Paulien Hogeweg
Encyclopedia
Paulien Hogeweg is a Dutch
theoretical biologist and complex system
s researcher studying biological systems as dynamic information processing systems at many interconnected levels. Together with Ben Hesper she coined the term Bioinformatics
in 1978 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.
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.
s 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
.
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, which is now common practice in sequence alignment and phylogeny.
At about the same time she pioneered folding algorithms for predicting RNA secondary
structures. RNA folding was also introduce to allow for a non-linear genotype to phenotype mapping to study evolution on complex fitness landscape
s
.
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.
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.
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
. 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.
Dutch people
The Dutch people are an ethnic group native to the Netherlands. They share a common culture and speak the Dutch language. Dutch people and their descendants are found in migrant communities worldwide, notably in Suriname, Chile, Brazil, Canada, Australia, South Africa, New Zealand, and the United...
theoretical biologist and complex system
Complex system
A complex system is a system composed of interconnected parts that as a whole exhibit one or more properties not obvious from the properties of the individual parts....
s researcher studying biological systems as dynamic information processing systems at many interconnected levels. Together with Ben Hesper she coined the term Bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
in 1978 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
Oxford English Dictionary
The Oxford English Dictionary , published by the Oxford University Press, is the self-styled premier dictionary of the English language. Two fully bound print editions of the OED have been published under its current name, in 1928 and 1989. The first edition was published in twelve volumes , and...
. In her research she stands out as a pioneer, being the first to develop new concepts and computational approaches in various areas of biology.
Biography
Paulien Hogeweg founded the Theoretical Biology & Bioinformatics groupat Utrecht University
Utrecht University
Utrecht University is a university in Utrecht, Netherlands. It is one of the oldest universities in the Netherlands and one of the largest in Europe. Established March 26, 1636, it had an enrollment of 29,082 students in 2008, and employed 8,614 faculty and staff, 570 of which are full professors....
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
Pattern formation
The science of pattern formation deals with the visible, orderly outcomes of self-organisation and the common principles behind similar patterns....
and pattern recognition
Pattern recognition
In machine learning, pattern recognition is the assignment of some sort of output value to a given input value , according to some specific algorithm. An example of pattern recognition is classification, which attempts to assign each input value to one of a given set of classes...
.
The first part of her scientific career she collaborated intensively with Ben Hesper.
Research
Starting with asynchronous extensions of L-systemL-system
An L-system or Lindenmayer system is a parallel rewriting system, namely a variant of a formal grammar, most famously used to model the growth processes of plant development, but also able to model the morphology of a variety of organisms...
s 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
.
This type of research later became popular in artificial life
Artificial life
Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...
.
When the first biological sequence data became available (from the EMBL) she developed a tree based algorithm
for multiple sequence alignment, which is now common practice in sequence alignment and phylogeny.
At about the same time she pioneered folding algorithms for predicting RNA secondary
structures. RNA folding was also introduce to allow for a non-linear genotype to phenotype mapping to study evolution on complex fitness landscape
Fitness landscape
In evolutionary biology, fitness landscapes or adaptive landscapes are used to visualize the relationship between genotypes and reproductive success. It is assumed that every genotype has a well-defined replication rate . This fitness is the "height" of the landscape...
s
.
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.
She pioneered the use of cellular automata for studying spatial ecological and evolutionary processes and demonstrated that spatial pattern formation
Pattern formation
The science of pattern formation deals with the visible, orderly outcomes of self-organisation and the common principles behind similar patterns....
can revert evolutionary selection pressures.
Extending the Cellular Potts model
Cellular Potts model
The cellular Potts model is a lattice-based computational modeling method to simulate the collective behavior of cellular structures. Other names for the CPM are extended large-q Potts model and Glazier and Graner model...
(CPM) to study morphogenesis and development
she modeled the complete life cycle of Dictyostelium discoideum
Dictyostelium discoideum
Dictyostelium discoideum is a species of soil-living amoeba belonging to the phylum Mycetozoa. D. discoideum, commonly referred to as slime mold, is a eukaryote that transitions from a collection of unicellular amoebae into a multicellular slug and then into a fruiting body within its lifetime. D...
using
simple rules for chemotaxis and differential adhesion
. 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.