People >> Prof. Erich Bornberg-Bauer

	Name: Erich Bornberg-Bauer Status: Head of Division Email: e.bornberguni-muenster.de

• Full Professor, School of Biological Sciences, The Westfalian Wilhelms University of Münster, Germany, 2003 - present.
• Senior Lecturer, School of Biological Sciences, The University of Manchester, UK, 2000-2003
• Project Manager, EML GmbH, Heidelberg, Germany, 1998-2000
• Postdoctoral Research Associate, Theoretical Bioinformatics Group, German Cancer Research Centre, Heidelberg, Germany, 1996-1998
• Assistant Professor (Univ. Ass.), Numerical Mathematics, Institute of Mathematics, University of Vienna, Austria, 1994-1996
• PhD in Computational Theoretical Biochemistry, University of Vienna, Austria, 1995
• Diploma (equ. to MSc) in Biochemistry, University of Vienna, Austria, 1992
• Studies in Biochemistry, Physics and Mathematics, University of Vienna, Austria, 1981-1991

Current Teaching:

• Bioinformatics 1 (molecular evolution, protein structures)
• Bioinformatics 2 (sequence analysis, genome analysis)
• several specialised courses on molecular evolution and computational biology

Research areas:

• Phenotypic Transition in Molecular Evolution
• Evolution of Complex Cellular Networks
• Modular Evolution of Genes and Proteins
• Adaptive, Parallel and Convergent Genome Evolution

Publications

 [PubMed Publication list]

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• Wissler L. Godmann L, and E. Bornberg-Bauer
  The macroevolutionary fate of simple sequence repeats: a comparison across 12 Drosophila species
  submitted


• A.R. Reineke, E. Bornberg-Bauer and J. Gu
  Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes
  Nucleic Acids research (2011) Vol. 39, No. 14 6029–6043
  [Online access]



• January Weiner 3rd, Francois Beaussart, Erich Bornberg-Bauer
  Rapid similarity search of proteins using alignments of domain arrangements
  submitted






• The Atta Genome Working Group
  The Genome Sequence of the Leaf-cutter Ant Atta cephalotes Reveals Insights into its Obligate Symbiotic Lifestyle
  PLoS Genet 7(2): e1002007. doi:10.1371/journal.pgen.1002007
  [S14] [S17]
[Online access][Cover picture Atta cephalotes]


• L. Wissler, F.C. Codoner, T.B.H. Reusch, J.L. Olsen, G. Procaccini and E. Bornberg-Bauer
  Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
    BMC Evolutionary Biology (2011) 11 :8
  [Online access ]


• A.M. Ernst, B. Ruping, S.B. Jekat, S. Nordzieke, A.R. Reineke, B. Müller , E. Bornberg-Bauer, D. Prüfer and G.A. Noll
  The sieve element occlusion gene family in dicotyledonous plants 
  Plant Signaling & Behavior, V6 (2011)
  [Online access ]


• B. Ruping, A.M. Ernst, S.B. Jekat, S. Nordzieke, A.R. Reineke, B. Müller , E. Bornberg-Bauer, D. Prüfer and G.A. Noll
  Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants
  BMC Plant Biology,10:219 (2010)
  [Online access]


• A. Schueler and E. Bornberg-Bauer
  The Evolution of Protein Interaction Networks
  in:Data Mining in Proteomics (Ed: Martin Eisenacher, Michael Hamacher and Christian Stephan), SpringerLink (2010)
  [Online access][Request reprint]


•  E. Bornberg-Bauer
  Signals: Tinkering with Domains
  Science Signaling, 3:139 (2010)
  [Online access][Request reprint]


• E. Bornberg-Bauer and  L. Kramer
  Robustness Versus Evolvability: A Paradigm Revisited.
  HFSP J. Volume 4, Issue 3 (2010)
  [Online access]


• T. Chen, D. Vernazobres, T. Yomo, E. Bornberg-Bauer and H. S. Chan
  Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model
  Biophysical Journal  2010, 98:11, 2487-2496 
  [online access ]



• A. D. Moore and E. Bornberg-Bauer
  Protein domains as evolutionary units
  in: Evolutionary Genomics and Systems Biology, Ed. G. Caetano-Anollés (2010)
  John Wiley & Sons
  [Wiley online][Request reprint]


• E. Bornberg-Bauer, A.-K. Huylmans, and T. Sikosek
  How do new proteins arise?
  Current Opinion in Structural Biology. 20:1-7 (2010)
  [Online access][Request reprint]


• T. Sikosek and E. Bornberg-Bauer
  Evolution after and before gene duplication?
  In: Evolution after gene duplication (Ed. D. Liberles and K. Dittmar), Wiley-Blackwell, (2010).
  [Online access][Request reprint ]


• The Nasonia Genome Working Group
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
Science, 327:5963 (2010)
[Online access][Request reprint]



• L. Wissler; E. Dattolo; A. D. Moore; T. B. H. Reusch; J. L. Olsen; M. Migliaccio; E. Bornberg-Bauer; G. Procaccini
  Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.
  Database, Vol. 2009: doi:10.1093/database/bap2009 (2009)
  
[Online access][Request reprint]


• J. Weiner 3rd, A. D. Moore, E. Bornberg-Bauer
  Just how versatile are domains?
  
  BMC Evol Biol , 8:285-299 (2008)
  [Free online access]


• A. D. Moore*, A. K. Bjoerklund*, D. Ekman, E. Bornberg-Bauer and A. Elofsson
  Arrangements in the modular evolution of proteins
  Trends in Biochemical Sciences, 33(9): 444-451 (2008)
  * these authors contributed equally to this work
  [online access]


• D. Whitehead, C. Wilke, D. Vernazobres, E. Bornberg-Bauer
  The look-ahead effect of phenotypic mutations
  Biology Direct , 3:18 (2008)


• F. Friedrichs, L. Henckaerts, S. Vermaire, T. Kucharzik, T. Seehafer, M. Krull, E. Bornberg-Bauer, M. Stoll, J. Weiner
  Discovery of a caspase recruitment domain in the Crohn's disease susceptibility gene DLG5 by sequence comparison and phylogenies
  J. Mol. Med., 86(4):423-432. (2008)
  online access


• Falb Michaela, Mueller Kerstin, Koenigsmaier Lisa, Oberwinkler Tanja, Horn Patrick, Gronau Susanne von, Orland Gonzales, Pfeiffer Friedhelm, Bornberg-Bauer Erich, Oesterhelt Dieter
  Metabolism of Halophilic Archaea
  Extremophiles, 12:177-196 (2008)
  online access


• H. Schulenburg, M. Hoeppner, J. Weiner III, E. Bornberg-Bauer
  Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans
  Immunobiol., 213(3-4):237-250. (2008) 
  online access


• Thorsten BH Reusch*, Amelie S Veron*, Christoph Sapper, January Weiner, Lothar Wissler, Alfred Beck, Sven Klages, Michael Kube, Richard Reinhardt and Erich Bornberg-Bauer
  Comparative analysis of expressed sequence tag libraries in the seagrass Zostera marina subjected to temperature stress
  Marine Biotech., 10(3):297-309 (2008)
   [ Online access]
  * these authors contributed equally to this work


• Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG
  A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network.
  BMC Systems Biology, 1:34 (2007)
  [Online access]


• Francois Beaussart, January Weiner 3rd, Erich Bornberg-Bauer
  Automated Improvement of Domain ANnotations using context analysis of Domain Arrangements (AIDAN)
  Supplementary material
  Bioinformatics (2007)
   [Online access]








• R. Wroe, H.S. Chan and E. Bornberg-Bauer
  A Structural Model of Latent Evolutionary Potentials Underlying Neutral Networks in Proteins
  HFSP J.,1:79 (2007)
  [See the cover of this issue]
  Supplementary Material
  
  
  • Please also note a parallel article which observes basically the same phenomenon for the latent evolution of enzymatic function:
    G. Amitai, R.D. Gupta and Dan S. Tawfik
    Latent evolutionary potentials under the neutral mutational drift of an enzyme
    HFSP J., 1:67 (2007) 
  
  
  • A commentary on both papers can be found here:
    Mark A. DePristo
    The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity
    HFSP J.,1:94 (2007)


• J. Kilian, D. Whitehead, J. Horak, D. Wanke, S. Weinl, O. Batistic, C. D'Angelo, E. Bornberg-Bauer, J. Kudla and K. Harter
  The AtGenExpress global stress expression data set: Protocols, evoluation and model data analysis of UV-B light, drought and cold stress responses
  Plant J., 50(2): 347-63 (2007)
  [Online access]


• A. Veron, K. Kaufmann, E. Bornberg-Bauer
  Evidence of interaction network evolution by whole genome duplications: a case-study in MADS-box proteins
  Mol Biol Evol, 24: 670-678 (2007) [MBE abstract].


• G. Amoutzias, A. Veron, J. Weiner, M. Robinson-Rechavi, E. Bornberg-Bauer, S. Oliver, D. Robertson
  One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity
  Mol Biol Evol, 24: 827-835 (2007) [MBE abstract]


• A. Veron, D. Whitehead and E. Bornberg-Bauer 
  Studying the evolution of regulatory networks 
  in: Biological Networks, Ed. F. Kepes, World Scientific (invited)(2007)


• Amoutzias G.D., Bornberg-Bauer E., Oliver S.G. and Robertson D.L.
  Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network
  BMC Genomics, 7:107-117 (2006)
  [ Free online access ]


• Gerke M, X Jiang, E Bornberg-Bauer and G. Fuellen
  Finding Common Protein Interaction Patterns Across Organisms
  Evolutionary Bioinformatics Online, 2:45-52(2006)
  [ Free online access ]


• J. Weiner, F. Beaussart, E. Bornberg-Bauer
  Domain Deletions and Substitutions in the Modular Protein Evolution
  FEBS J. 2006, 273:2037-2047 (2006)
  [ Request electronic reprint ]


• J. Weiner and E. Bornberg-Bauer
  Evolution of Circular Permutations in Multi-Domain Proteins
  Molecular Biology and Evolution, 23(4): 734-743 (2006)
  [ Request reprint]


• E. Bornberg-Bauer and Amelie Veron
  Evolution of regulatory networks
  Genetics, Genomics, Proteomics and Bioinformatics John Wiley & Sons (invited) (2005)
  [ Online access ]
  [ Request manuscript ]


• Teichmann SA, Bornberg-Bauer E, Luscombe NM
  Transcriptional Networking
  Genome Biol., 6(9): 344-347  (2005)
  [ Online access ]


• Wroe R, E. Bornberg-Bauer and HS Chan
  Comparing folding codes in simple heteropolymer models of protein evolutionary landscapes: How robust is the superfunnel paradigm?
  Biophys. J., 88(1):118-31 (2005)
  [ Free online access ]
  
  
• Weiner J, G. Thomas and E. Bornberg-Bauer
  Rapid Motif-Based Prediction of Circular Permutations in Multi-Domain Proteins
  Bioinformatics, 21(7):932-937 (2005)
  [ Request reprint ]



• E. Bornberg-Bauer, F Beaussart, S Kummerfeld, S Teichmann and J Weiner
  The Evolution of Domain Arrangements in Proteins and Interaction Networks (Review)
  CLMS,  62(4):435-445  (2005)
  [ Request reprint ]


• Malonek S, Bomke C, Bornberg-Bauer E, Rojas MC, Hedden P, Hopkins P, Tudzynski B.
  Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex
  Phytochemistry , 66(11):1296-1311 (2005)
  [ Request electronic reprint ]


• Amoutzias G, J Weiner and E. Bornberg-Bauer
  Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs
  Gene 347, (2):247-253  (2005)
  [ Request electronic reprint ]


• Amoutzias G, DL Robertson, SG Oliver and E. Bornberg-Bauer
  Convergent Evolution of Gene Networks by single-gene duplication in higher eukaryotes
  EMBO Reports; 5:274-279 (2004)
  [ Free online access ]


• Amoutzias G and E. Bornberg-Bauer
  Evolution of protein-protein interaction networks in homo- and heterodimerisng eukaryotic transcription factors
  Comparative and Functional Genomics ; 5:79 - 84 (2004)
  [ Online access ]
  [ Request reprint ]


• Mabey JE, MJ Anderson, PF Giles, CJ Miller, TK Attwood, NW Paton, E. Bornberg-Bauer, GD Robson, SG Oliver and DW Denning
  CADRE: The Central Aspergillus Data REpository
  Nucleic Acids Res.; 32:D401-D405 (2004)
  [ Free online access ]


• Do JH, MJ Anderson, DW Denning and E. Bornberg-Bauer
  Computational identification of TCA and glyoxylate cycle in Aspergillus fumigatus
  Journal of Microbiology and Biotechnology ; 14:74-80 (2004)
  [ Request reprint ]


• Gerrard DG and E. Bornberg-Bauer
  doMosaic: Analysis of the mosaic-like domain architecture in proteins
  Informatica; 27: 15-20(2003)
  [ Request reprint ]


• Bornberg-Bauer E.
  Randomness, Structural Uniqueness, Modularity, and Neutral Evolution in Sequence Space of Model Proteins.
  Z. Phys. Chem., 216: 139 -154 (2002)
  [ Request reprint ]


• Cui Y., W.H. Wong, E. Bornberg-Bauer, and H.S. Chan
  Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes
  Proc. Natl. Acad. Sci.  USA, 99: 809 - 814 (2002)
  [ Online access ]
  [ Request reprint ]


• Sirava M, T Schäfer, M Eigelsperger, M Kauffman, O Kohlbacher, E. Bornberg-Bauer and HP Lenhof
  BioMiner - Modeling, Analyzing and Visualizing Biochemical Pathways and Networks
  Bioinformatics; 18(S):219-230 (2002) [ECCB Proceedings Issue]
  [ Online access ]
  [ Request reprint ]


• Bornberg-Bauer E. and N. Paton
  Conceptual data modelling for bioinformatics (Review)
  Briefings in Bioinformatics, 3(2): 166 -180, (2002)
  [ Request reprint ]


• Rojas-Mujica I. and E. Bornberg-Bauer
  Database systems for the analysis of biochemical pathways; (invited)
  In Molecular Biology and Pathogenicity of Mycoplasmas , 201--220; (S. Razin and R. Herrmann, editors)(2002)
  Kluver Academic/Plenum Publishers (KAPP), New York


• Chan H.S. and E. Bornberg-Bauer
  Perspectives on Protein Evolution from simple exact models (Review)
  Applied Bioinformatics; 1:121-144, (2002)


• E. Bornberg-Bauer and January Weiner III
  Computational identification of a putative trancription factor responsible for mobility in Mycoplasma Pneumoniae (comment)
  Microbiology UK, 148:10-11,(2002)
  [ Online access ]
  [ Request reprint ]


• Rost U. and E. Bornberg-Bauer
  TreeWiz: Interactive exploration of huge trees
  Bioinformatics, 18(1): 109 - 114, (2002)
  [ Online access ]
  [ Request reprint ]


• E. Bornberg-Bauer, Mark Harvey and Andrew McMeekin
  Bioinformatics education: skills shortage or fundamental shift in skill creation and demand (invited). European Biopharmaceutical Review, 5: 104 -110 (2002)
  [ Free online access (free registration required) ]
• Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G.
  Switching from simple to complex oscillations in calcium signaling;
  Biophys J. 79(3):1188-1195, (2000) [ Online access ]


• Butler G., E. Bornberg-Bauer G. Grahne, F. Kurfess, C. Lam, J. Paquet, I. Rojas, R. Shinghal, L. Tao and A. Tsang;
  The BioIT Projects: Internet, Database and Software Technology Applied to Bioinformatics (invited);
  Proceeding of SSGRR'2000, IEEE - International conference on advances in infrastructure Rome, Italy; (2000).


• E. Bornberg-Bauer
  Integrating Biological data by Modelling Cellular processes (invited),
  In Proceedings of the Pharmaceuticals 2000 virtual conference


• Bornberg-Bauer E. and H.S. Chan;
  Modeling Evolutionary Landscapes: Mutational Stability, Topology and Superfunnels in Sequence Space;
  Proc. Natl. Acad. Sci., USA, track 2, 96(19): 10689 -10694, (1999).
  [ Online access ]


• Backofen R., S. Will and E. Bornberg-Bauer
  Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets;
  Bioinformatics, 15(3): 234 -242; (1999).
  [ Online access ]


• Krause A., P. Nicodeme, E. Bornberg-Bauer M. Rehmsmeier and M. Vingron;
  WWW-access to the SYSTERS Protein Sequence Cluster Set;
  Bioinformatics., 15(3): 262 -263, (1999).
  [ Online access ]


• Rojas-Mujica I. and E. Bornberg-Bauer
  A Comprehensible Database Model for the Computation of Biochemical Pathways (invited);
  In Proceedings of the Workshop on Computation of Biochemical Pathways and Genetic Networks 95-100, Logos, Berlin, (1999).


• Bornberg-Bauer E., E. Rivals and M. Vingron;
  Computational Approaches to Identify Leucine Zippers;
  Nucleic Acids Res., 26(11):2740 -2746, (1998).
  # [ Online access ]


• E. Bornberg-Bauer
  Simple folding model for HP lattice proteins;
  In German Conference on Bioinformatics Hofestaedt, R., T. Lengauer, T. Loeffler and D Schomburg, editors, Lecture Notes in Computer Science, vol. 1278:125-136, Springer, Berlin, (1997).


• Bornberg-Bauer E.;
  How are model protein structures distributed in sequence space?;
  Biophys.J., 73(5):2393 -2403, (1997).
  [ Free online access ]


• Renner A. and E. Bornberg-Bauer
  Exploring the fitness landscapes of lattice proteins;
  In Proceedings of the 1997 Pacific Symposium on Biocomputing (Altman, R., K. Dunker, L. Hunter and T. Klein, editors), 361 -373, World Scientific, London, (1997).


• E. Bornberg-Bauer
  Chain growth algorithms for HP type lattice proteins;
  In RECOMB Proceedings 47 -55, ACM press, New York, (1997).


• E. Bornberg-Bauer
  A simple folding model for HP-type lattice proteins;
  In Computer Science and Biology: Proceedings of German Conference on Bioinformatics
  (Hofestaedt, R., T. Lengauer, M Loeffler and D. Schomburg, editors, vol. IMISE Report No. 1, 72 - 77, University Leipzig, (1996).


• E. Bornberg-Bauer
  Random Structures and Evolution of Biopolymers: A Computational Case Study on RNA Secondary Structures;
  Pharm. Acta Helv., 71:79-85, (1996).


• E. Bornberg-Bauer
  Structure formation of biopolymers is complex, their evolution may be simple;
  In Proceedings of the 1996 Pacific Symposium on Biocomputing (Hunter, L. and T. Klein, editors), pp 97 -108, World Scientific, London, (1996).


• Tacker M., P. F. Stadler, E. Bornberg-Bauer, I. L. Hofacker and P. Schuster;
  Algorithm independent properties of RNA secondary structure predictions;
  Eur. Biophys. J. 25:115-130, ; (1996).


• Fontana W., P. F. Stadler, E. Bornberg-Bauer T. Griesmacher, I. L. Hofacker, M. Tacker, P. Tarazona, E.D. Weinberger and P. Schuster;
  RNA folding and combinatorial landscapes;
  Phys. Rev. E 47:2083 -2099, (1993).