???global.info.a_carregar???
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.
Ler resumo completo ↓
Identificação

Identificação pessoal

Nome completo
Rune Matthiesen

Nomes de citação

  • Matthiesen, Rune

Identificadores de autor

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

Domínios de atuação

  • Ciências Naturais - Ciências Biológicas - Bioquímica
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
  • Ciências Médicas e da Saúde - Biotecnologia Médica

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Dinamarquês (Idioma materno)
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Alemão Utilizador independente (B2) Utilizador proficiente (C2) Utilizador independente (B2) Utilizador proficiente (C2) Utilizador independente (B1)
Português Utilizador independente (B1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador independente (B1) Utilizador independente (B1)
Formação
Grau Classificação
2000/12/31 - 2003/12/16
Concluído
 Departmen of Life Science, University of Aalborg (Doutoramento)
Aalborg Universitet, Dinamarca
"Mass spectrometry in Proteomics" (TESE/DISSERTAÇÃO)
1998/07/01 - 1999/07/01
Concluído
 Molecular biology (Mestrado)
Aarhus Universitet, Dinamarca
"Crystallography of ternary complex of eIF2" (TESE/DISSERTAÇÃO)
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2016/08/01 - Atual Investigador principal (carreira) (Investigação) iNOVA4Health, Portugal
2013/08/01 - 2016/08/01 Investigador principal (carreira) (Investigação) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2008/08/01 - 2013/08/01 Investigador principal (carreira) (Investigação) 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 Investigador principal (carreira) (Investigação) CIC bioGUNE, Espanha
CIC bioGUNE, Espanha
2004/01/01 - 2006/01/01 Investigador Auxiliar (carreira) (Investigação) Syddansk Universitet, Dinamarca
Syddansk Universitet, Dinamarca
2004/01/01 - 2005/01/01 Investigador Auxiliar (carreira) (Investigação) European Bioinformatics Institute, Reino Unido
European Bioinformatics Institute, Reino Unido
Projetos

Bolsa

Designação Financiadores
2023/09/01 - Atual FCT LA LS4Future: 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

GREEN-IT, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal

Instituto Gulbenkian de Ciência, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade de Lisboa Centro de Estudos Comparatistas, Portugal

Universidade Nova de Lisboa, Portugal

Universidade Nova de Lisboa Molecular Structural and Cellular Microbiology, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2025/03/14 - 2026/03/13 Deciphering Response Variability in Non-Muscle Invasive Bladder Cancer: Investigating Heterogeneity Through Cancer Stem Cells and Exosomal Dynamics
NRC/CIMAGO 2024/2025
Universidade de Coimbra Instituto de Investigação Clínica e Biomédica de Coimbra, Portugal
 Liga Portuguesa Contra o Cancro Núcleo Regional do Centro
Em curso
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
Em curso
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
Desativado
2022/01/17 - 2025/01/17 Optimizing mass spectrometry based detection of biomarkers for immunotherapy response across urologic cancers
PTDC/BTM-TEC/1746/2021
Investigador responsável
Fundação para a Ciência e a Tecnologia
Em curso
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
Investigador
Liga Portuguesa Contra o Cancro
Em curso
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
Concluído

Projeto

Designação Financiadores
2023/09/01 - Atual 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
Em curso
2023/03/01 - 2024/08/31 Interação nutrição-obesidade através de vesículas extracelulares: retrato ômico no transplante fecal
2022.05764.PTDC
10.54499/2022.05764.PTDC
Universidade Nova de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2022/01/10 - 2024/01/09 Screening for new high potential therapeutic targets in duodenum against type 2 diabetes
EXPL/MED-PAT/0852/2021
10.54499/EXPL/MED-PAT/0852/2021
Universidade Nova de Lisboa, Portugal

Unidade de Ciências Biomoleculares Aplicadas, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal

iNOVA4Health, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
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
Em curso
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
Em curso
2018/10/01 - 2022/09/30 Remote ischemic post-conditioning in acute phase of ischemic stroke: disclosing novel circulating biomarkers and clinical trial for improving outcome
PTDC/MEC-NEU/28750/2017
Centro Hospitalar de Lisboa Ocidental EPE, Portugal

Universidade Nova de Lisboa, Portugal

Universidade Nova de Lisboa Medical School, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
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
Em curso
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
Concluído
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
Concluído
2010/06/01 - 2013/11/30 Dissection of the molecular role of O-GlcNAc in the multinucleation phenotype of the neoplasic cells in Hodgkin´s lymphoma.
PTDC/QUI-BIQ/099457/2008
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
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
Concluído
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
Concluído

Outro

Designação Financiadores
2016/06 - 2021/02/28 Implications of Medical Low Dose Radiation Exposure
755523
Bolseiro de Cientista Convidado
Em curso
Produções

Publicações

Artigo em conferência
  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". Trabalho apresentado em Perspectivas em Oncologia, Porto, 2022.
    Publicado
  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.
Artigo em revista
  1. Carlos Miguel Vital; José Manuel Inácio; Ana Sofia Carvalho; Hans Christian Beck; Rune Matthiesen; José António Belo. "Integrative Proteomics of Extracellular Vesicles from hiPSC-Derived Cardiac Organoids Reveals Heart Tissue-like Molecular Representativity". International Journal of Molecular Sciences (2026): https://doi.org/10.3390/ijms27020981.
    10.3390/ijms27020981
  2. Joao Vasco Ferreira; Luís Carvalho Ferraz; Ana da Rosa Soares; Mostafa Ejtehadifar; Ana Sofia Carvalho; Michael James Hall; Judit Morello; et al. "LAMP2A regulates endosomal protein composition and membrane identity in exosome biogenesis". iScience (2026): https://doi.org/10.1016/j.isci.2025.114305.
    10.1016/j.isci.2025.114305
  3. Paula de Oliveira; Inês Sofia Vala; Pedro Faísca; Joao C Guimaraes; Filomena Pina; Esmeralda Poli; Isabel Diegues; et al. "Subtherapeutic Dose of Ionizing Radiation Reprograms the Pre-Metastatic Lung Niche, Accelerating Its Formation and Promoting Metastasis". International Journal of Molecular Sciences (2025): https://doi.org/10.3390/ijms26136145.
    10.3390/ijms26136145
  4. Bergantim, Rui; Peixoto da Silva, Sara; Pinto, Vanessa; Pereira, J. M.; Sousa, Diana; fernanda trigo; Matthiesen, Rune; José Eduardo Guimarães; Vasconcelos, M. Helena. "MicroRNA-665 and its potential role in drug response and survival outcomes in Multiple Myeloma: a preliminary study". Frontiers in Pharmacology 16 (2025): https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2025.1465814/abstract.
    Aceite para publicação
  5. Mollet, Inês G.; Viana-Soares, Ricardo; Cardoso-Pires, Catarina; Soares, Nuno L.; Marto, João Pedro; Mendonça, Marcelo; Queiroga, Cláudia S.F.; et al. "Identification of human circulating factors following remote ischemic conditioning (RIC): Potential impact on stroke". Free Radical Biology and Medicine 224 (2024): 23-38. https://doi.org/10.1016/j.freeradbiomed.2024.08.017.
    10.1016/j.freeradbiomed.2024.08.017
  6. Pires, Carolina; Laine, Hugo; C., Ehlers Anna; Saramago, Ana; Moura, Margarida; Pojo, Marta; Cabrera, Rafael; et al. "Clinically relevant germline genetic variants and somatic fusions underlying paediatric thyroid cancer risk and aggressiveness". Endocrine Abstracts 101 (2024): http://dx.doi.org/10.1530/endoabs.101.op-06-04.
    Publicado • 10.1530/endoabs.101.op-06-04
  7. Serambeque, Beatriz; Mestre, Catarina; Hundarova, Kristina; Marto, Carlos Miguel; Oliveiros, Bárbara; Gomes, Ana Rita; Teixo, Ricardo; et al. "Proteomic Profile of Endometrial Cancer: A Scoping Review". Biology 13 8 (2024): 584. http://dx.doi.org/10.3390/biology13080584.
    Publicado • 10.3390/biology13080584
  8. João Vasco Ferreira; Ana da Rosa Soares; L. C. Ferraz; Ejtehadifar, Mostafa; Ana Carvalho; Michael James Hall; Morello, Judit; et al. "The role of LAMP2A in Endosomal Protein Composition: Implications for Membrane Identity, Endosomal Maturation and Exosome Biogenesis.". Journal of Extracellular Vesicles (2024):
    Em revisão
  9. Serambeque, Beatriz; Mestre, Catarina; Correia-Barros, Gabriela; Teixo, Ricardo; Marto, Carlos Miguel; Gonçalves, Ana Cristina; Caramelo, Francisco; et al. "Influence of Aldehyde Dehydrogenase Inhibition on Stemness of Endometrial Cancer Stem Cells". Cancers 16 11 (2024): 2031. http://dx.doi.org/10.3390/cancers16112031.
    Publicado • 10.3390/cancers16112031
  10. Pedro Baptista Pereira; Estefania 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". Nutrients (2024): https://doi.org/10.3390/nu16050736.
    10.3390/nu16050736
  11. Bernardino, Rui; Carvalho, Ana Sofia; Hall, Michael J.; Alves, Liliana; Leão, Ricardo; Sayyid, Rashid; Pereira, Hermínia; et al. "Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study". (2024): http://hdl.handle.net/10362/175460.
    https://doi.org/10.1038/s41598-024-75272-w
  12. Marto, João Pedro; Carvalho, Ana Sofia; G. Mollet, Inês; Mendonça, Marcelo; Salavisa, Manuel; Meira, Bruna; Fernandes, Marco; et al. "Proteomics to Identify New Blood Biomarkers for Diagnosing Patients With Acute Stroke". Journal of the American Heart Association 12 22 (2023): http://dx.doi.org/10.1161/jaha.123.030021.
  13. 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
  14. 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
  15. 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.
    Publicado • 10.1158/1557-3125.ras23-a006
  16. 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
  17. 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. Autor correspondente: Vicente Miranda, Hugo. "aSyn overexpression impairs oxidative phosphorylation, endocytosis, and synaptic vesicle dynamics in the midbrain (Under Preparation)". npj Parkinson's Disease (2023):
    Submetido
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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.
    Publicado • 10.3389/fimmu.2022.909880
  23. 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
  24. Mollet, Inês; Martins, Catarina; Ângelo-Dias, Miguel; Carvalho, Ana S.; Aloria, Kerman; Matthiesen, Rune; Viana-Baptista, Miguel; Borrego, Luís Miguel; Vieira, Helena L.A.. "Pilot study in human healthy volunteers on the mechanisms underlying remote ischemic conditioning (RIC) – Targeting circulating immune cells and immune-related proteins". Journal of Neuroimmunology 367 (2022): 577847. http://dx.doi.org/10.1016/j.jneuroim.2022.577847.
    10.1016/j.jneuroim.2022.577847
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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.
    Publicado
  30. 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..
    Publicado
  31. 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.
    10.3390/ijms23010319
  32. 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
  33. 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.
    10.3390/ijms222011004
  34. 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
  35. Ana Chegão; Mariana Guarda; Alexandre BM; Shvachiy, Liana; Mariana Temido-Ferreira; Inês Marques-Morgado; Bárbara Fernandes Gomes; et al. Autor correspondente: 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.
    Publicado
  36. 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.
    10.1016/j.ebiom.2021.103504
  37. 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.
    10.1038/s41598-021-94468-y
  38. 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):
    Submetido
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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.
    Publicado • 10.1007/s00018-018-2896-7
  57. 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
  58. 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
  59. 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.
    https://doi.org/10.1038/srep42190
  60. 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.
    10.1016/j.bbadis.2016.11.019
  61. 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.
    https://doi.org/10.1016/j.dib.2017.01.005
  62. 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
  63. 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.
    10.1038/srep42190
  64. 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
  65. 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
  66. 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.
    10.1007/s10689-015-9848-2
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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.
    10.1371/journal.pone.0104935
  80. 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
  81. 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
  82. 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
  83. Matthiesen R; Carvalho AS. "Methods and algorithms for quantitative proteomics by mass spectrometry.". (2013): http://europepmc.org/abstract/med/23666727.
    10.1007/978-1-62703-392-3_8
  84. Matthiesen R. "Algorithms for database-dependent search of MS/MS data.". (2013): http://europepmc.org/abstract/med/23666724.
    10.1007/978-1-62703-392-3_5
  85. Matthiesen R. "LC-MS spectra processing.". (2013): http://europepmc.org/abstract/med/23666721.
    10.1007/978-1-62703-392-3_2
  86. Matthiesen, R.. "Preface". Methods in Molecular Biology 1007 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84883172367&partnerID=MN8TOARS.
    10.1007/978-1-62703-392-3
  87. 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.
    10.1371/journal.pgen.1003349
  88. 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.
    doi:10.1371/journal.pgen.1003349
  89. 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.
    10.1186/1471-2105-13-288
  90. 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.
    10.1155/2012/875148
  91. Matthiesen, R.; Prieto, G.; Amorim, A.; Aloria, K.; Fullaondo, A.; Carvalho, A.S.; Arizmendi, J.M.. "SIR: Deterministic protein inference from peptides assigned to MS data". Journal of Proteomics 75 13 (2012): 4176-4183. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862659627&partnerID=MN8TOARS.
    10.1016/j.jprot.2012.05.010
  92. 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.
    10.1016/j.jprot.2011.12.001
  93. 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.
    10.1371/journal.pone.0018487
  94. Matthiesen, R.; Azevedo, L.; Amorim, A.; Carvalho, A.S.. "Discussion on common data analysis strategies used in MS-based proteomics". Proteomics 11 4 (2011): 604-619. http://www.scopus.com/inward/record.url?eid=2-s2.0-79551483264&partnerID=MN8TOARS.
    10.1002/pmic.201000404
  95. 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.
    10.1002/pmic.200900255
  96. Gubb E; Matthiesen R. "Introduction to omics.". (2010): http://europepmc.org/abstract/med/19957142.
    10.1007/978-1-60327-194-3_1
  97. Frades I; Matthiesen R. "Overview on techniques in cluster analysis.". (2010): http://europepmc.org/abstract/med/19957146.
    10.1007/978-1-60327-194-3_5
  98. Matthiesen R; Carvalho AS. "Methods and algorithms for relative quantitative proteomics by mass spectrometry.". (2010): http://europepmc.org/abstract/med/19957151.
    10.1007/978-1-60327-194-3_10
  99. Lasso G; Matthiesen R. "Computational methods for analysis of two-dimensional gels.". (2010): http://europepmc.org/abstract/med/19957153.
    10.1007/978-1-60327-194-3_12
  100. Matthiesen R; Amorim A; Matthiesen, R.; Amorim, A.. "Proteomics facing the combinatorial problem.". Methods in molecular biology (Clifton, N.J.) 593 (2010): 175-186. http://europepmc.org/abstract/med/19957150.
    10.1007/978-1-60327-194-3_9
  101. Hackenberg M; Matthiesen R. "Algorithms and methods for correlating experimental results with annotation databases.". (2010): http://europepmc.org/abstract/med/19957156.
    10.1007/978-1-60327-194-3_15
  102. 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.
    10.1264/jsme2.ME09185
  103. Pereira, F.; Carneiro, J.; Matthiesen, R.; Van Asch, B.; Pinto, N.; Gusmão, L.; Amorim, A.. "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 22 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650444073&partnerID=MN8TOARS.
    10.1093/nar/gkq865
  104. 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.
    10.1186/1471-2121-11-81
  105. 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
  106. 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.
  107. 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.
  108. 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.
  109. 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.
  110. 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
  111. 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.
  112. 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.
  113. 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
  114. 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
  115. 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
  116. 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.
  117. 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
  118. 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
  119. 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
  120. 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
  121. 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
  122. 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
  123. Matthiesen R; Mutenda KE. "Introduction to proteomics.". (2007): http://europepmc.org/abstract/med/17185767.
    10.1385/1-59745-275-0:1
  124. 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
  125. Gruhler A; Matthiesen R. "Quantitation with virtual expert mass spectrometrist.". (2007): http://europepmc.org/abstract/med/17185774.
    10.1385/1-59745-275-0:139
  126. 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
  127. Mutenda KE; Matthiesen R. "Analysis of carbohydrates by mass spectrometry.". (2007): http://europepmc.org/abstract/med/17185783.
    10.1385/1-59745-275-0:289
  128. 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
  129. 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
  130. 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
  131. 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
  132. 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
  133. 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
  134. 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
  135. 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
  136. 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.
  137. 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.
  138. 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.
  139. 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.
  140. 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.
  141. 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.
  142. 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.
  143. 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.
  144. 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.
  145. 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
  146. 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
  147. 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
  148. 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
  149. 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
  150. 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
  151. 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
  152. 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
  153. 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
  154. Matthiesen, Rune. "Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS v2.0.". Proteomics (2004):
  155. 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
  156. 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
  157. 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
Livro
  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
Poster em conferência
  1. Torrejón, Estefania; Inês Ferreira; Matthiesen, Rune; Macedo, Maria Paula; Anaïs Baudot; Rita Machado de Oliveira. "An adaptation of the Nichenet method to study targeted communication network mediated by extracellular vesicles". Trabalho apresentado em International Society of Extracellular, 2025.
  2. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Fabrizia Carli; et al. Autor correspondente: Rita Machado de Oliveira. "Gut derived Extracellular Vesicles reaching with Kupffer Cells: An alternative route for lipid transport and deposition in the liver". Trabalho apresentado em ISCB-LATAM SOIBIO CCBCOL 2024, 2024.
  3. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Fabrizia Carli; et al. Autor correspondente: Rita Machado de Oliveira. "Gut derived Extracellular Vesicles Reaching Kupffer Cells: An alternative route for lipid transport out of the gut". Trabalho apresentado em 28th Annual International Conference on Research in Computational Molecular Biology (RECOMB2024) and satellite RECOMB-Seq conference, 2024.
  4. Torrejón, Estefania; Teshima, Akiko; Ferreira, Ines; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Carli, Fabrizia; et al. Autor correspondente: Torrejón, Estefania. "Diabetogenic Gut derived Extracellular Vesicles Proteomics modulated by Oral Anti-Diabetic Drugs: A Lipidomic Connection". Trabalho apresentado em NOVA Medical School Research Week 2023, 2023.
  5. 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". Trabalho apresentado em EASD(European Association for the Study of Diabetes) 59th Annual meeting, 2023.
  6. Laranjo, Mafalda; Mestre, Catarina; Serambeque, B; Carvalho, Ana Sofia; Beck, Hans C; Botelho, Maria Filomena; Carvalho, Maria João da Silva Fernandes Leal; Matthiesen, Rune. Autor correspondente: Mestre, Catarina. "Looking for therapeutic targets on the proteome profile of endometrial cancer stem cells". Trabalho apresentado em ESMO 2023, 2023.
    https://doi.org/10.1016/j.annonc.2023.09.1545
  7. Torrejón, Estefania; Teshima, Akiko; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Macedo, Maria Paula; Rita Machado de Oliveira. Autor correspondente: Rita Machado de Oliveira. "Impact of oral anti-diabetic drugs on gut-derived extracellular vesicles: Proteomic Signature". Trabalho apresentado em International Society of Computational Biology Student Council Symposium 2023 and main event (ISMBECCB2023), 2023.
  8. Zahedi, Sara; Ejtehadifar, Mostafa; Carvalho, Ana Sofia; Matthiesen, Rune. Autor correspondente: Matthiesen, Rune. "Comparative proteome analysis of pleural fluid biomarkers obtained from mesothelioma patients, non malignant and malignant lung diseases". Trabalho apresentado em iMig2023, 2023.
  9. Ejtehadifar, Mostafa; Zahedi, Sara; Ana Sofia Carvalho; Matthiesen, Rune. Autor correspondente: Matthiesen, Rune. "Nucleobindin1 in a diffuse large B-cell lymphoma cell line is a potential drug-resistance biomarker". Trabalho apresentado em 2nd meeting of the Portuguese Network on extracellular vesicles, 2023.
  10. Torrejón, Estefania; Teshima, Akiko; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Macedo, Maria Paula; Rita Machado de Oliveira. "Gut-derived extracellular vesicles’ proteomic diabetogenic signature altered by oral anti-diabetic drugs". Trabalho apresentado em 2nd meeting of the Portuguese Network on Extracellular Vesicles, 2023.
  11. 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". Trabalho apresentado em XLVIII Annual Meeting Portuguese Socienty of Immunology, 2023.
  12. 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". Trabalho apresentado em XLVIII Annual Meeting Portuguese Society of Immunology, 2023.
  13. Serambeque, Beatriz; Carvalho, Maria João; Mestre, Catarina; Teixo, Ricardo; Marto, Carlos Miguel; Beck, Hans C; Carvalho, Ana Sofia; et al. "Endometrial cancer stem cells: exploring the role of ALDH in stemness". Trabalho apresentado em 4th SPLC-CRS Young Scientists Meeting, 2023.
  14. Ribeiro, Sónia; Pereira, Ana Rita S.; Rocha, Filipe; Vala, Inês Sofia; Pinto, Ana Teresa; Ministro, Augusto; Poli, Esmeralda; et al. Autor correspondente: Santos, Susana Constantino Rosa. "Cardiac tissue remodelling induced by ionizing radiation in a dosedependent manner is an early predictor of subclinical cardiac dysfunction.". Trabalho apresentado em European Radiation Protection Week 2022, 2022.
  15. 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". Trabalho apresentado em Champalimaud Research Symposium, 2022.
  16. 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)". Trabalho apresentado em 19th International Myeloma Society Annual Meeting, 2022.
  17. 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.
  18. 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)". Trabalho apresentado em 5th Annual Meeting STRATAGEM COST Action, 2022.
  19. Mestre, Catarina; Serambeque, B; Carvalho, Ana Sofia; Beck, Hans C; Carvalho, Maria João da Silva Fernandes Leal; Botelho, Maria Filomena; Matthiesen, Rune; Laranjo, Mafalda. Autor correspondente: Mestre, Catarina. "Clinical therapeutic targets in endometrial cancer stem cells: a proteomic overview". Trabalho apresentado em ASPIC 2022, 2022.
  20. 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?". Trabalho apresentado em XV CAML V NeurULisboa PhD Students meeting, 2022.
  21. 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". Trabalho apresentado em XLVII Annual Meeting Portuguese Society of Immunology, 2022.
  22. 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.". Trabalho apresentado em XVII Meeting of the Portuguese Society for Neuroscience (SPN2021), 2021.
  23. Inês Antunes Ferreira; de Oliveira RM; Teshima, Akiko; Matthiesen, Rune; Costa-Silva, Bruno; Macedo, Maria. Autor correspondente: Inês Antunes Ferreira. "Gut-derived exosomes in prediabetes: proteomics insight.". 2020.
  24. 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". Trabalho apresentado em Reunião Anual Sociedade Portuguesa de Hematologia (SPH), 2019.
  25. 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". Trabalho apresentado em 40th European Cystic Fibrosis Conference, 2017.
  26. 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". Trabalho apresentado em i3S retreat 2014, 2014.
Pré-impressão
  1. Ana Sofia Carvalho; Juan M. Falcón-Pérez’; Hans C Beck; Rune Matthiesen. "A Meta-Analysis of 515 Human Proteomes Defines the Core Composition and Contaminants of Plasma Extracellular Vesicles isolates". 2026. https://doi.org/10.64898/2026.01.28.702342.
    10.64898/2026.01.28.702342
  2. 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
  3. 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
  4. Borbinha, Jorge; Lourenço, Raquel; Brandão, Ana S.; Carvalho, Ana; Matthiesen, Rune; Jacinto, António. "Metabolic reprogramming regulates histone lactylation during zebrafish caudal fin regeneration". 2024. https://doi.org/10.1101/2024.09.28.615596.
    10.1101/2024.09.28.615596
  5. 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
Resumo em conferência
  1. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Anaïs Baudot; Macedo, Maria Paula; Rita Machado de Oliveira. Autor correspondente: Rita Machado de Oliveira. "Deciphering the Gut-to-Kupffer cell communication network mediated by gut-derived extracellular vesicles". Trabalho apresentado em EASL SLD Summit 2025 - EASL-The Home of Hepatology, Estoril, 2025.
  2. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Fabrizia Carli; et al. Autor correspondente: Macedo, Maria Paula. "Anti-Diabetic Drugs: Shaping the Protein Messages of the Diabetogenic Gut Derived Extracellular Vesicles". Trabalho apresentado em 58th Annual Scientific Meeting of the European Society for Clinial Investigation (ESCI 2024), Barcelona, 2024.
  3. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Fabrizia Carli; et al. Autor correspondente: Rita Machado de Oliveira. "Fármacos Antidiabéticos Orais Redefinem a Assinatura Proteómica das Vesículas Extracelulares Derivadas do Intestino Diabetogénico: implicações metabólicas". Trabalho apresentado em 20.º Congresso Português de Diabetes, 2024.
  4. Torrejón, Estefania; Teshima, Akiko; Inês Ferreira; Carvalho, Ana Sofia; Beck, Hans Christian; Matthiesen, Rune; Fabrizia Carli; et al. Autor correspondente: Rita Machado de Oliveira. "Diabetogenic Gut derived Extracellular Vesicles Reaching Kupffer Cells: A Lipidomic Connection". Trabalho apresentado em EVCA Winter Retreat, 2024.
  5. 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". Trabalho apresentado em Congresso Português de Endocrinologia - 75ª Reunião Anual da SPEDM, Vilamoura, 2024.
    Publicado
  6. 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". Trabalho apresentado em Congresso Português de Endocrinologia 2024 - 75ª Reunião Anual da SPEDM, Vilamoura, 2024.
    Publicado
  7. 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". Trabalho apresentado em NMS Research Week, Lisboa, 2023.
    Publicado
  8. 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.
  9. 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.
    Publicado
  10. Inês Ferreira; Rita Machado-Oliveira; Matthiesen, Rune; Bruno Costa-Silva; Macedo, M P. "Exossomas derivados do Intestino como Mensageiro de Pré-diabetes". Trabalho apresentado em 16º Congresso Português de Diabetes, 2020.
    Publicado
  11. de Oliveira RM; Inês Antunes Ferreira; Teshima, Akiko; Matthiesen, Rune; Costa-Silva, Bruno; Macedo, Maria. Autor correspondente: de Oliveira RM. "Prediabetes from the perspective of gut-derived exosomes". Vilamoura, 2020.
    Publicado
Revisão de livro
  1. Bernardino, Rui Miguel Marques; Leão, Ricardo; Henrique, Rui; Pinheiro, Luis Campos; Kumar, Prashant; Suravajhala, Prashanth; Beck, Hans Christian; Carvalho, Ana Sofia; Matthiesen, Rune. "Extracellular vesicle proteome in prostate cancer". (2021): http://hdl.handle.net/10362/130894.
    https://doi.org/10.3390/ijms222413605

Outros

Outra produção
  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
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2026/06/03 Tumor Secretome-Mediated Proteome Remodeling in Peripheral Immune Cells: Evidence from Lung Cancer and DLBCL Tumor Secretome-Mediated Proteome Remodeling in Peripheral Immune Cells: Evidence from Lung Cancer and DLBCL
European Society for Clinical Investigation (Lisbon, Portugal)
2026/03/11 Presenter of final overview of EVCA MEV projects. In last EVCA retreat. and Protein Arginine methylation in extracellular vesicles EVCA seminars
EVCA (Sesimbra, Portugal)
2026/02/11 Invited speaker in PhD student seminars, NMS, Decoding the Plasma EV Landscape: From Venn Diagrams and Quality Metrics to Biological Insight Decoding the Plasma EV Landscape: From Venn Diagrams and Quality Metrics to Biological Insight
Nova medical school (Lisbon, Portugal)
2025/12/15 Systemic Immune Suppression in DLBCL: Tumor-Derived Extracellular Vesicles Induce Polyubiquitination and Compromise PBMC Viability EVCA seminars
Nova medical school (Lisbon, Portugal)
2025/07/03 Decoding EVs: Diagnostic Applications in Oncology Decoding EVs: Diagnostic Applications in Oncology
I3S (Porto, Portugal)
2025/06/17 Maximizing Clinical Research Data Value Through AI”. In the NMS/eatris/GIMM event Maximizing Clinical Research Data Value Through AI”. In the NMS/eatris/GIMM event
Nova medical school (Lisbon, Portugal)
2025/04/04 Use of AI in science Use of AI in science
Lisbon stroke summit 2025 (Lisbon, Portugal)
2025/03/22 Unlocking the Diagnostic Potential of Extracellular Vesicles International Congress in Health Science Research: from molecule to community
International Congress in Health Science Research: from molecule to community (covilha, Portugal)
2024/11/07 Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation, Institute Curie, Paris, France Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation, Institute Curie, Paris, France
European Multidisciplinary Congress on Urological Cancers ( EMUC24) (Lisbon, Portugal)
2024/10/18 Invited speaker - Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation - XVIII Simpósio APU 2024 Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation
Associação Portuguesa de Urologia (Tróia Design Hotel, Portugal)
2024/02/28 Presentation of EVCA MEV project status, EVCA second winter retreat
EVCA (Lisbon, Portugal)
2023/12/06 Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study, invited presentation
(Paris, França)
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, Índia)
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, França)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2020/12/31 - 2024/01/01 Artifical agents in Metabolomics
Orientador
 iNOVA4Health - Programme in Translational Medicine, Universidade Nova de Lisboa – NMS|FCM (Doutoramento)
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
Coorientador
 iNOVA4Health - Programme in Translational Medicine, Universidade Nova de Lisboa – NMS|FCM (Doutoramento)
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
Orientador
 BioMedicine (Doutoramento)
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
Orientador
 BioMedicine (Doutoramento)
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
Coorientador
 Oncology (Doutoramento)
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
Orientador
 BioMedicine (Doutoramento)
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)
Orientador
 Biomedicine (Doutoramento)
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
Orientador
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal

Organização de evento

Nome do evento
Tipo de evento (Tipo de participação) 		Instituição / Organização
2026/04/26 - 2026/04/26 Organiser and speaker in symposium “Deconvoluting the EV Landscape: Bridging EV-function and Biomarkers via Systems Biology”, ISEV 2026, Puerto Rico (2026/04/26 - 2026/04/26)
Simpósio (Presidente da Comissão Organizadora)
 International Society for Extracellular Vesicles, Estados Unidos
2024/07/11 - 2024/07/12 Co-organiser of EVCA summer school on EV isolation and characterization (2024/07/11 - 2024/07/12)
Oficina (workshop) (Membro da Comissão Científica)
 Universidade Nova de Lisboa Medical School, Portugal
2019/02/26 - 2019/02/28 druggability of the ubiquitin system (2019/02/26 - 2019/02/28)
Conferência (Presidente da Comissão Organizadora)
 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)
Conferência (Presidente da Comissão Organizadora)
 Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2026/02/27 Identification of Molecular Biotypes of Prostate Cancer as a Basis for Precision Medicine (BIOChiP)
Arguente
 Belén Pastor Navarro (Doutoramento)
Fundación Instituto Valenciano de Oncología Servicio de Urología, Espanha
2022/07/28 Study of the protein cargo of extracellular vesicles released by Acute Myeloid Leukemia cell lines
Arguente
 Inês Adriana Miranda (Doutoramento)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2020/12/19 Extracellular vesicles: agents of gut communication in prediabetes scenario
Arguente
 Ines Antunes Ferreira (Doutoramento)
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
Arguente
 André Macedo (Doutoramento)
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
Arguente
 Diana Sousa (Doutoramento)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2019/03/06 Multi-omics Integration for Biomarker Discovery
Arguente
 Marc Clos Garcia (Doutoramento)
CIC bioGUNE, Espanha
2019/01/27 REGULATION OF THE RP- MDM2-P53 PATHWAY BY SUMO
Arguente
 Ahmed Hassan El Motiam (Doutoramento)
Universidade de Santiago de Compostela, Espanha
2017/06/20 The Endoplasmic Reticulum Quality Control: Dissecting Protein Networks in Cystic Fibrosis
Arguente
 Sara Canato (Doutoramento)
Universidade de Lisboa, Portugal
2017 Methods to compare the proteome of the parasite Trypanosome brucei isolated from two different tissues of its host
Arguente principal
 Mariana Sequeira (Doutoramento)
2017 Mass spectrometry-based proteomic strategies to define protein NEDDyation
Arguente principal
 Sofia Celeste Lobato (Doutoramento)
CIC bioGUNE, Espanha

Arbitragem científica em conferência

Nome da conferência Local da conferência
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

Comissão de avaliação

Descrição da atividade
Tipo de assessoria 		Instituição / Organização Entidade financiadora
2020/12/01 - Atual The Hellenic Foundation for Research and Innovation (HFRI)
Avaliador
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, Reino Unido
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.
Avaliador
 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
Avaliador
 Ministerio de Ciencia E innovacion, Espanha
2018/05/16 - 2018/06/30 Remote and local evaluation of H2020 projects. H2020 Framework program, Brussels, Belgium
Avaliador
 _H2020, Dinamarca EU Framework Programme for Research and Innovation Euratom
2016/01/01 - 2016/06/01 Bilateral Scientific Cooperation China" application to the Research Foundation Flanders
Avaliador
2014/01/01 - 2014/03/01 Czech-Norwegian Research Programme (CZ09)
Avaliador
2013/01/01 - 2013/03/01 Evaluator of FCT investigators
Avaliador
2010/01/01 - 2010/03/01 EU INDIGO projects in the area of biomarker discovery, bioinformatics and proteomics
Avaliador

Consultoria / Parecer

Descrição da atividade Instituição / Organização
2024/01/01 - 2025/01/01 External consultant Mursla, Cambridge.

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2020/01/01 - Atual 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
2026/04/14 - 2026/05/29 Yearly course on advanced computational proteomics and metabolomics Advanced Proteomics and Metabolomics (Mestrado) Universidade Nova de Lisboa, Portugal

Expedição científica

Descrição da atividade Instituição / Organização
2025/04/23 - 2025/04/27 Enhancing Extracellular Vesicle Characterization through High-Resolution Mass Spectrometry: Development of an R Package and Testing with Public Plasma Datasets International Society for Extracellular Vesicles, Estados Unidos
2024/12/02 - 2024/12/05 CelebrateMS, Odense, SDU, Denmark, poster presentation ”Proteome Alterations in Peripheral Immune Cells of DLBCL Patients and Evidence of Cancer Extracellular Vesicles Involvement” Syddansk Universitet, Dinamarca

Membro de associação

Nome da associação Tipo de participação
2023/06/01 - Atual 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

Membro de comissão

Descrição da atividade
Tipo de participação 		Instituição / Organização
2024/01/01 - Atual ISEV EV-TRACK task force member working group 3 focusing on outreach and future developments
Membro
2022/10/01 - 2025/10/10 Coordinator of EVCA board for internal funded EVCA projects.
Coordenador
 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
Coordenador
2020/09/01 - 2023/01/01 Editor on the journal Cancers
Membro
Distinções

Prémio

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, Dinamarca