Akos Dobay

Link to Research Group page (Prof. Dr. Barbara König)

Research Interests

I studied theoretical physics at the University of Lausanne where I did my Ms dissertation «On Supersymmetric Extensions of Poincaré Lie Superalgebra» with Jean-Jacques Loeffel and my PhD dissertation on «Physical and statistical properties of random knots» with Jacques Dubochet and Andrzej Stasiak. Together with Nicolas Monod, I also founded a book series, Arkhaï,  during my studies.

My current duties include research in forensic molecular genetics, supervision of master students, big data management and high-performance computing.

For students, I give a lecture series entitled Interdisciplinary Research Methods in Computational Biology.

Students

  • Tobias Wechsler (Master Student)

Tobias explores the intricate dynamics of bacteria engaged in cooperative behavior in silico. This work is done together with the group of Rolf Kümmerli. For additional details on this project, please also visit his page.

Microbes share secreted beneficial metabolites (i.e. public goods) among community members. This type of cooperative behavior can be weakened by cheater microbes that do not invest in public goods production, but take advantage of them nevertheless. From an evolutionary perspective, it is puzzling to understand why cooperation can be observed nowadays even if it is not favored by natural selection.

Computer simulation
Artwork showing a computer simulation snapshot (disks of various sizes) superimposed on a fluorescence  image microscopy of  P. aeruginosa. Green are cooperator cells and purple are cheaters. Image taken by Konstanze Schiess.

It turns out that there are many loopholes in such a simplistic reasoning. Our in silico experiments, based on a custom-made simulation environment that can run on large clusters (see the article in the Scientific Computing World), show that cooperation can nicely flourish in the presence of cheaters under the right environmental conditions.

Furthermore, bacteria are able to evolve what we would qualify as policy mechanims that prevent the emergence of cheaters in the community. We are currently exploring this phenomenon.

CV

Education and Professional Positions

2015 - present Research Associate, Institute of Forensic Medicine, University of Zurich, Switzerland (Department of Forensic Genetics)
2013 - present Post-doctoral researcher, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland (Group of Prof. Dr. Barbara König)
2012 -2013 Post-doctoral researcher, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland (Group of Prof. Dr. Homayoun Bagheri)
2010 - 2011 Post-doctoral researcher, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland (Group of Dr. Daniel J. Rankin)
2006 - 2009 Post-doctoral researcher, Department of Biology II, Ludwig-Maximilians-University, Munich, Germany (Group of Prof. Dr. Heinrich Leonhardt)
2006 Max-Delbrück-Center (MDC) Fellow, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany (Group of Dr. Cristina Cardoso)
2005 - 2006 SNF fellow (Advanced Researcher) with Dr. Eduardo Mendoza, Experimental Physics, Ludwig-Maximilians-University (LMU), Munich, Germany (Chair: Prof. Joachim Rädler)
2005 SNF fellow (Advanced Researcher), Arnold Sommerfeld Zentrum für theoretische Physik, Ludwig-Maximilians-University (LMU), Munich, Germany (Chair: Prof. Dr. Erwin Frey)
2002 - 2004 First assistant (Oberassistent), Laboratory of Ultrastructural Analysis (LAU), University of Lausanne, Switzerland
2004 Guest researcher at the University of North Carolina at Charlotte (UNCC), USA (Inviting Professor: Prof. Dr. Yuanan Diao)
2003 Guest researcher at the University of Santa Barbara in California (UCSB), USA (Inviting Professor: Prof. Dr. Kenneth Millett)
1997 - 2003 Doctoral studies at the University of Lausanne, Laboratory of Ultrastructural Analysis (LAU), Department of Biology, Switzerland (Department head: Prof. Jacques Dubochet) PhD degree with Prof. Dr. Jacques Dubochet and Dr. Andrzej Stasiak: «Physical and Statistical Properties of Random Knots»
1992 - 1997 Academic studies at the University of Lausanne, Department of Physics, Switzerland Master in Physics with Prof. Dr. Jean-Jacques Loeffel: «On Supersymmetric Extensions of Poincaré Lie Superalgebra»

Selected Publications

  • Manjarrez-Casas A., Bagheri HC., Dobay A. (2016). Transition from one- to two-dimensional development facilitates maintenance of multicellularity. Royal Society Open Science, 3(9):1-11. DOI: 10.1098/rsos.160554
  • Dobay A., Pilo P., Lindholm A., Origgi F., Bagheri H., König B. (2015). Epizootic of tularemia in a closely-monitored, free-roaming population of wild house mice. PLoS ONE. DOI: 10.1371/journal.pone.0141103
  • König B., Lindholm AK., Lopes PC., Dobay A., Steinert S., Buschmann FJ-U. (2015). A system for automatic recording of social behavior in a free-living wild house mouse population. Animal Biotelemetry, 3(1):39. DOI: 10.1186/s40317-015-0069-0
  • Kümmerli R., Santorelli LA., Granato ET., Dumas Z., Dobay A., Griffin AS., West SA. (2015). Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa. Journal of Evolutionary Biology, 28(12):2264-2274. DOI: 10.1111/jeb.12508
  • Dobay A., Bagheri HC., Messina A., Kümmerli R., Rankin D. (2014). Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes. Journal of Evolutionary Biology, 27(9):1869-1877 (featured by Silicon Graphics: "University of Zurich Boosts Delivery of Ground-Breaking Research with SGI") DOI: 10.1111/jeb.12437
  • Schneider K., Fuchs C., Dobay A., Rottach A., Qin W., Wolf P., Alvarez-Castro JM., Nalaskowski MM., Kremmer E., Schmid V., Leonhardt H., Schermelleh L. (2013). Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling. Nucleic Acids Research, 41(9):4860-4876. DOI: 10.1093/nar/gkt191
  • Dobay A., Gall GEC., Rankin DJ. and Bagheri HC. (2013). Renaissance model of an epidemic with quarantine. Journal of Theoretical Biology, 317:348-358 (featured on the portal of the journal in a Special Issue on Epidemiology) DOI: 10.1016/j.jtbi.2012.10.002
  • Dobay MP., Dobay A., Bantang J. and Mendoza E. (2011). How many trimers? Modeling influenza virus fusion yields a minimum aggregate size of six trimers, three of which are fusogenic. Molecular Biosystems, 7(10):2741-2749. DOI: 10.1039/c1mb05060e
  • Rawdon E., Dobay A., Kern JC., Millett KC., Piatek M., Plunkett P., Stasiak A. (2008). Scaling Behavior and Equilibrium Lengths of Knotted Polymers. Macromolecules 41: 4444–4451. DOI: 10.1021/ma8000803
  • Siebrasse JP., Veith R., Dobay A., Leonhardt H., Daneholt B., Kubitscheck U. (2008). Discontinuous movement of mRNP particles in nucleoplasmic regions devoid of chromatin. PNAS 105: 20291-20296 (reviewed in Faculty of 1000 Prime by Yaron Shav-Tal and Yosef Gruenbaum). DOI: 10.1073/pnas.0810692105
  • Plunkett P., Piatek M., Dobay A., Kern JC., Millett KC., Stasiak A., Rawdon EJ. (2007). Total Curvature and Total Torsion of Knotted Polymers. Macromolecules 40: 3860-3867. DOI: 10.1021/ma0627673
  • Diao Y., Dobay A., Stasiak A. (2005). The Average Inter-crossing Number of Equilateral Random Walks and Polygons. Journal of Physics A: Math. Gen. 36: 7601-7616.
  • Diao Y., Dobay A., Kusner RB., Millett K., Stasiak A. (2003). The average crossing number of equilateral random polygons. J. Phys. A: Math. Gen. 36: 11561-11574 (IOP select). DOI: 10.1088/0305-4470/36/46/002
  • Dobay A., Millett KC., Sottas PE., Dubochet J., Stasiak A. (2003). Scaling behavior of random knots. PNAS 100: 5611-5615. DOI: 10.1073/pnas.0330884100
  • Dobay A., Sottas PE., Dubochet J., Stasiak A. (2001). Predicting the Optimal Lengths of Random Knots. Lett. Math. Phys. 55:239-247. DOI: 10.1023/A:1010921318473
  • Stasiak A., Dobay A., Dubochet J., Dietler G. (1999). Knotted Fishing Line, Covalent Bonds and Breaking Points. Science 286: 5437, 11. DOI: 10.1126/science.286.5437.11a

Book chapters:

  • Dobay A., Dobay MP. (2013). DDBJ genome resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay A., Dobay MP. (2013). EBI genome resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay MP., Dobay A. (2013). Metabolic disease resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay MP., Dobay A. (2013). Metagenomics resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay A., Dobay MP. (2013). NCBI Bioproject genome resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay MP., Dobay A. (2013). NCBI viral genomes resources. In Encyclopedia of Systems Biology, 1st ed. (Dubitzky W, Wolkenhauer O, Yokota H and Cho KH eds.). Springer-Verlag
  • Dobay A., Sottas PE., Dubochet J., Stasiak A. (2002). Bringing an Order into Random Knots. In Physical Knotting proceedings volume in the Contemporary Math series (J. A. Calvo, K. C. Millett, E. Rawdon eds.). AMS: 115-124

Transdisciplinary articles:

  • Acevedo-Rocha C., Yu J., Dobay A. (2010). Entgrenzung – Transcending boundaries across scientific disciplines. Arkhai 14: 23-40
  • Dobay A., van Toledo W. (2008). Informational processing of morphological and topological transitions in biology. Arkhai 13: 5-16