Researchers regularly publish articles on various Complex Systems topics.

2016

  • Péli, G. (2016). Analyzing complex organizational arguments with logical model building. In. Kuckertz, A., Berger, E. (eds.) Complexity in entrepreneurship, innovation and technology research - Applications of emergent and neglected methods. FGF Studies in Small Business and Entrepreneurship. Springer: Berlin. pp. 139-159.
  • S.Battiston, J.D.Farmer, A.Flache, D.Garlaschelli, A.Haldane, H.Heesterbeek, C.Hommes, C.Jaeger, R.May & M.Scheffer (2016). Complexity Theory and Financial Regulation: Economic policy needs interdisciplinary network analysis and behavioral modeling. Science.

2015

  • Ariotti S., Beltman J.B., Borsje R., Hoekstra M.E., Halford W.P., Haanen J.B., De Boer R.J. & Schumacher T.N. (2015). Subtle CXCR3-Dependent Chemotaxis of CTLs within Infected Tissue Allows Efficient Target Localization. J. Immunol., 195: 5285-5295
  • Bezemer D., Cori A., Ratmann O., Van Sighem A., Hermanides H.S., Dutilh B.E., Gras L., Rodrigues Faria N., Van den Hengel R., Duits A.J., Reiss P., De Wolf F. & Fraser C. (2015). Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. PLoS. Med., 12: e1001898.
  • Buskens, V.W. & Snijders, C. (2015). Effects of Network Characteristics on Reaching the Payoff-Dominant Equilibrium in Coordination Games - A Simulation StudyDynamic Games and Applications, (pp. 1-18).
  • Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2015b). A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors. Mol. Biol. Evol., 32: 2149-2160.
  • Costa A.I., Koning D., Ladell K., McLaren J.E., Grady B.P., Schellens I.M., Van Ham P., Nijhuis M., Borghans J.A., Kesmir C., Price D.A. & Van Baarle D. (2015). Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1. J. Virol., 89: 110-119.
  • Coutinho F.H., Meirelles P.M., Moreira A.P., Paranhos R.P., Dutilh B.E. & Thompson F.L. (2015). Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review. PeerJ., 3: e1008.
  • García-Díaz C, van Witteloostuijn A, Péli G (2015). Micro-Level Adaptation, Macro-Level Selection, and the Dynamics of Market Partitioning. PLoS ONE, 10(12): e0144574. doi:10.1371/journal.pone.0144574
  • Garza D.R. & Dutilh B.E. (2015). From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol. Life Sci., 72: 4287-4308.
  • Heesterbeek, Hans et al. (2015). Modeling infectious disease dynamics in the complex landscape of global health. Science, 347 , pp. aaa4339.
  • Hermsen R., Okano H., You C., Werner N. & Hwa T. (2015). A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Mol. Syst. Biol., 11: 801. 
  • Koster M.J., Snel B. & Timmers H.T. (2015). Genesis of chromatin and transcription dynamics in the origin of species. Cell, 161: 724-736.
  • Niculescu I., Textor J. & De Boer R.J. (2015). Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration. PLoS. Comput. Biol., 11: e1004280.
  • Westermann J., Lange T., Textor J. & Born J. (2015). System Consolidation During Sleep - A Common Principle Underlying Psychological and Immunological Memory Formation. Trends Neurosci., 38: 585-597.

2014

  • De Boer F.K. & Hogeweg P. (2014). Mutation Rates and Evolution of Multiple Coding in RNA-based Protocells. J. Mol. Evol., 79: 193-203.
  • Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2014). Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus. Front. Immunol., 5: 20.
  • Colizzi E.S. & Hogeweg P. (2014). Evolution of functional diversification within quasispecies. Genome Biol. Evol., 6: 1990-2007.
  • Corten, R. (2014). Computational Approaches to Studying the Co-evolution of Networks and Behavior in Social Dilemmas. Chichester: John Wiley & Sons.
  • Cuypers T.D. & Hogeweg P. (2014). A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. PLoS. Comput. Biol., 10: e1003547.
  • van Dolder, Dennie & Buskens, Vincent (2014). Individual choices in dynamic networks. PLoS ONE [E], 9(4)
  • Van Dorp C.H., Van Boven M. & De Boer R.J. (2014). Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution. PLoS Comput. Biol., 10: e1003899.
  • Dutilh B.E. (2014). Metagenomic ventures into outer sequence space. Bacteriophage, 0: e979664.
  • Gadhamsetty S., Maree A.F., Beltman J.B. & De Boer R.J. (2014). A general functional response of cytotoxic T lymphocyte-mediated killing of target cells. Biophys. J., 106: 1780-1791.
  • Mahonen A.P., Ten Tusscher K., Siligato R., Smetana O., Diaz-Trivino S., Salojarvi J., Wachsman G., Prasad K., Heidstra R. & Scheres B. (2014). PLETHORA gradient formation mechanism separates auxin responses. Nature, 515: 125-129.
  • Morbitzer, Dominik, Buskens, Vincent, Rosenkranz, Stephanie & Raub, Werner (2014). How Farsightedness Affects Network Formation. Analyse und Kritik, 36, pp. 103-133.
  • Pandit A. & De Boer R.J. (2014). Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants. Retrovirology., 11: 56.
  • Perie L., Hodgkin P.D., Naik S.H., Schumacher T.N., De Boer R.J. & Duffy K.R. (2014). Determining lineage pathways from cellular barcoding experiments. Cell Rep., 6: 617-624.
  • Selakovic, S., de Ruiter, P.C. & Heesterbeek, J.A.P. (2014): Infectious disease agents mediate interaction in food webs and ecosystems. Proc. R. Soc. B 281, 20132709.
  • Stein, Mart L., Van Steenbergen, Jim E., Buskens, Vincent, Van Der Heijden, Peter G M, Chanyasanha, Charnchudhi, Tipayamongkholgul, Mathuros, Thorson, Anna E., Bengtsson, Linus, Lu, Xin & Kretzschmar, Mirjam E E (2014). Comparison of contact patterns relevant for transmission of respiratory pathogens in Thailand and The Netherlands using respondent-driven sampling. PLoS ONE [E], 9(11)
  • Textor J., Henrickson S.E., Mandl J.N., Von Andrian U.H., Westermann J., De Boer R.J. & Beltman J.B. (2014). Random migration and signal integration promote rapid and robust T cell recruitment. PLoS. Comput. Biol., 10: e1003752.

2013

  • Van Berkel K., De Boer R.J., Scheres B. & Ten Tusscher K. (2013). Polar auxin transport: models and mechanisms. Development, 140: 2253-2268.
  • Carrillo-Bustamante P., Kesmir C. & De Boer R.J. (2013). Virus encoded MHC-like decoys diversify the inhibitory KIR repertoire. PLoS. Comput. Biol., 9: e1003264. 
  • Deris J.B., Kim M., Zhang Z., Okano H., Hermsen R., Groisman A. & Hwa T. (2013). The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science, 342: 1237435.
  • Diekmann, O., Heesterbeek, J.A.P. & T. Britton: Mathematical Tools for Understanding Infectious Disease Dynamics. Princeton University Press, 2013, 500pp.
  • Funk, S., Cecchi, F., Nishiura, H., Heesterbeek, J.A.P. & J. Edmunds (2013): Identifying transmission cycles at the human-animal interface: the role of animal reservoirs in maintaining gambiense Human African Trypanosomiasis. PLoS Comp. Biol., 9: e1002855.
  • Gerlach C., Rohr J.C., Perie L., Van Rooij N., Van Heijst J.W., Velds A., Urbanus J., Naik S.H., Jacobs H., Beltman J.B., De Boer R.J. & Schumacher T.N. (2013). Heterogeneous differentiation patterns of individual CD8+ T cells. Science, 340: 635-639.
  • Roberts, M.G. & J.A.P. Heesterbeek (2013): Characterizing the next-generation matrix and basic reproduction number in ecological epidemiology. J. Math. Biol., 66,  1045-1064.
  • Tsvetkova, M. & Buskens, V.W. (2013). Coordination on egalitarian networks from asymmetric relations in a social game of chicken. Advances in Complex Systems, 16.
  • Ten Tusscher K.H. (2013). Mechanisms and constraints shaping the evolution of body plan segmentation. Eur. Phys. J. E, 36: 54.
  • Weise L.D. & Panfilov A.V. (2013). A discrete electromechanical model for human cardiac tissue: effects of stretch-activated currents and stretch conditions on restitution properties and spiral wave dynamics. PLoS. One., 8: e59317.

2012

  • De Boer F.K. & Hogeweg P. (2012). Less can be more: RNA-adapters may enhance coding capacity of replicators. PLoS. One., 7: e29952.
  • De Boer R.J. (2012). Which of our modeling predictions are robust? PLoS. Comput. Biol., 8: e1002593.
  • Corten, R. (2012). Composition and structure of a large online social network in the Netherlands. PLoS ONE [E], 7(4 e34760)
  • Cuypers T.D. & Hogeweg P. (2012). Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining. Genome Biol. Evol., 4: 212-229.
  • Groenenboom M.A. & Hogeweg P. (2012). Modelling the dynamics of viral suppressors of RNA silencing. J. R. Soc. Interface, 9: 436-447.
  • Hogeweg P. (2012). Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. Adv. Exp. Med. Biol., 751: 195-224.
  • Mostowy R., Kouyos R.D., Hoof I., Hinkley T., Haddad M., Whitcomb J.M., Petropoulos C.J., Kesmir C. & Bonhoeffer S. (2012). Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. PLoS. Comput. Biol., 8: e1002525.
  • Reijniers, J., Davis, S., Begon, M., Heesterbeek, J.A.P., Agayev, V.S. & H. Leirs (2012): A curve of thresholds governs plague epizootics in Central Asia. Ecol. Letters, 15, 554-560.
  • Takeuchi N. & Hogeweg P. (2012a). Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life. Phys. Life Rev., 9: 219-263.
  • Takeuchi N. & Hogeweg P. (2012b). Reply to the commentaries on ''Evolutionary dynamics of rna-like replicator systems: A bioinformatic approach to the origin of life''. Phys. Life Rev., 9: 279 - 284.
  • Vroomans R.M., Maree A.F., De Boer R.J. & Beltman J.B. (2012). Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens. PLoS. Comput. Biol., 8: e1002763. 
  • Weise L.D. & Panfilov A.V. (2012). Emergence of spiral wave activity in a mechanically heterogeneous reaction-diffusion-mechanics system. Phys. Rev. Lett., 108: 228104.

2011

  • Alonso S., Bar M. & Panfilov A.V. (2011). Effects of reduced discrete coupling on filament tension in excitable media. Chaos., 21: 013118.
  • Beltman J.B., Allen C.D., Cyster J.G. & De Boer R.J. (2011). B cells within germinal centers migrate preferentially from dark to light zone. Proc. Natl. Acad. Sci. U.S.A., 108: 8755-8760.
  • Bojanowski, M.J. & Buskens, V.W. (2011). Coordination in dynamic social networks under heterogeneity. Journal of Mathematical Sociology, 35, pp. 249-286.
  • Groenenboom M.A. & Hogeweg P. (2011). Modelling the dynamics of viral suppressors of RNA silencing. J R Soc Interface.
  • Hogeweg P. (2011).The roots of bioinformatics in theoretical biology. PLoS. Comput. Biol., 7: e1002021.
  • Takeuchi N., Hogeweg P. & Koonin E.V. (2011). On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems. PLoS. Comput. Biol., 7: e1002024.
  • Ten Tusscher K. & Scheres B. (2011). Joining forces: feedback and integration in plant development. Curr. Opin. Genet. Dev., 21: 799-805. 
  • Ten Tusscher K.H. & Hogeweg P. (2011). Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. PLoS. Comput. Biol., 7: e1002208.
  • Weise L.D., Nash M.P. & Panfilov A.V. (2011). A discrete model to study reaction-diffusion-mechanics systems. PLoS. One., 6: e21934. 
  • Weise L.D. & Panfilov A.V. (2011). New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system. PLoS. One., 6: e27264. 

2010

  • Althaus C.L. & De Boer R.J. (2010). Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy. Mol. Syst. Biol., 6: 348.
  • De Boer F.K. & Hogeweg P. (2010). Eco-evolutionary Dynamics, Coding Structure and the Information Threshold. BMC. Evol. Biol., 10: 361.
  • Hogeweg P. (2010). Multilevel cellular automata as a tool for studying bioinformatic processes. In: Hoekstra A.G., Kroc J. & Sloot P.M.A., eds., Simulating Complex Systems by Cellular Automata, Understanding Complex Systems, pp. 19-28. Springer, 1st edn.
  • Keldermann R.H., Nash M.P., Gelderblom H., Wang V.Y. & Panfilov A.V. (2010). Electromechanical wavebreak in a model of the human left ventricle. Am. J. Physiol. Heart. Circ. Physiol., 299: H134-H143.
  • Schmid B.V., Kesmir C. & De Boer R.J. (2010). Quantifying how mhc polymorphism prevents pathogens from adapting to the antigen presentation pathway. Epidemics, 2: 99 - 108.
  • Sridhar S., Sinha S. & Panfilov A.V. (2010). Anomalous drift of spiral waves in heterogeneous excitable media. Phys. Rev. E, 82: 051908.

Before 2010

  • Corten, R. & Cook, K.S. (2009). Cooperation and reputation in dynamic networks. In M. Paolucci (Eds.), Proceedings of the First International Conference on Reputation: Theory and Technology pp. 20-34.
  • Weesie, J., Snijders, C.C.P. & Buskens, V.W. (2009). The rationale of rationality. Rationality and Society, 21, pp. 249-277.
  • Buskens, V.W., Corten, R. & Weesie, H.M. (2008). Consent or conflict: coevolution of coordination and networks. Journal of Peace Research, 45, pp. 205-222.
  • Davis, S.A., Trapman, J.P., Leirs, H., Begon, M. & J.A.P. Heesterbeek (2008). The abundance threshold for plague as a critical percolation phenomenon. Nature, 454, 634-637.
  • Weisbuch, G., Buskens, V.W. & Vuong, L. (2008). Heterogeneity and increasing returns may drive socio-economic transitions. Computational & Mathematical Organization Theory, 14, pp. 376-390.
  • Neutel, A.M., Heesterbeek, J.A.P., van de Koppel, J., Hoenderboom, G., Vos, A., Kaldeway, C., Berendse, F. & P.C. de Ruiter (2007). Reconciling complexity with stability in naturally assembling food webs.Nature, 449, 599-602.
  • Neutel, A.M., Heesterbeek, J.A.P. & P.C. De Ruiter (2002): Weak links in long loops enhance stability in real food webs. Science, 296, 1120-1123.