Załącznik
do Komunikatu Dziekana w sprawie dodatkowej rekrutacji na studia doktoranckie
w ramach międzynarodowego programu KNOW „Poznańskie Konsorcjum RNA”
na Wydziale Biologii Uniwersytetu im. Adama Mickiewicza w Poznaniu
Projekt rozprawy doktorskiej
planowanej do realizacji w ramach międzynarodowego programu studiów
doktoranckich KNOW „Poznańskie Konsorcjum RNA” w latach 2015-2018
na Wydziale Biologii Uniwersytetu im. Adama Mickiewicza w Poznaniu
1. Wnioskodawca (kierownik projektu): dr hab. Borys Wróbel
2. Tytuł projektu: Ewoluujące sztuczne sieci regulacji genowej inspirowane biochemią w świecie
RNA (Evolving artificial gene networks inspired by RNA world biochemistry)
3. Dyscyplina naukowa (właściwą podkreślić): biologia, biochemia, biotechnologia
4. Krótki opis projektu w j. angielskim (maksymalnie 1 strona; Autorzy zakwalifikowanych projektów
zostaną poproszeni o przygotowanie streszczeń w j. angielskim oraz j. polskim, które zostaną zamieszczone
na stronie internetowej Wydziału Biologii):
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. Źródła finansowania badań w ramach proponowanego projektu rozprawy doktorskiej
(wskazać źródło finansowania, okres i miejsce realizacji, charakter udziału w projekcie oraz budżet
projektu):
Dodatkowe finansowanie będzie możliwe dzięki projektom Biomerge (NCN Opus ST6; od
2012-08-31 do 2015-08-30, wniosek o przedłużenie do 2016-08-30; 586 950 zł) i EvoSN
(NCN Harmonia ST6; od 2013-10-09 do 2016-10-08 , wniosek o przedłużenie do 2017-1008, 643 500 zł)
6. Lista najlepszych publikacji kierownika projektu z ostatnich 5 lat (5 publikacji wraz ze
wskaźnikiem oddziaływania i liczbą cytowań).
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: 0,745; liczba cytowań 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.