Annex
to the Dean’s announcement on the recruitment of candidates
for the international PhD program of KNOW „RNA Research Centre in Poznań”
at the Faculty of Biology of the Adam Mickiewicz University in Poznań
The description of a PhD research project at the graduate school of
KNOW RNA Research Centre in Poznań at
the Faculty of Biology of Adam Mickiewicz University, for years 2015-2018
1. Project leader: Borys Wróbel, PhD, Habil
2. Project title: Evolving artificial gene networks inspired by RNA world biochemistry
3. Scientific discipline: biology, biochemistry, biotechnology
4. Short description in English:
Biologically inspired computation is a discipline of science and engineering that aims to understand
and build complex systems using computational methods based on the design principles found in
nature. One such inspiration is the way regulatory interactions between genes in biological cells
control the behaviour of the cell; this inspiration stands behind artificial genetic networks (AGNs) or
artificial gene regulatory networks (aGRNs). Computationally, these devices are similar to artificial
neural networks and cellular automata; the differences lie in the details, affecting mostly the
connectivity of the networks, and how this connectivity is determined---in the case of AGNs, usually
through a process based on biological evolution.
A well known fact in the field, if perhaps little advertised, is that AGNs, in contrast to known natural
genetic networks appear to be much more connected. High density of connections result in high
computational costs of calculating the state of the system over time, which limits the practical
applicability of these computational devices. It is less obvious if there are any computational tasks
which are difficult to accomplish with AGNs with high connectivity.
Most existing AGN models draw their inspirations from the way protein-coding genes are regulated by
proteins. This project will aim to follow closer the idealised and hypothetical biochemistry of preprotein/pre-DNA protocells, in which one large RNA molecule will be responsible for storing the
genetical information and small RNA molecules will play the regulatory and functional roles. We will
investigate how closer---although strict abstract---following of the biological inspiration in which the
regulatory relations depend on hybridization of a small number of molecules, and in which the large
molecules evolve by point mutations of discrete elements (‘nucleotides’) and splicing the RNA
strands, will affect the connectivity and the computational properties of the evolved complex systems.
A successful PhD candidate will need programming skills (C++, Matlab or R), and can have
background in bioinformatics, computer science or other computational disciplines (mathematics,
physics).
5. Source of funding for the research project.
Additional funding will be provided through projects Biomerge (NCN Opus ST6; from 2012-08-
31 till 2015-08-30, application for extension till 2016-08-30; 586 950 zł) i EvoSN (NCN
Harmonia ST6; from 2013-10-09 till 2016-10-08 , application for extension till 2017-10-08,
643 500 zł)
6. 5 selected papers of the project leader from last 5 years.
Joachimczak M., Wróbel B. (2009) Complexity of the search space in a model of artificial
evolution of gene regulatory networks controlling 3D multicellular development. Adv.
Complex Syst., 12, 347-369. [IF 2011: 0.74, citations in WoS: 2]
Joachimczak M., Wróbel B. (2009) Evolution of the morphology and patterning of artificial
embryos: scaling the tricolour problem to the third dimension. Lecture Notes in
Computer Science, 5777, 33-41.
Joachimczak, M., Wróbel, B. (2012). Co-evolution of morphology and control of soft-bodied
multicellular animats. In Soule, T. et al., editors, Proceedings of the Fourteenth
International Conference on Genetic and Evolutionary Computation, GECCO '12, strony
561-568, New York, NY, USA. ACM.
Joachimczak B., Wróbel B. (2012) Evolution of robustness to damage in artificial 3dimensional development. BioSystems, 109, 498-505. [IF 1,497; cytowania WoS: 2]
Joachimczak, M., Kowaliw, T., Doursat, R., Wróbel, B. (2012). Brainless bodies:
Controlling the development and behavior of multicellular animats by gene regulation
and diffusive signals. In Adami, C., Bryson, D. M., Ofria, C., and Pennock, R. T., editors,
Artificial Life XIII: Proceedings of the Thirteenth International Conference on the
Simulation and Synthesis of Living Systems, strony 349-356, Cambridge, MA. MIT
Press.