao J, Nemr K, Flick R, Brown G, Mahadevan R, Edwards EA, Yakunin AF. (2018) Biosynthesis and Activity of Prenylated FMN Cofactors. Cell Chemical Biology, 5 (25) 560-570.e6

10.1016/j.foodres.2022.112112 Wang J, Ossemond J, Jardin J, Briard-Bion V, Henry G, Le Gouar Y, Ménard O, Lê S, Madadlou A, Dupont D, Pédrono F. (2022) Encapsulation of DHA oil with heat-denatured whey protein in Pickering emulsion improves its bioaccessibility. Food Research International, Pt B (162) 112112

10.3390/ijms23169352 Wang X, Davanture M, Zivy M, Bailly C, Nambara E, Corbineau F. (2022) Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. International Journal of Molecular Sciences, 16 (23) 9352

10.3389/fpls.2022.832246 Zang L, Tarkowski Łukasz P, Paven MCML, Zivy M, Balliau T, Clochard T, Bahut M, Balzergue S, Pelletier S, Landès C, Limami AM, Montrichard F. (2022) The Nitrate Transporter MtNPF6.8 Is a Master Sensor of Nitrate Signal in the Primary Root Tip of Medicago truncatula. Frontiers in Plant Science, (13) 832246

10.1128/aem.02959-20 Zhang B, Lingga C, Bowman C, Hackmann TJ. (2021) A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. Applied and Environmental Microbiology, 14 (87) e02959-20

10.1111/tpj.14461 Zhang W, Cochet F, Ponnaiah M, Lebreton S, Matheron L, Pionneau C, Boudsocq M, Resentini F, Huguet S, Blázquez M, Bailly C, Puyaubert J, Baudouin E. (2019) The MPK8‐TCP14 pathway promotes seed germination in Arabidopsis. The Plant Journal, 4 (100) 677-692

10.1038/s41598-023-43282-9 Zhang B, Lingga C, De Groot H, Hackmann TJ. (2023) The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella. Scientific Reports, 1 (13) 16429

10.1101/2024.05.17.594647 Zhang X, Ling T, Jin Z, Xu S, Gao Z, Sun B, Qiu Z, Dong N, Wang G, Wang G, Li L, Abdul-Mageed M, Lakshmanan LVS, Ouyang W, Chang C, Sun S. (2024) π-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing. bioRxiv, () 2024.05.17.594647

10.1038/s41467-024-55021-3 Zhang X, Ling T, Jin Z, Xu S, Gao Z, Sun B, Qiu Z, Wei J, Dong N, Wang G, Wang G, Li L, Abdul-Mageed M, Lakshmanan LVS, He F, Ouyang W, Chang C, Sun S. (2025) π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing. Nature Communications, 1 (16) 267

10.1016/j.talanta.2025.128055 Zohouri D, Mai TD, Reyre M, Smadja C, Krupova Z, Talbot L, Taverna M. (2025) Elucidation of extracellular vesicles behavior during capillary isoelectric focusing. Talanta, (293) 128055

10.3390/microorganisms10091808 da Luz BSR, de Rezende Rodovalho V, Nicolas A, Chabelskaya S, Jardin J, Briard-Bion V, Le Loir Y, de Carvalho Azevedo VA, Guédon Éric. (2022) Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles. Microorganisms, 9 (10) 1808

10.1186/s12866-023-03112-4 da Silva TF, Glória RA, de Sousa TJ, Americo MF, Freitas AS, Viana MVC, de Jesus LCL, da Silva Prado LC, Daniel N, Ménard O, Cochet MF, Dupont D, Jardin J, Borges AD, Fernandes SOA, Cardoso VN, Brenig B, Ferreira E, Profeta R, Aburjaile FF, de Carvalho RDO, Langella P, Le Loir Y, Cherbuy C, Jan G, Azevedo V, Guédon Éric. (2023) Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain. BMC Microbiology, 1 (23) 364

10.1016/j.foodhyd.2021.106787 de Figueiredo Furtado G, Ménard O, Yu X, Ossemond J, Henry G, Jardin J, Briard-Bion V, Deglaire A, Hubinger MD, Dupont D. (2021) In vitro dynamic digestion of model infant formulae containing lactoferrin and medium chain triacylglycerols. Food Hydrocolloids, (118) 106787

10.7554/elife.81196 de Nies L, Busi SB, Kunath BJ, May P, Wilmes P. (2022) Mobilome-driven segregation of the resistome in biological wastewater treatment. eLife, (11) e81196

10.1093/femsml/uqad029 de Rezende Rodovalho V, da Luz BSR, Nicolas A, Jardin J, Briard-Bion V, Folador EL, Santos AR, Jan G, Le Loir Y, de Carvalho Azevedo VA, Guédon Éric. (2023) Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles. microLife, (4) uqad029

10.1128/aem.02263-20 de Rezende Rodovalho V, da Luz BSR, Nicolas A, do Carmo FLR, Jardin J, Briard-Bion V, Jan G, Le Loir Y, de Carvalho Azevedo VA, Guédon E. (2020) Environmental Conditions Modulate the Protein Content and Immunomodulatory Activity of Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii. Applied and Environmental Microbiology, 4 (87) e02263-20

10.3389/fmicb.2020.01544 de Rezende Rodovalho V, da Luz BSR, Rabah H, do Carmo FLR, Folador EL, Nicolas A, Jardin J, Briard-Bion V, Blottière H, Lapaque N, Jan G, Le Loir Y, de Carvalho Azevedo VA, Guédon E. (2020) Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway. Frontiers in Microbiology, (11) 1544

10.3389/fmicb.2018.01807 do Carmo FLR, Silva WM, Tavares GC, Ibraim IC, Cordeiro BF, Oliveira ER, Rabah H, Cauty C, da Silva SH, Viana MVC, Caetano ACB, dos Santos RG, de Oliveira Carvalho RD, Jardin J, Pereira FL, Folador EL, Le Loir Y, Figueiredo HCP, Jan G, Azevedo V. (2018) Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129. Frontiers in Microbiology, (9) 1807

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