Paulien Hogeweg

Summary

Affiliation: Utrecht University
Country: The Netherlands

Publications

  1. doi request reprint Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability
    Paulien Hogeweg
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Adv Exp Med Biol 751:195-224. 2012
  2. pmc RNA silencing can explain chlorotic infection patterns on plant leaves
    Marian A C Groenenboom
    Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Syst Biol 2:105. 2008
  3. pmc The dynamics and efficacy of antiviral RNA silencing: A model study
    Marian A C Groenenboom
    Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Syst Biol 2:28. 2008
  4. pmc The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation
    Kirsten H W J Ten Tusscher
    Department of Scientific Computing, Simula Research Laboratory, 1325 Lysaker, Norway
    BMC Evol Biol 9:159. 2009
  5. pmc Eco-evolutionary dynamics, coding structure and the information threshold
    Folkert K de Boer
    Utrecht University, Netherlands
    BMC Evol Biol 10:361. 2010
  6. pmc The roots of bioinformatics in theoretical biology
    Paulien Hogeweg
    Theoretical Biology and Bioinformatics Group, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 7:e1002021. 2011
  7. pmc Evolution of evolvability in gene regulatory networks
    Anton Crombach
    Theoretical Biology and Bioinformatics Group, Utrecht University, The Netherlands
    PLoS Comput Biol 4:e1000112. 2008
  8. ncbi request reprint The role of complex formation and deleterious mutations for the stability of RNA-like replicator systems
    Nobuto Takeuchi
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    J Mol Evol 65:668-86. 2007
  9. ncbi request reprint The role of mutational dynamics in genome shrinkage
    Milan J A van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Mol Biol Evol 24:2485-94. 2007
  10. ncbi request reprint Metabolic adaptation after whole genome duplication
    Milan J A van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Mol Biol Evol 26:2441-53. 2009

Detail Information

Publications29

  1. doi request reprint Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability
    Paulien Hogeweg
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Adv Exp Med Biol 751:195-224. 2012
    ..Is it also what did happen in biological evolution? I will discuss some data that suggest that it did. In any case, these results provide us with novel search images to tackle the wealth of biological data...
  2. pmc RNA silencing can explain chlorotic infection patterns on plant leaves
    Marian A C Groenenboom
    Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Syst Biol 2:105. 2008
    ..These results strongly indicate that the interaction between virus growth and RNA silencing plays a role in the formation of infection patterns on leaves. However, how RNA silencing leads to the intricate patterns is not known...
  3. pmc The dynamics and efficacy of antiviral RNA silencing: A model study
    Marian A C Groenenboom
    Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Syst Biol 2:28. 2008
    ..Mathematical modeling is important to provide insight in the complicated pathway of RNA silencing. RNA silencing is an RNA based mechanism that is widely used by eukaryotes to fight viruses, and to control gene expression...
  4. pmc The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation
    Kirsten H W J Ten Tusscher
    Department of Scientific Computing, Simula Research Laboratory, 1325 Lysaker, Norway
    BMC Evol Biol 9:159. 2009
    ..The organisms compete in a multi-niche environment, imposing selection for phenotypic differentiation...
  5. pmc Eco-evolutionary dynamics, coding structure and the information threshold
    Folkert K de Boer
    Utrecht University, Netherlands
    BMC Evol Biol 10:361. 2010
    ..In this setup, where both the ecosystem and the individual genomes can evolve their structure, we study how populations cope with high mutation rates and accordingly how the information threshold might be alleviated...
  6. pmc The roots of bioinformatics in theoretical biology
    Paulien Hogeweg
    Theoretical Biology and Bioinformatics Group, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 7:e1002021. 2011
    ..In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging...
  7. pmc Evolution of evolvability in gene regulatory networks
    Anton Crombach
    Theoretical Biology and Bioinformatics Group, Utrecht University, The Netherlands
    PLoS Comput Biol 4:e1000112. 2008
    ..In other words, evolution in an alternating environment leads to a network that is sensitive to a small class of beneficial mutations, while the majority of mutations remain neutral: an example of evolution of evolvability...
  8. ncbi request reprint The role of complex formation and deleterious mutations for the stability of RNA-like replicator systems
    Nobuto Takeuchi
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    J Mol Evol 65:668-86. 2007
    ..Furthermore, we investigate the effect of deleterious mutations. Surprisingly, high mutation rates can weaken the exploitation of the catalyst by the parasite...
  9. ncbi request reprint The role of mutational dynamics in genome shrinkage
    Milan J A van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Mol Biol Evol 24:2485-94. 2007
    ..aphidicola can be explained by the clustering of genes in operons. Therefore, we show that selection has little effect on the clustering of deleted genes after the WGD in yeast, while it has during genome shrinkage in B. aphidicola...
  10. ncbi request reprint Metabolic adaptation after whole genome duplication
    Milan J A van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Mol Biol Evol 26:2441-53. 2009
    ..This explains why WGD, while pivotal in the evolution of many lineages and an apparent "easy" genetic operator, occurs relatively rarely...
  11. pmc Evolution of complexity in RNA-like replicator systems
    Nobuto Takeuchi
    Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Biol Direct 3:11. 2008
    ..Therefore, to obtain a more complete picture of the evolution of complexity, we must study the evolution of both information and organization...
  12. pmc The effect of stochasticity on the lac operon: an evolutionary perspective
    Milan van Hoek
    Theoretical Biology Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 3:e111. 2007
    ..Moreover, we demonstrate that in silico evolution in a quantitative model, by mutating the parameters of interest, is a promising way to unravel the functional properties of biological systems...
  13. pmc The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription
    Nobuto Takeuchi
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    Biol Direct 3:33. 2008
    ..Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement...
  14. pmc Phenotypic error threshold; additivity and epistasis in RNA evolution
    Nobuto Takeuchi
    Theoretical Biology Bioinformatics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Evol Biol 5:9. 2005
    ..A previous study formulated the error threshold in terms of phenotypes, and their results showed that a rather low degree of mutational neutrality can increase the error threshold unlimitedly...
  15. pmc Coevolution of gene families in prokaryotes
    Otto X Cordero
    Theoretical Biology and Bioinformatics, University of Utrecht, 3584 CH Utrecht, The Netherlands
    Genome Res 18:462-8. 2008
    ..3) "Long-range" coevolutionary relationships, caused mostly by large family expansions or contractions, reveal high-level evolutionary organization of cellular processes in prokaryotes...
  16. pmc Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability
    Kirsten H Ten Tusscher
    Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 7:e1002208. 2011
    ..Finally, we observe that, as a free side effect of evolving segmentation and differentiation in combination, we obtained in-silico developmental mechanisms resembling mechanisms used in vertebrate development...
  17. pmc Less can be more: RNA-adapters may enhance coding capacity of replicators
    Folkert K de Boer
    Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
    PLoS ONE 7:e29952. 2012
    ..Protocells can successfully use RNA-adapters to modify their genotype-phenotype mapping in order to enhance the coding capacity of their genome and fit more information on smaller sized genomes...
  18. pmc The impact of long-distance horizontal gene transfer on prokaryotic genome size
    Otto X Cordero
    Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8 3584 CH, Utrecht, The Netherlands
    Proc Natl Acad Sci U S A 106:21748-53. 2009
    ....
  19. ncbi request reprint Feed-forward loop circuits as a side effect of genome evolution
    Otto X Cordero
    Department of Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands
    Mol Biol Evol 23:1931-6. 2006
    ..The mechanism here proposed and the analysis of the yeast data show that regulator duplication could have played an important role in FFL evolution...
  20. pmc Gene duplications contribute to the overrepresentation of interactions between proteins of a similar age
    Like Fokkens
    Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
    BMC Evol Biol 12:99. 2012
    ..There are several theories explaining this phenomenon, but despite the importance of gene duplication in genome evolution, none consider protein family dynamics as a contributing factor...
  21. ncbi request reprint Chromosome rearrangements and the evolution of genome structuring and adaptability
    Anton Crombach
    Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan, Utrecht, The Netherlands
    Mol Biol Evol 24:1130-9. 2007
    ..In other words, our model provides a "proof of principle" that genomes can structure themselves in order to increase the beneficial effect of chromosome rearrangements...
  22. pmc Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization
    Nobuto Takeuchi
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 5:e1000542. 2009
    ..Different multilevel selection mechanisms can produce a difference in the long-term evolutionary trend of identical microscopic entities...
  23. pmc Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining
    Thomas D Cuypers
    Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
    Genome Biol Evol 4:212-29. 2012
    ..We propose that the complex genotype to phenotype mapping in virtual cells as well as in their biological counterparts drives genome size dynamics, due to an emerging interplay between adaptation, neutrality, and evolvability...
  24. pmc Evolution of resource cycling in ecosystems and individuals
    Anton Crombach
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    BMC Evol Biol 9:122. 2009
    ..In this study, our basic questions are how does a community evolve its resource usage and how are resource cycles partitioned?..
  25. pmc A synergism between adaptive effects and evolvability drives whole genome duplication to fixation
    Thomas D Cuypers
    Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands
    PLoS Comput Biol 10:e1003547. 2014
    ..Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change. ..
  26. ncbi request reprint Auxin transport is sufficient to generate a maximum and gradient guiding root growth
    Verônica A Grieneisen
    Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
    Nature 449:1008-13. 2007
    ..Directional permeability and diffusion can fully account for stable auxin maxima and gradients that can instruct morphogenesis...
  27. pmc Is RNA-dependent RNA polymerase essential for transposon control?
    Anton Crombach
    Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    BMC Syst Biol 5:104. 2011
    ..Hence two important questions are: is RdRP truly a necessary component for transposon control, and are the alternative RNA-based strategies also capable of controlling transposable elements?..
  28. pmc Moving forward moving backward: directional sorting of chemotactic cells due to size and adhesion differences
    Jos Käfer
    Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
    PLoS Comput Biol 2:e56. 2006
    ..The mechanisms we describe can easily be overlooked in studies of differential cell movement, hence certain experimental observations may be misinterpreted...
  29. ncbi request reprint Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome
    Can Kesmir
    Theoretical Biology Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Immunogenetics 55:437-49. 2003
    ..Thus, our analysis provides evidence that the immunoproteasome has co-evolved with the major histocompatibility complex to optimize antigen presentation in vertebrate cells...