EDUCATION AND EMPLOYMENT
2008-2011:   Editorial board member of the Oxford journal Bioinformatics
2007-2009:   Editor on “Bioinformatics in clinical omics”, Humana Press 
2008-2013:   Researcher, IPATIMUP, Porto, Portugal
2006-2008:   Principle investigator, CIC bioGUNE, Bilbao Spain
2004-2006:   Assistant Professor, Protein research group, University of Southern Denmark
2004-2006:   Editor on “Mass Spectrometry Data Analysis in Proteomics”, Humana Press 
2003-2004:   Assistant Professor, EBI, Hinxton and University of Southern Denmark
2000-2003:   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


PUBLICATIONS

Carvalho AS, Harduin-Lepers A, Magalhães A, Machado E, Mendes N, Costa LT, Matthiesen R, Almeida R, Costa J, Reis CA. Differential expression of alpha-2,3-sialyltransferases and alpha-1,3/4-fucosyltransferases regulates the levels of sialyl Lewis a and sialyl Lewis x in gastrointestinal carcinoma cells.Int J Biochem Cell Biol. 2009

Rune Matthiesen and Finn Kirpekar. Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping. Nucleic Acids Res. 2009 37(6):e48.

Hackenberg M, Lasso G, Matthiesen R. ContDist: a tool for the analysis of quantitative gene and promoter properties. BMC Bioinformatics. 2009, 7,10:7.

Henrik Molina, Rune Matthiesen, Kumaran Kandasamy, and Akhilesh Pandey. Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation. Anal Chem. 2008, 80, 4825-35

Hackenberg, Michael, Matthiesen, Rune Annotation-Modules: A tool for finding significant combinations of multisource annotations in gene lists. Bioinformatics, 2008, 24, 1386-93

Martinez Chantar, Maria, Vazquez-Chantada, Mercedes Ariz, Usue, Martínez-Lopez, Nuria, Varela, Marta, Luka, Zigmund, Capdevila, Antonieta, Rodríguez, Juan, Matthiesen, Rune, Yang, Heping, Calvisi, Diego, Esteller, Manel, Fraga, Mario, Lu, Shelly, Wagner, Conrad, Mato, Jose.  Loss of the GNMT gene leads to steatosis and hepatocellular carcinoma in mice. Hepatology, 2008, 47, 1191-9

Hägglund P, Matthiesen R, Elortza F, Højrup P, Roepstorff P, Jensen ON, Bunkenborg J. An enzymatic deglycosylation scheme enabling identification of core fucosylated N-glycans and O-glycosylation site mapping of human plasma proteins. J Proteome Res. 2007, 6, 3021-31.

Omaetxebarria MJ, Elortza F, Rodríguez-Suárez E, Aloria K, Arizmendi JM, Jensen ON and Matthiesen R. Computational approach for identification and characterization of GPI-anchored peptides in proteomics experiments. Proteomics. 2007, 7, 2815-32.

Matthiesen R. Methods, algorithms and tools in computational MS-based proteomics: a practical point of view. Proteomics. 2007, 7, 2815-32.

Erba EB, Matthiesen R, Bunkenborg J, Schulze WX, Stefano PD, Cabodi S, Tarone G, Defilippi P, Jensen ON. Quantitation of Multisite EGF Receptor Phosphorylation Using Mass Spectrometry and a Novel Normalization Approach. J Proteome Res. 2007, 6, 2768-85.

Mutenda KE, Matthiesen R and Roepstorff P. Differential fragmentation patterns of pectin oligogalacturonides observed by nanoelectrospray quadrupole ion-trap mass spectrometry using automated spectra interpretation. J Mass Spectrom,2007, 42, 428-39.

Laukens K, Matthiesen R, Lemiere F, Esmans E, Onckelen HV, Jensen ON, Witters E. Integration of gel-based proteome data with pProRep. Bioinformatics, 2006, 22, 2838-40.

Alloza I, Baxter A, Chen Q, Matthiesen R, Vandenbroeck K. Celecoxib inhibits interleukin-12 alphabeta and beta2 folding and secretion by a novel COX2-independent mechanism involving chaperones of the endoplasmic reticulum. Mol Pharmacol, 2006, 69, 1579-87.

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 colourless strawberry mutant. Proteomics, 2006, 6, 1574-87.

Fierro-Monti I, Mohammed S, Matthiesen R, Santoro R, Burns JS, Williams DJ, Proud CG, Kassem M, Jensen ON and Roepstorff P. Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly as a novel partner for eukaryotic initiation factor 4E. J. Proteome Res, 2006, 5, 1367-78.

Beck HC, Jensen EC, Matthiesen R, Jensen LH, Finn P, Grauslund M, Hansen AM, and Jensen ON. Quantitative proteomic analysis of post-translational modifications of human histones. Mol. Cell. Proteomics 2006, 5, 1314-1325.

Matthiesen R, Sørensen M, Bunkenborg J, Højrup P, and Jensen ON. VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J. Proteome Res 2005, 4, 2338–47.

Gruhler A, Schulze W, Matthiesen R, Mann M, Jensen ON. Stable isotope labeling of Arabidopsis thalinana suspension cells and analysis of differential protein expression by mass spectrometry. Mol. Cell. Proteomics 2005, 4, 1697–709.

Matthiesen R, Bauw G, Welinder KG. Use of performic acid oxidation to expand the mass distribution of tryptic peptides. Anal. Chem.2004, 76, 6848-6852.

Matthiesen R, Bunkenborg J, Stensballe A, Jensen ON, Welinder KG, Bauw G. Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS v2.0. Proteomics 2004, 9, 2583-93.

Matthiesen R, Lundsgaard M, Welinder KG and Bauw G. Interpreting peptide mass spectra by VEMS. Bioinformatics 2003, 19, 792-93.

Pedersen NR, Wimmer R, Matthiesen R, Pedersen LH, Gessesse A. Synthesis of sucrose laurate using a new alkaline protease. Tetrahedron: Asymmetry 2003, 14, 667-73.

Pedersen NR, Halling PJ, Pedersen LH, Wimmer R, Matthiesen R, Veltman OR. Efficient transesterification of sucrose catalysed by the metalloprotease thermolysin in dimethylsulfoxide. FEBS Lett., 2002, 519, 181-184


BOOK CHAPTERS

Introduction to omics. Gubb E, Matthiesen R. Methods Mol Biol. 2010;593:1-23. PMID: 19957142

SNP-PHAGE: high-throughput SNP discovery pipeline. Aransay AM, Matthiesen R, Regueiro MM. Methods Mol Biol. 2010;593:49-65. PMID: 19957144

Overview on techniques in cluster analysis. Frades I, Matthiesen R. Methods Mol Biol. 2010;593:81-107. PMID: 19957146

Proteomics facing the combinatorial problem. Matthiesen R, Amorim A. Methods Mol Biol. 2010;593:175-86. PMID: 19957150

Methods and algorithms for relative quantitative proteomics by mass spectrometry. Matthiesen R, Carvalho AS. Methods Mol Biol. 2010;593:187-204. PMID: 19957151

Computational methods for analysis of two-dimensional gels. Lasso G, Matthiesen R. Methods Mol Biol. 2010;593:231-62. PMID: 19957153

Algorithms and methods for correlating experimental results with annotation databases. Hackenberg M, Matthiesen R. Methods Mol Biol. 2010;593:315-40. PMID: 19957156

Analysis of mass spectrometry data in proteomics. Methods Mol Biol. 2008, Matthiesen R and Jensen ON, 453, 105-22.

Introduction to proteomics. Methods Mol Biol. 2006, 367, 1-36. R. Matthiesen and K. E. Mutenda PMID: 17185767

Extracting monoisotopic single-charge peaks from liquid chromatography-electrospray ionization-mass spectrometry. Methods Mol Biol. 2006, 367, 37-48. R. Matthiesen and O. N. Jensen. PMID: 17185768

Virtual Expert Mass Spectrometrist v3.0: An Integrated Tool for Proteome Analysis . Methods Mol Biol. 2006, 367, 121-38. R. Matthiesen PMID: 17185773

Quantitation with virtual expert mass spectrometrist. Methods Mol Biol. 2006, 367, 139-52. A. Gruhler and R. Matthiesen. PMID: 17185774

Sequence Handling by Sequence Analysis Toolbox v1.0. Methods Mol Biol. 2006, 367, 153-68. C.R.Ingrell, R. Matthiesen and O.N. Jensen. PMID: 17185775

Interpretation of collision-induced fragmentation tandem mass spectra of posttranslationally modified peptides. Methods Mol Biol. 2006, 367, 169-94. J. Bunkenborg and R. Matthiesen. PMID: 17185776

Organisation of Proteomics Data with YassDB. Methods Mol Biol. 2006, 367, 271-88
A. L. Thomsen, K. Laukens, R. Matthiesen, O. N. Jensen. PMID: 17185782

Analysis of carbohydrates by mass spectrometry. Methods Mol Biol. 2006, 367, 289-302 K. Mutenda and R. Matthiesen. PMID: 17185783

Useful mass spectrometry programs freely available on the internet. Methods Mol Biol. 2006, 367, 303-6 R. Matthiesen. PMID: 17185784

Analysis of Proteomics Data. R. Matthiesen, O. N. Jensen.

Annotation of class I peroxidase genes in Arabidopsis thaliana VI INTERNATIONAL PLANT PEROXIDASES SYMPOSIUM Proceedings 2002, Murcia, Spain,163-166. R. Matthiesen, L. Duroux and K. G. Welinder. available on publishers’ homepage


SELECTED RECENT ORAL COMMUNICATIONS
2008 Sep: Computational methods for biomarker characterization, XXXI Congreso de la SEBBM, Bilbao, Spain
2008 June: Quantitative methods in Mass spectrometry, CNIO, Madrid, Spain
2008 May: Computational methods for analysis of MSMS data of complex modification, CIMA, Pamplona, Spain
2007 Oct: Opponent on PhD thesis: “Computational methods in high-throughput proteomics research”, Department of Informatics, Bergen University, Norway
2007 Oct: Invited speaker: “Novel computational approaches for improved identification of post-translational modifications”, HUPO 6th Annual World Congress, Seoul 2007
2007 Feb: Invited speaker: Integrated data analysis platform for analysis of OMICs data, iMath, Coruña, Spain
2007 Feb: Teaching lecture on quantitative proteomics for ProteoRed, Salamanca University, Spain
2007 Teaching lecture on Proteomics Data analysis, CNIO, Madrid, Spain
2006 Sep: Selected speaker: A New Combinatorial Algorithm for the Identification of GPI Anchored Peptides in MS/MS Data, 17th International Mass Spectrometry Conference, Prague, 2006
2006 A New Combinatorial Algorithm for the Identification of GPI Anchored Peptides in MS/MS Data, Computational proteomics meeting, Berlin

REVIEWING DUTIES
Assigned as editor on Mass Spectrometry Data Analysis in Proteomics, Humana Press
Reviewed manuscripts for Bioinformatics, Proteomics, Journal of Proteome Research, Journal of Mass Spectrometry

EDITOR WORK
Editor on Bionformatics in clinical omics, in preparation
Editor on Mass Spectrometry Data Analysis in Proteomics, Humana press, 2006

RESEARCH GRANTS

Current:
2010-2013: PTDC/QUI-BIQ/099457/2008 “Clarificacão do papel da O-GlcNAc na multinucleacão das células neoplásicas do lymphoma de Hodgkin´s” (Principal Investigator)
2010-2013: PTDC/EIA-EIA/099458/2008 “Sistema de avaliação universal de doenças com base em marcadores moleculares” (Principal Investigator)
2010-2013: PTDC/SAU-FCF/100930/2008 “Abordagens Molecular e Nanotecnológica para a melhoria da actividade antitumoral de pequenas moléculas” (Research member)
Contract with Novo Nordisk

Previous:
Ramon Cajal (Rune Matthiesen), Carlsberg foundation (Rune Matthiesen), Etortek Research Programs 2005 / 2006 (CIC bioGUNE), Profit (Gaiker), La Caixa (María Luz Martínez Chantar), EU Temblor (Ole N Jensen)

TECHNICAL EXPERTISE
Bio computing: Delphi, R package, Python, C++, Java, XML, Mysql, Postgresql
Protein chemistry: Mass spectrometry, HPLC, FPLC, gel electrophoresis, isoelectric focusing, ultra centrifugation, crystallization, protein purification, chromatography, in vitro translation, enzyme assays
Molecular biology: Vector cloning, in vitro transcription, polyclonal antibodies, RNA purification