Research overview (KEBB)

Systems Medicine: from systems genomics to systems biology

Our systems medicine projects aim to advance our understanding of biological systems in health and disease by either pursuing a top-down (systems genomics) or a bottom-up (systems biology) approach. Systems genomics mostly involve the (statistical) analyses of (multi-)omics data, while systems biology approaches focus on mathematical modelling.

Information Management

Our information management research focusses on the analysis, integration and/or use of public biomedical databases and the development of knowledge bases.

Selected publications Systems Medicine

  1. Doorenspleet ME, Klarenbeek PL, de Hair MJH, van Schaik BDC, Esveldt REE, van Kampen aHC, Gerlag DM, Musters a, Baas F, Tak PP, de Vries N (2014) Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity. Annals of the rheumatic diseases 73:756-762.
  2. Klarenbeek PL, Tak PP, van Schaik BDC, Zwinderman AH, Jakobs ME, Zhang Z, van Kampen AHC, van Lier RAW, Baas F, de Vries N (2010) Human T-cell memory consists mainly of unexpanded clones. Immunology letters 133:42-48.
  3. Reshetova P., Smilde AK, Westerhuis JA, van Kampen AHC (2015) Using Petri nets for experimental design in a multi-organ elimination pathway. Computers in Biology and Medicine. Accepted for publication.
  4. van Schaik B, Klarenbeek P, Doorenspleet M, van Kampen A, Moody DB, de Vries N, Van Rhijn I (2014) Discovery of Invariant T Cells by Next-Generation Sequencing of the Human TCR α-Chain Repertoire. Journal of immunology.
  5. Willemsen AM, Hendrickx DM, Hoefsloot HC, Hendriks MM, Wahl SA, Teusink B, Smilde AK, van Kampen AH (2015) MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Molecular bioSystems 11 (1):137-145.

Selected publications Information Management

  1. S. Shahand, M. Santcroos, A. H. C. van Kampen, and S. D. Olabarriaga. “A grid-enabled gateway for biomedical data analysis”. Journal of Grid Computing, 10(4):725–742, 2012
  2. Stobbe MD, Houten SM, Jansen GA, van Kampen AHC, Moerland PD (2011) Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC systems biology 5:165.
  3. Stobbe MD, Houten SM, van Kampen AH, Wanders RJ, Moerland PD (2012) Improving the description of metabolic networks: the TCA cycle as example. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 26 (9):3625-3636.
  4. Stobbe MD, Jansen GA, Moerland PD, van Kampen AH (2014) Knowledge representation in metabolic pathway databases. Briefings in bioinformatics 15 (3):455-470.
  5. Stobbe MD, Swertz MA, Thiele I, Rengaw T, van Kampen AHC, Moerland PD (2013) Consensus and conflict cards for metabolic pathway databases. BMC systems biology 7:50.
  6. Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ (2013) A community-driven global reconstruction of human metabolism. Nature biotechnology 31:419-425.
  7. Willemsen AM, Jansen GA, Komen JC, van Hooff S, Waterham HR, Brites PMT, Wanders RJA, van Kampen AHC (2008) Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. Bioinformatics (Oxford, England) 24:i21-27.

Bioinformatics Laboratory

Prof dr Antoine H.C. van Kampen
Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)
Academic Medical Center

Visiting address
Meibergdreef 9
Location J1B-208
Amsterdam Zuidoost

Postal address
P.O. Box 22700
1100 DE Amsterdam
the Netherlands

Tel.: +31-20-5667096
Mobile: 06-41768067

Skype
antoine.van.kampen

Contact