Publications
2022
Scholarly publications
von der Dunk, S. H. A., Snel, B., & Hogeweg, P. (2022). Evolution of Complex Regulation for Cell-Cycle Control. Genome Biology and Evolution, 14(5), [evac056]. https://doi.org/10.1093/gbe/evac056
Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., Hogeweg, P., Khatri, B. S., Krug, J., Louis, A. A., Martin, N. S., Payne, J. L., Tarnowski, M. J., & Weiß, M. (2022). The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics". Physics of Life Reviews, 42, 19-24. https://doi.org/10.1016/j.plrev.2022.05.007
https://dspace.library.uu.nl/bitstream/handle/1874/425925/Reply_to_comment.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/425925/Reply_to_comment.pdf?sequence=1
Colizzi, E. S., Hogeweg, P., & Vroomans, R. M. A. (2022). Modelling the evolution of novelty: a review. Essays in Biochemistry, 66(6), 727-735. https://doi.org/10.1042/EBC20220069
2021
Scholarly publications
Hogeweg, P. (2021). Modeling Complex Biological Systems: Tackling the Parameter Curse Through Evolution. In A. Crombach (Ed.), Evolutionary Systems Biology: Advances, Questions, and Opportunities (pp. 19-33). Springer. https://doi.org/10.1007/978-3-030-71737-7_2
https://dspace.library.uu.nl/bitstream/handle/1874/428205/978_3_030_71737_7_2.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/428205/978_3_030_71737_7_2.pdf?sequence=1
Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., Hogeweg, P., Khatri, B. S., Krug, J., Louis, A. A., Martin, N. S., Payne, J. L., Tarnowski, M. J., & Weiß, M. (2021). From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Physics of Life Reviews, 38, 55-106. https://doi.org/10.1016/j.plrev.2021.03.004
Hickinbotham, S. J., Stepney, S., & Hogeweg, P. (2021). Nothing in evolution makes sense except in the light of parasitism: evolution of complex replication strategies. Royal Society Open Science, 8(8), 1-15. [210441]. https://doi.org/10.1098/rsos.210441
2020
Scholarly publications
Meijer, J., van Dijk, B., & Hogeweg, P. (2020). Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves. Communications Biology, 3, [401]. https://doi.org/10.1038/s42003-020-1107-x
2019
Scholarly publications
Rutten, J. P., Hogeweg, P., & Beslon, G. (2019). Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure. BMC Evolutionary Biology, 19(1), [191]. https://doi.org/10.1186/s12862-019-1507-z
Colizzi, E. S., & Hogeweg, P. (2019). Transcriptional mutagenesis prevents ribosomal DNA deterioration: The Role of Duplications and Deletions. Genome Biology and Evolution, 11(11), 3207-3217. https://doi.org/10.1093/gbe/evz235
van Dijk, B., Meijer, J., Cuypers, T. D., & Hogeweg, P. (2019). Trusting the hand that feeds: microbes evolve to anticipate a serial transfer protocol as individuals or collectives. BMC Evolutionary Biology, 19(1), [201]. https://doi.org/10.1186/s12862-019-1512-2
2018
Scholarly publications
Vroomans, R. M. A., Hogeweg, P., & ten Tusscher, K. H. W. J. (2018). Around the clock: Gradient shape and noise impact the evolution of oscillatory segmentation dynamics. EvoDevo, 9(1), [24]. https://doi.org/10.1186/s13227-018-0113-2
2017
Scholarly publications
von der Dunk, S. H. A., Colizzi, E., & Hogeweg, P. (2017). Evolutionary Conflict Leads to Innovation: Symmetry Breaking in a Spatial Model of RNA-Like Replicators. Life (Basel, Switzerland), 7(4), [43]. https://doi.org/10.3390/life7040043
Takeuchi, N., Hogeweg, P., & Kaneko, K. (2017). Conceptualizing the origin of life in terms of evolution. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 375(2109), [20160346]. https://doi.org/10.1098/rsta.2016.0346
https://dspace.library.uu.nl/bitstream/handle/1874/361715/20160346.full.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/361715/20160346.full.pdf?sequence=1
Takeuchi, N., Hogeweg, P., & Kaneko, K. (2017). The origin of a primordial genome through spontaneous symmetry breaking. Nature Communications, 8, [250]. https://doi.org/10.1038/s41467-017-00243-x
Cuypers, T. D., Hogeweg, P., & Rutten, J. P. (2017). Evolution of evolvability and phenotypic plasticity in virtual cells. BMC Evolutionary Biology, 17(1), [60]. https://doi.org/10.1186/s12862-017-0918-y
2016
Scholarly publications
Takeuchi, N., Kaneko, K., & Hogeweg, P. (2016). Evolutionarily stable disequilibrium: endless dynamics of evolution in a stationary population. Proceedings of the Royal Society B: Biological Sciences, 283(1830), [20153109]. https://doi.org/10.1098/rspb.2015.3109
Colizzi, E. S., & Hogeweg, P. (2016). High cost enhances cooperation through the interplay between evolution and self-organisation. BMC Evolutionary Biology, 16(31), 31. https://doi.org/10.1186/s12862-016-0600-9
Colizzi, E. S., & Hogeweg, P. (2016). Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation. PLoS Computational Biology, 12(4), [e1004902]. https://doi.org/10.1371/journal.pcbi.1004902
Hogeweg, P., ten Tusscher, K. H. W. J., Davis, GK., Patel, NH., Peel, A., Akam, M., Couso, JP., Budd, GE., Seaver, EC., Minelli, A., Fusco, G., Tautz, D., Jacobs, DK., Hughes, NC., Fitz-Gibbon, ST., Winchell, CJ., Blair, SS., Wanninger, A., Kristof, A., ... Ruddle, FH. (2016). In silico evo-devo: reconstructing stages in the evolution of animal segmentation. EvoDevo, 7(1), 14. https://doi.org/10.1186/s13227-016-0052-8
van Dijk, B., & Hogeweg, P. (2016). In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility. Genome Biology and Evolution, 8(1), 176-88. https://doi.org/10.1093/gbe/evv255
2015
Scholarly publications
Vroomans, R. M. A., Hogeweg, P., & ten Tusscher, K. H. W. J. (2015). Segment-Specific Adhesion as a Driver of Convergent Extension. PLoS Computational Biology, 11(2), [e1004092]. https://doi.org/10.1371/journal.pcbi.1004092
https://dspace.library.uu.nl/bitstream/handle/1874/324896/92.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/324896/92.pdf?sequence=1
2014
Scholarly publications
Cuypers, T. D., Hogeweg, P., & Hogeweg, P. (2014). A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. PLoS Computational Biology, 10(4), e1003547. https://doi.org/10.1371/journal.pcbi.1003547
Colizzi, E. S., Hogeweg, P., & Hogeweg, P. (2014). Evolution of functional diversification within quasispecies. Genome Biology and Evolution, 6(8), 1990-2007. https://doi.org/10.1093/gbe/evu150
Hogeweg, P., & de Boer, F. K. (2014). Mutation rates and evolution of multiple coding in RNA-based protocells. Journal of Molecular Evolution, 79(5-6), 193-203. https://doi.org/10.1007/s00239-014-9648-6
2012
Scholarly publications
Hogeweg, P., & Hogeweg, P. (2012). Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. Advances in Experimental Medicine and Biology, 751, 195-224. https://doi.org/10.1007/978-1-4614-3567-9_10
de Boer, F. K., & Hogeweg, P. (2012). Less can be more: RNA-adapters may enhance coding capacity of replicators. PLoS One, 7(1).
Hogeweg, P. (2012). Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. Advances in Experimental Medicine and Biology, 9, 436-447.
Grieneisen, V., Scheres, B. J. G., Hogeweg, P., & Maree, A. F. M. (2012). Morphogengineering roots: comparing mechanisms of morphogen gradient formation. BMC Systems Biology, 6, 37-37.
Takeuchi, N., & Hogeweg, P. (2012). Reply to the commentaries on 'Evolutionary dynamics of rna-like replicator systems: A bioinformatic approach to the origin of life'. Physics of Life Reviews, 9, 279-284.
Fokkens, L., Hogeweg, P., & Snel, B. (2012). Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age. BMC Evolutionary Biology, 12, 99.
Takeuchi, N., & Hogeweg, P. (2012). Evolutionary dynamics of RNA-like replicator systems: a bioinformatic approach to the origin of life. Physics of Life Reviews, 9, 219-263.
Cuypers, T. D., & Hogeweg, P. (2012). Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining. Genome Biology and Evolution, 4, 212-229.
2011
Scholarly publications
Crombach, A. B. M., & Hogeweg, P. (2011). Is RNA-dependent RNA polymerase essential for transposon control? BMC Systems Biology, 5, 104.
Hogeweg, P. (2011). The roots of bioinformatics in theoretical biology. PLoS Computational Biology, 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 Computational Biology, 7, e1002024.
Groenenboom, M. A. C., & Hogeweg, P. (2011). Modelling the dynamics of viral suppressors of RNA silencing. Journal of the Royal Society Interface, 0, 0.
ten Tusscher, K. H. W. J., & Hogeweg, P. (2011). Evolution of networks for body plan patterning; interplay of modularity robustness and evolvability. PLoS Computational Biology, 7, e1002208.
2010
Scholarly publications
ten Tusscher, K. H. W. J., & Hogeweg, P. (2010). The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. Experimental Physiology, 9, 159.
Other output
de Boer, F. K., & Hogeweg, P. (2010). Eco-evolutionary dynamics, coding structure and the information threshold. BMC Evolutionary Biology, 10(DOI. MEDLINE. DownLoad PDF), 361.
2009
Scholarly publications
Takeuchi, N., & Hogeweg, P. (2009). Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization. PLoS Computational Biology, 5, e1000542.
Crombach, A. B. M., & Hogeweg, P. (2009). Evolution of resource cycling in ecosystems and individuals. BMC Evolutionary Biology, 9, 122.
Takeuchi, N., & Hogeweg, P. (2009). Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization. PLoS Computational Biology, 5.
van der Post, D. J., Ursem, B., & Hogeweg, P. (2009). Resource distributions affect social learning on multiple timescales. Behavioral Ecology and Sociobiology, 63, 1643-1658.
van der Post, D. J., & Hogeweg, P. (2009). Cultural inheritance and diversification of diet in variable environments. Animal Behaviour, 78, 155-166.
van Hoek, M. J. A., & Hogeweg, P. (2009). Metabolic adaptation after whole genome duplication. Molecular Biology and Evolution, 0.
Cordero, O. X., & Hogeweg, P. (2009). Regulome size in prokaryotes: universality and lineage-specific variations. Trends in Genetics, 25, 285-286.
ten Tusscher, K. H. W. J., & Hogeweg, P. (2009). The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. BMC Evolutionary Biology, 9, 159.
Cordero, O. X., & Hogeweg, P. (2009). The consequences of basepair composition biases for regulatory network organization in prokaryotes. Molecular Biology and Evolution, 26, 2171-2173.
Cordero, O. X., & Hogeweg, P. (2009). The impact of long-distance horizontal gene transfer on prokaryotic genome size. Proceedings of the National Academy of Sciences of the United States of America, 0.
2008
Scholarly publications
Groenenboom, M. A. C., & Hogeweg, P. (2008). The dynamics and efficacy of antiviral RNA silencing: A model study. BMC Systems Biology, 2, 28-DOI. Medline.
van der Post, D. J., & Hogeweg, P. (2008). Diet traditions and cumulative cultural processes as side-effects of grouping. Animal Behaviour, 75, 133-144.
Crombach, A. B. M., & Hogeweg, P. (2008). Evolution of evolvability in gene regulatory networks. PLoS Computational Biology, 4, e1000112-MEDLINE.
Groenenboom, M. A. C., & Hogeweg, P. (2008). RNA silencing can explain chlorotic infection patterns on plant leaves. BMC Systems Biology, 2, 105-DOI. Medline.
Takeuchi, N., & Hogeweg, P. (2008). Evolution of complexity in RNA-like replicator systems. Biology Direct, 3, 11-MEDLINE.
Takeuchi, N., Salazar, L., Poole, A. M., & Hogeweg, P. (2008). The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription. Biology Direct, 3, 33-MEDLINE.
Laskowski, M., Grieneisen, V., Hofhuis, H. F., ten Hove, C. A., Hogeweg, P., Maree, A. F. M., & Scheres, B. J. G. (2008). Root system architecture from coupling cell shape to auxin transport. PloS Biology [E], 6, e307-DOI. MEDLINE.
Cordero Sanchez, O. X., Snel, B., & Hogeweg, P. (2008). Coevolutions of gene families in prokaryotes. Cytogenetic and Genome Research, 18, MEDLINE.
Professional publications
Burgers, G., Doelman, A., Frenken, K., Hogeweg, P., van der Hommes, C., Maas, H., Mulder, B., van Stam, C., Van Steen, M., & Zandee, L. (2008). Complexity. Outline of the NWO strategic theme "Dynamics of Complex Systems". NWO. http://www.nwo.nl
2007
Scholarly publications
Crombach, A. B. M., & Hogeweg, P. (2007). Chromosome rearrangements and the evolution of genome structuring and adaptabillity. Molecular Biology and Evolution, 24, 1130-1139.
Cordero, O. X., & Hogeweg, P. (2007). Large changes in regulome size herald the main prokaryotic lineages. Trends in Genetics, 23(10), 488-493. https://doi.org/10.1016/j.tig.2007.07.006
Takeuchi, N., & Hogeweg, P. (2007). Error-threshold exists in fitness landscapes with lethal mutants. BMC Evolutionary Biology, 7, [15]. https://doi.org/10.1186/1471-2148-7-15
Maree, A. F. M., Grieneisen, V., & Hogeweg, P. (2007). The cellular potts model and biophysical properties of cells, tissues and morphogenesis. In Single-cell-based models in Biology and Medicine (pp. 107-136). Birkhaüser.
van Hoek, M. J. A., & Hogeweg, P. (2007). The role of mutational dynamics in genome shrinkage. Molecular Biology and Evolution, 24, 2485-2494.
Takeuchi, N., & Hogeweg, P. (2007). The role of complex formation and deleterious mutations for the stability of RNA-like replicator systems. Journal of Molecular Evolution, 6, 668-686.
van der Post, D. J., & Hogeweg, P. (2007). Diet traditions and cumulative cultural processes as side-effects of grouping. Animal Behaviour, 10, 1016-1016.
van Hoek, M. J. A., & Hogeweg, P. (2007). The effect of stochasticity on the lac operon: an evolutionary perspective. PLoS Computational Biology, 22, e111-e111.
Grieneisen, V., Xu, J., Maree, A. F. M., Hogeweg, P., & Scheres, B. J. G. (2007). Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature, 449, 1008-1013.
Hogeweg, P. (2007). From population dynamics to ecoinformatics: Ecosystems as multilevel information processing systems. Ecological Informatics, 2, 103-111.
2006
Scholarly publications
van der Post, D. J., & Hogeweg, P. (2006). Resource distributions and diet development by trial-and-order learning. Behavioral Ecology and Sociobiology, 61, 65-80.
Merks, R. M., Hoekstra, A. G., Kaandorp, J., Sloot, P. M. A., & Hogeweg, P. (2006). Problem-solving environments for biological morphogenesis. Computing in science & engineering, 8, 61-72.
Van Hoek, M. J. A., & Hogeweg, P. (2006). In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose. Biophysical Journal, 91(8), 2833-2843. https://doi.org/10.1529/biophysj.105.077420
Cordero Sanchez, O. X., & Hogeweg, P. (2006). Feed-forward loop circuits as a side effect of genome evolution. Molecular Biology and Evolution, 23, 1931-1936.
Kafer, J., Hogeweg, P., & Maree, A. F. M. (2006). Moving forward moving backward: directional sorting of chemotactic cells due to size and adhesion differences. PLoS Computational Biology, 2 e56, 1-12.
2005
Scholarly publications
Takeuchi, N., Poorthuis, P. H., & Hogeweg, P. (2005). Phenotypic error threshold; additivity and epistasis in RNA evolution. BMC Evolutionary Biology, 5, 9-9.
Hogeweg, P. (2005). Interlocking of selforganization and evolution. In Self-organization and evolution of Social Systems (ed. C.K. Hemelrijk) (pp. 166-189). Cambridge University Press.
Groenenboom, M. A. C., Maree, A. F. M., & Hogeweg, P. (2005). The RNA silencing pathway: the bits and pieces that matter. PLoS Computational Biology, 2, 155-165.
Hogeweg, P. (2005). Multilevel particle systems and the study of biological evolution. Markov Processes and Related Fields, 1005, 291-312.
2004
Scholarly publications
van der Post, D. J., & Hogeweg, P. (2004). Learning what to eat: Studying inter-relations between learning, grouping and environmental conditions in an artificial world. Lecture Notes in Computer Science, 3305, 492-501.
https://dspace.library.uu.nl/bitstream/handle/1874/11445/Post_BC8CDE58d01.pdf?sequence=2
https://dspace.library.uu.nl/bitstream/handle/1874/11445/Post_BC8CDE58d01.pdf?sequence=2
2003
Scholarly publications
Kesmir, C., van Noort, V., de Boer, R. J., & Hogeweg, P. (2003). Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Immunogenetics, 55, 437-449.
Hogeweg, P. (2003). Computing an organism: on the interface between informatic and dynamic processes. In S. Kumar, & J. Bentley (Eds.), On Growth, Form and Computers Elsevier.
Hogeweg, P., & Takeuchi, N. (2003). Multilevel selection in models of prebiotic evolution: compartments and spatial self-organization. Origins of life and evolution of the biosphere, 33, 375-403.
2002
Scholarly publications
Hogeweg, P. (2002). Computing an organism: On the interface between informatic and dynamic processes. BioSystems, 64(1-3), 97-109. https://doi.org/10.1016/S0303-2647(01)00178-2
Groenenboom, M. A. C., & Hogeweg, P. (2002). Space and the persistence of male-killing endosymbionts in insect populations. Proceedings of the Royal Society B-Biological Sciences, 269, 2509-2518.
Hogeweg, P. (2002). Multilevel processes in evolution and development: computational models and biological insights. In M. Laessig, & A. Valleriani (Eds.), Biological Evolution and Statistical Physics (pp. 217-239). Springer.
Hogeweg, P. (2002). Computing an organism: on the interface between informatic and ynamic processes. BioSystems, 64, 97-109.
Hogeweg, P. (2002). Multilevel evolution: The fate of duplicated genes. Zeitschrift fur Physikalische Chemie, 216, 77-90.
Marée, A. F. M., & Hogeweg, P. (2002). Modelling Dictyostelium discoideum morphogenesis: the culmination. Bulletin of Mathematical Biology, 64, 327-353.
Professional publications
Hogeweg, P. (2002). From bioinformatic pattern analysis to evolutionary dynamics. Nieuw archief voor wiskunde. Serie 5, 3(2), 132-138.
https://dspace.library.uu.nl/bitstream/handle/1874/314082/32.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/314082/32.pdf?sequence=1
2001
Scholarly publications
Marée, A. F. M., & Hogeweg, P. (2001). How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum. Proceedings of the National Academy of Sciences of the United States of America, 98(7), 3879-3883. https://doi.org/10.1073/pnas.061535198
2000
Scholarly publications
Hogeweg, P. (2000). Shapes in the shadow: evolutionary dynamics of morphogenesis. Artificial Life, 6(1), 85-101.
Hogeweg, P. (2000). Evolving mechanisms of morphogenesis: On the interplay between differential adhesion and cell differentiation. Journal of Theoretical Biology, 203(4), 317-333. https://doi.org/10.1006/jtbi.2000.1087
1999
Scholarly publications
Pagie, L. W. P., & Hogeweg, P. (1999). Colicin diversity: a result of eco-evolutionary dynamics. Journal of Theoretical Biology, 196(2), 251-261.
Savill, N. J., & Hogeweg, P. (1999). Competition and dispersal in predator-prey waves. Theoretical Population Biology, 56, 243-263.
Yamamoto, T., & Hogeweg, P. (1999). Evolution to complexity: replication, elongation and assembly in an RNA world Advances in Artificial Life. In D. Floreano, J-D. Nicoud, & F. Mondada (Eds.), Lecture Notes in Artificial Intelligence (pp. 422-426). Springer.
Marée, A. F. M., Panfilov, A. V., & Hogeweg, P. (1999). Phototaxis during the slug stage of Dictyostelium discoideum: a model study. Proceedings of the Royal Society B-Biological Sciences, 266(1426), 1351-1360. https://doi.org/10.1098/rspb.1999.0787
Marée, A. F. M., Panfilov, A. V., & Hogeweg, P. (1999). "Migration and thermotaxis of Dictyostelium discoideum slugs, a model study". Journal of Theoretical Biology, 199, 297-309.
1998
Scholarly publications
Savill, N. J., & Hogeweg, P. (1998). Spatially induced speciation prevents extinction: The evolution of dispersal distance in oscillatory predator-prey models. Philosophical transactions / Royal Society of London. Biological sciences, 265(1390), 25-32. https://doi.org/10.1098/rspb.1998.0259
Van Doorn, G. S., Noest, A. J., & Hogeweg, P. (1998). Sympatric speciation and extinction driven by environment dependent sexual selection. Proceedings - Royal Society. Biological sciences , 265(1408), 1915-1919.
1997
Scholarly publications
Savill, N. J., & Hogeweg, P. (1997). Evolutionary stagnation due to pattern-pattern interactions in a coevolutionary predator-prey model. Artificial Life, 3(2), 81-100.
Savill N.J, N. V., Rohani, P., & Hogeweg, P. (1997). Erratum: (Journal of Theoretical Biology (1997) 188 (11-20)). Journal of Theoretical Biology, 188(4), 525-526. https://doi.org/10.1006/jtbi.1997.0556
1995
Scholarly publications
Van der Laan, J. D., & Hogeweg, P. (1995). Predator-prey coevolution: Interactions across different timescales. Proceedings - Royal Society. Biological sciences , 259(1354), 35-42.
Van der Laan, J. D., Lhotka, L., & Hogeweg, P. (1995). Sequential predation: A multi-model study. Journal of Theoretical Biology, 174(2), 149-167. https://doi.org/10.1006/jtbi.1995.0088
Panfilov, A. V., & Hogeweg, P. (1995). Mechanisms of cardiac fibrillation. Science, 270(5239), 1223-1224; author reply 1224-1225.
1994
Scholarly publications
Huynen, M. A., & Hogeweg, P. (1994). Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes. Journal of Molecular Evolution, 39(1), 71-79.
1993
Scholarly publications
Boerlijst, M. C., Lamers, M. E., & Hogeweg, P. (1993). Evolutionary consequences of spiral waves in a host-parasitoid system. Proceedings - Royal Society. Biological sciences , 253(1336), 15-18.
Huynen, M. A., Konings, D. A. M., & Hogeweg, P. (1993). Multiple coding and the evolutionary properties of RNA secondary structure. Journal of Theoretical Biology, 165(2), 251-267. https://doi.org/10.1006/jtbi.1993.1188
1992
Scholarly publications
Huynen, M. A., Konings, D. A. M., & Hogeweg, P. (1992). Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure. Journal of Molecular Evolution, 34(4), 280-291. https://doi.org/10.1007/BF00160235
1990
Scholarly publications
Van Ooyen, A., & Hogeweg, P. (1990). Iterative character weighting based on mutation frequency: A new method for constructing phyletic trees. Journal of Molecular Evolution, 31(4), 330-342.
Kwakman, J. H. J. M., Konings, D. A. M., Hogeweg, P., Pel, H. J., & Grivell, L. A. (1990). Structural analysis of a group II intron by chemical modifications and minimal energy calculations. Journal of Biomolecular Structure and Dynamics, 8(2), 413-430.
1989
Scholarly publications
De Boer, R. J., & Hogeweg, P. (1989). Memory but no suppression in low-dimensional symmetric idiotypic networks. Bulletin of Mathematical Biology, 51(2), 223-246.
De Boer, R. J., & Hogeweg, P. (1989). Stability of symmetric idiotypic networks--a critique of Hoffmann's analysis. Bulletin of Mathematical Biology, 51(2), 217-222.
De Boer, R. J., & Hogeweg, P. (1989). Unreasonable implications of reasonable idiotypic network assumptions. Bulletin of Mathematical Biology, 51(3), 381-408.
de Boer, R. J., & Hogeweg, P. (1989). Idiotypic networks incorporating T-B cell co-operation. The conditions for percolation. Journal of Theoretical Biology, 139(1), 17-38.
Konings, D. A. M., & Hogeweg, P. (1989). Pattern analysis of RNA secondary structure. Similarity and consensus of minimal-energy folding. Journal of Molecular Biology, 207(3), 597-614. https://doi.org/10.1016/0022-2836(89)90468-3
Hogeweg, P. (1989). Local T-T cell and T-B cell interactions: A cellular automaton approach. Immunology Letters, 22(2), 113-122. https://doi.org/10.1016/0165-2478(89)90177-6
Hogeweg, P., Rizki, M., & Trenary, R. (1989). Simplicity and complexity in MIRROR universes. BioSystems, 23(2-3), 231-246. https://doi.org/10.1016/0303-2647(89)90029-4
1988
Scholarly publications
Konings, D. A. M., Bredenbeek, P. J., Noten, J. F. H., Hogeweg, P., & Spaan, W. J. M. (1988). Differential premature termination of transcription as a proposed mechanism for the regulation of coronavirus gene expression. Nucleic Acids Research, 16(22), 10849-10860. https://doi.org/10.1093/nar/16.22.10849
1987
Scholarly publications
De Boer, R. J., & Hogeweg, P. (1987). Immunological discrimination between self and non-self by precursor depletion and memory accumulation. Journal of Theoretical Biology, 124(3), 343-369. https://doi.org/10.1016/S0022-5193(87)80121-2
Konings, D. A. M., Van Duijn, L. P., Voorma, H. O., & Hogeweg, P. (1987). Minimal energy foldings of eukaryotic mRNAs form a separate leader domain. Journal of Theoretical Biology, 127(1), 63-78. https://doi.org/10.1016/S0022-5193(87)80161-3
Konings, D. A. M., Hogeweg, P., & Hesper, B. (1987). Evolution of the primary and secondary structures of the E1a mRNAs of the adenovirus. Molecular Biology and Evolution, 4(3), 300-314.
De Boer, R. J., & Hogeweg, P. (1987). Self-nonself discrimination due to immunological nonlinearities: the analysis of a series of models by numerical methods. IMA journal of mathematics applied in medicine and biology, 4(1), 1-32.
1986
Scholarly publications
De Boer, R. J., Michelson, S., & Hogeweg, P. (1986). Concomitant immunization by the fully antigenic counterparts prevents modulated tumor cells from escaping cellular immune elimination. Journal of Immunology, 136(11), 4319-4327.
De Boer, R. J., & Hogeweg, P. (1986). Interactions between macrophages and T-lymphocytes: Tumor sneaking through intrinsic to helper T cell dynamics. Journal of Theoretical Biology, 120(3), 331-351.
1985
Scholarly publications
De Boer, R. J., Hogeweg, P., & Dullens, H. F. J. (1985). Macrophage T lymphocye interactions in the anti-tumor immune response: A mathematical model. Journal of Immunology, 134(4), 2748-2758.
Hogeweg, P., & Hesper, B. (1985). Socioinformatic processes: MIRROR modelling methodology. Journal of Theoretical Biology, 113(2), 311-330.
De Boer, R. J., & Hogeweg, P. (1985). Tumor escape from immune elimination: simplified precursor bound cytotoxicity models. Journal of Theoretical Biology, 113(4), 719-736. https://doi.org/10.1016/S0022-5193(85)80189-2
1984
Scholarly publications
Hogeweg, P., & Hesper, B. (1984). The alignment of sets of sequences and the construction of phyletic trees: An integrated method. Journal of Molecular Evolution, 20(2), 175-186.
Hogeweg, P., & Konings, D. A. M. (1984). U1 snRNA: The evolution of its primary and secondary structure. Journal of Molecular Evolution, 21(4), 323-333. https://doi.org/10.1007/BF02115650