Computational and Experimental Biology


Rune Matthiesen

Principal Investigator
2004-2006: Assistant Professor, Protein research group, University of Southern Denmark
2004-2005: Assistant Professor, EBI, Hinxton and University of Southern Denmark
2000-2004: Ph.D. thesis: Mass spectrometry in Proteomics, University of Aalborg
1999-2000: Research Assistant, Developmental biology, EMBL, Heidelberg
1998-1999: Cand. Scient in Crystallography, Aarhus University

Google Scholar citations



Campus Sant'Ana
Pólo de Investigação, NMS, UNL
Rua Câmara Pestana, nº 6
1150-082 Lisboa, Portugal

Phone: (+351) 218 803 101
Fax: (+351) 218 851 920
E-mail: rune.matthiesen(at)

Main Interests:

We are mainly interested in elucidating drug resistance mechanisms in cancer by large scale biological experiments using model systems followed by biomarker validation in clinical samples.

Research Areas:

The computational and experimental biology group (CEB) aims at being forefront in clinical proteogenomics research. We have established experimental and computational quantitative technologies for MS-based profiling useful for clinical proteomics (e.g. label free quantitation, triple dimethyl labeling, SILAC and tandem tags). More specifically we have over the last eight years obtained considerably experience in global MS-based drug profiling used in combination with genomics technologies such as next generation sequencing methodologies (Proteogenomics). We are furthermore heavily involved in the COST Action PROTEOSTASIS BM1307. Our collaborations in this network have opened new doors to combine biochemical methods in Proteostasis with mass spectrometry in novel ways. We have experience in using proteogenomics in clinical samples, human cell lines and in multi drug resistance bacteria. Our main interest is to apply our technologies on lung cancer, cardiovascular diseases and hematological diseases. Although the main focus is on chronic diseases, pathogens are also questioned to address the role of host-pathogen interactions in chronic diseases. In other words, we work in the interface between clinicians, biomedical and biochemistry researchers.



FCT investigator program 2012 (Principal Investigator) – five year group leader salary.
2014-2019: National representative for the COST action PROTEOSTASIS
2014-2019: COST action Proteostasis. We have so far been selected for two post doctoral exchange grants (Principal Investigator).
2016-2019: PTDC/BBB-BEP/2463/2014 ProbeCOPD. Protease activity-based probes for Chronic Obstructive Pulmonary Disease diagnostics ~200,000.00 Euro.
2014-2017: Remote ischemic per-conditioning in acute stroke – clinical trial for improving outcome and disclosing novel circulating biomarkers, iNOVA for health, (Research member) - 100,000.00 Euro.
2016-2021: Invited participant for the recent approved COST action network Transautophagy.

2013-2015: PTDC-BEX-GMG-0242-2012 “Evaluating the role of proteolysis in the male reproductive system through the study of KLK (19q13.4) and WFDC (20q13) gene clusters.” (Research member)- ~200,000.00 Euro.
2014-2015: EXPL/DTP-PIC/0616/2013 “Global MS-based profiling of bronchial aspirate: targeting lung cancer specific modifications” (Principal Investigator) - 49,800.00 Euro.
2010-2013: PTDC/QUI-BIQ/099457/2008 “Dissection of the molecular role of O-GlcNAc in the multinucleation phenotype of the neoplasic cells in Hodgkin´s lymphoma.” (Principal Investigator) ~200,000.00 Euro.
2010-2013: PTDC/EIA-EIA/099458/2008 “Computational disease prediction system based on molecular markers” (Principal Investigator) ~50,000.00 Euro.
2010-2013: PTDC/SAU-FCF/100930/2008 “Molecular and nanotechnology-based approaches to improve the antitumor activity of small molecules” (Research member) ~200,000.00 Euro.
2010-2013: PTDC/SAU-GMG/101229/2008 “Search for genomic structural variants in azoospermia: a study in Portuguese population”
Contract with Novo Nordisk (2010) - 10,000.00 Euro.
Ramon Cajal (Principal Investigator) – five year group leader salary.
Carlsberg foundation (Principal Investigator) – two year post doc salary.
Etortek Research Programs 2005 / 2006 (CIC bioGUNE) (Principal Investigator).
Profit (Gaiker), (research member).
La Caixa (research member).
EU Temblor (research member).



1. Prof. John Fields, Leonor Mota and Cristina Barba, Felix Elortza We are currently preparing a
manuscript where bronchoaviolar lavage of ~100 potential lung cancer patients have been analyzed by LCMS.

2. Dr. Wenjie Sun, Tulane University School of Public Health and Tropical Medicine, New Orleans, US,
Lung inflammasome and lung cancer biomarkers.

3. Mission Therapeutics – 1) Chemical probes for cancer therapies and diagnostics and 2) MS-based
global drug profiling for novel cancer drugs.

4. Dr. Manuel S. Rodriguez, France –A) Role of protein ubiquitylation in Mantle Cell Lymphoma
resistance to Bortezomib (120 LC-MS runs), B) New insights into host-parasite ubiquitin proteome
dynamics in P. falciparum infected red blood cells using TUBEs-MS approach (160 LC-MS runs) and C)
Next generation Ubiquitin and SUMO traps.

5. Professor David C Lyden and Ayuko Hoshino, Weill Cornell Medical College; Bruno Costa-Silva,
Champalimaud, Lisbon; Henrik Molina, Rockefeller University – Exosome biomarkers.

6. Dr. Carmen Rivas, Spain - PI3K signalling in cancer

7. Director of Human genetics, João Lavinha, National institute of health, Lisbon, Portugal. Sickle cell

8. Professor Helena Viera and Prof. Miguel Viana-Baptista, director of Hospital São Francisco Xavier.
Clinical trial for improving outcome and disclosing novel circulating biomarkers.

9. Manuela Caniça, National institute of Health, Lisbon, responsible for infectious disease control. A)
Metagenomics of soil samples, B) global drug profiling of drug resistant E. coli and C) NGS sequencing of
drug resistant E. coli strain.

10. Professor Margarida D. Amaral, EMBO chair and Dr. Carlos Farinha. Dissecting the endoplasmic

reticulum quality control - differential protein interactions as new therapeutic targets in Cystic Fibrosis.

11. Dr. Susana Seixas, researcher, IPATIMUP, Porto, Portugal and Felix Elortza LC-MS runs of infertile
patients and controls (Proteogenomics).

12. Dr. Sílvia Gomes, NGS sequencing of bronchoaviolar lavage microbiome.

13. Dr. Paulo Matos, Targeting Rac1-signaling to enhance iodide-related therapy in breast cancer.

14. Dr. Susana Lucas, COPD biomarkers

15. MD Amélia Feliciano, kerman Aloria - OSA biomarkers

Motivated students (Undergraduate, Master and PhD) are encouraged to apply. Interested candidates, please send your CV, a letter explaining your interests and the name/contact information for 1-3 references to rune.matthiesen(at)