Publications

A list is also available at google scholar or pubmed.

# indicates equal contribution.

Key

E. Bosdriesz, J. Fernandes Neto, A. Sieber, R. Bernards,N. Blüthgen and L.F.A. Wessels, ‘Identifying selective drug combinations using Comparative Network Reconstruction’. bioRxiv 2020.12.17.423240; doi:10.1101/2020.12.17.423240, 2020.
Shows that Comperative Network Reconstruction can be be used to predict which low-dose multi-drug combinations that are likely to selective, using an isogenic cell-line pair.
Code and Data

J. Fernandes Neto, E. Nadal#, E. Bosdriesz#, S. N. Ooft, L. Farre, C. McLean, S. Klarenbeek, A. Jurgens, H. Hagen, L. Wang, E. Felip, A. Martinez-Marti, A. Vidal, E. Voest, L.F.A. Wessels, O. van Tellingen, A. Villanueva and & R. Bernards, ‘Multiple Low Dose Therapy as an Effective Strategy to Treat EGFR Inhibitor-Resistant NSCLC Tumours.’ Nature Communications, 11 (1): 3157. doi:10.1038/s41467-020-16952-9, 2020.
Shows that combining multiple drugs at low dose is effective, prevents emergence resistance, and is well tolerated by mice.

E. Bosdriesz, A. Prahallad, B. Klinger, A. Sieber, A. Bosma, R. Bernards, N. Blüthgen and L.F.A. Wessels, ‘Comparative Network Reconstruction Using Mixed Integer Programming’, Bioinformatics, 34:i997–1004. doi:10.1093/bioinformatics/bty616, 2018.
Method to reconstruct and compare signaling networks based on perturbation data using Mixed Integer Quadratic programming.
Code - Notebooks

A. Ressa#, E. Bosdriesz#, J. de Ligt, S. Mainardi, G. Maddalo, A. Prahallad, M. Jager, L. de la Fonteijne, M. Fitzpatrick, S. Groten, A.F.M. Altelaar, R. Bernards, E. Cuppen, L.F.A Wessels and J.R. Heck, ‘A System-Wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells’, Molecular & Cellular Proteomics, 17(10):1892-1908. doi:10.1074/mcp.RA117.000486, 2018.
Transcriptomic, proteomic and phosphoproteomic, time-course analysis of cancer cells in response to targeted inhibitors:
Code

E. Bosdriesz, D. Molenaar, B. Teusink, and F.J. Bruggeman, ‘How Fast-Growing Bacteria Robustly Tune Their Ribosome Concentration to Approximate Growth-Rate Maximization.’, FEBS Journal, 282(10):2029-2044. doi:10.1111/febs.13258, 2015.
Uses mechanistic, minimal models to understand the design principles of how bacteria control their macromolecular composition:
model

Pre-prints

E. Bosdriesz, J. Fernandes Neto, A. Sieber, R. Bernards,N. Blüthgen and L.F.A. Wessels, ‘Identifying selective drug combinations using Comparative Network Reconstruction’. bioRxiv 2020.12.17.423240; doi:10.1101/2020.12.17.423240, 2020.

Peer-reviewed articles

J. Fernandes Neto, E. Nadal#, E. Bosdriesz#, S. N. Ooft, L. Farre, C. McLean, S. Klarenbeek, A. Jurgens, H. Hagen, L. Wang, E. Felip, A. Martinez-Marti, A. Vidal, E. Voest, L.F.A. Wessels, O. van Tellingen, A. Villanueva and & R. Bernards, ‘Multiple Low Dose Therapy as an Effective Strategy to Treat EGFR Inhibitor-Resistant NSCLC Tumours.’ Nature Communications, 11 (1): 3157.doi:10.1038/s41467-020-16952-9, 2018.

T. Sustic, E. Bosdriesz, S. van Wageningen, L.F.A. Wessels and R. Bernards, ‘RUNX2/CBFB modulates the response to MEK inhibitors through activation of receptor tyrosine kinases in KRAS-mutant colorectal cancer’, Translational Oncology, 13(2):201-211. doi:10.1016/j.tranon.2019.10.006, 2020.

E. Bosdriesz, A. Prahallad, B. Klinger, A. Sieber, A. Bosma, R. Bernards, N. Blüthgen and L.F.A. Wessels, ‘Comparative Network Reconstruction Using Mixed Integer Programming’, Bioinformatics, 34:i997–1004. doi:10.1093/bioinformatics/bty616, 2018.

A. Ressa#, E. Bosdriesz#, J. de Ligt, S. Mainardi, G. Maddalo, A. Prahallad, M. Jager, L. de la Fonteijne, M. Fitzpatrick, S. Groten, A.F.M. Altelaar, R. Bernards, E. Cuppen, L.F.A Wessels and J.R. Heck , ‘A System-Wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells’, Molecular & Cellular Proteomics, 17(10):1892-1908. doi:10.1074/mcp.RA117.000486, 2018.

T. Šuštić#, S. van Wageningen#, E. Bosdriesz, R.J.D. Reid, J. Dittmar, C. Lieftink, R.L. Beijersbergen, L.F.A. Wessels, R. Rothstein and R. Bernards, ‘A Role for the Unfolded Protein Response Stress Sensor ERN1 in Regulating the Response to MEK Inhibitors in KRAS Mutant Colon Cancers’, Genome Medicine, 10:90. doi:10.1186/s13073-018-0600-z, 2018.

L. Wang#, R. Leite de Oliveira#, S. Huijberts, E. Bosdriesz, N. Pencheva, D. Brunen, A. Bosma, J.Y. Song, J. Zevenhoven, G. T. Los-de Vries, H. Horlings, B. Nuijen, J.H. Beijnen, J.H.M. Schellens and R. Bernards. ‘An Acquired Vulnerability of Drug-Resistant Melanoma with Therapeutic Potential’. Cell, 173(6):1413-1425.e14. doi:10.1016/j.cell.2018.04.012, 2018.

M. Dorel, B. Klinger, T. Gross, A. Sieber, A. Prahallad, E. Bosdriesz, L.F.A. Wessels and N. Blüthgen, ‘Modelling Signalling Networks from Perturbation Data’, Bioinformatics, 34(23):4079–4086. doi:10.1093/bioinformatics/bty473, 2018.

Z. Xue, D.J. Vis, A. Bruna, T. Šuštić, S. Van Wageningen, A. Sati Batra, O.M. Rueda, E. Bosdriesz, C. Caldas, L.F.A. Wessels and R. Bernards. ‘MAP3K1 and MAP2K4 Mutations Are Associated with Sensitivity to MEK Inhibitors in Multiple Cancer Models’. Cell Research, 28:719–729. doi:10.1038/s41422-018-0044-4, 2018.

E. Bosdriesz#, M.T. Wortel#, J.R. Haanstra, M.J. Wagner, P. de la Torre Cortés, and B. Teusink, ‘Low Affinity Uniporter Carrier Proteins Can Increase Net Substrate Uptake Rate by Reducing Efflux’, Scientific Reports, 8:5576. doi:10.1038/s41598-018-23528-7, 2018.

M.T. Wortel#, E. Bosdriesz#, B. Teusink, and F.J. Bruggeman. ‘Evolutionary Pressures on Microbial Metabolic Strategies in the Chemostat’. Scientific Reports, 6:29503. doi:10.1038/srep29503, 2016.

E. Bosdriesz, D. Molenaar, B. Teusink, and F.J. Bruggeman, ‘How Fast-Growing Bacteria Robustly Tune Their Ribosome Concentration to Approximate Growth-Rate Maximization.’, FEBS Journal, 282(10):2029-2044. doi:10.1111/febs.13258, 2015.

E. Bosdriesz, S. Magnúsdóttir, F.J. Bruggeman, B. Teusink, and D. Molenaar, ‘Binding Proteins Enhance Specific Uptake Rate by Increasing the Substrate-Transporter Encounter-Rate’, FEBS Journal, 282:2394–2407. doi:10.1111/febs.13289, 2015.

J. Berkhout, E. Bosdriesz, E. Nikerel, D. Molenaar, D. de Ridder, B. Teusink and F.J. Bruggeman, ‘How Biochemical Constraints of Cellular Growth Shape Evolutionary Adaptations in Metabolism.’, Genetics, 194:505–512. doi:10.1534/genetics.113.150631, 2013.