Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W.
The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities.
J Biol Chem. 2018 Sep 17. pii: jbc.RA118.004185. doi: 10.1074/jbc.RA118.004185. [Epub ahead of print]

Mylonas R, Beer I, Iseli C, Chong C, Pak HS, Gfeller D, Coukos G, Xenarios I, Müller M, Bassani-Sternberg M.
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.
Mol Cell Proteomics. 2018 Aug 31. pii: mcp.RA118.000877. doi: 10.1074/mcp.RA118.000877. [Epub ahead of print]

Schumacher P, Demarsy E, Waridel P, Petrolati LA, Trevisan M, Fankhauser C.
A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process.
Nat Commun. 2018, 9(1):2403.

Chennupati V, Veiga DF, Maslowski KM, Andina N, Tardivel A, Yu EC, Stilinovic M, Simillion C, Duchosal MA, Quadroni M, Roberts I, Sankaran VG, MacDonald HR, Fasel N, Angelillo-Scherrer A, Schneider P, Hoang T, Allam R.
Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 mRNA translation.
J Clin Invest. 2018, 128(4):1597-1614.



Presotto D, Erdes E, Duong MN, Allard M, Regamey PO, Quadroni M, Doucey MA, Rufer N, Hebeisen M.
Fine-Tuning of Optimal TCR Signaling in Tumor-Redirected CD8 T Cells by Distinct TCR Affinity-Mediated Mechanisms.
Front Immunol. 2017, 8:1564. doi: 10.3389/fimmu.2017.01564. eCollection 2017.

Debelyy MO, Waridel P, Quadroni M, Schneiter R, Conzelmann A.
Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins.
PLoS One. 2017, 12(10):e0186840.

Weidenauer L, Wang T, Joshi S, Chiosis G, Quadroni M.
Proteomic interrogation of HSP90 and insights for medical research.
Expert Rev Proteomics. 2017, 14(12):1105-1117.

Martin Campos T, Mylonas R, Masselot A, Waridel P, Petricevic T, Xenarios I, Quadroni M.
MsViz, a graphical software tool for in-depth manual validation and quantitation of post-translational modifications.
J Proteome Res. 2017, 16(8): 3092-3101.

Salamin K, Eugster PJ, Jousson O, Waridel P, Grouzmann E, Monod M.
AoS28D, a proline-Xaa carboxypeptidase secreted by Aspergillus oryzae.
Appl Microbiol Biotechnol. 2017, 101(10):4129-4137.

Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN,  Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulic V, Naef F, Gachon F.
Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver.
Cell Metabolism 2017, 25(1): 102-117.



LeBoeuf AC, Waridel P, Brent CS, Gonçalves AN, Menin L, Ortiz D, Koto A, Privman E, Soares ZG, Miska EA, Benton R, Keller L.
Oral transfer of chemical cues, growth proteins and hormones in social insects.
eLife 2016, 5:e20375.

Fumagalli F, Noack J, Bergmann TJ, Presmanes EC, Pisoni GB, Fasana E, Fregno I, Galli C, Loi M, Soldà T, D'Antuono R, Raimondi A, Jung M, Melnyk A, Schorr S, Schreiber A, Simonelli L, Varani L, Wilson-Zbinden C, Zerbe O, Hofmann K, Peter M, Quadroni M, Zimmermann R, Molinari M.
Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery.
Nat Cell Biol. 2016, 18(11):1173-1184.

Gat-Yablonski G, Finka A, Pinto G, Quadroni M, Shtaif B, Goloubinoff P.
Quantitative proteomics of rat livers shows that unrestricted feeding is stressful for proteostasis with implications on life span.
Aging (Albany NY) 2016, 8(8): 1735-1758.

Rognon B, Barrera C, Monod M, Valot B, Roussel S, Quadroni M, Jouneau S, Court-Fortune I, Caillaud D, Fellrath JM, Dalphin JC, Reboux G, Millon L.
Identification of Antigenic Proteins from Lichtheimia corymbifera for Farmer's Lung Disease Diagnosis.
PLoS One. 2016, 11(8):e0160888. doi: 10.1371/journal.pone.0160888.

Di Micco A, Frera G, Lugrin J, Jamilloux Y, Hsu ET, Tardivel A, De Gassart A, Zaffalon L, Bujisic B, Siegert S, Quadroni M, Broz P, Henry T, Hrycyna CA, Martinon F.
AIM2 inflammasome is activated by pharmacological disruption of nuclear envelope integrity.
Proc Natl Acad Sci U S A. 2016, 113(32):E4671-80.

Tran VDT, De Coi N, Feuermann M, Schmid-Siegert E, Bagut¸ E-T, Mignon B, Waridel P, Peter C, Pradervand S, Pagni M, Monod M.
RNA sequencing-based genome reannotation of the dermatophyte Arthroderma benhamiae and characterization of its secretome and whole gene expression profile during infection.
mSystems 2016, 1(4):00036-16. doi:10.1128/mSystems.00036-16.

Martin R, Desponds C, Eren RO, Quadroni M, Thome M, Fasel N.
Caspase-mediated cleavage of raptor participates in the inactivation of mTORC1 during cell death.
Cell Death Discovery 2016, 2: 16024.

Sobel JA, Waridel P, Gori I, Quadroni M, Canny GO.
Proteome-Wide Effect of 17-β-Estradiol and Lipoxin A4 in an Endometriotic Epithelial Cell Line.
Front. Endocrinol. 2016, 6:192.

Borgatta M, Waridel P, Decosterd LA, Buclin T, Chèvre N.
Multigenerational effects of the anticancer drug tamoxifen and its metabolite 4-hydroxy-tamoxifen on Daphnia pulex.
Sci Total Environ. 2016, 545-46:21-29.



Bhuiyan T, Waridel P, Kapuria V, Zoete V, Herr W.
Distinct OGT-Binding Sites Promote HCF-1 Cleavage.
PLoS One 2015, 10(8): e0136636. doi:10.1371/journal.pone.0136636.

Finka A, Sood V, Quadroni M, Rios PL, Goloubinoff P.
Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.
Cell Stress Chaperones. 2015 20(4):605-20.

Borgatta M, Decosterd LA, Waridel P, Buclin T, Chèvre N.
The anticancer drug metabolites endoxifen and 4-hydroxy-tamoxifen induce toxic effects on Daphnia pulex in a two-generation study.
Sci Total Environ. 2015, 520:232-240.

Quadroni M, Potts A, Waridel P.
Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome.
J Proteomics. 2015, 120:215-29.

Roja Murcia N, Lee X, Waridel P, Maspoli A, Imker HJ, Chai T, Walsh CT, Reimmann C.
The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor.
Front Microbiol. 2015, 6:170. eCollection 2015.

Borgatta M, Hernandez C, Decosterd LA, Chèvre N, Waridel P.
Shotgun ecotoxicoproteomics of Daphnia pulex: biochemical effects of the anticancer drug tamoxifen.
J Proteome Res. 2015, 14(1): 279-291.



Barrera C, Millon L, Rognon B, Quadroni M, Roussel S, Dalphin JC, Court-Fortune I, Caillaud D, Jouneau S, Fellrath JM, Zaugg C, Reboux G, Monod M.
Immunoreactive proteins of Saccharopolyspora rectivirgula for farmer's lung serodiagnosis.
Proteomics Clin Appl. 2014, 8(11-12):971-81.

Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F.
Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.
Proc Natl Acad Sci U S A. 2014, 111(1):167-72.

Hernandez C, Waridel P, Quadroni M.
Database Construction and Peptide Identification Strategies for Proteogenomic Studies on Sequenced Genomes.
Curr Top Med Chem. 2014, 14(3): 425-434.

Morikawa K, Gouttenoire J, Hernandez C, Thi VL, Tran HT, Lange CM, Dill MT, Heim MH, Donzé O, Penin F, Quadroni M, Moradpour D.
Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease.
Hepatology 2014, 59(2): 423-433.



Fierro-Monti I, Echeverria P, Racle J, Hernandez C, Picard D, Quadroni M.
Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy.
PLoS One 2013, 8(11): e80425. doi:10.1371/journal.pone.0080425.

Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M.
A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor.
PLoS One 2013, 8(11): e80423. doi:10.1371/journal.pone.0080423.



Ythier M, Resch G, Waridel P, Panchaud A, Gfeller A, Majcherczyk P, Quadroni M, Moreillon P.
Proteomic and transcriptomic profiling of Staphylococcus aureus surface LPXTG-proteins: correlation with agr genotypes and adherence phenotypes.
Mol Cell Proteomics 2012, 11: 1123-1139, M111.014191.

Millon L, Roussel S, Rognon B, Quadroni M, Salamin K, Reboux G, Barrera C, Fellrath JM, Aubert JD, Dalphin JC, Monod M.
Aspergillus species recombinant antigens for serodiagnosis of farmer's lung disease.
J Allergy Clin Immunol. 2012, 130(3):803-805.

Wigginton KR, Menin L, Sigstam T, Gannon G, Cascella M, Hamidane HB, Tsybin YO, Waridel P, Kohn T. UV Radiation Induces Genome-Mediated, Site-Specific Cleavage in Viral Proteins.
ChemBioChem 2012, 13(6): 837-845.

Groß O, Yazdi AS, Thomas CJ, Masin M, Heinz LX, Guarda G, Quadroni M, Drexler SK, Tschopp J. Inflammasome Activators Induce Interleukin-1α Secretion via Distinct Pathways with Differential Requirement for the Protease Function of Caspase-1. Immunity 2012, 36(3): 388-400.

Waridel P, Ythier M, Gfeller A, Moreillon P, Quadroni M.
Evidence for a new post-translational modification in Staphylococcus aureus: Hydroxymethylation of asparagine and glutamine.
J Proteomics 2012, 75(6): 1742-1751.

Grill B, Chen L, Tulgren ED, Baker ST, Bienvenut W, Anderson M, Quadroni M, Jin Y, Garner CC.
RAE-1, a Novel PHR Binding Protein, Is Required for Axon Termination and Synapse Formation in Caenorhabditis elegans.
J Neurosci. 2012, 32(8): 2628-2636.

Heinz LX, Rebsamen M, Rossi DC, Staehli F, Schroder K, Quadroni M, Gross O, Schneider P, Tschopp J.
The death domain-containing protein Unc5CL is a novel MyD88-independent activator of the pro-inflammatory IRAK signaling cascade.
Cell Death Differ. 2012, 19(4):722-31.



Sriranganadane D, Waridel P, Salamin K, Feuermann M, Mignon B, Staib P, Neuhaus J-M, Quadroni M, Monod M.
Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH.
Proteomics 2011, 11(22): 4422-4433.

Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Waridel P, Quadroni M, et al. Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma.
PLoS ONE 2011, 6(4): e18369.

Logette E, Schuepbach-Mallepell S, Mirjam JE, Leo XH, Jaccard B, Manzl C, Tardivel A, Villunger A, Quadroni M, Gaide O, Tschopp J.
PIDD orchestrates translesion DNA synthesis in response to UV irradiation.
Cell Death Differ. 2011, 18(6): 1036-1045.

Sriranganadane D, Reichard U, Salamin K, Fratti M, Jousson O, Waridel P, Quadroni M, Neuhaus JM, Monod M.
Secreted glutamic protease rescues aspartic protease Pep deficiency in Aspergillus fumigatus during growth in acidic protein medium.
Microbiology 2011, 157(Pt 5): 1541-1550.

Capotosti F, Guernier S, Lammers F, Waridel P, Cai Y, Jin J, Conaway JW, Conaway RC, Herr W.
O-GlcNAc Transferase Catalyzes Site-Specific Proteolysis of HCF-1.
Cell 2011, 144(3): 376-388.

Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M.
Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides.
J Proteome Res. 2011, 10(2): 800-811.

Tinel A, Eckert MJ, Logette E, Lippens S, Janssens S, Jaccard B, Quadroni M, Tschopp J.
Regulation of PIDD auto-proteolysis and activity by the molecular chaperone Hsp90.
Cell Death Differ. 2011, 18(3): 506-15.

Roussel S, Rognon B, Barrera C, Reboux G, Salamin K, Grenouillet F, Thaon I, Dalphin JC, Tillie-Leblond I, Quadroni M, Monod M, Millon L.
Immuno-reactive proteins from Mycobacterium immunogenum useful for serodiagnosis of metalworking fluid hypersensitivity pneumonitis.
Int J Med Microbiol. 2011, 301(2): 150-156.



Sriranganadane D, Waridel P, Salamin K, Reichard U, Grouzmann E, Neuhaus J-M, Quadroni M, Monod M.
Aspergillus Protein Degradation Pathways with Different Secreted Protease Sets at Neutral and Acidic pH.
J Proteome Res. 2010, 9(7): 3511–3519.

Priego-Capote F, Scherl A, Müller M, Waridel P, Lisacek F, Sanchez J-C.
Glycation Isotopic Labelling (GIL) with 13C-reducing Sugars for Quantitative Analysis of Glycated Proteins in Human Plasma.
Mol Cell Proteomics 2010, 9(3): 579-592.

Roussel S, Reboux G, Rognon B, Monod M, Grenouillet F, Quadroni M, Fellrath JM, Aubert JD, Dalphin JC, Millon L.
Comparison of three antigenic extracts of Eurotium amstelodami in serological diagnosis of farmer's lung disease.
Clin Vaccine Immunol. 2010, 17(1):160-7.

Vaezzadeh AR, Deshusses JMP, Waridel P, François P, Zimmermann-Ivol CG, Lescuyer P,  Schrenzel J, Hochstrasser DF.
Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes.
J. Microbiol. Meth. 2010, 80(1): 56-62.



Maerki S, Olma MH, Staubli T, Steigemann P, Gerlich DW, Quadroni M, Sumara I, Peter M.
The Cul3-KLHL21 E3 ubiquitin ligase targets aurora B to midzone microtubules in anaphase and is required for cytokinesis.
J Cell Biol. 2009, 187(6):791-800.

Colzani M, Bienvenut WV, Faes E, Quadroni M.
Precursor ion scans for the targeted detection of stable-isotope-labeled peptides.
Rapid Commun. Mass Spectrom. 2009, 23(22): 3570-3578.

Colzani M., Waridel P., Laurent J., Faes E., Rüegg C., Quadroni M.
Metabolic Labeling and Protein Linearization Technology Allow the Study of Proteins Secreted by Cultured Cells in Serum-Containing Media.
J Proteome Res. 2009, 8(10): 4779-4788.

Olma MH, Roy M, Le Bihan T, Sumara I, Maerki S, Larsen B, Quadroni M, Peter M, Tyers M, Pintard L.
An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases.
J Cell Sci. 2009, 122(7): 1035-1044.



Baruthio F, Quadroni M, Rüegg C, Mariotti A.
Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage.
Proteomics 2008, 8(22): 4733-4747.

Da Cruz S, Parone PA, Gonzalo P, Bienvenut WV, Tondera D, Jourdain A, Quadroni M, Martinou JC. SLP-2 interacts with prohibitins in the mitochondrial inner membrane and contributes to their stability.
Biochim Biophys Acta. 2008, 1783(5):904-911.

Colzani M, Schütz F, Potts A, Waridel P, Quadroni M.
Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS).
Mol Cell Proteomics 2008, 7(5): 927-937.

Barelli S, Canellini G, Thadikkaran L, Crettaz D, Quadroni M, Rossier JS, Tissot JD, Lion N.
Oxidation of proteins: Basic principles and perspectives for blood proteomics.
Proteomics Clin Appl. 2008, 2(2):142-57.



Grill B, Bienvenut WV, Brown HM, Ackley BD, Quadroni M, Jin Y.
C. elegans RPM-1 regulates axon termination and synaptogenesis through the Rab GEF GLO-4 and the Rab GTPase GLO-1.
Neuron. 2007, 55(4):587-601.

Giddey K, Monod M, Barblan J, Potts A, Waridel P, Zaugg C, Quadroni M.
Comprehensive analysis of proteins secreted by Trichophyton rubrum and Trichophyton violaceum under in vitro conditions.
J Proteome Res. 2007, 6(8):3081-92.

Sumara I, Quadroni M, Frei C, Olma MH, Sumara G, Ricci R, Peter M.
A Cul3-based E3 ligase removes Aurora B from mitotic chromosomes, regulating mitotic progression and completion of cytokinesis in human cells.
Dev Cell. 2007,12(6):887-900.

Tinel A, Janssens S, Lippens S, Cuenin S, Logette E, Jaccard B, Quadroni M, Tschopp J.
Autoproteolysis of PIDD marks the bifurcation between pro-death caspase-2 and pro-survival NF-kappaB pathway.
EMBO J. 2007, 26(1):197-208.

Giddey K, Favre B, Quadroni M, Monod M.
Closely related dermatophyte species produce different patterns of secreted proteins.
FEMS Microbiol Lett. 2007, 267(1):95-101.



Arrigoni G, Resjo S, Levander F, Nilsson R, Degerman E, Quadroni M, Pinna LA, James P.
Chemical derivatization of phosphoserine and phosphothreonine containing peptides to increase sensitivity for MALDI-based analysis and for selectivity of MS/MS analysis.
Proteomics 2006, 6(3):757-66.

Walker J, Acestor N, Gongora R, Quadroni M, Segura I, Fasel N, Saravia NG.
Comparative protein profiling identifies elongation factor-1beta and tryparedoxin peroxidase as factors associated with metastasis in Leishmania guyanensis.
Mol Biochem Parasitol. 2006, 145(2):254-64.



Owen HR, Quadroni M, Bienvenut W, Buerki C, Hottiger MO.
Identification of novel and cell type enriched cofactors of the transcription activation domain of RelA (p65 NF-kappaB).
J Proteome Res. 2005, 4(4):1381-90.

P.M. Palagi, D. Walther, M. Quadroni, S. Catherinet, J. Burgess, C.G. Zimmermann-Ivol, J.C. Sanchez, P.-A. Binz, D.F. Hochstrasser and R.D. Appel,
MSight: an image analysis software for liquid chromatography-mass spectrometry.
Proteomics 2005, 5(9):2381-4.



Jousson O, Lechenne B, Bontems O, Mignon B, Reichard U, Barblan J, Quadroni M, Monod M.
Secreted subtilisin gene family in Trichophyton rubrum.
Gene 2004, 339:79-88.

Crettaz D, Sensebe L, Vu DH, Schneider P, Depasse F, Bienvenut WV, Quadroni M, Tissot JD.
Proteomics of methylene blue photo-treated plasma before and after removal of the dye by an absorbent filter.
Proteomics 2004, 4(3):881-91.

Jousson O, Lechenne B, Bontems O, Capoccia S, Mignon B, Barblan J, Quadroni M, Monod M.
Multiplication of an ancestral gene encoding secreted fungalysin preceded species differentiation in the dermatophytes Trichophyton and Microsporum.
Microbiology 2004, 150(Pt 2):301-10.

Grill B, Wilson GM, Zhang KX, Wang B, Doyonnas R, Quadroni M, Schrader JW.
Activation/division of lymphocytes results in increased levels of cytoplasmic activation/proliferation-associated protein-1: prototype of a new family of proteins.
J Immunol. 2004 , 172(4):2389-400.



Vuadens F, Benay C, Crettaz D, Gallot D, Sapin V, Schneider P, Bienvenut WV, Lemery D, Quadroni M, Dastugue B, Tissot JD.
Identification of biologic markers of the premature rupture of fetal membranes: proteomic approach.
Proteomics 2003, 3(8):1521-5.

Gongora R, Acestor N, Quadroni M, Fasel N, Saravia NG, Walker J.
Mapping the proteome of Leishmania Viannia parasites using two-dimensional polyacrylamide gel electrophoresis and associated technologies.
Biomedica 2003, 23(2):153-60.

Vuadens F, Crettaz D, Scelatta C, Servis C, Quadroni M, Bienvenut WV, Schneider P, Hohlfeld P, Applegate LA, Tissot JD.
Plasticity of protein expression during culture of fetal skin cells.
Electrophoresis 2003, 24(7-8):1281-91.



Acestor N, Masina S, Walker J, Saravia NG, Fasel N, Quadroni M.
Establishing two-dimensional gels for the analysis of Leishmania proteomes.
Proteomics 2002, 2(7):877-9.

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