Paulien Hogeweg

Paulien Hogeweg
Born 1943
Nationality Dutch
Fields theoretical biologist
Institutions Utrecht University
Known for coined the term Bioinformatics in 1978

Paulien Hogeweg (born 1943) is a Dutch theoretical biologist and complex systems researcher studying biological systems as dynamic information processing systems at many interconnected levels. Together with Ben Hesper she coined the term Bioinformatics in 1978 [1][2] as the study of informatic processes in biotic systems. The first use of this now so popular term was identified by the Oxford English dictionary. In her research she stands out as a pioneer, being the first to develop new concepts and computational approaches in various areas of biology.

Contents

Biography

Paulien Hogeweg founded the Theoretical Biology & Bioinformatics group at Utrecht University in 1977 and has been its group leader until 2009. She graduated from the University of Amsterdam in 1969 and received her PhD at Utrecht University in 1976 on the thesis "Topics in Biological Pattern Analysis" on biological pattern formation and pattern recognition. The first part of her scientific career she collaborated intensively with Ben Hesper.

Research

Starting with asynchronous extensions of L-systems she pioneered agent-based modeling studying development of social structure in animal societies, using the opportunity based "ToDo" principle where agents "do what there is to do", and a "DoDom" principle for dominance ranking also known as the winner-loser effect .[3] This type of research later became popular in artificial life.

When the first biological sequence data became available (from the EMBL) she developed a tree based algorithm for multiple sequence alignment,[4] which is now common practice in sequence alignment and phylogeny. At about the same time she pioneered folding algorithms for predicting RNA secondary structures.[5] RNA folding was also introduce to allow for a non-linear genotype to phenotype mapping to study evolution on complex fitness landscapes .[6]

The first phase-phase trajectory of a chaotic attractor in an ecological food-chain model of three differential equations appeared long before chaos became popular.[7] She pioneered the use of cellular automata for studying spatial ecological and evolutionary processes and demonstrated that spatial pattern formation can revert evolutionary selection pressures.[8]

Extending the Cellular Potts model (CPM) to study morphogenesis and development she modeled the complete life cycle of Dictyostelium discoideum using simple rules for chemotaxis and differential adhesion .[9] This CPM approach is now used for modeling in various areas of developmental biology, and the migration of immune cells in lymphoid tissues. Finally the CPM is used for EvoDevo research.

Current work is on gene regulation networks, prebiotic evolution and properties of fitness landscapes of RNA replicators.

References

  1. ^ Hogeweg, P. (1978). "Simulating the growth of cellular forms". Simulation 31 (3): 90–96. doi:10.1177/003754977803100305.  edit
  2. ^ Hogeweg, P. (2011). Searls, David B.. ed. "The Roots of Bioinformatics in Theoretical Biology". PLoS Computational Biology 7 (3): e1002021. Bibcode 2011PLSCB...7E0020H. doi:10.1371/journal.pcbi.1002021. PMC 3068925. PMID 21483479. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3068925.  edit
  3. ^ Hogeweg, P. and B. Hesper (1985) Socioinformatic processes, a MIRROR modelling methodology. J Theor Biol 113: 311-330; Hogeweg, P. and B. Hesper (1983) The ontogeny of the interaction structure in BumbleBee colonies: a MIRROR model. Behav Ecol Sociobiol 12: 271-283.
  4. ^ Hogeweg, P. and B. Hesper B. (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20: 175-186.
  5. ^ Hogeweg, P. and B. Hesper (1984) Energy directed folding of RNA sequences. NAR 12: 67-74.
  6. ^ Huynen, M.A. and Hogeweg, P. (1994) Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes. J Mol Evol 39:71-79; Konings, D.A.M. and P. Hogeweg (1989) Pattern analysis for RNA secondary structure. Similarity and consensus of minimal-energy folding. J Mol Biol 207: 596-614.
  7. ^ Hogeweg, P. and Hesper, B. (1978) Interactive instruction on population interactions. Comput Biol Med 8:319-27.
  8. ^ Boerlijst M.A. and Hogeweg P. (1991) Spiral wave structure in pre-biotic evolution: Hypercycles stable against parasites. Physica D 48:17-28; Hogeweg, P. and B. Hesper (1981a) Two predators and a prey in a patchy environment: An application of MICMAC modelling. J Theor Biol 93: 411-432.
  9. ^ Maree A.F.M. & Hogeweg P. (2001) How amoeboids self-organize into a fruiting body: Multicellular coordination in Dictyostelium discoideum. Proc Natl Acad Sci USA 98: 3879-3883; Savill, N.J. and Hogeweg, P. (1997) Modeling morphogenesis: from single cells to crawling slugs. J Theor Biol 184: 229-235.

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