Key publications

Bonzanni N, Garg A, Feenstra KA, Schütte J, Kinston S, Miranda-Saavedra D, Heringa J, Xenarios I, Göttgens B. Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinformatics. 2013 Jul 1;29(13):i80-8. doi: 10.1093/bioinformatics/btt243.

De Vries-van Leeuwen IJ, da Costa Pereira D, Flach KD, Piersma SR, Haase C, Bier D, Yalcin Z, Michalides R, Feenstra KA, Jiménez CR, de Greef TF, Brunsveld L, Ottmann C, Zwart W, de Boer AH. Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface. Proc Natl Acad Sci U S A. 2013 May 28;110(22):8894-9. doi: 10.1073/pnas.1220809110. Epub 2013 May 15.

Daleke MH, Ummels R, Bawono P, Heringa J, Vandenbroucke-Grauls CM, Luirink J, Bitter W. General secretion signal for the mycobacterial type VII secretion pathway. Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11342-7. doi: 10.1073/pnas.1119453109. Epub 2012 Jun 25.

Hou Q, Lensink MF, Heringa J, Feenstra KA. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation approach to Scoring Docking Decoys. PLoS ONE (2016). doi:10.1371/journal.pone.0155251.

Jacobsen A, Heijmans N, Verkaar F, Smit MJ, Heringa J, van Amerongen R, Feenstra KA. Construction and Experimental Validation of a Petri Net Model of Wnt/β-catenin Signaling. PLoS ONE (2016). doi:10.1371/journal.pone.0155743.

van Dijk E, Varilly P, Knowles TPJ, Frenkel D, Abeln S. Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation. Physical Review Letters. 19 February 2016; 116(7).

Dinkla K*, El-Kebir M*, Bucur CI, Siderius M, Smit MJ, Westenberg MA, Klau GW. eXamine: Exploring annotated modules in networks. BMC Bioinformatics (2014) 15:201. *joint first authors