Paulien_HogewegProf. Dr. Paulien Hogeweg
Theoretical Biology and Bioinformatics Group
Faculty of Science, Utrecht University
Kruytgebouw, room Z530
Padualaan 8
3584 CH  Utrecht
The Netherlands
Tel. +31-(0)30-253 3692
Fax +31-(0)30-253 3655
e-mail: p.hogeweg@uu.nl

Curriculum Vitae

Paulien Hogeweg studied biology at the University of Amsterdam. She performed her graduate studies in Utrecht and received her PhD in1976. She coined the term Bioinformatics for the study of informatic processes in biotic systems and has headed her own research group in this area since 1976. In 1991 she became full professor at the Theoretical Biology and Bioinformatics Group at the Department of Biology at Utrecht University. Since 2009 she is honorary professor in this group.

Research summary

The aim of our research is to understand biotic systems as dynamic information processing systems at many interconnected levels. To this end we develop and use large scale computational modeling approaches.  We apply this work concept in various area’s of biology:  e.g. intracellular regulation, development,  behavior, ecology. In all these area’s we focus on the role of spatial pattern formation and other emergent properties. Research projects in all these area’s are available. Currently the main focus is on multilevel evolution, a part of the emerging field of evolutionary systems biology.

Ever since Darwin, most evolutionary theory has considered a direct coupling between mutations and changes in phenotypic traits on which selection takes place. This is obviously a simplification as the transformation between genomes and phenotypes is very complex, non-linear and multi-layered. Moreover this transformation is  of course a product of evolution, as is the genome structure itself. We investigate the (evolutionary)  consequences of this complex genotype phenotype mapping, as well as its evolution.

We do this by investigating generic properties of Darwinian evolution in in silico systems which are defined in such a way that evolution can shape the the genome structure and the genotype-phenotype mapping. We have shown that given enough degrees of freedom, evolution leads to long term information integration, and thereby to e.g. evolution of evolvability.  Our models shed light on many surprising features of biological evolution, such as the large ancestral genomes gleaned from phylogenetic reconstruction, elucidate the role of whole genome duplication in adaptation to changing environments and as a source of complexity,  and debug long held assumption on the structure of regulatory networks.

The primary aim of our research is to elucidate these fundamental biological processes. However our approaches also contribute to technological applications of artificial evolution.

For more information, visit the group website at http://www-binf.bio.uu.nl/ph/

Lab members

Technical support
Jan Kees van Amerongen – j.k.van Amerongen@uu.nl

Ph.D. students
Thomas Cuypers – thomas.cuypers@gmail.com
Bram van Dijk – bramvandijk88@gmail.com

Publications

Cuypers TD, Rutten JP, Hogeweg P. Evolution of evolvability and phenotypic plasticity in virtual cells. BMC Evol Biol. 2017 Feb 28;17(1):60. doi: 10.1186/s12862-017-0918-y.

van Dijk B, Hogeweg P. In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility. Genome Biol Evol. 2015 Dec 28;8(1):176-88. doi: 10.1093/gbe/evv255.

Hogeweg P. Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. Adv Exp Med Biol. 2012;751:195-224. Review. PubMed PMID: 22821460.

Takeuchi N, Hogeweg P. Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life. Phys Life Rev. 2012 Sep;9(3):219-63. doi: 10.1016/j.plrev.2012.06.001. Epub 2012 Jun 13. PubMed PMID: 22727399; PubMed Central PMCID: PMC3466355.

Hogeweg P. The roots of bioinformatics in theoretical biology. PLoS Comput Biol. 2011 Mar;7(3):e1002021. Epub 2011 Mar 31. PubMed PMID: 21483479; PubMed Central PMCID: PMC3068925.