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1.
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10 p, 859.5 KB |
Predicting AT(N) pathologies in Alzheimer's disease from blood-based proteomic data using neural networks
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Zhang, Y. (University of Oxford) ;
Ghose, U. (University of Oxford) ;
Buckley, N.J. (University of Oxford) ;
Engelborghs, S. (Vrije Universiteit Brussel) ;
Sleegers, K. (University of Antwerp) ;
Frisoni, G.B. (Department of Psychiatry. University of Geneva) ;
Wallin, A. (University of Gothenburg) ;
Lleó, Alberto (Institut d'Investigació Biomèdica Sant Pau) ;
Popp, J. (University of Zürich) ;
Martinez-Lage, P. (CITA-Alzheimer Foundation) ;
Legido-Quigley, C. (Steno Diabetes Center) ;
Barkhof, F. (University College London) ;
Zetterberg, H. (Kong Kong Center for Neurodegenerative Diseases) ;
Visser, P.J. (VU University Medical Center) ;
Bertram, L. (University of Oslo) ;
Lovestone, S. (Janssen RD) ;
Nevado-Holgado, Alejo (University of Oxford) ;
Shi, L. (University of Oxford) ;
Universitat Autònoma de Barcelona
Background and objective: Blood-based biomarkers represent a promising approach to help identify early Alzheimer's disease (AD). Previous research has applied traditional machine learning (ML) to analyze plasma omics data and search for potential biomarkers, but the most modern ML methods based on deep learning has however been scarcely explored. [...]
2022 -  10.3389/fnagi.2022.1040001
Frontiers in aging neuroscience, Vol. 14 (29 2022) , p. 1040001
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2.
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16 p, 3.5 MB |
Biomarkers Found in the Tumor Interstitial Fluid may Help Explain the Differential Behavior Among Keratinocyte Carcinomas
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Matas-Nadal, Clara (Hospital de Santa Caterina (Salt, Girona)) ;
Bech-Serra, Joan-Josep (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Gatius, Sònia (Hospital Universitari Arnau de Vilanova) ;
Gomez, Xavier (Universitat de Lleida. Departament de Ciències Mèdiques Bàsiques) ;
Ribes-Santolaria, Marina (Universitat de Lleida. Departament de Ciències Mèdiques Bàsiques) ;
Guasch-Vallés, Marta (Universitat de Lleida. Departament de Ciències Mèdiques Bàsiques) ;
Pedraza, Neus (Universitat de Lleida. Departament de Ciències Mèdiques Bàsiques) ;
Casanova, Josep M. (Hospital Universitari Arnau de Vilanova) ;
De La Torre Gómez, Gisela Carolina (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Gari, Eloi (Universitat de Lleida. Departament de Ciències Mèdiques Bàsiques) ;
Aguayo-Ortiz, Rafael S. (Hospital Universitari Arnau de Vilanova)
Basal cell carcinomas (BCCs) and cutaneous squamous cell carcinomas (SCCs) are the most frequent types of cancer, and both originate from the keratinocyte transformation, giving rise to the group of tumors called keratinocyte carcinomas (KCs). [...]
2023 - 10.1016/j.mcpro.2023.100547
Molecular and Cellular Proteomics, Vol. 22 Núm. 6 (june 2023) , p. 100547
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3.
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15 p, 1.5 MB |
ApoL1 levels in high density lipoprotein and cardiovascular event presentation in patients with familial hypercholesterolemia
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Cubedo, Judit (Hospital de la Santa Creu i Sant Pau (Barcelona, Catalunya)) ;
Padró, Teresa (Institut d'Investigació Biomèdica Sant Pau) ;
Alonso, Rodrigo (Jimenez Diaz Foundation) ;
Mata, Pedro (Fundación Hipercolesterolemia Familiar) ;
Badimon, Lina (Institut d'Investigació Biomèdica Sant Pau) ;
Universitat Autònoma de Barcelona
HDL composition rather than HDL-cholesterol (HDL-C) levels seems to be a key determinant of HDL-induced atheroprotection. Heterozygous familial hypercholesterolemia (FH) patients, with lifelong exposure to high LDL levels, show a high prevalence of premature coronary artery disease. [...]
2016 - 10.1194/jlr.P061598
Journal of Lipid Research, Vol. 57 Núm. 6 (june 2016) , p. 1059-1073
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4.
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50 p, 28.5 MB |
Pan-cancer proteogenomics connects oncogenic drivers to functional states
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Li, Yize (Washington University in St. Louis) ;
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Tokheim, Collin (Harvard T.H. Chan School of Public Health) ;
Bailey, Matthew H. (Brigham Young University) ;
Yaron, Tomer (Weill Cornell Medicine) ;
Stathias, Vasileios (University of Miami Miller School of Medicine) ;
Geffen, Yifat (Massachusetts General Hospital) ;
Imbach, Kathleen (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Cao, Song (McDonnell Genome Institute) ;
Anand, Shankara (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Akiyama, Yo (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Liu, Wenke (NYU Grossman School of Medicine) ;
Wyczalkowski, Matthew A. (McDonnell Genome Institute) ;
Song, Yizhe (McDonnell Genome Institute) ;
Storrs, Erik P. (McDonnell Genome Institute) ;
Wendl, Michael C. (Washington University in St. Louis) ;
Zhang, Wubing (Dana-Farber Cancer Institute (Boston, Estats Units)) ;
Sibai, Mustafa (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Liang, Wen-Wei (McDonnell Genome Institute) ;
Terekhanova, Nadezhda V. (McDonnell Genome Institute) ;
Martins Rodrigues, Fernanda (McDonnell Genome Institute) ;
Clauser, Karl R. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Heiman, David I. (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhang, Qing (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Aguet, Francois (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Calinawan, Anna Pamela (Icahn School of Medicine at Mount Sinai) ;
Dhanasekaran, Saravana Mohan (University of Michigan) ;
Birger, Chet (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Satpathy, Shankha (Broad Institute of Massachusetts Institute of Technology and Harvard) ;
Zhou, Daniel Cui (McDonnell Genome Institute) ;
Wang, Liang-Bo (McDonnell Genome Institute) ;
Baral, Jessika (McDonnell Genome Institute) ;
Johnson, Jared L. (Weill Cornell Medicine) ;
Huntsman, Emily M. (Weill Cornell Medicine) ;
Pugliese, Pietro (University of Sannio (Benevento, Itàlia)) ;
Colaprico, Antonio (University of Miami Miller School of Medicine) ;
Iavarone, Antonio (University of Miami Miller School of Medicine) ;
Chheda, Milan G. (Washington University in St. Louis) ;
Ricketts, Christopher J. (National Institutes of Health) ;
Fenyö, David (NYU Grossman School of Medicine) ;
Payne, Samuel H. (Brigham Young University) ;
Rodriguez, Henry (Office of Cancer Clinical Proteomics Research) ;
Robles, Ana I. (Office of Cancer Clinical Proteomics Research) ;
Gillette, Michael A. (Harvard Medical School) ;
Kumar-Sinha, Chandan (University of Michigan) ;
Lazar, Alexander (The University of Texas MD Anderson Cancer Center) ;
Cantley, Lewis (Weill Cornell Medicine) ;
Getz, Gad A. (Harvard Medical School) ;
Ding, Li (Siteman Cancer Center) ;
An, Eunkyung ;
Anurag, Meenakshi ;
Bavarva, Jasmin ;
Birrer, Michael J. ;
Ceccarelli, Michele ;
Chan, Daniel W. ;
Chinnaiyan, Arul M. ;
Cho, Hanbyul ;
Chowdhury, Shrabanti ;
Cieslik, Marcin P. ;
da Veiga Leprevost, Felipe ;
Day, Corbin ;
Domagalski, Marcin J. ;
Dou, Yongchao ;
Druker, Brian J. ;
Edwards, Nathan ;
Ellis, Matthew J. ;
Selvan, Myvizhi Esai ;
Foltz, Steven M. ;
Francis, Alicia ;
Gonzalez Robles, Tania J. ;
Gosline, Sara J. C. ;
Gümüş, Zeynep H. ;
Hiltke, Tara ;
Hong, Runyu ;
Hostetter, Galen ;
Hu, Yingwei ;
Huang, Chen ;
Huntsman, Emily ;
Jaehnig, Eric J. ;
Jewel, Scott D. ;
Ji, Jiayi ;
Jiang, Wen ;
Katsnelson, Lizabeth ;
Ketchum, Karen A. ;
Kolodziejczak, Iga ;
Lei, Jonathan T. ;
Liao, Yuxing ;
Lindgren, Caleb M. ;
Liu, Tao ;
Ma, Weiping ;
McKerrow, Wilson ;
Nesvizhskii, Alexey I. ;
Newton, Chelsea ;
Oldroyd, Robert ;
Omenn, Gilbert S. ;
Paulovich, Amanda G. ;
Petralia, Francesca ;
Reva, Boris ;
Rodland, Karin D. ;
Ruggles, Kelly V. ;
Rykunov, Dmitry ;
Savage, Sara R. ;
Schadt, Eric E. ;
Schnaubelt, Michael ;
Schraink, Tobias ;
Shi, Zhiao ;
Smith, Richard D. ;
Song, Xiaoyu ;
Tan, Jimin ;
Thangudu, Ratna R. ;
Tignor, Nicole ;
Wang, Joshua M. ;
Wang, Pei ;
Wang, Ying Cindy ;
Wen, Bo ;
Wiznerowicz, Maciej ;
Yi, Xinpei ;
Zhang, Bing ;
Zhang, Hui ;
Zhang, Xu ;
Zhang, Zhen ;
Universitat Autònoma de Barcelona
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. [...]
2023 - 10.1016/j.cell.2023.07.014
Cell, Vol. 186 Núm. 18 (31 2023) , p. 3921-3944.e25
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13 p, 3.5 MB |
Proteomic Analysis of Human iPSC-Derived Neural Stem Cells and Motor Neurons Identifies Proteasome Structural Alterations
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Álvarez Pérez, Iñaki (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Tirado-Herranz, Adrián (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Alvarez-Palomo, Belén (Banc de Sang i Teixits (Barcelona, Catalunya)) ;
Osete, Jordi Requena (Oslo University Hospital (Oslo, Noruega)) ;
Edel, Michael J (Universitat Autònoma de Barcelona. Departament de Ciències Morfològiques)
Background: Proteins targeted by the ubiquitin proteasome system (UPS) are identified for degradation by the proteasome, which has been implicated in the development of neurodegenerative diseases. Major histocompatibility complex (MHC) molecules present peptides broken down by the proteasome and are involved in neuronal plasticity, regulating the synapse number and axon regeneration in the central or peripheral nervous system during development and in brain diseases. [...]
2023 - 10.3390/cells12242800
Cells, Vol. 12 (december 2023)
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9 p, 745.8 KB |
The EMIF-AD Multimodal Biomarker Discovery study : Design, methods and cohort characteristics
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Bos, Isabelle (Maastricht University) ;
Vos, Stephanie (Maastricht University) ;
Vandenberghe, Rik (Katholieke Universiteit Leuven) ;
Scheltens, Philip (Amsterdam UMC. University Medical Center) ;
Engelborghs, Sebastiaan (University of Antwerp) ;
Frisoni, Giovanni (IRCCS Instituto Centro San Giovanni di Dio Fatebenefratelli) ;
Molinuevo, José Luis (Fundació Pasqual Maragall) ;
Wallin, Anders (Institute of Neuroscience and Physiology) ;
Lleó, Alberto (Institut d'Investigació Biomèdica Sant Pau) ;
Popp, Julius (Lausanne University Hospital) ;
Martinez-Lage, Pablo (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ;
Baird, Alison (University of Oxford) ;
Dobson, Richard (NIHR University College London Hospitals) ;
Legido-Quigley, Cristina (King's College London) ;
Sleegers, Kristel (University of Antwerp) ;
Van Broeckhoven, Christine (University of Antwerp) ;
Bertram, Lars (University of Oslo) ;
Ten Kate, Mara (Amsterdam UMC. University Medical Center) ;
Barkhof, Frederik (Amsterdam UMC. University Medical Center) ;
Zetterberg, Henrik (UK Dementia Research Institute) ;
Lovestone, Simon (University of Oxford) ;
Streffer, Johannes (Janssen Pharmaceutical Companies) ;
Visser, Pieter Jelle (Vrije Universiteit Amsterdam) ;
Universitat Autònoma de Barcelona
There is an urgent need for novel, noninvasive biomarkers to diagnose Alzheimer's disease (AD) in the predementia stages and to predict the rate of decline. Therefore, we set up the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study. [...]
2018 - 10.1186/s13195-018-0396-5
Alzheimer's research & therapy, Vol. 10 Núm. 1 (june 2018) , p. 64
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11 p, 783.1 KB |
Discovery and validation of plasma proteomic biomarkers relating to brain amyloid burden by SOMAscan assay
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Shi, Liu (University of Oxford) ;
Westwood, Sarah (University of Oxford) ;
Baird, Alison L. (University of Oxford) ;
Winchester, Laura (University of Oxford) ;
Dobricic, Valerija (University of Lübeck) ;
Kilpert, Fabian (University of Lübeck) ;
Hong, Shengjun (University of Lübeck) ;
Franke, Andre (Christian-Albrechts-University of Kiel) ;
Hye, Abdul (King's College London) ;
Ashton, Nicholas J. (South London and Maudsley NHS Foundation) ;
Morgan, Angharad R. (Cardiff University) ;
Bos, Isabelle (Maastricht University) ;
Vos, Stephanie J.B. (Amsterdam UMC. University Medical Center) ;
Buckley, Noel J (University of Oxford) ;
Kate, Mara ten (Amsterdam UMC. University Medical Center) ;
Scheltens, Philip (Amsterdam UMC. University Medical Center) ;
Vandenberghe, Rik (University Hospitals Leuven (Bèlgica)) ;
Gabel, Silvy (Laboratory for Cognitive Neurology) ;
Meersmans, Karen (Laboratory for Cognitive Neurology) ;
Engelborghs, Sebastiaan (VUB University Hospital Brussels (UZ Brussel)) ;
De Roeck, Ellen E. (Institute Born-Bunge. University of Antwerp) ;
Sleegers, Kristel (Center for Molecular Neurology. VIB) ;
Frisoni, Giovanni B. (IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli) ;
Blin, Olivier (Aix-Marseille Université) ;
Richardson, Jill C. (GlaxoSmithKline R&D) ;
Bordet, Régis (University of Lille) ;
Molinuevo, José Luis (Hospital Clínic i Provincial de Barcelona) ;
Rami, Lorena (Universitat Pompeu Fabra) ;
Wallin, Anders (Sahlgrenska Academy at University of Gothenburg) ;
Kettunen, Petronella (University of Oxford) ;
Tsolaki, Magda (AHEPA University Hospital (Grècia)) ;
Verhey, Frans (Maastricht University) ;
Lleó, Alberto (Institut d'Investigació Biomèdica Sant Pau) ;
Alcolea, Daniel (Institut d'Investigació Biomèdica Sant Pau) ;
Popp, Julius (Geneva University Hospitals) ;
Peyratout, Gwendoline (Lausanne University Hospital) ;
Martinez-Lage, Pablo (Fundación CITA-Alzhéimer Fundazioa) ;
Tainta, Mikel (CITA-Alzheimer Foundation) ;
Johannsen, Peter Copenhagen University Hospital ;
Teunissen, Charlotte E. (Vrije Universiteit Amsterdam) ;
Freund-Levi, Yvonne (King's College London) ;
Frölich, Lutz (University of Heidelberg) ;
Legido-Quigley, Cristina (Steno Diabetes Center) ;
Barkhof, Frederik (UCL Institutes of Neurology and Healthcare Engineering) ;
Blennow, Kaj (Sahlgrenska University Hospital (Suècia)) ;
Zetterberg, Henrik (UCL Institute of Neurology (Regne Unit)) ;
Baker, Susan (Janssen R&D) ;
Morgan, B.Paul (Cardiff University) ;
Streffer, Johannes (Janssen R&D. LLC) ;
Visser, Pieter Jelle (Karolinska Institutet (Estocolm, Suècia)) ;
Bertram, Lars (University of Oslo) ;
Lovestone, Simon (University of Oxford) ;
Nevado-Holgado, Alejo (University of Oxford) ;
Universitat Autònoma de Barcelona
Plasma proteins have been widely studied as candidate biomarkers to predict brain amyloid deposition to increase recruitment efficiency in secondary prevention clinical trials for Alzheimer's disease. [...]
2019 - 10.1016/j.jalz.2019.06.4951
Alzheimer's & Dementia, Vol. 15 Núm. 11 (november 2019) , p. 1478-1488
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15 p, 2.7 MB |
Plasma proteomic profiling identifies CD33 as a marker of HIV control in natural infection and after therapeutic vaccination
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Duran-Castells, Clara (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Prats, Anna (Institut Germans Trias i Pujol. Fundació Lluita Contra les Infeccions) ;
Oriol-Tordera, Bruna (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Llano Montero, Anuska (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Gálvez, Cristina (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Martínez Picado, Francisco Javier (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Ballana, Ester (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
García Vidal, Edurne (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Clotet Sala, Bonaventura (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Muñoz-Moreno, Jose A. (Institut Germans Trias i Pujol. Fundació Lluita Contra les Infeccions) ;
Hanke, Thomas (University of Oxford. The Jenner Institute) ;
Moltó, José (Institut Germans Trias i Pujol. Fundació Lluita Contra les Infeccions) ;
Mothe, Beatriz (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa) ;
Brander, Christian (Universitat Autònoma de Barcelona. Departament de Medicina) ;
Ruiz Riol, Marta (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. [...]
2023 - 10.1016/j.ebiom.2023.104732
EBioMedicine, Vol. 95 (september 2023)
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10.
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13 p, 162.5 KB |
Validation of plasma proteomic biomarkers relating to brain amyloid burden in the EMIF-Alzheimer's disease multimodal biomarker discovery cohort
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Westwood, Sarah (University of Oxford) ;
Baird, Alison L (University of Oxford) ;
Anand, Sneha N. (University of Oxford) ;
Nevado-Holgado, Alejo (University of Oxford) ;
Kormilitzin, Andrey (University of Oxford) ;
Shi, Liu (University of Oxford) ;
Hye, Abdul (King's College London) ;
Ashton, Nicholas J (University of Gothenburg) ;
Morgan, Angharad R. (Cardiff University) ;
Bos, Isabelle (Maastricht University) ;
Vos, Stephanie J.B. (Maastricht University) ;
Baker, Susan (Janssen R and D) ;
Buckley, Noel J (University of Oxford) ;
Ten Kate, Mara (Vrije Universiteit University Medical Center) ;
Scheltens, Philip (Vrije Universiteit University Medical Center) ;
Teunissen, Charlotte E. (Vrije Universiteit University Medical Center) ;
Vandenberghe, Rik (University Hospitals Leuven (Bèlgica)) ;
Gabel, Silvy (Ku Leuven) ;
Meersmans, Karen (Ku Leuven) ;
Engelborghs, Sebastiaan (Vrije Universiteit Brussel (VUB)) ;
De Roeck, Ellen E. (Vrije Universiteit Brussel (VUB)) ;
Sleegers, Kristel (Center for Molecular Neurology) ;
Frisoni, Giovanni B. (Irccs Istituto Centro San Giovanni di Dio Fatebenefratelli) ;
Blin, Olivier (Aix-Marseille Université) ;
Richardson, Jill C. (GlaxoSmithKline R and D) ;
Bordet, Régis (University of Lille) ;
Molinuevo, José Luis (Hospital Clínic i Provincial de Barcelona) ;
Rami, Lorena (Universitat Pompeu Fabra) ;
Wallin, Anders (Sahlgrenska Academy at University of Gothenburg) ;
Kettunen, Petronella (Sahlgrenska Academy at University of Gothenburg) ;
Tsolaki, Magda (AHEPA University Hospital (Grècia)) ;
Verhey, Frans (Maastricht University) ;
Lleó, Alberto (Institut d'Investigació Biomèdica Sant Pau) ;
Sala, Isabel (Institut d'Investigació Biomèdica Sant Pau) ;
Popp, Julius (Geneva University Hospitals) ;
Peyratout, Gwendoline (Lausanne University Hospital) ;
Martinez-Lage, Pablo (Geneva University Hospitals) ;
Tainta, Mikel (CITA-Alzheimer Foundation) ;
Johannsen, Peter (Copenhagen University Hospital) ;
Freund-Levi, Yvonne (Karolinska Institutet (Estocolm, Suècia)) ;
Frölich, Lutz (University of Heidelberg) ;
Dobricic, Valerija (University of Lübeck) ;
Legido-Quigley, Cristina (Steno Diabetes Center) ;
Bertram, Lars (University of Oslo) ;
Barkhof, Frederik (Ucl Institutes of Neurology and Healthcare Engineering) ;
Zetterberg, Henrik (Ucl Institute of Neurology) ;
Morgan, B.Paul (Cardiff University) ;
Streffer, Johannes (Janssen R and D. Llc) ;
Visser, Pieter Jelle (Vu University Medical Center) ;
Lovestone, Simon (Janssen R and D) ;
Universitat Autònoma de Barcelona
We have previously investigated, discovered, and replicated plasma protein biomarkers for use to triage potential trials participants for PET or cerebrospinal fluid measures of Alzheimer's disease (AD) pathology. [...]
2020 - 10.3233/JAD-190434
Journal of Alzheimer's disease, Vol. 74 Núm. 1 (2020) , p. 213-225
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