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Systems Biology


Systems Biology

Most important publications of the RPA Systems Biology (2013-2017).


  1. Barberis M., R.G. Todd, L. van der Zee (2017) Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models. FEMS Yeast Research 17: 1-15. DOI: 10.1093/femsyr/fow103
  2. Haanstra J.R., A. Gerding, A.M. Dolga, F.J. Sorgdrager, M. Buist-Homan, F. du Toit, K.N. Faber, H.G. Holzhütter, B. Szöör, K.R. Matthews, J.L. Snoep, H.V. Westerhoff, B.M. Bakker (2017) Targeting pathogen metabolism without collateral damage to the host. Scientific Reports 7, 40406. DOI: 10.1038/srep40406
  3. Linke C., A. Chasapi, A. González-Novo, I. Al Sawad, S. Tognetti, E. Klipp, M. Loog, S. Krobitsch, F. Posas, I. Xenarios, M. Barberis (2017) A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. Nature Publishing Journal Systems Biology and Applications 7, 3. DOI:10.1038/s41540-017-0008-1
  4. Magnani L., G. Frigè G, R.M. Gadaleta, et al. (2017) Acquired CYP19A1 amplification is an early specific mechanism of aromatase inhibitor resistance in ERα metastatic breast cancer. Nature Genetics 49, 444-450. DOI: 10.1038/ng.3773
  5. Ostrow A.Z., R. Kalhor, Y. Gan, S.K. Villwock, C. Linke, M. Barberis, L. Chen, O.M. Aparicio (2017) Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proceedings of the National Academy of Sciences U S A 114, E2411-E2419. DOI: 10.1073/pnas.1612422114


  1. Brussaard, C.P.D., L. Peperzak, S. Beggah, et al., (2016) Immediate ecotoxicological effects of short-lived oil spills on marine biota. Nature Communications 7, 11206. DOI:10.1038/ncomms11206
  2. Cúcio, C, A.H. Engelen, R. Costa, G. Muyzer (2016) Rhizosphere microbiomes of European seagrasses are selected by the plant, but are not species specific. Frontiers in Microbiology 7: 440. DOI: 10.3389/fmicb.2016.00440
  3. Jacobsen A., N. Heijmans, F. Verkaar, M.J. Smit, J. Heringa, R. van Amerongen, K.A. Feenstra (2016) Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling. PLoS One 11, e0155743. DOI: 10.1371/journal.pone.0155743
  4. Widder, S, Allen, RJ, Pfeiffer, T, Curtis, TP, Wiuf, C, et al. (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME
  5. Journal 10: 2557-2568. DOI: 10.1038/ismej.2016.45
  6. Müller A., M. Wenzel, H. Strahl, F. Grein, T.N. Saaki, B. Kohl, T. Siersma, J.E. Bandow, H.G. Sahl, T. Schneider, L.W. Hamoen (2016) Daptomycin inhibits cell envelope synthesis by interfering with fluid membrane microdomains. Proceedings of the National Academy of Sciences U S A 113, E7077-E7086. DOI: 10.1073/pnas.1611173113
  7. Sandrini, G., R.P. Tann, J.M. Schuurmans, S.A.M. van Beusekom, H.C.P. Matthijs, J. Huisman. (2016) Diel variation in gene expression of the CO2-concentrating mechanism during a harmful cyanobacterial bloom. Frontiers in Microbiology 7:551. DOI: 10.3389/fmicb.2016.00551
  8. Sandrini, G., X. Ji, J.M.H. Verspagen, R.P. Tann, P.C. Slot, V.M. Luimstra, J.M. Schuurmans, H.C.P. Matthijs, J. Huisman (2016) Rapid adaptation of harmful cyanobacteria to rising CO2. Proceedings of the National Academy of Sciences of the United States of America 113: 9315-9320. DOI: 10.1073/pnas.1602435113
  9. Vavourakis, C.D., R. Ghai , F. Rodriguez-Valera, D.Y. Sorokin, S.G. Tringe, P. Hugenholtz, G. Muyzer (2016) Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology 7:211. DOI: 10.3389/fmicb.2016.00211
  10. Wijchers, P.J., P.L. Krijger, G. Geeven, et al., (2016) Cause and consequence of tethering a subTAD to different nuclear compartments. Molecular Cell 61, 461.DOI: 10.1016/j.molcel.2016.01.001


Bastiaens, P., M.R. Birtwistle, N. Blüthgen, et al. (2015) Silence on the relevant literature and errors in implementation, Nature Biotechnology 33, 336-339. DOI: 10.1038/nbt.3185

Gamba P., M.J. Jonker, L.W. Hamoen (2015) A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence. PLoS Genetics 11, e1005047. DOI: 10.1371/journal.pgen.100504

Kempe H., A. Schwabe, F. Crémazy, P.J. Verschure, F.J. Bruggeman (2015) The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Molecular Biology of the Cell 26, 797-804. DOI: 10.1091/mbc.E14-08-1296

Kröel-Dulay, G., J. Ransijn, I. Kappel Schmidt, et al. (2015) Increased sensitivity to climate change in disturbed ecosystems. Nature Communications 6, 6682. DOI:10.1038/ncomms7682

Muntyan, M.S., D.A. Cherepanov, A.M. Malinen, D.A. Bloch, D.Y. Sorokin, I.I. Severina, T.V. Ivashina, R. Lahti, G. Muyzer, V.P. Skulachev (2015) Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase. Proceedings of the National Academy of Sciences of the United States of America 112: 7695-7700. DOI:10.1073/pnas.1417071112

Naldi A., P.T. Monteiro, C. Müssel; Consortium for Logical Models and Tools, et al. (2015) Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 31, 1154-1159. DOI: 10.1093/bioinformatics/btv013

Reichstein, B. L. Persson, A.M. de Roos (2015) Ontogenetic asymmetry modulates population biomass production and response to harvest. Nature Communications 6, 6441. DOI: 10.1038/ncomms7441

Rybakova K.N., A. Tomaszewska, S. van Mourik, J. Blom, H.V. Westerhoff, C. Carlberg, F.J. Bruggeman (2015) Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model. Nucleic Acids Research 43, 153-161. DOI: 10.1093/nar/gku1272

Rybakova K.N., F.J. Bruggeman, A. Tomaszewska, M.J. Moné, C. Carlberg, H.V. Westerhoff (2015) Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Computational Biology 11, e1004236. DOI: 10.1371/journal.pcbi.1004236

Sorokin, D.Y., H.L. Banciu, G. Muyzer (2015) Functional microbiology of soda lakes. Current Opinion in Microbiology 25: 88-96. DOI: 10.1016/j.mib.2015.05.004

Strahl, H., S. Ronneau, B. Solana González, D. Klutsch, C. Schaffner-Barbero, L.W. Hamoen (2015) Transmembrane protein sorting driven by membrane curvature. Nature Communications 6, 8728. DOI: 10.1038/ncomms9728

Westerhoff H.V., S. Nakayama, T.D. Mondeel, M. Barberis (2015) Systems Pharmacology: An opinion on how to turn the impossible into grand challenges. Drug Discovery Today Technology 15, 23-31. DOI: 10.1016/j.ddtec.2015.06.006

Worden, A.Z., M.J. Follows, S.J. Giovannoni, S. Wilken, A.E. Zimmerman, P.J. Keeling (2015) Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347, 735. DOI: 10.1126/science.1257594


Liu, Q.X., P.M. Herman, W.M. Mooij, J. Juisman, M. Scheffer, H. Olff, J. van de Koppel (2014) Pattern formation at multiple spatial scales drives the resilience of mussel bed ecosystems. Nature Communications 5, 5234. DOI: 10.1038/ncomms6234

Sandrini, G., H.C.P. Matthijs, J.M.H. Verspagen, G. Muyzer, J. Huisman (2014) Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis. The ISME Journal 8: 589-600. DOI:10.1038/ismej.2013.179

Sorokin, D.Y., V.M. Gumerov, A.L. Rakitin, A.V. Beletsky, J.S. Sinninghe Damsté, G. Muyzer, A.V. Mardanov, N.V. Ravin (2014) Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3' Environmental Microbiology 16: 1549-1565. DOI: 10.1111/1462-2920.12284

Strahl, H., F. Bürmann, L.W. Hamoen (2014) The actin homologue MreB organizes the bacterial cell membrane. Nature Communications 5, 3442. DOI: 10.1038/ncomms4442

Suzuki, S., J.G. Kuenen, K. Schippers, S. van der Velde, S. Ishii, A. Wu, D.Y. Sorokin, A. Tenney, X. Meng, P.L. Morril, Y. Kamagata, G. Muyzer, K.H. Nealson (2014) Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site. Nature Communications 5, 3900. DOI: 10.1038/ncomms4900

Verspagen, J.M.H., D.B. van de Waal, J.F. Finke, P.M. Visser, E. van Donk, J. Huisman (2014) Rising CO2 levels will intensify phytoplankton blooms in eutrophic and hypertrophic lakes. PLoS One 9: e104325. DOI:10.1371/journal.pone.0104325


Bachmann H., M. Fischlechner, I. Rabbers, N. Barfa, F. Branco dos Santos, D. Molenaar, B. Teusink (2013). Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A 110: 14302-14307. DOI: 10.1073/pnas.1308523110

Cavalca, L, A. Corsini, P. Zaccheo, V. Andreoni, G. Muyzer (2013) Microbial transformations of arsenic: perspectives for biological removal of arsenic from water. Future Microbiology 8:753-768. DOI: 10.2217/FMB.13.38


Duman R., S. Ishikawa, I. Celik, H. Strahl, N. Ogasawara, P. Troc, J. Löwe, L.W. Hamoen (2013) Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring. Proceedings of the National Academy of Sciences U S A 110: E4601-E4610

Firczuk, H., S. Kannambath, J. Pahle, A. Claydon, R. Beynon, J. Duncan, H. Westerhoff, P. Mendes, J. McCarthy (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9, 635. DOI: 10.1038/msb.2012.73

Geenen, S., F.B. du Preez, J.L. Snoep, A.J. Foster, S. Sarda, J.G. Kenna, I.D. Wilson, (2013) Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy (2013) Biochimica et Biophysica Acta 1830: 4943-4959. DOI: 10.1016/j.bbagen.2013.04.014

Kolodkin, A., N. Sahin, A. Phillips, S.R. Hood, F.J. Bruggeman, H.V. Westerhoff (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4: 1792. DOI: 10.1038/ncomms2799

Lim, X., S.H. Tan, W.L. Koh, R.M. Chau, K.S. Yan, C.J. Kuo, R. van Amerongen, A.M. Klein, R. Nusse (2013) Interfollicular epidermal stem cells self-renew via autocrine wnt signaling. Science 342: 1226-1230. DOI: 10.1126/science.1239730

Sheik, A.R., C.P.D. Brussaard, G. Lavik, R.A. Foster, N. Musat, B. Adam, M.M.M. Kuypers (2013) Viral infection of Phaeocystis globosa impedes release of chitinous star-like structures: quantification using single cell approaches. Environmental Microbiology 15: 1441-1451. DOI: 10.1111/j.1462-2920.2012.02838.x

Thiele, I., N. Swainston, R.M. Fleming, et al. (2013) A community-driven global reconstruction of human metabolism. Nature Biotechnology 31: 419-425. DOI: 10.1038/nbt.2488

van Heeswijk W.C., H.V. Westerhoff, F.C. Boogerd (2013) Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiology and Molecular Biology Reviews 77, 628-695. DOI: 10.1128/MMBR.00025-13