Département de biologie structurale et bioinformatique

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2017

Scientific Articles

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Annotation of functional impact of voltage-gated sodium channel mutationsHinard, Valérie; Britan, Aurore; Schaeffer, Mathieu; Zahn, Monique; ... Gaudet, Pascale
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Anti-Apolipoprotein A-1 IgG Predict All-Cause Mortality and Are Associated with Fc Receptor-Like 3 PolymorphismsAntiochos, Panagiotis; Marques-Vidal, Pedro; Virzi, Julien; Pagano, Sabrina; ... Vuilleumier, Nicolas
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Association of Lectin Pathway Protein Levels and Genetic Variants Early after Injury with Outcomes after Severe Traumatic Brain Injury: A Prospective Cohort StudyOsthoff, Michael; Walder, Bernhard; Delhumeau-Cartier, Cécile; Trendelenburg, Marten; Turck, Natacha
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Characterisation of extracellular vesicle-subsets derived from brain endothelial cells and analysis of their protein cargo modulation after TNF exposureDozio, Vito; Sanchez, Jean-Charles;
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Clinical Mass spectrometry proteomics (cMSP) for medical laboratory: What does the future hold?Lehmann, Sylvain; Brede, Cato; Lescuyer, Pierre; Cocho, José A.; ... Hirtz, Christophe
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Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolismRoomp, Kirsten; Kristinsson, Hjalti; Schvartz, Domitille; Ubhayasekera, Kumari; ... Bergsten, Peter
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Effects of interpersonal violence-related post-traumatic stress disorder (PTSD) on mother and child diurnal cortisol rhythm and cortisol reactivity to a laboratory stressor involving separationCordero, Maria I; Moser, Dominik A; Manini, Aurelia; Suardi, Francesca; ... Schechter, Daniel
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Efficacy of intravitreal aflibercept in macular telangiectasia type 1 is linked to the ocular angiogenic profileKowalczuk, Laura; Matet, Alexandre; Dirani, Ali; Daruich, Alejandra; ... Behar-Cohen, Francine
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Extracellular Vesicles in Bile as Markers of Malignant Biliary StenosesSeverino, Valeria; Dumonceau, Jean-Marc; Delhaye, Myriam; Moll, Solange; ... Farina, Annarita
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From the Cover: High Susceptibility of Lrig1 Sebaceous Stem Cells to TCDD in MiceFontao, Fabienne; Barnes, Laurent; Kaya, Gurkan; Saurat, Jean-Hilaire; Sorg, Olivier
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H-FABP: A new biomarker to differentiate between CT-positive and CT-negative patients with mild traumatic brain injuryLagerstedt, Linnéa; Egea-Guerrero, Juan José; Bustamante, Alejandro; Montaner, Joan; ... Sanchez, Jean-Charles
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Impact of CD14 Polymorphisms on Anti-Apolipoprotein A-1 IgG-Related Coronary Artery Disease Prediction in the General PopulationAntiochos, Panagiotis; Marques-Vidal, Pedro; Virzi, Julien; Pagano, Sabrina; ... Vuilleumier, Nicolas
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Pharmacological Intervention to Modulate HDL: What Do We Target?Woudberg, Nicholas J; Pedretti, Sarah; Lecour, Sandrine; Schulz, Rainer; ... Frias, Miguel A
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Proteomic discovery and verification of serum amyloid A as a predictor marker of patients at risk of post-stroke infection: a pilot studyAzurmendi Gil, Leire; Lapierre, Vanessa; Schneider, J; Montaner, J; ... Sanchez, Jean-Charles
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Risk factors for community-acquired acute kidney injury in patients with and without chronic kidney injury and impact of its initial management on prognosis: a prospective observational studyStucker, Fabien Jérôme; Ponte, Belen; De La Fuente, Victoria; Alves, Cyrielle; ... Saudan, Patrick
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The neXtProt knowledgebase on human proteins: 2017 updateGaudet, Pascale; Michel, Pierre-André Albert; Zahn, Monique; Britan, Aurore; ... Bairoch, Amos Marc
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Triage by ranking to support the curation of protein interactionsMottin, Luc; Pasche, Emilie; Gobeill, Julien; Rech De Laval, Valentine; ... Ruch, Patrick

Professional Articles

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Diagnostic des hémoglobinopathies par spectrométrie de masseCoelho Graca, Didia; Scherl, Alexander; Samii, Kaveh; Hochstrasser, Denis; Lescuyer, Pierre

2016

Scientific Articles

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A systems proteomics view of the endogenous human claudin protein familyLiu, Fei; Koval, Michael; Ranganathan, Shoba; Fanayan, Susan; ... Baker, Mark S
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Anti-ApoA-1 IgG serum levels predict worse post-stroke outcomesCarbone, Federico; Satta, Nathalie; Montecucco, Fabrizio; Virzi, Julien; ... Vuilleumier, Nicolas
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Anti-apolipoprotein A-1 auto-antibodies as active modulators of atherothrombosisPagano, Sabrina; Carbone, Federico; Burger, Fabienne; Roth, Aline; ... Vuilleumier, Nicolas
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Association between anti-apolipoprotein A-1 antibodies and cardiovascular disease in the general population. Results from the CoLaus studyAntiochos, Panagiotis; Marques-Vidal, Pedro; Virzi, Julien; Pagano, Sabrina; ... Vuilleumier, Nicolas
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Blood DNA Yield but Not Integrity or Methylation Is Impacted After Long-Term StorageBulla, Alexandre; De Witt, Brian; Ammerlaan, Wim; Betsou, Fay; Lescuyer, Pierre
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Cerebral ischemic events in patients with pancreatic cancer: A retrospective cohort study of 17 patients and a literature reviewBonnerot, Mathieu; Humbertjean, Lisa; Mione, Gioia; Lacour, Jean-Christophe; ... Richard, Sébastien
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Comparison of Cardiac and Non-Cardiac Biomarkers for Risk Stratification in Elderly Patients with Non-Massive Pulmonary EmbolismVuilleumier, Nicolas; Simona, Aurélien; Méan, Marie; Limacher, Andreas; ... Righini, Marc Philip
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Detection of busulfan adducts on proteinsAcosta Martin, Adelina Elena; Antinori Malaspina, Paola; Uppugunduri Satyanarayana, Chakradhara Rao; Daali, Youssef; ... Lescuyer, Pierre
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Diagnostic performance of peroxiredoxin 1 to determine time-of-onset of acute cerebral infarctionRichard, Sébastien; Lapierre, Vanessa; Girerd, Nicolas; Bonnerot, Mathieu; ... Sanchez, Jean-Charles
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Evaluation and identification of dioxin exposure biomarkers in human urine by high-resolution metabolomics, multivariate analysis and in vitro synthesisJeanneret, Fabienne; Tonoli, David; Hochstrasser, Denis; Saurat, Jean-Hilaire; ... Rudaz, Serge
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Evaluation of steroidomics by liquid chromatography hyphenated to mass spectrometry as a powerful analytical strategy for measuring human steroid perturbationsJeanneret, Fabienne; Tonoli, David; Rossier, Michel; Saugy, Martial; ... Rudaz, Serge
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Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016Van Eyk, Jennifer E; Corrales, Fernando Jose; Aebersold, Ruedi; Cerciello, Ferdinando; ... Omenn, Gilbert S
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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1Deutsch, Eric W; Overall, Christopher M; Van Eyk, Jennifer E; Baker, Mark S; ... Omenn, Gilbert S
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ICEPO: the ion channel electrophysiology ontologyHinard, Valérie; Britan, Aurore; Rougier, Jean-Sébastien; Bairoch, Amos Marc; ... Gaudet, Pascale
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Intraplaque Expression of C-Reactive Protein Predicts Cardiovascular Events in Patients with Severe Atherosclerotic Carotid Artery StenosisBonaventura, Aldo; Mach, François; Roth, Aline; Lenglet, Sébastien; ... Carbone, Federico
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LacaScore: a novel plasma sample quality control tool based on ascorbic acid and lactic acid levelsTrezzi, Jean-Pierre; Bulla, Alexandre; Bellora, Camille; Rose, Michael; ... Betsou, Fay
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Looking for missing proteins in the proteome of human spermatozoa: an updateVandenbrouck, Yves; Lane, Lydie; Carapito, Christine; Duek, Paula Debora; ... Pineau, Charles
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Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational ModificationsOmenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Beavis, Ronald C; ... Deutsch, Eric W
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New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approachZufferey Bakos, Anne; Ibberson, Mark; Reny, Jean-Luc; Nolli, Severine; ... Fontana, Pierre
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neXtA5: accelerating annotation of articles via automated approaches in neXtProtMottin, Luc; Gobeill, Julien; Pasche, Emilie; Michel, Pierre-André Albert; ... Ruch, Patrick
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PepPSy: a web server to prioritize gene products in experimental and biocuration workflowsSallou, Olivier; Duek, Paula Debora; Darde, Thomas A; Collin, Olivier; ... Chalmel, Frédéric
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Profound hyponatraemia in the emergency department: seasonality and risk factorsHuwyler, Tibor; Stirnemann, Jérôme; Vuilleumier, Nicolas; Martin, Christopher; ... Rutschmann, Olivier Thierry
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Prognostic value of PCSK9 levels in patients with acute coronary syndromesGencer, Baris; Montecucco, Fabrizio; Nanchen, David; Carbone, Federico; ... Mach, François
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Proteomic and lipidomic analyses of paraoxonase defined high density lipoprotein particles: association of paraoxonase with the anti-coagulant, protein S.Moren, Xenia; Lhomme, Marie; Bulla, Alexandre; Sanchez, Jean-Charles; ... James, Richard W
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The Associations of Blood Kidney Injury Molecule-1 and Neutrophil Gelatinase-Associated Lipocalin with Progression from CKD to ESRD.Alderson, Helen V; Ritchie, James P; Pagano, Sabrina; Middleton, Rachel J; ... Kalra, Philip A
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The missing protein landscape of human chromosomes 2 and 14: progress and current statusDuek, Paula; Bairoch, Amos Marc; Gateau, Alain; Vandenbrouck, Yves; Lane, Lydie
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Vitamin D receptor is expressed within human carotid plaques and correlates with pro-inflammatory M1 macrophagesCarbone, Federico; Satta, Nathalie; Burger, Fabienne; Roth, Aline; ... Montecucco, Fabrizio

Doctoral Thesis

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Blood proteome characterization of the interplay between glycation and aspirin-mediated acetylation in vitro and in diabetic patientsFinamore, Francesco;

2015

Scientific Articles

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A Population-Based Model to Consider the Effect of Seasonal Variation on Serum 25(OH)D and Vitamin D StatusVuistiner, Philippe; Rousson, Valentin; Henry, Hugues; Lescuyer, Pierre; ... Guessous, Idris
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Anti-apoA-1 auto-antibodies increase mouse atherosclerotic plaque vulnerability, myocardial necrosis and mortality triggering TLR2 and TLR4Montecucco, Fabrizio; Braunersreuther, Vincent; Burger, Fabienne; Lenglet, Sébastien; ... Vuilleumier, Nicolas
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Aryl Hydrocarbon Receptor Activation in Acne Vulgaris Skin: A Case Series from the Region of Naples, ItalyFabbrocini, Gabriella; Kaya, Gurkan; Caseiro Silverio, Patricia; De Vita, Valerio; ... Saurat, Jean-Hilaire
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Aspirin-mediated acetylation of haemoglobin increases in presence of high glucose concentration and decreases protein glycationFinamore, Francesco; Priego-Capote, Feliciano; Nolli, Severine; Fontana, Pierre; Sanchez, Jean-Charles
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Association between Agent Orange Exposure and Nonmelanotic Invasive Skin Cancer: A Pilot StudySorg, Olivier;
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Auto-antibodies as possible markers and mediators of ischemic, dilated, and rhythmic cardiopathiesSatta, Nathalie; Vuilleumier, Nicolas;
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Biomarkers for cardiovascular risk assessment in autoimmune diseasesTeixeira, Priscila Camillo; Ferber, Philippe; Vuilleumier, Nicolas; Cutler, Paul;
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C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc1 Complex Assembly and Supercomplex StabilizationDesmurs-Rousseau, Marjorie; Foti, Michelangelo; Raemy, Etienne; Vaz, Frédéric Maxime; ... Lane, Lydie
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Cardiac biomarkers and clinical scores for risk stratification in elderly patients with non-high-risk pulmonary embolismVuilleumier, Nicolas; Limacher, Andreas; Méan, M; Choffat, J; ... Righini, Marc Philip
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CD14 as a Mediator of the Mineralocorticoid Receptor-Dependent Anti-apolipoprotein A-1 IgG Chronotropic Effect on CardiomyocytesMannic, Tiphaine; Satta, Nathalie; Pagano, Sabrina; Python, Magaly; ... Vuilleumier, Nicolas
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Cerebrospinal fluid angiotensin-converting enzyme for diagnosis of neurosarcoidosisBridel, Claire; Courvoisier, Delphine; Vuilleumier, Nicolas; Lalive, Patrice H;
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Characterisation of the influences of aspirin-acetylation and glycation on human plasma proteinsFinamore, Francesco; Priego-Capote, Feliciano; Nolli, Severine; Zufferey Bakos, Anne; ... Sanchez, Jean-Charles
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Comparative analysis of cerebrospinal fluid from the meningo-encephalitic stage of T. b. gambiense and rhodesiense sleeping sickness patients using TMT quantitative proteomicsTiberti, Natalia; Sanchez, Jean-Charles;
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Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14Carapito, Christine; Lane, Lydie; Benama, Mohamed; Opsomer, Alisson; ... Vandenbrouck, Yves
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Converting neXtProt into Linked Data and nanopublicationsChichester, Christine; Karch, Olivier; Gaudet, Pascale; Lane, Lydie; ... Bairoch, Amos Marc
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Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreatBabbitt, Patricia C; Bagos, Pantelis G; Bairoch, Amos Marc; Bateman, Alex; ... Vriend, Gerrit
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Data from proteomic characterization of the role of Snail1 in murine mesenchymal stem cells and 3T3-L1 fibroblasts differentiationPeláez-García, A; Barderas, R; Mendes, M; Lopez-Lucendo, M; ... Casal, J I
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De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteinsSquillaro, Tiziana; Severino, Valeria; Alessio, Nicola; Farina, Annarita; ... Galderisi, Umberto
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Deep Question Answering for protein annotationGobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; ... Ruch, Patrick
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Devising a Consensus Framework for Validation of Novel Human Coding LociBruford, Elspeth A; Lane, Lydie; Harrow, Jennifer;
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Diabetogenic milieus induce specific changes in mitochondrial transcriptome and differentiation of human pancreatic isletsBrun, Thierry; Li, Ning; Jourdain, Alexis; Gaudet, Pascale; ... Maechler, Pierre
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Diagnostic and prognostic value of autoantibodies anti-apolipoprotein A-1 and anti-phosphorylcholine in acute non-ST elevation myocardial infarctionRubini Gimenez, Maria; Pagano, Sabrina; Virzi, Julien; Montecucco, Fabrizio; ... Mueller, Christian
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E-selectin and vascular cell adhesion molecule-1 as biomarkers of 3-month outcome in cerebrovascular diseasesRichard, Sébastien; Lagerstedt, Linnéa; Burkhard, Pierre; Debouverie, Marc; ... Sanchez, Jean-Charles
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Ethical Criteria for Human Trials of Stem-Cell-Derived Dopaminergic Neurons in Parkinson's DiseaseHurst, Samia; Mauron, Alex; Momjian, Shahan Marc; Burkhard, Pierre;
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Evaluation of electrode position in deep brain stimulation by image fusion (MRI and CT)Barnaure, I; Pollak, Pierre; Momjian, Shahan Marc; Horvath, Judit; ... Vargas Gomez, Maria Isabel
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Gastric bypass in morbid obese patients is associated with reduction in adipose tissue inflammation via N-oleoylethanolamide (OEA)-mediated pathwaysMontecucco, Fabrizio; Lenglet, Sébastien; Quercioli, Alessandra; Burger, Fabienne; ... Pataky, Zoltan
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Gene Ontology Consortium: going forwardGaudet, Pascale;
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Genetic deletion of the adaptor protein p66Shc increases susceptibility to short-term ischaemic myocardial injury via intracellular salvage pathwaysAkhmedov, Alexander; Montecucco, Fabrizio; Braunersreuther, Vincent; Camici, Giovanni G; ... Lüscher, Thomas F
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Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome ProjectJumeau, Fanny; Com, Emmanuelle; Lane, Lydie; Duek, Paula Debora; ... Pineau, Charles
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Human sweat metabolomics for lung cancer screeningCalderón-Santiago, Mónica; Priego-Capote, Feliciano; Turck, Natacha; Robin, Xavier; ... Luque de Castro, María D
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Identification of hemoglobin variants by top-down mass spectrometry using selected diagnostic product ionsCoelho Graca, Didia; Hartmer, Ralf; Jabs, Wolfgang; Beris, Photis; ... Lescuyer, Pierre
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Impact of systemic inflammation and autoimmune diseases on apoA-I and HDL plasma levels and functionsMontecucco, Fabrizio; Favari, Elda; Norata, Giuseppe Danilo; Ronda, Nicoletta; ... Vuilleumier, Nicolas
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Improving reconstituted HDL composition for efficient post-ischemic reduction of ischemia reperfusion injuryBrulhart-Meynet, Marie-Claude; Braunersreuther, Vincent; Brinck, Jonas; Montecucco, Fabrizio; ... Frias, Miguel
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Key challenges for the creation and maintenance of specialist protein resourcesHolliday, Gemma L; Bairoch, Amos Marc; Bagos, Pantelis G; Chatonnet, Arnaud; ... Bateman, Alex
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L-Tryptophan as a Novel Potential Pharmacological Treatment for Wound Healing via Aryl Hydrocarbon Receptor ActivationBarouti, Neda; Mainetti, Carlo; Fontao, Lionel; Sorg, Olivier;
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Mass spectrometry-based quantification of malignant biliary stenosis biomarkers in human bileFarina, Annarita; Adrait, Annie; Dumonceau, Jean-Marc; Delhaye, Myriam; ... Coute, Yohann
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Measuring Serum Amyloid A for Infection Prediction in Aneurysmal Subarachnoid HemorrhageAzurmendi Gil, Leire; Degos, Vincent; Tiberti, Natalia; Kapandji, Natacha; ... Sanchez, Jean-Charles
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Mechanisms of local invasion in enteroendocrine tumors: Identification of novel candidate cytoskeleton-associated proteins in an experimental mouse model by a proteomic approach and validation in human tumorsCouderc, Christophe; Bollard, Julien; Coute, Yohann; Massoma, Patrick; ... Roche, Colette
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Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein IdentificationOmenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Beavis, Ronald C; ... Deutsch, Eric W
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N-terminome analysis of the human mitochondrial proteomeVaca Jacome, Alvaro Sebastian; Rabilloud, Thierry; Schaeffer-Reiss, Christine; Rompais, Magali; ... Carapito, Christine
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Neopterin plasma concentrations in patients with aneurysmal subarachnoid hemorrhage: correlation with infection and long-term outcomeAzurmendi Gil, Leire; Degos, Vincent; Tiberti, Natalia; Kapandji, Natacha; ... Sanchez, Jean-Charles
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Neuropathology of Parkinsonism in Alzheimer's diseaseKovari, Eniko Veronika; Bouras, Constantin; Herrmann, François; Burkhard, Pierre; ... Xekardaki, Aikaterini
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Pathophysiology and Treatments of Oxidative Injury in Ischemic Stroke: Focus on the Phagocytic NADPH Oxidase 2Carbone, Federico; Teixeira, Priscila Camillo; Braunersreuther, Vincent; Mach, François; ... Montecucco, Fabrizio
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Potent Anti-HIV Chemokine Analogs Direct Post-Endocytic Sorting of CCR5Boensch, Claudia; Munteanu, Nicoleta Mihaela; Rossitto-Borlat, Irène; Fuerstenberg, Alexandre; Hartley, Oliver
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Proteomics in mechanistic toxicology: history, concepts, achievements, caveats and potentialRabilloud, Thierry; Lescuyer, Pierre;
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Quantification Of HER2 By Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer TissuesSteiner, Carine; Tille, Jean-Christophe; Lamerz, Jens; Kux van Geijtenbeek, Sabine; ... Ducret, Axel
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Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome ProjectHorvatovich, Péter; Lane, Lydie;
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