Centre intégratif de génomique

Equipe principale | CIG Services communs | Genomics Technologies Facility (GTF) | Group Benton | Group Desvergne | Group Fajas | Group Fankhauser | Group Franken | Group Gambetta | Group Gatfield | Group Hernandez | Group Herr | Group Michalik | Group Reymond | Group Stasiak | Group Thorens | Group Wahli | Group van Leeuwen | Mouse Metabolic Evaluation Facility (MEF) | Protein Analysis Facility (PAF)
Publications | Mémoires et thèses

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72 publications

2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 |
Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.
Golumbeanu M., Desfarges S., Hernandez C., Quadroni M., Rato S., Mohammadi P., Telenti A., Beerenwinkel N., Ciuffi A., 2019/01/18. Scientific reports, 9 (1) p. 213. Peer-reviewed.
Molecular evolution of juvenile hormone esterase-like proteins in a socially exchanged fluid.
LeBoeuf A.C., Cohanim A.B., Stoffel C., Brent C.S., Waridel P., Privman E., Keller L., Benton R., 2018/12/13. Scientific reports, 8 (1) p. 17830. Peer-reviewed.
 
A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process.
Schumacher P., Demarsy E., Waridel P., Petrolati L.A., Trevisan M., Fankhauser C., 2018/06/19. Nature communications, 9 (1) p. 2403. Peer-reviewed.
Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 translation.
Chennupati V., Veiga D.F., Maslowski K.M., Andina N., Tardivel A., Yu E.C., Stilinovic M., Simillion C., Duchosal M.A., Quadroni M. et al., 2018. The Journal of Clinical Investigation, 128 (4) pp. 1597-1614. Peer-reviewed.
 
Proteomic interrogation of HSP90 and insights for medical research.
Weidenauer L., Wang T., Joshi S., Chiosis G., Quadroni M.R., 2017/12. Expert review of proteomics, 14 (12) pp. 1105-1117. Peer-reviewed.
BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance.
Zhang B., Holmlund M., Lorrain S., Norberg M., Bakó L., Fankhauser C., Nilsson O., 2017/08/22. eLife, 6 pp. e26759. Peer-reviewed.
 
MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.
Martín-Campos T., Mylonas R., Masselot A., Waridel P., Petricevic T., Xenarios I., Quadroni M., 2017/08/04. Journal of proteome research, 16 (8) pp. 3092-3101. Peer-reviewed.
 
AoS28D, a proline-Xaa carboxypeptidase secreted by Aspergillus oryzae.
Salamin K., Eugster P.J., Jousson O., Waridel P., Grouzmann E., Monod M., 2017/05. Applied microbiology and biotechnology, 101 (10) pp. 4129-4137. Peer-reviewed.
Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins.
Debelyy M.O., Waridel P., Quadroni M., Schneiter R., Conzelmann A., 2017. PLoS One, 12 (10) pp. e0186840. Peer-reviewed.
Fine-Tuning of Optimal TCR Signaling in Tumor-Redirected CD8 T Cells by Distinct TCR Affinity-Mediated Mechanisms
Presotto D., Erdes E., Duong M.N., Allard M., Regamey P.O., Quadroni M., Doucey M.A., Rufer N., Hebeisen M., 2017. Frontiers in Immunology, 8 p. 1564. Peer-reviewed.
Fine-Tuning of Optimal TCR Signaling in Tumor-Redirected CD8 T Cells by Distinct TCR Affinity-Mediated Mechanisms.
Presotto D., Erdes E., Duong M.N., Allard M., Regamey P.O., Quadroni M., Doucey M.A., Rufer N., Hebeisen M., 2017. Frontiers in Immunology, 8 p. 1564. Peer-reviewed.
Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver.
Wang J., Mauvoisin D., Martin E., Atger F., Galindo A.N., Dayon L., Sizzano F., Palini A., Kussmann M., Waridel P. et al., 2017. Cell Metabolism, 25 (1) pp. 102-117. Peer-reviewed.
Oral transfer of chemical cues, growth proteins and hormones in social insects.
LeBoeuf A.C., Waridel P., Brent C.S., Gonçalves A.N., Menin L., Ortiz D., Riba-Grognuz O., Koto A., Soares Z.G., Privman E. et al., 2016/11/29. eLife, 5 pp. e20375. Peer-reviewed.
 
Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery.
Fumagalli F., Noack J., Bergmann T.J., Cebollero E., Pisoni G.B., Fasana E., Fregno I., Galli C., Loi M., Soldà T. et al., 2016/11. Nature cell biology, 18 (11) pp. 1173-1184. Peer-reviewed.
AIM2 inflammasome is activated by pharmacological disruption of nuclear envelope integrity.
Di Micco A., Frera G., Lugrin J., Jamilloux Y., Hsu E.T., Tardivel A., De Gassart A., Zaffalon L., Bujisic B., Siegert S. et al., 2016/08/09. Proceedings of the National Academy of Sciences of the United States of America, 113 (32) pp. E4671-80. Peer-reviewed.
Quantitative proteomics of rat livers shows that unrestricted feeding is stressful for proteostasis with implications on life span.
Gat-Yablonski G., Finka A., Pinto G., Quadroni M., Shtaif B., Goloubinoff P., 2016/08. Aging, 8 (8) pp. 1735-1758. Peer-reviewed.
Caspase-mediated cleavage of raptor participates in the inactivation of mTORC1 during cell death.
Martin R., Desponds C., Eren R.O., Quadroni M., Thome M., Fasel N., 2016. Cell Death Discovery, 2 p. 16024. Peer-reviewed.
Identification of Antigenic Proteins from Lichtheimia corymbifera for Farmer's Lung Disease Diagnosis.
Rognon B., Barrera C., Monod M., Valot B., Roussel S., Quadroni M., Jouneau S., Court-Fortune I., Caillaud D., Fellrath J.M. et al., 2016. PLoS One, 11 (8) pp. e0160888. Peer-reviewed.
 
Multigenerational effects of the anticancer drug tamoxifen and its metabolite 4-hydroxy-tamoxifen on Daphnia pulex.
Borgatta M., Waridel P., Decosterd L.A., Buclin T., Chèvre N., 2016. Science of the Total Environment, 545-546 pp. 21-29.
RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.
Tran V.D., De Coi N., Feuermann M., Schmid-Siegert E., Băguţ E.T., Mignon B., Waridel P., Peter C., Pradervand S., Pagni M. et al., 2016. mSystems, 1 (4) pp. e00036. Peer-reviewed.
Distinct OGT-Binding Sites Promote HCF-1 Cleavage.
Bhuiyan T., Waridel P., Kapuria V., Zoete V., Herr W., 2015. Plos One, 10 (8) pp. e0136636. Peer-reviewed.
 
Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome.
Quadroni M., Potts A., Waridel P., 2015. Journal of Proteomics, 120 pp. 215-229.
Proteome-Wide Effect of 17-β-Estradiol and Lipoxin A4 in an Endometriotic Epithelial Cell Line.
Sobel J.A., Waridel P., Gori I., Quadroni M., Canny G.O., 2015. Frontiers in Endocrinology, 6 p. 192.
 
Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.
Finka A., Sood V., Quadroni M., Rios Pde L, Goloubinoff P., 2015. Cell Stress and Chaperones, 20 (4) pp. 605-620. Peer-reviewed.
 
The anticancer drug metabolites endoxifen and 4-hydroxy-tamoxifen induce toxic effects on Daphnia pulex in a two-generation study.
Borgatta M., Decosterd L.A., Waridel P., Buclin T., Chèvre N., 2015. Science of the Total Environment, 520 pp. 232-240.
 
Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.
Mauvoisin D., Wang J., Jouffe C., Martin E., Atger F., Waridel P., Quadroni M., Gachon F., Naef F., 2014. Proceedings of the National Academy of Sciences of the United States of America, 111 (1) pp. 167-172.
 
Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.
Hernandez C., Waridel P., Quadroni M., 2014. Current Topics in Medicinal Chemistry, 14 (3) pp. 425-434.
 
Immunoreactive proteins of Saccharopolyspora rectivirgula for farmer's lung serodiagnosis.
Barrera C., Millon L., Rognon B., Quadroni M., Roussel S., Dalphin J.C., Court-Fortune I., Caillaud D., Jouneau S., Fellrath J.M. et al., 2014. Proteomics. Clinical Applications, 8 (11-12) pp. 971-981.
 
Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease.
Morikawa K., Gouttenoire J., Hernandez C., Dao Thi V.L., Tran H.T., Lange C.M., Dill M.T., Heim M.H., Donzé O., Penin F. et al., 2014. Hepatology, 59 (2) pp. 423-433. Peer-reviewed.
 
Shotgun Ecotoxicoproteomics of Daphnia pulex: Biochemical Effects of the Anticancer Drug Tamoxifen.
Borgatta M., Hernandez C., Decosterd L.A., Chèvre N., Waridel P., 2014. Journal of Proteome Research, 14 (1) pp. 279-291.
A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor.
Fierro-Monti I., Racle J., Hernandez C., Waridel P., Hatzimanikatis V., Quadroni M., 2013. PLoS One, 8 (11) pp. e80423.
Dynamic impacts of the inhibition of the molecular chaperone hsp90 on the T-cell proteome have implications for anti-cancer therapy.
Fierro-Monti I., Echeverria P., Racle J., Hernandez C., Picard D., Quadroni M., 2013. PLoS One, 8 (11) pp. e80425.
 
Aspergillus species recombinant antigens for serodiagnosis of farmer's lung disease.
Millon L., Roussel S., Rognon B., Quadroni M., Salamin K., Reboux G., Barrera C., Fellrath J.M., Aubert J.D., Dalphin J.C. et al., 2012. Journal of Allergy and Clinical Immunology, 130 (3) pp. 803-805.e6.
 
Evidence for a new post-translational modification in Staphylococcus aureus: Hydroxymethylation of asparagine and glutamine.
Waridel P., Ythier M., Gfeller A., Moreillon P., Quadroni M., 2012. Journal of Proteomics, 75 (6) pp. 1742-1751.
 
Inflammasome activators induce interleukin-1α secretion via distinct pathways with differential requirement for the protease function of caspase-1.
Gross O., Yazdi A.S., Thomas C.J., Masin M., Heinz L.X., Guarda G., Quadroni M., Drexler S.K., Tschopp J., 2012. Immunity, 36 (3) pp. 388-400.
 
Proteomic and transcriptomic profiling of Staphylococcus aureus surface LPXTG-proteins: correlation with agr genotypes and adherence phenotypes.
Ythier M., Resch G., Waridel P., Panchaud A., Gfeller A., Majcherczyk P., Quadroni M., Moreillon P., 2012. Molecular and Cellular Proteomics, 11 (11) pp. 1123-1139. Peer-reviewed.
RAE-1, a novel PHR binding protein, is required for axon termination and synapse formation in Caenorhabditis elegans.
Grill B., Chen L., Tulgren E.D., Baker S.T., Bienvenut W., Anderson M., Quadroni M., Jin Y., Garner C.C., 2012. Journal of Neuroscience, 32 (8) pp. 2628-2636.
 
The death domain-containing protein Unc5CL is a novel MyD88-independent activator of the pro-inflammatory IRAK signaling cascade.
Heinz L.X., Rebsamen M., Rossi D.C., Staehli F., Schroder K., Quadroni M., Gross O., Schneider P., Tschopp J., 2012. Cell Death and Differentiation, 19 (4) pp. 722-731.
 
Addressing trypsin bias in large scale (phospho)proteome analysis by size exclusion chromatography and secondary digestion of large post-trypsin peptides.
Tran B.Q., Hernandez C., Waridel P., Potts A., Barblan J., Lisacek F., Quadroni M., 2011. Journal of Proteome Research, 10 (2) pp. 800-811.
 
Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH.
Sriranganadane D., Waridel P., Salamin K., Feuermann M., Mignon B., Staib P., Neuhaus J.M., Quadroni M., Monod M., 2011. Proteomics, 11 (22) pp. 4422-4433.
 
Immuno-reactive proteins from Mycobacterium immunogenum useful for serodiagnosis of metalworking fluid hypersensitivity pneumonitis.
Roussel S., Rognon B., Barrera C., Reboux G., Salamin K., Grenouillet F., Thaon I., Dalphin J.C., Tillie-Leblond I., Quadroni M. et al., 2011. International Journal of Medical Microbiology, 301 (2) pp. 150-156.
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
Valsesia A., Rimoldi D., Martinet D., Ibberson M., Benaglio P., Quadroni M., Waridel P., Gaillard M., Pidoux M., Rapin B. et al., 2011. PLoS One, 6 (4) pp. e18369. Peer-reviewed.
 
PIDD orchestrates translesion DNA synthesis in response to UV irradiation.
Logette E., Schuepbach-Mallepell S., Eckert M.J., Leo X.H., Jaccard B., Manzl C., Tardivel A., Villunger A., Quadroni M., Gaide O. et al., 2011. Cell Death and Differentiation, 18 (6) pp. 1036-1045.
 
Regulation of PIDD auto-proteolysis and activity by the molecular chaperone Hsp90.
Tinel A., Eckert M.J., Logette E., Lippens S., Janssens S., Jaccard B., Quadroni M., Tschopp J., 2011. Cell Death and Differentiation, 18 (3) pp. 506-515.
 
Secreted glutamic protease rescues aspartic protease Pep deficiency in Aspergillus fumigatus during growth in acidic protein medium.
Sriranganadane D., Reichard U., Salamin K., Fratti M., Jousson O., Waridel P., Quadroni M., Neuhaus J.M., Monod M., 2011. Microbiology, 157 (5) pp. 1541-1550.
 
Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes.
Vaezzadeh A.R., Deshusses J.M., Waridel P., François P., Zimmermann-Ivol C.G., Lescuyer P., Schrenzel J., Hochstrasser D.F., 2010. Journal of Microbiological Methods, 80 (1) pp. 56-62.
 
Aspergillus protein degradation pathways with different secreted protease sets at neutral and acidic pH.
Sriranganadane D., Waridel P., Salamin K., Reichard U., Grouzmann E., Neuhaus J.-M., Quadroni M., Monod M., 2010. Journal of Proteome Research, 9 (7) pp. 3511-3519.
 
Comparison of three antigenic extracts of Eurotium amstelodami in serological diagnosis of farmer's lung disease.
Roussel Sandrine, Reboux Gabriel, Rognon Benedicte, Monod Michel, Grenouillet Frederic, Quadroni Manfredo, Fellrath Jean-Marc, Aubert John-David, Dalphin Jean-Charles, Millon Laurence, 2010. Clinical and Vaccine Immunology, 17 (1) pp. 160-167.
 
An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases.
Olma M.H., Roy M., Le Bihan T., Sumara I., Maerki S., Larsen B., Quadroni M., Peter M., Tyers M., Pintard L., 2009. Journal of cell science, 122 (Pt 7) pp. 1035-1044. Peer-reviewed.
 
Metabolic labeling and protein linearization technology allow the study of proteins secreted by cultured cells in serum-containing media.
Colzani M., Waridel P., Laurent J., Faes E., Rüegg C., Quadroni M., 2009. Journal of Proteome research, 8 (10) pp. 4779-4788.
 
Precursor ion scans for the targeted detection of stable-isotope-labeled peptides.
Colzani M., Bienvenut W.V., Faes E., Quadroni M., 2009. Rapid communications in mass spectrometry, 23 (22) pp. 3570-3578. Peer-reviewed.
 
Profiling of T-cell receptor signaling complex assembly in human CD4 T-lymphocytes using RP protein arrays.
Brembilla N.C., Cohen-Salmon I., Weber J., Rüegg C., Quadroni M., Harshman K., Doucey M.A., 2009. Proteomics, 9 (2) pp. 299-309.
The Cul3-KLHL21 E3 ubiquitin ligase targets aurora B to midzone microtubules in anaphase and is required for cytokinesis.
Maerki S., Olma M.H., Staubli T., Steigemann P., Gerlich D.W., Quadroni M., Sumara I., Peter M., 2009. Journal of Cell Biology, 187 (6) pp. 791-800.
 
SLP-2 interacts with prohibitins in the mitochondrial inner membrane and contributes to their stability.
Da Cruz S., Parone P.A., Gonzalo P., Bienvenut W.V., Tondera D., Jourdain A., Quadroni M., Martinou J.C., 2008/02. Biochimica et Biophysica Acta, 1783 (5) pp. 904-911. Peer-reviewed.
 
c-Cbl expression levels regulate the functional responses of human central and effector memory CD4 T cells.
Brembilla N.C., Weber J., Rimoldi D., Pradervand S., Schütz F., Pantaleo G., Rüegg C., Quadroni M., Harshman K., Doucey M.A., 2008. Blood, 112 (3) pp. 652-660.
 
Oxidation of proteins: Basic principles and perspectives for blood proteomics.
Barelli S., Canellini G., Thadikkaran L., Crettaz D., Quadroni M., Rossier J.S., Tissot J.D., Lion N., 2008. Proteomics. Clinical Applications, 2 (2) pp. 142-157. Peer-reviewed.
 
Proteomic analysis of membrane rafts of melanoma cells identifies protein patterns characteristic of the tumor progression stage.
Baruthio F., Quadroni M., Rüegg C., Mariotti A., 2008. Proteomics, 8 (22) pp. 4733-4747. Peer-reviewed.
 
Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS)
Colzani M., Schutz F., Potts A., Waridel P., Quadroni M., 2008. Molecular and Cellular Proteomics, 7 (5) pp. 927-937. Peer-reviewed.
 
C. elegans RPM-1 regulates axon termination and synaptogenesis through the Rab GEF GLO-4 and the Rab GTPase GLO-1.
Grill B., Bienvenut W.V., Brown H.M., Ackley B.D., Quadroni M., Jin Y., 2007/08. Neuron, 55 (4) pp. 587-601. Peer-reviewed.
 
Comprehensive analysis of proteins secreted by Trichophyton rubrum and Trichophyton violaceum under in vitro conditions.
Giddey K., Monod M., Barblan J., Potts A., Waridel P., Zaugg C., Quadroni M., 2007/08. Journal of proteome research, 6 (8) pp. 3081-3092. Peer-reviewed.
 
A Cul3-based E3 ligase removes Aurora B from mitotic chromosomes, regulating mitotic progression and completion of cytokinesis in human cells.
Sumara I., Quadroni M., Frei C., Olma M.H., Sumara G., Ricci R., Peter M., 2007/06. Developmental cell, 12 (6) pp. 887-900. Peer-reviewed.
Closely related dermatophyte species produce different patterns of secreted proteins.
Giddey K., Favre B., Quadroni M., Monod M., 2007/02. Fems Microbiology Letters, 267 (1) pp. 95-101. Peer-reviewed.
 
Autoproteolysis of PIDD marks the bifurcation between pro-death caspase-2 and pro-survival NF-kappaB pathway.
Tinel A., Janssens S., Lippens S., Cuenin S., Logette E., Jaccard B., Quadroni M., Tschopp J., 2007/01. EMBO Journal, 26 (1) pp. 197-208. Peer-reviewed.
 
Chemical derivatization of phosphoserine and phosphothreonine containing peptides to increase sensitivity for MALDI-based analysis and for selectivity of MS/MS analysis.
Arrigoni G., Resjö S., Levander F., Nilsson R., Degerman E., Quadroni M., Pinna L.A., James P., 2006/02. Proteomics, 6 (3) pp. 757-766. Peer-reviewed.
 
Comparative protein profiling identifies elongation factor-1beta and tryparedoxin peroxidase as factors associated with metastasis in Leishmania guyanensis.
Walker J., Acestor N., Gongora R., Quadroni M., Segura I., Fasel N., Saravia N.G., 2006. Molecular and Biochemical Parasitology, 145 (2) pp. 254-264. Peer-reviewed.
 
Identification of novel and cell type enriched cofactors of the transcription activation domain of RelA (p65 NF-kappaB).
Owen H.R., Quadroni M., Bienvenut W., Buerki C., Hottiger M.O., 2005. Journal of proteome research, 4 (4) pp. 1381-1390. Peer-reviewed.
 
MSight: an image analysis software for liquid chromatography-mass spectrometry.
Palagi P.M., Walther D., Quadroni M., Catherinet S., Burgess J., Zimmermann-Ivol C.G., Sanchez J.C., Binz P.A., Hochstrasser D.F., Appel R.D., 2005. Proteomics, 5 (9) pp. 2381-4. Peer-reviewed.
 
Activation/division of lymphocytes results in increased levels of cytoplasmic activation/proliferation-associated protein-1: prototype of a new family of proteins.
Grill B., Wilson G.M., Zhang K.X., Wang B., Doyonnas R., Quadroni M., Schrader J.W., 2004. Journal of Immunology, 172 (4) pp. 2389-2400. Peer-reviewed.
 
Multiplication of an ancestral gene encoding secreted fungalysin preceded species differentiation in the dermatophytes Trichophyton and Microsporum.
Jousson O., Léchenne B., Bontems O., Capoccia S., Mignon B., Barblan J., Quadroni M., Monod M., 2004. Microbiology, 150 (Pt 2) pp. 301-310. Peer-reviewed.
 
Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics.
Quadroni M., Ducret A., Stöcklin R., 2004. Proteomics, 4 (8) pp. 2211-2215.
 
Secreted subtilisin gene family in Trichophyton rubrum.
Jousson O., Léchenne B., Bontems O., Mignon B., Reichard U., Barblan J., Quadroni M., Monod M., 2004. Gene, 339 pp. 79-88. Peer-reviewed.
 
Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session.
Binz P.A., Abdi F., Affolter M., Allard L., Barblan J., Bhardwaj S., Bienvenut W.V., Bulet P., Burgess J., Carrette O. et al., 2003. Proteomics, 3 (8) pp. 1562-1566. Peer-reviewed.
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