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Dr. Matthiesen has master in X-ray crystallography from University of Arhus Denmark (1998) under the supervision of Prof. Jens Nyborg famous for solving the ternary complex of EF-Tu. Dr. Matthiesen worked one and half year in EMBL, Heidleberg as a research assistant where he learned a multitude of laboratory techniques related to protein science, cell biology and drosophila development under supervision of Prof Anne Ephrussi. He obtained his PhD in computational proteomics in 2003 from Aalborg University under supervision by Prof. Karen Welinder and the thesis was evaluated by Prof Mathias Mann. During his PhD he developed a hybrid MSMS search engine with the capability to identify complex modification in semi open search by combining database dependent search with de novo sequencing. The thesis opened the door to a first post doc position in the prestigious laboratory in mass spectrometry based proteomics at University of Southern Denmark which at the time were led by pioneers in the field Prof Mathias Mann, Prof. Ole N Jensen and Prof. Peter Roepstorff. In 2006 Dr Matthiesen became group leader of bioinformatics group in CIC bioGUNE Spain. Since 2016 to current, Dr Matthiesen has led the experimental and computational biology group at NOVA medical school (NMS). In NMS Dr Matthiesen has been responsible for multiple courses and co-responsible for a master program. Dr. Matthiesen has been Principal Investigator on 15 research projects focusing on mainly clinical proteomics and data integration with clinical samples, securing more than 3.5 Million Euros (excluding salary awards) in funding from e.g. H2020, Carlsberg foundation, and Fundação para a Ciência e a Tecnologia Portugal. Currently, Dr. Matthiesen plays a pivotal role as the coordinator of the prestigious EU project, EVCA - Centre for Excellence in Diagnostic and Advanced Therapeutics based on Extracellular Vesicles (Horizon2020 GA n° 101079264, EVCA). Awards a) Since my PhD all my research activities have been funded by competitive calls from research funding agencies. These awards are 1) Carlsberg foundation (2004-2006), Ramon Cajal (2006-2008), Ciência Viva (2008-2013), FCT investigator (2013-2018, maximum score in all criteria) and CEEC investigator (2018-2025, the highest evaluation in scientific domain). b) Obtained funding from EU in the project “Excellence in Diagnostic and Advanced Therapeutics based on Extracellular Vesicles (Horizon2020 GA n° 101079264, EVCA)”. International networks: Dr. Matthiesen served as national representative in cost action Proteostasis. Dr. Matthiesen is currently national representative and work group leader in ProteoCure. Coordinator of EU project EVCA. Dissemination: Dr. Matthiesen takes a proactive role in knowledge dissemination by organizing conferences, workshops, winter retreats, and summer schools tailored for both early and senior career researchers. These events serve as platforms for knowledge exchange, skill development, and networking, empowering the next generation of scientists within the EVCA community. International networks: Supervision: PhD Matthiesen has supervised 2 bachelors, 4 master and 9 PhD students supervisor and co-supervisor and been responsible for eight post docs/senior researchers. He has also been opponent on 12 international PhD defenses and a number of national defenses. PhD Matthiesen co-established the master program in Computational Biology and Bioinformatics (MCBBI) of University NOVA Lisbon, which enrolls 20-30 master students per year. He is responsible for the semester course advanced metabolomics and proteomics and also provide lectures in the other course modules of the master program. These activities provide a source of students for his research laboratory.
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Identification

Personal identification

Full name
Rune Matthiesen

Citation names

  • Matthiesen, Rune

Author identifiers

Ciência ID
BB1A-A606-EE77
ORCID iD
0000-0002-6353-2616

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Medical Biotechnology

Languages

Language Speaking Reading Writing Listening Peer-review
Danish (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
German Upper intermediate (B2) Proficiency (C2) Upper intermediate (B2) Proficiency (C2) Intermediate (B1)
Portuguese Intermediate (B1) Intermediate (B1) Beginner (A1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2000/12/31 - 2003/12/16
Concluded
 Departmen of Life Science, University of Aalborg (Doutoramento)
Aalborg Universitet, Denmark
"Mass spectrometry in Proteomics" (THESIS/DISSERTATION)
1998/07/01 - 1999/07/01
Concluded
 Molecular biology (Mestrado)
Aarhus Universitet, Denmark
"Crystallography of ternary complex of eIF2" (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution 		Employer
2016/08/01 - Current Principal Investigator (Research) iNOVA4Health, Portugal
2013/08/01 - 2016/08/01 Principal Investigator (Research) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2008/08/01 - 2013/08/01 Principal Investigator (Research) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2006/01/01 - 2008/08/01 Principal Investigator (Research) CIC bioGUNE, Spain
CIC bioGUNE, Spain
2004/01/01 - 2006/01/01 Auxiliary Researcher (Research) Syddansk Universitet, Denmark
Syddansk Universitet, Denmark
2004/01/01 - 2005/01/01 Auxiliary Researcher (Research) European Bioinformatics Institute, United Kingdom
European Bioinformatics Institute, United Kingdom
Projects

Grant

Designation Funders
2022/10/01 - 2025/10/01 Centre for Excellence in Diagnostic and Advanced Therapeutics based on Extracellular Vesicles (EVCA)
101079264
Coordinator
Universidade Nova de Lisboa, Portugal
 EU Framework Programme for Research and Innovation Euratom
Ongoing
2022/10 - 2025/10 Centre for Excellence in Diagnostic and Advanced Therapeutics based on Extracellular Vesicles (EVCA)
101079264
Coordinator
EU Framework Programme for Research and Innovation Euratom
Cancelled
2022/01/17 - 2025/01/17 Optimizing mass spectrometry based detection of biomarkers for immunotherapy response across urologic cancers
PTDC/BTM-TEC/1746/2021
Principal investigator
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01 - 2022/12 Immune- and microenvironment- proteogenomics profiling for classifying lung cancer patients
02/SAICT/2017, 30088
 Science and Technology Foundation
2019/01 - 2022/12 Impact of B-cell deregulated pathways on tumor immune evasion - relevance for Diffuse Large B-Cell Lymphoma therapy response
02/SAICT/2017, 30087
 Science and Technology Foundation
2021/06/01 - 2022/06/01 How could we predict Intraductal and Cribriform Prostate Cancer in Prostate Biopsies?
a2018775d
Researcher
Liga Portuguesa Contra o Cancro
Ongoing
2018/01 - 2021/12 UBICODE
Project ID: 765445
 _H2020
2019/01/01 - 2019/10/31 iNOVA4Health - Programme in Translational Medicine (iBET, CEDOC/FCM, IPOLFG and ITQB)
UID/Multi/04462/2019
Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal

Universidade Nova de Lisboa, Portugal

Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal

Universidade Nova de Lisboa Medical School, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2023/09/01 - Current Life Sciences for a Healthy and Sustainable Future
LA/P/0087/2020
10.54499/LA/P/0087/2020
Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal

Universidade Nova de Lisboa Molecular Structural and Cellular Microbiology, Portugal

Universidade Nova de Lisboa, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Instituto Gulbenkian de Ciência, Portugal

Universidade de Lisboa Centro de Estudos Comparatistas, Portugal

BioResources 4 Sustainability, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/10/01 - 2022/09/30 Implementação de um teste de diagnóstico para avaliação clínica de doentes com cancro do pulmão com base na análise proteómica das características imunológicas e do micro-ambiente do tumor.
PTDC/BTM-TEC/30088/2017
Universidade Nova de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/10/01 - 2022/09/30 Sodium-iodide symporter posttranslational interactome: identification of novel targets to enhance iodide-related cancer therapy
PTDC/BIA-MOL/31787/2017
Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/10/01 - 2021/09/30 Diffuse Large B-cell lymphoma blood based proteome signatures
PTDC/BTM-TEC/30087/2017
Universidade Nova de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/06/01 - 2019/12/31 ProbeCOPD. Protease activity-based probes for Chronic Obstructive Pulmonary Disease diagnostics
PTDC/BBB-BEP/2463/2014
Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2014/03/01 - 2015/06/30 Identificação global por Espectrometria de Massa de aspirados bronquiais: visando modificações específicas do cancro do pulmão.
EXPL/DTP-PIC/0616/2013
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/06 - 2013/11 Molecular and nanotechnology-based approaches to improve the antitumor activity of small molecules
Provided by PTCRIS: 100930
100930
PTDC/SAU-FCF/100930/2008
Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Universidade do Porto Faculdade de Farmácia, Portugal

Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Cooperativa de Ensino Superior Politécnico e Universitário CRL, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 3 - 2011-2012
PEst-C/SAU/LA0003/2011
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2016/06 - 2021/02/28 Implications of Medical Low Dose Radiation Exposure
755523
Invited Scientist Fellow
Ongoing
Outputs

Publications

Book
  1. Matthiesen, R.. Preface. 2013.
    10.1007/978-1-62703-392_3
  2. Matthiesen, R.. Algorithms for database-dependent search of MS/MS data. 2013.
    10.1007/978-1-62703-392-3-5
  3. Fonseca, C.; Voabil, P.; Carvalho, A.S.; Matthiesen, R.. Tools for protein posttranslational modifications analysis: FAK, a case study. 2013.
    10.1007/978-1-62703-392-3-15
  4. Matthiesen, R.; Carvalho, A.S.. Methods and algorithms for quantitative proteomics by mass spectrometry. 2013.
    10.1007/978-1-62703-392-3-8
  5. Bunkenborg, J.; Matthiesen, R.. Interpretation of tandem mass spectra of posttranslationally modified peptides. 2013.
    10.1007/978-1-62703-392-3-6
  6. Matthiesen, R.. LC-MS spectra processing. 2013.
    10.1007/978-1-62703-392-3-2
  7. Matthiesen, R.; Bunkenborg, J.. Introduction to mass spectrometry-based proteomics. 2013.
    10.1007/978-1-62703-392-3-1
Conference abstract
  1. Pires, Carolina; Lainé, Hugo; Ehlers, Anna C.; Saramago, Ana; Moura, Margarida; Pojo, Marta; Cabrera, Rafael; et al. "MULTIOMICS APPROACH REVEALS ALTERATIONS UNDERLYING PAEDIATRIC THYROID CANCER RISK AND AGGRESSIVENESS". Paper presented in Congresso Português de Endocrinologia - 75ª Reunião Anual da SPEDM, Vilamoura, 2024.
    Published
  2. Pires, Carolina; Lainé, Hugo; Ehlers, Anna C.; Saramago, Ana; Moura, Margarida; Pojo, Marta; Cabrera, Rafael; et al. "Multiomics approach reveals alterations underlying paedriatic thyroid cancer risk and aggressiveness". Paper presented in Congresso Português de Endocrinologia 2024 - 75ª Reunião Anual da SPEDM, Vilamoura, 2024.
    Published
  3. Pires, Carolina; Lainé, Hugo; Ehlers, Anna C.; Saramago, Ana; Moura, Margarida; Cabrera, Rafael; Hamelmann, Stefan; et al. "Identification of novel genetic alterations that increase the risk and aggressiveness of paediatric thyroid cancer with impact in diagnosis and treatment". Paper presented in NMS Research Week, Lisboa, 2023.
    Published
  4. Ricardo Rodrigues; Ana Pinto; Marta Pojo; Diana Pacheco Sousa; Ana Sofia Carvalho; Hans C. Beck; Matthiesen, Rune; et al. Corresponding author: Ana Pinto.. "SPRY4 COMO POTENCIAL MEDIADOR DO PAPEL ANTI-TUMORAL DOS MACRÓFAGOS NO CARCINOMA ANAPLÁSICO DA TIRÓIDE". 2023.
  5. Rodrigues, Ricardo; Pinto, Ana Teresa; Pojo, Marta; Pacheco, Diana Sousa; Carvalho, Ana Sofia; Beck, Hans C.; Matthiesen, Rune; Pires, Carolina; et al.. "SPRY4 como potencial mediador do papel anti-tumoral dos macrófagos no carcinoma anaplásico da tiroide". Vilamoura, 2023.
    Published
  6. Inês Ferreira; Rita Machado-Oliveira; Matthiesen, Rune; Bruno Costa-Silva; Macedo, M P. "Exossomas derivados do Intestino como Mensageiro de Pré-diabetes". Paper presented in 16º Congresso Português de Diabetes, 2020.
    Published
  7. de Oliveira RM; Inês Antunes Ferreira; Teshima, Akiko; Matthiesen, Rune; Costa-Silva, Bruno; Macedo, Maria. Corresponding author: de Oliveira RM. "Prediabetes from the perspective of gut-derived exosomes". Vilamoura, 2020.
    Published
Conference paper
  1. Velosa Ferreira, Bruna; Ana Filipa Barahona Afonso; Pestana, Carolina; Ana Raquel lopes; Matthiesen, Rune; Caetano, Joana. "Extrecellular vesicle proteins as biomarker of outcome in multiple myeloma patients: a real world study". Paper presented in Perspectivas em Oncologia, Porto, 2022.
    Published
  2. Jones-Dias, Daniela; Carvalho, Ana Sofia; Moura, Inês Barata; Dill, Brian; Molina, Henrik; Manageiro, Vera; Caniça, Manuela; Matthiesen, Rune. "Quantitative proteome analysis of an Escherichia coli exposed to tetracycline reveals multiple affected cytoplasmic metabolic processes". 2016.
  3. Feliciano, Amelia; Bozanic, Vesna; Torres, Vukosava Milic; Matthiesen, Rune; Carvalho, Ana S.; Almeida, Andreia; Alexandre, Bruno; et al. "Proteomics of Red Blood Cells from Patients with Obstructive Sleep Apnea". 2015.
  4. Seabra, Catarina; Carvalho, Filipa; Gonçalves, João; Matthiesen, Rune; Fernandes, Susana; Ana, Neto; de Sousa, Mário; et al. "Validation of Rare Structural Variants in Portuguese Azoospermic Patients". 2012.
Conference poster
  1. Teshima, Akiko; Torrejon, Estefania; Ana Carvalho; Beck, Hans Christian; Matthiesen, Rune; Macedo, Maria Paula; de Oliveira RM. "Oral anti-diabetic drugs reverse diabetogenic proteomic signature of gut-derived extracellular vesicles". Paper presented in EASD(European Association for the Study of Diabetes) 59th Annual meeting, 2023.
  2. Zahedi, Sara; Ejtehadifar, Mostafa; Carvalho, Ana Sofia; Matthiesen, Rune. Corresponding author: Matthiesen, Rune. "Comparative proteome analysis of pleural fluid biomarkers obtained from mesothelioma patients, non malignant and malignant lung diseases". Paper presented in iMig2023, 2023.
  3. Ejtehadifar, Mostafa; Zahedi, Sara; Ana Sofia Carvalho; Matthiesen, Rune. Corresponding author: Matthiesen, Rune. "Nucleobindin1 in a diffuse large B-cell lymphoma cell line is a potential drug-resistance biomarker". Paper presented in 2nd meeting of the Portuguese Network on extracellular vesicles, 2023.
  4. Ana Raquel lopes; Caetano, Joana; Ana Filipa Barahona; Velosa Ferreira, Bruna; Diana Lourenço; Ana C. Queirós; Matthiesen, Rune; et al. "Insights on how multiple myeloma-derived extracellular vesicles modulate the bone marrow immune niche". Paper presented in XLVIII Annual Meeting Portuguese Socienty of Immunology, 2023.
  5. Lopes, Raquel; Caetano, Joana; Ana Filipa Barahona Afonso; Velosa Ferreira, Bruna; Diana Lourenço; QUEIRÓS, ANA; Matthiesen, Rune; et al. "Insights on how multiple myeloma-derived extracellular vesicles modulate the bone marrow niche". Paper presented in XLVIII Annual Meeting Portuguese Society of Immunology, 2023.
  6. Ribeiro, Sónia; Pereira, Ana Rita S.; Rocha, Filipe; Vala, Inês Sofia; Pinto, Ana Teresa; Ministro, Augusto; Poli, Esmeralda; et al. Corresponding author: Santos, Susana Constantino Rosa. "Cardiac tissue remodelling induced by ionizing radiation in a dosedependent manner is an early predictor of subclinical cardiac dysfunction.". Paper presented in European Radiation Protection Week 2022, 2022.
  7. Lopes, Raquel; Caetano, Joana; Ana Filipa Barahona Afonso; Pestana, Carolina; Velosa Ferreira, Bruna; Diana Lourenço; QUEIRÓS, ANA; et al. "Are you talking to me? How multiple myeloma-derived extracellular vesicles reprogramme the bone marrow immune niche". Paper presented in Champalimaud Research Symposium, 2022.
  8. Bergantim, Rui; Peixoto da Silva, Sara; Pereira, Joana; Pinto, Vanessa; Sousa, Diana; Matthiesen, Rune; Guimarães, José E.; Vasconcelos, M. Helena. "Identifying microRNAs as potential biomarkers of drug resistance in Multiple Myeloma patients: proof-of-concept study (co-author; presented by Rui Bergantim)". Paper presented in 19th International Myeloma Society Annual Meeting, 2022.
  9. Rodrigues, Ricardo; Pinto, Ana; Pojo, Marta; Pacheco, Diana; Carvalho, A. S.; Beck, H. C.; Matthiesen, Rune; et al. "The dual role of tumour-associated macrophages in anaplastic thyroid cancer.". 2022.
  10. Bergantim, Rui; Peixoto da Silva, Sara; Pereira, Joana; Pinto, Vanessa; Sousa, Diana; Matthiesen, Rune; Guimarães, José Eduardo; Vasconcelos, M. Helena. "Circulating microRNAs as drug resistance biomarkers in Multiple Myeloma patients (co-author; presented by Rui Bergantim)". Paper presented in 5th Annual Meeting STRATAGEM COST Action, 2022.
  11. Lopes, Raquel; Caetano, Joana; Ana Filipa Barahona Afonso; Pestana, Carolina; Velosa Ferreira, Bruna; Diana Lourenço; QUEIRÓS, ANA; et al. "Unraveling the crosstalk beterrn multiple myeloma and the bone marrow immune microenvironment: a role for myeloma-derived extracellular vesicles?". Paper presented in XV CAML V NeurULisboa PhD Students meeting, 2022.
  12. Lopes, Raquel; Caetano, Joana; Ana Filipa Barahona Afonso; Pestana, Carolina; Velosa Ferreira, Bruna; Diana Lourenço; QUEIRÓS, ANA; et al. "Multiple myeloma-derived extracellular vesicles induce an immunosuppressive bone marrow microenvironment". Paper presented in XLVII Annual Meeting Portuguese Society of Immunology, 2022.
  13. Neves-Silva, Dalila; Martins, Isaura; de Sena-Tomás, Carmen; Rebocho da Costa, Mariana; Quitéria, Raquel; Matthiesen, Rune; Carvalho, Ana Sofia; et al. "Mimicking the Zebrafish Extracellular Matrix Profile in Mammals to Promote Spinal Cord Repair.". Paper presented in XVII Meeting of the Portuguese Society for Neuroscience (SPN2021), 2021.
  14. Inês Antunes Ferreira; de Oliveira RM; Teshima, Akiko; Matthiesen, Rune; Costa-Silva, Bruno; Macedo, Maria. Corresponding author: Inês Antunes Ferreira. "Gut-derived exosomes in prediabetes: proteomics insight.". 2020.
  15. Arnault Carneiro, Emilie; Velosa Ferreira, Bruna; Barahona, AF; Caetano, Joana; Lopes, Raquel; Lucio, Paulo; Matthiesen, Rune; et al. "Extracellular vesicles proteins and their potential as biomarkers of multiple myeloma aggressiveness". Paper presented in Reunião Anual Sociedade Portuguesa de Hematologia (SPH), 2019.
  16. Canato, S; Carvalho, AS; Botelho, Hugo M; Aloria, K; Matthiesen, Rune; Amaral, Margarida; Falcão, AO; Farinha, CM. "Modulation of protein traffic networks to rescue F508del-CFTR from the endoplasmic reticulum". Paper presented in 40th European Cystic Fibrosis Conference, 2017.
  17. Raquel T. Lima; Sousa, Diana; Mendes, Nuno; Matthiesen, Rune; Gomes, Ana Sara; Pinto, Madalena M. M; Sousa, Emília; Vasconcelos, M. Helena. "TXA1.HCl induces autophagy in NCI-H460 cells and reduces the growth of these lung cancer cells xenografted in nude mice". Paper presented in i3S retreat 2014, 2014.
Journal article
  1. Ana Teresa Pinto; Marta Pojo; Ricardo Rodrigues; Diana Pacheco Sousa; Rune Matthiesen; Ana Sofia Carvalho; Hans C. Beck; et al. "SPRY4 as a Potential Mediator of the Anti-Tumoral Role of Macrophages in Anaplastic Thyroid Cancer Cells". Cancers (2023): https://doi.org/10.3390/cancers15174387.
    10.3390/cancers15174387
  2. Neuza Domingues; Joana Gaifem; Rune Matthiesen; Diana P. Saraiva; Luís Bento; André R.A. Marques; Maria I.L. Soares; et al. "Cholesteryl hemiazelate identified in CVD patients causes in vitro and in vivo inflammation". Journal of Lipid Research (2023): https://doi.org/10.1016/j.jlr.2023.100419.
    10.1016/j.jlr.2023.100419
  3. Martins, Flavia; Machado, Ana L.; Carvalho, Patricia D.; Carvalho, Joana; Matthiesen, Rune; Backman, Vadim; Velho, Sergia. "Abstract A006: Chromatin remodeling as a potential epigenetic mechanism of tolerance to KRAS loss". Molecular Cancer Research 21 5_Suppleme (2023): A006-A006. http://dx.doi.org/10.1158/1557-3125.ras23-a006.
    Published • 10.1158/1557-3125.ras23-a006
  4. Mostafa Ejtehadifar; Sara Zahedi; Paula Gameiro; José Cabeçadas; Maria Gomes da Silva; Hans C. Beck; Ana Sofia Carvalho; Rune Matthiesen. "Meta-Analysis of MS-Based Proteomics Studies Indicates Interferon Regulatory Factor 4 and Nucleobindin1 as Potential Prognostic and Drug Resistance Biomarkers in Diffuse Large B Cell Lymphoma". Cells (2023): https://doi.org/10.3390/cells12010196.
    10.3390/cells12010196
  5. Chegão, Ana; Alexandre, Bruno M; Matthiesen, Rune; Lopes, Luísa V.; Anjos-Gomes, Ricardo; GOMES-ALVES, Patrícia; Coelho, Joana Esteves ; Outeiro, Tiago Fleming; Vicente Miranda, Hugo. Corresponding author: Vicente Miranda, Hugo. "aSyn overexpression impairs oxidative phosphorylation, endocytosis, and synaptic vesicle dynamics in the midbrain (Under Preparation)". npj Parkinson's Disease (2023):
    Submitted
  6. Ana Chegão; Mariana Guarda; Bruno M. Alexandre; Liana Shvachiy; Mariana Temido-Ferreira; Inês Marques-Morgado; Bárbara Fernandes Gomes; et al. "Glycation modulates glutamatergic signaling and exacerbates Parkinson’s disease-like phenotypes". npj Parkinson's Disease 8 1 (2022): https://doi.org/10.1038/s41531-022-00314-x.
    10.1038/s41531-022-00314-x
  7. Rune Matthiesen; Paula Gameiro; Andreia Henriques; Cristian Bodo; Maria Carolina Strano Moraes; Bruno Costa-Silva; José Cabeçadas; et al. "Extracellular Vesicles in Diffuse Large B Cell Lymphoma: Characterization and Diagnostic Potential". International Journal of Molecular Sciences (2022): https://doi.org/10.3390/ijms232113327.
    10.3390/ijms232113327
  8. Sara Zahedi; Ana Sofia Carvalho; Mostafa Ejtehadifar; Hans C. Beck; Nádia Rei; Ana Luis; Paula Borralho; António Bugalho; Rune Matthiesen. "Assessment of a Large-Scale Unbiased Malignant Pleural Effusion Proteomics Study of a Real-Life Cohort". Cancers (2022): https://doi.org/10.3390/cancers14184366.
    10.3390/cancers14184366
  9. Nuno Couto; Julia Elzanowska; Joana Maia; Silvia Batista; Catarina Esteves Pereira; Hans Christian Beck; Carvalho AS; et al. "IgG+ Extracellular Vesicles Measure Therapeutic Response in Advanced Pancreatic Cancer". Cells (2022): https://www.mdpi.com/2073-4409/11/18/2800.
    10.3390/cells11182800
  10. Lopes, Raquel; Caetano, Joana; Barahona, Filipa; Pestana, Carolina; Ferreira, Bruna Velosa; Lourenço, Diana; Queirós, Ana C.; et al. "Multiple Myeloma-Derived Extracellular Vesicles Modulate the Bone Marrow Immune Microenvironment". Frontiers in Immunology 13 (2022): http://dx.doi.org/10.3389/fimmu.2022.909880.
    Published • 10.3389/fimmu.2022.909880
  11. Ferreira, Bruna Velosa; Carneiro, Emilie Arnault; Pestana, Carolina; Barahona, Filipa; Caetano, Joana; Lopes, Raquel; Lúcio, Paulo; et al. "Patient-Derived Extracellular Vesicles Proteins as New Biomarkers in Multiple Myeloma - A Real-World Study". Frontiers in Oncology 12 (2022): http://dx.doi.org/10.3389/fonc.2022.860849.
    10.3389/fonc.2022.860849
  12. Inês Ferreira; Rita Machado de Oliveira; Ana Sofia Carvalho; Akiko Teshima; Hans Christian Beck; Rune Matthiesen; Bruno Costa-Silva; Maria Paula Macedo. "Messages from the Small Intestine Carried by Extracellular Vesicles in Prediabetes: A Proteomic Portrait". Journal of Proteome Research 21 4 (2022): 910-920. https://doi.org/10.1021/acs.jproteome.1c00353.
    10.1021/acs.jproteome.1c00353
  13. João Vasco Ferreira; Ana da Rosa Soares; José Ramalho; Catarina Máximo Carvalho; Maria Helena Cardoso; Petra Pintado; Ana Sofia Carvalho; et al. "LAMP2A regulates the loading of proteins into exosomes". Science Advances 8 12 (2022): https://doi.org/10.1126/sciadv.abm1140.
    10.1126/sciadv.abm1140
  14. Grégoire Quinet; Wendy Xolalpa; Diana Reyes-Garau; Núria Profitós-Pelejà; Mikel Azkargorta; Laurie Ceccato; Maria Gonzalez-Santamarta; et al. "Constitutive Activation of p62/Sequestosome-1-Mediated Proteaphagy Regulates Proteolysis and Impairs Cell Death in Bortezomib-Resistant Mantle Cell Lymphoma". Cancers (2022): https://www.mdpi.com/2072-6694/14/4/923.
    10.3390/cancers14040923
  15. Nicolai Bjødstrup Palstrøm; Rune Matthiesen; Lars Melholt Rasmussen; Hans Christian Beck. "Recent Developments in Clinical Plasma Proteomics—Applied to Cardiovascular Research". Biomedicines (2022): https://doi.org/10.3390/biomedicines10010162.
    10.3390/biomedicines10010162
  16. Lopes, Raquel; Caetano, Joana; Ana Filipa Barahona Afonso; Pestana, Carolina; Bruna Velosa Ferreira; Diana Lourenço; QUEIRÓS, ANA; et al. "Multiple myeloma-derived extracelular vesicles modulate the bone marrow immune microenvironment.". Frontiers in Immunology (2022): https://doi.org/10.3389/fimmu.2022.909880.
    Published
  17. Velosa Ferreira, Bruna; Arnault Carneiro, Emilie; Pestana, Carolina; Ana Filipa Barahona Afonso; Caetano, Joana; Lopes, Raquel; Lucio, Paulo; et al. "Patient-derived extracelullar vesicles proteins as new biomarkers in multiple myeloma: a real-world study". Frontiers in Oncology (2022): https://doi.org/10.3389/fonc.2022.860849..
    Published
  18. Nicolai Bjødstrup Palstrøm; Aleksandra M. Rojek; Hanne E. H. Møller; Charlotte Toftmann Hansen; Rune Matthiesen; Lars Melholt Rasmussen; Niels Abildgaard; Hans Christian Beck. "Classification of Amyloidosis by Model-Assisted Mass Spectrometry-Based Proteomics". International Journal of Molecular Sciences (2021): https://doi.org/10.3390/ijms23010319.
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  19. Rui Miguel Marques Bernardino; Ricardo Leão; Rui Henrique; Luis Campos Pinheiro; Prashant Kumar; Prashanth Suravajhala; Hans Christian Beck; Ana Sofia Carvalho; Rune Matthiesen. "Extracellular Vesicle Proteome in Prostate Cancer: A Comparative Analysis of Mass Spectrometry Studies". International Journal of Molecular Sciences (2021): https://doi.org/10.3390/ijms222413605.
    10.3390/ijms222413605
  20. Carvalho AS; Henrique Baeta; Andreia Almeida Henriques; Mostafa Ejtehadifar; Erin M. Tranfield; Ana Laura Sousa; Ana Farinho; et al. "Proteomic Landscape of Extracellular Vesicles for Diffuse Large B-Cell Lymphoma Subtyping". International Journal of Molecular Sciences (2021): https://www.mdpi.com/1422-0067/22/20/11004.
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  21. Bernardino, Rui; Henrique, Rui; Pereira, Herminia; Severo, Luis; Matthiesen, Rune; Pimentel, João; Pinheiro, Luis Campos. "MP33-02 UNRAVELING GENOMIC ALTERATIONS OF CRIBRIFORM AND INTRADUCTAL PROSTATE CANCER". Journal of Urology 206 Supplement (2021): http://dx.doi.org/10.1097/ju.0000000000002042.02.
    10.1097/ju.0000000000002042.02
  22. Ana Chegão; Mariana Guarda; Alexandre BM; Shvachiy, Liana; Mariana Temido-Ferreira; Inês Marques-Morgado; Bárbara Fernandes Gomes; et al. Corresponding author: Vicente Miranda, Hugo. "Exacerbation of Parkinson¿s disease-like phenotypes by glycation involves glutamatergic signaling". BioRxiv (2021): https://doi.org/10.1101/2021.08.24.457507.
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  23. Rune Matthiesen; Chris Lauber; Julio L. Sampaio; Neuza Domingues; Liliana Alves; Mathias J. Gerl; Manuel S. Almeida; et al. "Shotgun mass spectrometry-based lipid profiling identifies and distinguishes between chronic inflammatory diseases". EBioMedicine 70 (2021): 103504-103504. https://doi.org/10.1016/j.ebiom.2021.103504.
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  24. Seixas, Susana; Kolbe, Allison R.; Gomes, Sílvia; Sucena, Maria; Sousa, Catarina; Vaz Rodrigues, Luís; Teixeira, Gilberto; et al. "Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-94468-y.
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  25. Velosa Ferreira, Bruna; Arnault Carneiro, Emilie; Pestana, Carolina; Barahona, AF; Caetano, J; Lopes, Raquel; Lucio, P; et al. "Extracellular vesicles protein cargo as new prognostic biomarker for Multiple Myeloma - a real-life observational study". Blood Advances (2021):
    Submitted
  26. Maia, Joana; Otake, Andreia Hanada; Poças, Juliana; Carvalho, Ana Sofia; Beck, Hans Christian; Magalhães, Ana; Matthiesen, Rune; Strano Moraes, Maria Carolina; Costa-Silva, Bruno. "Transcriptome Reprogramming of CD11b+ Bone Marrow Cells by Pancreatic Cancer Extracellular Vesicles". Frontiers in Cell and Developmental Biology 8 (2020): http://dx.doi.org/10.3389/fcell.2020.592518.
    10.3389/fcell.2020.592518
  27. Carvalho AS; Maria Carolina Strano Moraes; Chan Hyun Na; Ivo Fierro-Monti; Andreia Almeida Henriques; Sara Zahedi; Cristian Bodo; et al. "Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer?". Cancers (2020): https://www.mdpi.com/2072-6694/12/11/3450.
    10.3390/cancers12113450
  28. Diana Sousa; Rune Matthiesen; Raquel T. Lima; M. Helena Vasconcelos. "Deep Sequencing Analysis Reveals Distinctive Non-Coding RNAs When Comparing Tumor Multidrug-Resistant Cells and Extracellular Vesicles with Drug-Sensitive Counterparts". Cancers 12 1 (2020): 200-200. https://doi.org/10.3390/cancers12010200.
    10.3390/cancers12010200
  29. Rune Matthiesen. "MS-Based Biomarker Discovery in Bronchoalveolar Lavage Fluid for Lung Cancer". PROTEOMICS – Clinical Applications (2020): 1900077-1900077. https://doi.org/10.1002/prca.201900077.
    10.1002/prca.201900077
  30. Matthiesen, Rune. "Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_7.
    10.1007/978-1-4939-9744-2_7
  31. Matthiesen, Rune. "Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_8.
    10.1007/978-1-4939-9744-2_8
  32. Matthiesen, Rune. "Extra-cellular vesicles carry proteome of cancer hallmarks.". Frontiers in bioscience (Landmark edition) (2020): https://doi.org/10.2741/4811.
    10.2741/4811
  33. Matthiesen, Rune. "LC-MS Spectra Processing.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_2.
    10.1007/978-1-4939-9744-2_2
  34. Matthiesen, Rune. "Solution to Dark Matter Identified by Mass-Tolerant Database Search.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_9.
    10.1007/978-1-4939-9744-2_9
  35. Matthiesen, Rune. "Comparing Peptide Spectra Matches Across Search Engines.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_5.
    10.1007/978-1-4939-9744-2_5
  36. Matthiesen, Rune. "Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_13.
    10.1007/978-1-4939-9744-2_13
  37. Matthiesen, Rune. "Introduction to Mass Spectrometry-Based Proteomics.". Methods in molecular biology (Clifton, N.J.) (2020): https://doi.org/10.1007/978-1-4939-9744-2_1.
    10.1007/978-1-4939-9744-2_1
  38. Sousa, Diana; Matthiesen, Rune; Lima, Raquel T.; Helena Vasconcelos, M.; NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM); Centro de Estudos de Doenças Crónicas (CEDOC). "Deep sequencing analysis reveals distinctive non-coding RNAs when comparing tumor multidrug-resistant cells and extracellular vesicles with drug-sensitive counterparts". (2020): http://hdl.handle.net/10362/93190.
    https://doi.org/10.3390/cancers12010200
  39. Matthiesen, Rune. "WNK1 phosphorylation sites in TBC1D1 and TBC1D4 modulate cell surface expression of GLUT1.". Archives of biochemistry and biophysics (2019): https://doi.org/10.1016/j.abb.2019.108223.
    10.1016/j.abb.2019.108223
  40. Gomes, Sílvia; Cavadas, Bruno; Ferreira, Joana Catarina; Marques, Patrícia Isabel; Monteiro, Catarina; Sucena, Maria; Sousa, Catarina; et al. "Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma". Scientific reports (2019): http://hdl.handle.net/10451/39649.
    10.1038/s41598-019-49195-w 1
  41. Santos, Joao D.; Canato, Sara; Carvalho, Ana S.; Botelho, Hugo M.; Aloria, Kerman; Amaral, Margarida D.; Matthiesen, Rune; et al. "Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum". Cells (2019): http://hdl.handle.net/10362/77021.
    https://doi.org/10.3390/cells8040353
  42. Matthiesen, Rune. "The Antitumor Activity of a Lead Thioxanthone is Associated with Alterations in Cholesterol Localization.". Molecules (Basel, Switzerland) (2018): https://europepmc.org/articles/PMC6321308.
    10.3390/molecules23123301
  43. Canato, Sara; Santos, João D.; Carvalho, Ana S.; Aloria, Kerman; Amaral, Margarida D.; Matthiesen, Rune; Falcao, André O.; Farinha, Carlos M.. "Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation". Cellular and Molecular Life Sciences 75 24 (2018): 4495-4509. http://dx.doi.org/10.1007/s00018-018-2896-7.
    Published • 10.1007/s00018-018-2896-7
  44. Lima, Raquel T.; Sousa, Diana; Gomes, Ana Sara; Mendes, Nuno; Matthiesen, Rune; Pedro, Madalena; Marques, Franklim; et al. "The antitumor activity of a lead thioxanthone is associated with alterations in cholesterol localization". (2018): http://www.scopus.com/inward/record.url?scp=85058769923&partnerID=8YFLogxK.
    https://doi.org/10.3390/molecules23123301
  45. Matthiesen, Rune. "Red Blood Cells in Clinical Proteomics.". Methods in molecular biology (Clifton, N.J.) (2017): https://doi.org/10.1007/978-1-4939-7057-5_13.
    10.1007/978-1-4939-7057-5_13
  46. Carvalho, Ana Sofia; Cuco, Célia Marina; Lavareda, Carla; Miguel, Francisco; Ventura, Mafalda; Almeida, Sónia; Pinto, Paula; et al. "Bronchoalveolar Lavage Proteomics in Patients with Suspected Lung Cancer". (2017): http://hdl.handle.net/10362/32589.
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  47. Feliciano, Amélia; Vaz, Fátima; Torres, Vukosava M.; Coelho, Cristina Valentim; Silva, Rita; Prosinecki, Vesna; Alexandre, Bruno M.; et al. "Evening and morning peroxiredoxin-2 redox/oligomeric state changes in obstructive sleep apnea red blood cells : correlation with polysomnographic and metabolic parameters". (2017): http://hdl.handle.net/10451/27393.
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  48. Feliciano, Amélia; Vaz, Fátima; Valentim-Coelho, Cristina; Torres, Vukosava M; Silva, Rita; Prosinecki, Vesna; Alexandre, Bruno M; et al. "Evening and morning alterations in Obstructive Sleep Apnea red blood cell proteome". (2017): http://hdl.handle.net/10362/24631.
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  49. Jones-Dias, Daniela; Carvalho, Ana Sofia; Moura, Inês Barata; Manageiro, Vera; Igrejas, Gilberto; Caniça, Manuela; Matthiesen, Rune. "Quantitative proteome analysis of an antibiotic resistant Escherichia coli exposed to tetracycline reveals multiple affected metabolic and peptidoglycan processes". (2017): http://hdl.handle.net/10400.18/4696.
    10.1016/j.jprot.2016.12.017
  50. Carvalho, Ana Sofia; Cuco, Célia Marina; Lavareda, Carla; Miguel, Francisco; Ventura, Mafalda; Almeida, Sónia; Pinto, Paula; et al. "Bronchoalveolar lavage proteomics in patients with suspected lung cancer". (2017): http://hdl.handle.net/10451/39963.
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  51. Mata-Cantero L; Azkargorta M; Aillet F; Xolalpa W; LaFuente MJ; Elortza F; Carvalho AS; et al. "New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach.". (2016): http://europepmc.org/abstract/med/26972027.
    10.1016/j.jprot.2016.03.004
  52. Cui H; Mu Y; Yu L; Xi YG; Matthiesen R; Su X; Sun W. "Methylation of the miR-126 gene associated with glioma progression.". (2016): http://europepmc.org/abstract/med/26463235.
    10.1007/s10689-015-9846-4
  53. Cui, H.; Mu, Y.; Yu, L.; Xi, Y.; Matthiesen, R.; Su, X.; Sun, W.. "Erratum to: Methylation of the miR-126 gene associated with glioma progression(Familial Cancer, Doi:10.1007/s10689-015-9846-4)". Familial Cancer 15 2 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84948161229&partnerID=MN8TOARS.
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  54. Mata-Cantero, L.; Azkargorta, M.; Aillet, F.; Xolalpa, W.; LaFuente, M.J.; Elortza, F.; Carvalho, A.S.; et al. "New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach". (2016): http://hdl.handle.net/10400.18/3819.
    10.1016/j.jprot.2016.03.004
  55. Feliciano, Amélia; Vaz, Fátima; Torres, Vukosava M.; Valentim-Coelho, Cristina; Silva, Rita; Prosinecki, Vesna; Alexandre, Bruno M.; et al. "Evening and morning peroxiredoxin-2 redox/oligomeric state changes in obstructive sleep apnea red blood cells: Correlation with polysomnographic and metabolic parameters". (2016): http://hdl.handle.net/10400.18/4140.
    10.1016/j.bbadis.2016.11.019
  56. Marques, Patrícia Isabel; Fonseca, Filipa; Carvalho, Ana Sofia; Puente, Diana A.; Damião, Isabel; Almeida, Vasco; Barros, Nuno; et al. "Sequence variation at KLK and WFDC clusters and its association to semen hyperviscosity and other male infertility phenotypes". (2016): http://hdl.handle.net/10400.18/4541.
    10.1093/humrep/dew267
  57. Cui, Hongwei; Mu, Yongping; Yu, Lei; Xi, Ya-guang; Matthiesen, Rune; Su, Xiulan; Sun, Wenjie. "Methylation of the miR-126 gene associated with glioma progression". (2016): http://hdl.handle.net/10400.18/4546.
    10.1007/s10689-015-9846-4
  58. Carvalho, A.S.; Molina, H.; Matthiesen, Rune; Carvalho AS; Molina H; Matthiesen R. "New insights into functional regulation in MS-based drug profiling". (2016): http://hdl.handle.net/10400.18/3818.
    10.1038/srep18826
  59. Carvalho AS; Penque D; Matthiesen R. "Bottom up proteomics data analysis strategies to explore protein modifications and genomic variants.". (2015): http://europepmc.org/abstract/med/25684358.
    10.1002/pmic.201400186
  60. Feliciano A; Torres VM; Vaz F; Carvalho AS; Matthiesen R; Pinto P; Malhotra A; Bárbara C; Penque D. "Overview of proteomics studies in obstructive sleep apnea.". (2015): http://europepmc.org/abstract/med/25770042.
    10.1016/j.sleep.2014.11.014
  61. Frades I; Andreasson E; Mato JM; Alexandersson E; Matthiesen R; Martínez-Chantar ML. "Integrative genomic signatures of hepatocellular carcinoma derived from nonalcoholic Fatty liver disease.". (2015): http://europepmc.org/abstract/med/25993042.
    10.1371/journal.pone.0124544
  62. Carvalho, Ana; Matthiesen, Rune; Penque, Deborah. "Bottom up proteomics data analysis strategies to explore protein modifications and genomic variant". (2015): http://hdl.handle.net/10400.18/3458.
    10.1002/pmic.201400186
  63. Feliciano, Amélia; Torres, Vukosava M.; Vaz, Fatima; Carvalho, Ana Sofia; Matthiesen, Rune; Pinto, Paula; Malhotra, Atul; Bárbara, Cristina; Penque, Deborah. "Overview of proteomics studies in obstructive sleep apnea". (2015): http://hdl.handle.net/10400.18/3093.
    10.1016/j.sleep.2014.11.014
  64. Carvalho AS; Ribeiro H; Voabil P; Penque D; Jensen ON; Molina H; Matthiesen R. "Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress.". (2014): http://europepmc.org/abstract/med/25128556.
    10.1074/mcp.M113.034363
  65. Gomes S; Marques PI; Matthiesen R; Seixas S. "Adaptive evolution and divergence of SERPINB3: a young duplicate in great Apes.". (2014): http://europepmc.org/abstract/med/25133778.
    10.1371/journal.pone.0104935
  66. Gomes, Silvia; Marques, Patricia; Matthiesen, Rune; Seixas, Susana. "Adaptive evolution and divergence of SERPINB3: a young duplicate in great Apes". (2014): http://hdl.handle.net/10400.18/2581.
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  67. Matthiesen R; Bunkenborg J. "Introduction to mass spectrometry-based proteomics.". (2013): http://europepmc.org/abstract/med/23666720.
    10.1007/978-1-62703-392-3_1
  68. Bunkenborg J; Matthiesen R. "Interpretation of tandem mass spectra of posttranslationally modified peptides.". (2013): http://europepmc.org/abstract/med/23666725.
    10.1007/978-1-62703-392-3_6
  69. Fonseca C; Voabil P; Carvalho AS; Matthiesen R. "Tools for protein posttranslational modifications analysis: FAK, a case study.". (2013): http://europepmc.org/abstract/med/23666734.
    10.1007/978-1-62703-392-3_15
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  71. Matthiesen R. "Algorithms for database-dependent search of MS/MS data.". (2013): http://europepmc.org/abstract/med/23666724.
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    10.1007/978-1-62703-392-3_2
  73. Matthiesen, R.. "Preface". Methods in Molecular Biology 1007 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84883172367&partnerID=MN8TOARS.
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  74. Lopes, A.M.; Aston, K.I.; Thompson, E.; Carvalho, F.; Gonçalves, J.; Huang, N.; Matthiesen, R.; et al. "Human Spermatogenic Failure Purges Deleterious Mutation Load from the Autosomes and Both Sex Chromosomes, including the Gene DMRT1". PLoS Genetics 9 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875985784&partnerID=MN8TOARS.
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  75. Lopes, Alexandra; Aston, Kenneth I.; Thompson, Emma E; Carvalho, Filipa; Gonçalves, João; Huang, N.; Matthiesen, Rune; et al. "Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1". (2013): http://hdl.handle.net/10400.18/2157.
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  76. Prieto, G.; Aloria, K.; Osinalde, N.; Fullaondo, A.; Arizmendi, J.M.; Matthiesen, R.. "PAnalyzer: A software tool for protein inference in shotgun proteomics". BMC Bioinformatics 13 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84868261119&partnerID=MN8TOARS.
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  77. Da Silva-Ferrada, E.; Lopitz-Otsoa, F.; Lang, V.; Rodríguez, M.S.; Matthiesen, R.. "Strategies to identify recognition signals and targets of SUMOylation". Biochemistry Research International (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864935256&partnerID=MN8TOARS.
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  79. Lopitz-Otsoa, F.; Rodriguez-Suarez, E.; Aillet, F.; Casado-Vela, J.; Lang, V.; Matthiesen, R.; Elortza, F.; Rodriguez, M.S.. "Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs)". Journal of Proteomics 75 10 (2012): 2998-3014. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861344026&partnerID=MN8TOARS.
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  80. Moleirinho, A.; Carneiro, J.; Matthiesen, R.; Silva, R.M.; Amorim, A.; Azevedo, L.. "Gains, losses and changes of function after gene duplication: Study of the metallothionein family". PLoS ONE 6 4 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79955562969&partnerID=MN8TOARS.
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  82. Rodríguez-Suárez E; Gubb E; Alzueta IF; Falcón-Pérez JM; Amorim A; Elortza F; Matthiesen R. "Virtual expert mass spectrometrist: iTRAQ tool for database-dependent search, quantitation and result storage.". (2010): http://europepmc.org/abstract/med/20140907.
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  88. Hackenberg M; Matthiesen R. "Algorithms and methods for correlating experimental results with annotation databases.". (2010): http://europepmc.org/abstract/med/19957156.
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  89. Tanthanuch, W.; Tittabutr, P.; Mohammed, S.; Matthiesen, R.; Yamabhai, M.; Manassila, M.; Jensen, O.N.; Boonkerd, N.; Teaumroong, N.. "Identification of salt-tolerant Sinorhizobium sp. strain Bl3 membrane proteins based on proteomics". Microbes and Environments 25 4 (2010): 275-280. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650057543&partnerID=MN8TOARS.
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  91. Vellón, L.; Royo, F.; Matthiesen, R.; Torres-Fuenzalida, J.; Lorenti, A.; Parada, L.A.. "Functional blockade of a5ß1 integrin induces scattering and genomic landscape remodeling of hepatic progenitor cells". BMC Cell Biology 11 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77957923168&partnerID=MN8TOARS.
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  92. Quental, R.; Azevedo, L.; Matthiesen, R.; Amorim, A.. "Comparative analyses of the Conserved Oligomeric Golgi (COG) complex in vertebrates". BMC Evolutionary Biology 10 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77954557058&partnerID=MN8TOARS.
    10.1186/1471-2148-10-212
  93. Rodríguez-Suárez, E.; Gubb, E.; Alzueta, I.F.; Falcón-Pérez, J.M.; Amorim, A.; Elortza, F.; Matthiesen, R.. "Virtual Expert Mass Spectrometrist: iTRAQ tool for database-dependent search, quantitation and result storage". Proteomics 10 9 (2010): 1545-1556. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951672231&partnerID=MN8TOARS.
  94. Lasso, G.; Matthiesen, R.. "Computational methods for analysis of two-dimensional gels.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 231-262. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649084214&partnerID=MN8TOARS.
  95. Gubb, E.; Matthiesen, R.. "Introduction to omics.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 1-23. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649093407&partnerID=MN8TOARS.
  96. Matthiesen, R.; Carvalho, A.S.. "Methods and algorithms for relative quantitative proteomics by mass spectrometry.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 187-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649124570&partnerID=MN8TOARS.
  97. Aransay, A.M.; Matthiesen, R.; Regueiro, M.M.; Aransay AM; Matthiesen R; Regueiro MM. "SNP-PHAGE: high-throughput SNP discovery pipeline.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 49-65. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649107859&partnerID=MN8TOARS.
    10.1007/978-1-60327-194-3_3
  98. Frades, I.; Matthiesen, R.. "Overview on techniques in cluster analysis.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 81-107. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649106493&partnerID=MN8TOARS.
  99. Hackenberg, M.; Matthiesen, R.. "Algorithms and methods for correlating experimental results with annotation databases.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 315-340. http://www.scopus.com/inward/record.url?eid=2-s2.0-75649111622&partnerID=MN8TOARS.
  100. Carvalho, A.S.; Harduin-Lepers, A.; Magalhães, A.; Machado, E.; Mendes, N.; Costa, L.T.; Matthiesen, R.; et al. "Differential expression of a-2,3-sialyltransferases and a-1,3/4-fucosyltransferases regulates the levels of sialyl Lewis a and sialyl Lewis x in gastrointestinal carcinoma cells". International Journal of Biochemistry and Cell Biology 42 1 (2010): 80-89. http://www.scopus.com/inward/record.url?eid=2-s2.0-70649087034&partnerID=MN8TOARS.
    10.1016/j.biocel.2009.09.010
  101. Matthiesen, R.; Kirpekar, F.. "Identification of RNA molecules by specific enzyme digestion and mass spectrometry: Software for and implementation of RNA mass mapping". Nucleic Acids Research 37 6 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-64549101995&partnerID=MN8TOARS.
    10.1093/nar/gkp139
  102. Hackenberg, M.; Lasso, G.; Matthiesen, R.. "ContDist: A tool for the analysis of quantitative gene and promoter properties". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-60549105392&partnerID=MN8TOARS.
    10.1186/1471-2105-10-7
  103. Matthiesen, R.; Jensen, O.N.. "Analysis of mass spectrometry data in proteomics.". Methods in molecular biology (Clifton, N.J.) 453 (2008): 105-122. http://www.scopus.com/inward/record.url?eid=2-s2.0-53449090217&partnerID=MN8TOARS.
  104. Matthiesen R; Jensen ON. "Analysis of mass spectrometry data in proteomics.". (2008): http://europepmc.org/abstract/med/18712299.
    10.1007/978-1-60327-429-6_4
  105. Conde-Vancells, J.; Rodriguez-Suarez, E.; Embade, N.; Gil, D.; Matthiesen, R.; Valle, M.; Elortza, F.; et al. "Characterization and comprehensive proteome profiling of exosomes secreted by hepatocytes". Journal of Proteome Research 7 12 (2008): 5157-5166. http://www.scopus.com/inward/record.url?eid=2-s2.0-61349173156&partnerID=MN8TOARS.
    10.1021/pr8004887
  106. Matthiesen, R.; Jensen, O.N.. "Analysis of mass spectrometry data in proteomics". Methods in Molecular Biology 453 (2008): 105-122. http://www.scopus.com/inward/record.url?eid=2-s2.0-53449090217&partnerID=MN8TOARS.
    10.1007/978-1-60327-429-6-4
  107. Molina, H.; Matthiesen, R.; Kandasamy, K.; Pandey, A.. "Comprehensive comparison of collision induced dissociation and electron transfer dissociation". Analytical Chemistry 80 13 (2008): 4825-4835. http://www.scopus.com/inward/record.url?eid=2-s2.0-46849098407&partnerID=MN8TOARS.
    10.1021/ac8007785
  108. Hackenberg, M.; Matthiesen, R.. "Annotation-modules: A tool for finding significant combinations of multisource annotations for gene lists". Bioinformatics 24 11 (2008): 1386-1393. http://www.scopus.com/inward/record.url?eid=2-s2.0-44349171852&partnerID=MN8TOARS.
    10.1093/bioinformatics/btn178
  109. Martínez-Chantar, M.L.; Vázquez-Chantada, M.; Ariz, U.; Martínez, N.; Varela, M.; Luka, Z.; Capdevila, A.; et al. "Loss of the glycine N-methyltransferase gene leads to steatosis and hepatocellular carcinoma in mice". Hepatology 47 4 (2008): 1191-1199. http://www.scopus.com/inward/record.url?eid=2-s2.0-42249100305&partnerID=MN8TOARS.
    10.1002/hep.22159
  110. Matthiesen R; Mutenda KE. "Introduction to proteomics.". (2007): http://europepmc.org/abstract/med/17185767.
    10.1385/1-59745-275-0:1
  111. Matthiesen R. "Extracting monoisotopic single-charge peaks from liquid chromatography-electrospray ionization-mass spectrometry.". (2007): http://europepmc.org/abstract/med/17185768.
    10.1385/1-59745-275-0:37
  112. Gruhler A; Matthiesen R. "Quantitation with virtual expert mass spectrometrist.". (2007): http://europepmc.org/abstract/med/17185774.
    10.1385/1-59745-275-0:139
  113. Bunkenborg J; Matthiesen R. "Interpretation of collision-induced fragmentation tandem mass spectra of posttranslationally modified peptides.". (2007): http://europepmc.org/abstract/med/17185776.
    10.1385/1-59745-275-0:169
  114. Mutenda KE; Matthiesen R. "Analysis of carbohydrates by mass spectrometry.". (2007): http://europepmc.org/abstract/med/17185783.
    10.1385/1-59745-275-0:289
  115. Matthiesen R. "Useful mass spectrometry programs freely available on the internet.". (2007): http://europepmc.org/abstract/med/17185784.
    10.1385/1-59745-275-0:303
  116. Matthiesen R. "Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis.". (2007): http://europepmc.org/abstract/med/17185773.
    10.1385/1-59745-275-0:121
  117. Ingrell CR; Matthiesen R; Jensen ON. "Sequence handling by sequence analysis toolbox v1.0.". (2007): http://europepmc.org/abstract/med/17185775.
    10.1385/1-59745-275-0:153
  118. Erba, E.B.; Matthiesen, R.; Bunkenborg, J.; Schulze, W.X.; Di Stefano, P.; Cabodi, S.; Tarone, G.; Defilippi, P.; Jensen, O.N.. "Quantitation of multisite EGF receptor phosphorylation using mass spectrometry and a novel normalization approach". Journal of Proteome Research 6 7 (2007): 2768-2785. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547167010&partnerID=MN8TOARS.
    10.1021/pr060675m
  119. Omaetxebarria, M.J.; Elortza, F.; Rodríguez-Suárez, E.; Aloria, K.; Arizmendi, J.M.; Jensen, O.N.; Matthiesen, R.. "Computational approach for identification and characterization of GPI-anchored peptides in proteomics experiments". Proteomics 7 12 (2007): 1951-1960. http://www.scopus.com/inward/record.url?eid=2-s2.0-34347373519&partnerID=MN8TOARS.
    10.1002/pmic.200700068
  120. Mutenda, K.E.; Matthiesen, R.; Roepstorff, P.. "Differential fragmentation patterns of pectin oligogalacturonides observed by nanoelectrospray quadrupole ion-trap mass spectrometry using automated spectra interpretation". Journal of Mass Spectrometry 42 4 (2007): 428-439. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247517373&partnerID=MN8TOARS.
    10.1002/jms.1169
  121. Hägglund, P.; Matthiesen, R.; Elortza, F.; Højrup, P.; Roepstorff, P.; Jensen, O.N.; Bunkenborg, J.. "An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins". Journal of Proteome Research 6 8 (2007): 3021-3031. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548186744&partnerID=MN8TOARS.
    10.1021/pr0700605
  122. Matthiesen, R.. "Methods, algorithms and tools in computational proteomics: A practical point of view". Proteomics 7 16 (2007): 2815-2832. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548396821&partnerID=MN8TOARS.
    10.1002/pmic.200700116
  123. Mutenda, K.E.; Matthiesen, R.. "Analysis of carbohydrates by mass spectrometry.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 289-301. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049196233&partnerID=MN8TOARS.
  124. Gruhler, A.; Matthiesen, R.. "Quantitation with virtual expert mass spectrometrist.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 139-152. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049177168&partnerID=MN8TOARS.
  125. Ingrell, C.R.; Matthiesen, R.; Jensen, O.N.. "Sequence handling by sequence analysis toolbox v1.0.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 153-168. http://www.scopus.com/inward/record.url?eid=2-s2.0-37249008061&partnerID=MN8TOARS.
  126. Matthiesen, R.. "Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 121-138. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049184740&partnerID=MN8TOARS.
  127. Matthiesen, R.. "Useful mass spectrometry programs freely available on the internet.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 303-305. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049179321&partnerID=MN8TOARS.
  128. Bunkenborg, J.; Matthiesen, R.. "Interpretation of collision-induced fragmentation tandem mass spectra of posttranslationally modified peptides.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 169-194. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049186670&partnerID=MN8TOARS.
  129. Matthiesen, R.. "Extracting monoisotopic single-charge peaks from liquid chromatography-electrospray ionization-mass spectrometry.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 37-48. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049183145&partnerID=MN8TOARS.
  130. Thomsen, A.L.; Laukens, K.; Matthiesen, R.; Jensen, O.N.. "Organization of proteomics data with YassDB.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 271-287. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049184863&partnerID=MN8TOARS.
  131. Matthiesen, R.; Mutenda, K.E.. "Introduction to proteomics.". Methods in molecular biology (Clifton, N.J.) 367 (2007): 1-35. http://www.scopus.com/inward/record.url?eid=2-s2.0-39049184264&partnerID=MN8TOARS.
  132. Thomsen AL; Laukens K; Matthiesen R; Jensen ON. "Organization of proteomics data with YassDB.". (2007): http://europepmc.org/abstract/med/17185782.
    10.1385/1-59745-275-0:271
  133. Laukens, K.; Matthiesen, R.; Lemière, F.; Esmans, E.; Onckelen, H.V.; Jensen, O.N.; Witters, E.. "Integration of gel-based proteome data with pProRep". Bioinformatics 22 22 (2006): 2838-2840. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751020580&partnerID=MN8TOARS.
    10.1093/bioinformatics/btl487
  134. Beck, H.C.; Nielsen, E.C.; Matthiesen, R.; Jensen, L.H.; Sehested, M.; Finn, P.; Grauslund, M.; Hansen, A.M.; Jensen, O.N.. "Quantitative proteomic analysis of post-translational modifications of human histones". Molecular and Cellular Proteomics 5 7 (2006): 1314-1325. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746298724&partnerID=MN8TOARS.
    10.1074/mcp.M600007-MCP200
  135. Fierro-Monti, I.; Mohammed, S.; Matthiesen, R.; Santoro, R.; Burns, J.S.; Williams, D.J.; Proud, C.G.; et al. "Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E". Journal of Proteome Research 5 6 (2006): 1367-1378. http://www.scopus.com/inward/record.url?eid=2-s2.0-33744980686&partnerID=MN8TOARS.
    10.1021/pr0504539
  136. Alloza, I.; Baxter, A.; Chen, Q.; Matthiesen, R.; Vandenbroeck, K.. "Celecoxib inhibits interleukin-12 aß and ß2 folding and secretion by a novel COX2-independent mechanism involving chaperones of the endoplasmic reticulum". Molecular Pharmacology 69 5 (2006): 1579-1587. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645813833&partnerID=MN8TOARS.
    10.1124/mol.105.020669
  137. Hjernø, K.; Alm, R.; Canbäck, B.; Matthiesen, R.; Trajkovski, K.; Björk, L.; Roepstorff, P.; Emanuelsson, C.. "Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless strawberry mutant". Proteomics 6 5 (2006): 1574-1587. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645065565&partnerID=MN8TOARS.
    10.1002/pmic.200500469
  138. Gruhler, A.; Schulze, W.X.; Matthiesen, R.; Mann, M.; Jensen, O.N.. "Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry". Molecular and Cellular Proteomics 4 11 (2005): 1697-1709. http://www.scopus.com/inward/record.url?eid=2-s2.0-28644448658&partnerID=MN8TOARS.
    10.1074/mcp.M500190-MCP200
  139. Matthiesen, R.; Trelle, M.B.; Højrup, P.; Bunkenborg, J.; Jensen, O.N.. "VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins". Journal of Proteome Research 4 6 (2005): 2338-2347. http://www.scopus.com/inward/record.url?eid=2-s2.0-29144535689&partnerID=MN8TOARS.
    10.1021/pr050264q
  140. Matthiesen, R.; Bauw, G.; Welinder, K.G.. "Use of performic acid oxidation to expand the mass distribution of tryptic peptides". Analytical Chemistry 76 23 (2005): 6848-6852. http://www.scopus.com/inward/record.url?eid=2-s2.0-10044293272&partnerID=MN8TOARS.
    10.1021/ac049032l
  141. Matthiesen, Rune. "Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS v2.0.". Proteomics (2004):
  142. Matthiesen, R.; Lundsgaard, M.; Welinder, K.G.; Bauw, G.. "Interpreting peptide mass spectra by VEMS". Bioinformatics 19 6 (2003): 792-793. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037433752&partnerID=MN8TOARS.
    10.1093/bioinformatics/btg059
  143. Pedersen, N.R.; Wimmer, R.; Matthiesen, R.; Pedersen, L.H.; Gessesse, A.. "Synthesis of sucrose laurate using a new alkaline protease". Tetrahedron Asymmetry 14 6 (2003): 667-673. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037459153&partnerID=MN8TOARS.
    10.1016/S0957-4166(03)00086-7
  144. Pedersen, N.R.; Halling, P.J.; Pedersen, L.H.; Wimmer, R.; Matthiesen, R.; Veltman, O.R.. "Efficient transesterification of sucrose catalysed by the metalloprotease thermolysin in dimethylsulfoxide". FEBS Letters 519 1-3 (2002): 181-184. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037157127&partnerID=MN8TOARS.
    10.1016/S0014-5793(02)02753-9
Preprint
  1. Pedro Baptista Pereira; Estefa Torrejón; Inês Ferreira; Ana Sofia Carvalho; Akiko Teshima; Inês Sousa-Lima; Hans Christian Beck; et al. "Proteomic Profiling of Plasma and Gut-Derived Extracellular Vesicles in Obesity". 2024. https://doi.org/10.20944/preprints202401.0856.v1.
    10.20944/preprints202401.0856.v1
  2. Martins, Flávia; Machado, Ana Luísa; Ribeiro, Andreia; Oliveira, Susana Mendonça; Carvalho, Joana; Matthiesen, Rune; Backman, Vadim; Velho, Sérgia. "KRAS silencing impacts chromatin organization and transcriptional activity in colorectal cancer cells". 2024. http://dx.doi.org/10.21203/rs.3.rs-3752760/v2.
    10.21203/rs.3.rs-3752760/v2
  3. Martins, Flávia; Machado, Ana Luísa; Ribeiro, Andreia; Oliveira, Susana Mendonça; Carvalho, Joana; Matthiesen, Rune; Velho, Sérgia. "KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells". 2023. http://dx.doi.org/10.21203/rs.3.rs-3752760/v1.
    10.21203/rs.3.rs-3752760/v1

Other

Other output
  1. Glycation modulates glutamatergic signalling and exacerbates Parkinson’s disease-like phenotypes. 2021. Ana Chegão; Mariana Guarda; Bruno M. Alexandre; Liana Shvachiy; Mariana Temido-Ferreira; Inês Marques-Morgado; Bárbara Fernandes Gomes; et al. https://doi.org/10.1101/2021.08.24.457507.
    10.1101/2021.08.24.457507
  2. Shotgun mass spectrometry-based lipid profiling identifies and distinguishes between chronic inflammatory diseases. 2021. Rune Matthiesen; Chris Lauber; Julio L. Sampaio; Neuza Domingues; Liliana Alves; Mathias J. Gerl; Manuel S. Almeida; et al. https://doi.org/10.1101/2021.03.08.21252659.
    10.1101/2021.03.08.21252659
  3. Messages From the Small Intestine Carried by Extracellular Vesicles in Prediabetes: a Proteomic Portrait. 2021. Inês Ferreira; Rita Machado de Oliveira; Ana Sofia Carvalho; Hans Christian Beck; Rune Matthiesen; Bruno Costa-Silva; Maria Paula Macedo. https://doi.org/10.1101/2021.02.19.431856.
    10.1101/2021.02.19.431856
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/02/13 From lung cancer to prostate cancer CAncer Prostate Consortium of India ( CAPCI) meeting
CAncer Prostate Consortium of India (Birla Institute of Scientific Research (BISR), India, India)
2020/12/18 R package for proteome quality control of extracellular vesicles First Workshop of the Portuguese Network on Extracellular Vesicles
IPATIMUP (Porto)
2019/02/26 Proteostasis factors in cancer exosomes druggability of the ubiquitin system
CEDOC (Lsibon, Portugal)
2019/02/15 Cancer diagnostic potential of exosome proteome Invited presentation
IMM, Lisbon (Lisbon)
2018/04/16 Diagnostic potential of exosome proteome BIOSAM
University of Lisbon (Lisbon)
2018/02/18 Bioconductor R package for Proteostasis factors UBICODE
University of Toulouse (Toulouse, France)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/12/31 - 2024/01/01 Artifical agents in Metabolomics
Supervisor
 iNOVA4Health - Programme in Translational Medicine, Universidade Nova de Lisboa – NMS|FCM (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2020/01/01 - 2024/01/01 Microenvironment, the shelter of brain malignancies: bidirectional communication between glia and brain tumors
Co-supervisor
 iNOVA4Health - Programme in Translational Medicine, Universidade Nova de Lisboa – NMS|FCM (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2020/01/01 - 2024/01/01 Urine extracellular vesicle proteome for classification of cribriform and intraductal patterns
Supervisor
 BioMedicine (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/12/01 - 2023/01/01 Urinary proteomics: new insights in overac$ve bladder syndrome
Supervisor
 BioMedicine (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/01/01 - 2023/01/01 Identification of therapeutic targets and disease biomarkers for mutant KRAS cancer patients: fulfilling an unmet clinical need
Co-supervisor
 Oncology (PhD)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2019/01/01 - 2022/01/01 Correlation of phospho protein network in immune and cancer cells from patients with clinical outcome
Supervisor
 BioMedicine (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/01/01 - 2022/01/01 Ubiquitin proteasome system in cancer and immune cells of patients with Diffuse Large B-Cell Lymphoma (DLBCL)
Supervisor
 Biomedicine (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/01/01 - 2020/12/18 Diffuse Large B-cell Lymphoma current classification based extracellular vesicle proteome
Supervisor
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/02/26 - 2019/02/28 druggability of the ubiquitin system (2019/02/26 - 2019/02/28)
Conference (President of the Organising Committee)
 Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2016/11/07 - 2016/11/09 Proteostasis cost action meeting (2016/11/07 - 2016/11/09)
Conference (President of the Organising Committee)
 Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2022/07/28 Study of the protein cargo of extracellular vesicles released by Acute Myeloid Leukemia cell lines
(Thesis) Arguer
 Inês Adriana Miranda (PhD)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2020/12/19 Extracellular vesicles: agents of gut communication in prediabetes scenario
(Thesis) Arguer
 Ines Antunes Ferreira (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2020/12/18 VENCODE – A VERSATILE ENTRY CODE FOR POST-DNA DELIVERY IDENTIFICATION OF TARGET CELLS
(Thesis) Arguer
 André Macedo (PhD)
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/11/03 Studying extracellular vesicles from P-glycoprotein overexpressing multidrug resistant cells: New insight into their cargo and release
(Thesis) Arguer
 Diana Sousa (PhD)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2019/03/06 Multi-omics Integration for Biomarker Discovery
(Thesis) Arguer
 Marc Clos Garcia (PhD)
CIC bioGUNE, Spain
2019/01/27 REGULATION OF THE RP- MDM2-P53 PATHWAY BY SUMO
(Thesis) Arguer
 Ahmed Hassan El Motiam (PhD)
Universidade de Santiago de Compostela, Spain
2017/06/20 The Endoplasmic Reticulum Quality Control: Dissecting Protein Networks in Cystic Fibrosis
(Thesis) Arguer
 Sara Canato (PhD)
Universidade de Lisboa, Portugal
2017 Methods to compare the proteome of the parasite Trypanosome brucei isolated from two different tissues of its host
(Thesis) Main arguer
 Mariana Sequeira (PhD)
2017 Mass spectrometry-based proteomic strategies to define protein NEDDyation
(Thesis) Main arguer
 Sofia Celeste Lobato (PhD)
CIC bioGUNE, Spain

Association member

Society Organization name Role
2023/06/01 - Current Vice president of Portuguese network of extracellular vesicles accounting
2018/01/01 - 2022/01/01 UBICODE https://euraxess.ec.europa.eu/jobs/277683 Memeber
2014/01/01 - 2019/01/01 Proteostasis National representative

Committee member

Activity description
Role 		Institution / Organization
2024/01/01 - Current ISEV EV-TRACK task force member working group 3 focusing on outreach and future developments
Member
2022/10/01 - 2025/10/10 Coordinator of EVCA board for internal funded EVCA projects.
Coordinator
 Universidade NOVA de Lisboa NOVA Medical School, Portugal
2023/01/28 - 2023/01/29 Coordinator of extracellular vesicles in clinical applications (EVCA) kick off meeting, Ericeia, Portugal
Coordinator
2020/09/01 - 2023/01/01 Editor on the journal Cancers
Member

Conference scientific committee

Conference name Conference host
2024/05/07 - 2024/05/10 Scientific advisory board in ProteoCure meeting in Warsaw Poland Warsaw Poland
2023/11/24 - 2023/11/24 Workshop on arginine methylation extracellular vesicles and cancer Nova medical school, Lisbon
2023/06/01 - 2023/06/03 Organiser of Portuguese Network on Extracellular Vesicles (PNEV) meeting Nova medical school, Lisbon
2019/03/26 - 2019/03/29 druggability of the ubiquitin system CEDOC
2016/11/07 - 2016/11/09 Proteostasis cost action meeting CEDOC

Consulting

Activity description Institution / Organization
2024/01/01 - 2025/01/01 External consultant Mursla, Cambridge.

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2020/01/01 - Current Cofounder of master program and responsible for advanced metabolomics and proteomcis course. MSc in Computational Biology and Bioinformatics (MCBBI) (Mestrado) Universidade Nova de Lisboa, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2020/12/01 - Current The Hellenic Foundation for Research and Innovation (HFRI)
Evaluator
2022/10/01 - 2025/10/01 Coordinator of twining project “Centre for Excellence in Diagnostic and Advanced Therapeutics based on Extracellular Vesicles” Universidade NOVA de Lisboa NOVA Medical School, Portugal
2022/01/01 - 2022/01/02 GrantsUKRI, University of Oxford University of Oxford - Old Road Campus, United Kingdom
2011/01/01 - 2020/01/01 Evaluator and rapporteur of national projects submitted to the research council of Romania (bioinformatics, proteomics and clinical projects) and evaluator for the national BrainMap investigator program.
Evaluator
 uefiscdi.gov.ro
2009/01/01 - 2020/01/01 Evaluator of Spanish National projects (MEC projects) https://www.mineco.gob.es/evalua/jsp/menu/menu.do?operacion=pintaMenu
Evaluator
 Ministerio de Ciencia E innovacion, Spain
2018/05/16 - 2018/06/30 Remote and local evaluation of H2020 projects. H2020 Framework program, Brussels, Belgium
Evaluator
 _H2020, Denmark EU Framework Programme for Research and Innovation Euratom
2016/01/01 - 2016/06/01 Bilateral Scientific Cooperation China" application to the Research Foundation Flanders
Evaluator
2014/01/01 - 2014/03/01 Czech-Norwegian Research Programme (CZ09)
Evaluator
2013/01/01 - 2013/03/01 Evaluator of FCT investigators
Evaluator
2010/01/01 - 2010/03/01 EU INDIGO projects in the area of biomarker discovery, bioinformatics and proteomics
Evaluator
Distinctions

Award

2023 Prémio SPAVC/ Stroke Biomarkers
2021 Urinary EV proteomics can we distinguise cribriform and intraductral carcinoma of the prostate
2020 Molecular Characterization of Intraductal and Cribriform Prostate Cancer: The future of Exosomes as Biomarkers
Associação Portuguesa de Urologia, Portugal
2020 Urinary extracellular vesicle proteomics
2019 CEEC position (FCT); https://doi.org/10.54499/CEECIND/03906/2017/CP1421/CT0004
Fundação para a Ciência e a Tecnologia, Portugal
2016 SPP/ Pfizer Vaccines
2013 FCT investigator
Fundação para a Ciência e a Tecnologia, Portugal
2008 Ciencia
Fundação para a Ciência e a Tecnologia, Portugal
2006 Ramón y Cajal (RYC)
2004 Carlsberg foundation
Carlsbergfondet, Denmark