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Thesis

• Evolution of Metabolism in a graph-based Toy-Universe

Papers

• In Silico Evolution of Early Metabolism
  Alexander Ullrich, Christoph Flamm, Markus Rohrschneider and Peter F. Stadler
  Artificial Life (MIT Press), Spring 2011, Vol. 17, No. 2, Pages 87-108
  
  
• Visual Network Analysis of Dynamic Metabolic Pathways
  Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, and Gerik Scheuermann
  6th International Symposium, ISVC 2010, Las Vegas, NV, USA
  Advances in Visual Computing, LNCS 6453
  
  
• In Silico Evolution of Early Metabolism
  Alexander Ullrich, Christoph Flamm, Markus Rohrschneider and Peter F. Stadler
  ALIFE XII, 2010
  Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, pp.57-64, MIT Press, 2010.
  
  
• Evolution of Metabolic Networks: A Computational Framework
  Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider,Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker and Peter F. Stadler
  Journal of Systems Chemistry, 2010, 1/1/4
  
  
• k-PathA: k-shortest Path Algorithm
  Alexander Ullrich and Christian V. Forst
  In Proceedings of High Performance Computational Systems Biology (HiBi 2009), pp. 23-30, IEEE Computer Society, 2009.
  
• A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms
  Alexander Ullrich and Christoph Flamm
  European Conference on Artificial Life, ECAL 2009
  ECAL, LNCS/LNAI 5777/5778
  
  
• Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe
  Alexander Ullrich and Christoph Flamm
  Computational Methods in Systems Biology, 6th International Conference, CMSB 2008, Proceedings: 23-48
  CMSB, LNCS/LNBI 5307
  
  BibTex

Abstracts

• Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms
  Alexander Ullrich, Christoph Flamm and Lukas Endler
  Artificial Life XI, Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems: 813
  BibTex

Posters

• Robustness, Flexibility and Modularity in Complex Biological Systems.
  14. Biotechnologietag, Dresden (D) 2011
• In Silico Evolution of early Metabolism.
  Multi-scale dynamics and evolvability of biological networks, MPI Workshop, Leipzig (D) 2010
• From the evolution of metabolic pathways to the emergence of complex properties.
  VW Project Meeting, Berlin (D) 2009
• Metabolic Pathway Analysis in Studying Evolution of Metabolism and the Emergence of Network Properties
  ICSB, Gothenburg (SWE) 2008
• Evolution of Metabolism in a Graph-based Toy-Universe
  ISMB, Toronto (CA) 2008

Talks

• Robustness and Modularity in Metabolic Networks.
  TBI Winterseminar, Bled (SLO) 2011
• In Silico Evolution of early Metabolism. (the long story)
  JCB Seminar, Jena (D) 2010
• In Silico Evolution of early Metabolism.
  ALIFE XII, Odense (DK) 2010
• Analysis of Metabolic Networks: Structure, Properties, Visualization
  TBI Winterseminar, Bled (SLO) 2010
• Evolution and Analysis of Metabolic Networks
  IZBI Herbstseminar, Studeny (CZ) 2009
• k-PathA: k-shortest Path Algorithm
  HiBi, Trento (IT) 2009
• A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms
  ECAL, Budapest (HU) 2009
• A new simulation approach: going metabolic
  IZBI Herbstseminar, Studeny (CZ) 2008
• Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe
  CMSB, Warnemuende (D) 2008
• Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms
  Artificial Life XI, Winchester (UK) 2008
• The binary Null-Space-Approach
  IZBI Herbstseminar, Studeny (CZ) 2007

Protocolls

• non-coding RNA's in teleost fish
  Martin Horn and Alexander Ullrich
• Conserved RNA secondary structure of spumaretrovirae
  Ronny Lorenz and Alexander Ullrich