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Thomas Wilhelm's publications

(papers are available as pdf on request)

  1. J. Hollunder, M. Friedel, M. Kuiper, T. Wilhelm. DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics 26 (2010) 987-989.
  2. P. Lorenz, S. Dietmann, T. Wilhelm, D. Koczan, S. Autran, S. Gad, G. Wen, G. Ding, Y. Li, M.-F. Rousseau-Merck, H.-J. Thiesen. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics 11 (2010) 206. 
  3. T. Aho, H. Almusa, J. Matilainen, A. Larjo, P. Ruusuvuori, K.-L. Aho, T. Wilhelm, H. Lähdesmäki, A. Beyer, M. Harju, S. Chowdhury, K. Leinonen, C. Roos, O. Yli-Harja. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PLoS One 5 (2010) e10662.
  4. T. Wilhelm. The smallest chemical reaction system with bistability. BMC  Systems Biology 3 (2009) 90.
  5. M. Friedel, S. Nikolajewa, J. Sühnel, T. Wilhelm. DiProGB: the dinucleotide properties genome browser. Bioinformatics 25 (2009) 2603-2604.
  6. M. Friedel, S. Nikolajewa, J. Sühnel, T. Wilhelm. DiProDB: a database for dinucleotide properties. Nucleic Acids Res. 37 (2009) D37-D40.
  7. J. Kim, T. Wilhelm. What is a complex graph? Physica A 387 (2008) 2637–2652. 
  8. M. Friedel, S. Nikolajewa, T. Wilhelm. The Decomposition Tree for Analyses of Boolean Functions. Math. Struct. in Comp. Science 18 (2008) 411-426.
  9. J. Behre, T. Wilhelm, A. von Kamp, E. Ruppin, S. Schuster. Structural robustness of metabolic networks with respect to multiple knockouts. J. Theor. Biol. 252 (2008) 433–441.
  10. T. Wilhelm, J. Hollunder. Information theoretic description of networks. Physica A 385 (2007) 385-396.
  11. T. Wilhelm. Analysis of structures causing instabilities. Phys. Rev. E 76 (2007) 011911.
    Article also selected for Vir. J. Bio. Phys. Res. 14(3) (2007).
  12. D. Pohlers, A. Beyer, D. Koczan, T. Wilhelm, H.-J. Thiesen, R. W. Kinne. Constitutive upregulation of the TGF-β pathway in rheumatoid arthritis synovial fibroblasts. Arthritis Research & Therapy 9 (2007) R59.
  13. R. Brockmann, A. Beyer, J. J. Heinisch, T. Wilhelm. Post-transcriptional expression regulation: What determines translation rates? PLoS Comput. Biol. 3(3) (2007) 531-539.
  14. J. Hollunder, A. Beyer, T. Wilhelm. Protein subcomplexes – molecular machines with highly specialized functions. IEEE Trans. Nanobiosci. 6 (2007) 86-93.
  15. J. Hollunder, M. Friedel, A. Beyer, C. Workman, T. Wilhelm. DASS: efficient discovery and p-value calculation of substructures in unordered data. Bioinformatics 23 (2007) 77-83.
  16. S. Nikolajewa, M. Friedel, T. Wilhelm. Boolean Networks with biologically relevant rules show ordered behavior. BioSystems 90 (2007) 40-47.
  17. T. Wilhelm, M. Friedel. Lead structures for drugs. (2006) US patent Appl.No.60/829,894.
  18. T. Aho, T. Wilhelm, A. Beyer, O. Yli-Harja. Finding infeasible reactions in metabolic networks: comparison of methods. Proc. 4th TICSP workshop on Computational Systems Biology (WCSB 2006), pp. 23-26. TICSP Series 32, University of Tampere, Finland .
  19. T. Wilhelm, J. Hollunder, J.-K. Kim, A. Beyer. General Classification of networks. Proceeedings of AISB (2006): Adaptation in Artificial and Biological Systems. T. Kovacs, J.A.R. Marshall (eds.). Vol.III, 189-194. University of Bristol, Bristol, UK
  20. A. Beyer, C. Workman, J. Hollunder, D. Radke, U. Möller, T. Wilhelm, T. Ideker. Integrated assessment and prediction of transcription factor binding. PLoS Comput. Biol. 2 (2006) 615-626.
  21. S. Nikolajewa, M. Friedel, A. Beyer, T. Wilhelm. The new classification scheme of the genetic code, tRNA usage and early code evolution. J. Bioinf. Comput. Biol. 4 (2006) 609-620.
  22. J. Hollunder, A. Beyer, T. Wilhelm. Exploiting combinatorial complexity - searching for new functional entities in the cell. Proc. of "Foundations of Systems Biology in Engineering" (FOSBE 2005), Univ.of California - Santa Barbara Campus, 363-366.
  23. S. Nikolajewa, A. Beyer, M. Friedel, J. Hollunder, T. Wilhelm. Common patterns in type II restriction enzyme binding sites. Nucleic Acids Research 33 (2005) 2726-2733.
  24. A. Beyer, T. Wilhelm. Dynamic simulation of protein complex formation on a genomic scale. Bioinformatics 21 (2005) 1610-1616.
  25. J. Hollunder, A. Beyer, T. Wilhelm. Identification and characterization of protein subcomplexes in yeast. Proteomics 5 (2005) 2082-2089.
  26. S. Nikolajewa, M. Friedel, A. Beyer, T. Wilhelm. Purine-Pyrimidine patterns in the genetic code and in restriction enzyme recognition sequences. Proc. of the Int. Moscow Conference on Comput. Mol. Biol., Juli 18-21 (2005) 250-252.
  27. T. Wilhelm. A study of equal node models for food webs. Ecol. Model. 181 (2005) 215-227.
  28. A. Beyer, J. Hollunder, H.-P. Nasheuer, T. Wilhelm. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.  Mol. Cell. Prot. 3.11 (2004) 1083-1092.
    Recommended by the Faculty of 1000 http://www.f1000biology.com/article/id/1022898/evaluation
  29. T. Wilhelm, A. Beyer, J. Hollunder. Patterns in weighted networks. Proceedings of the “8th World Multiconference on Systemics, Cybernetics and Informatics” (SCI 2004), Orlando, Florida , Vol.III, 217-221.
  30. T. Wilhelm, J. Behre, S. Schuster. Analysis of structural robustness of metabolic networks. Systems Biology 1 (2004) 114-120. (now published as: IET Systems Biology)
  31. T. Wilhelm, S. Nikolajewa. A Purine-Pyrimidine Classification Scheme of the Genetic Code. BIOforum Europe 06 (2004) 46-49.
  32. T. Wilhelm, S. Nikolajewa. A new classification scheme of the genetic code. J. Mol. Evol. 59 (2004) 598-605.
  33. T. Wilhelm, H.-P. Nasheuer, S. Huang. Physical and functional modularity of the protein network in yeast. Mol. Cell. Prot. 2.5 (2003) 292-298.
  34. T. Wilhelm, P. Hänggi. Power-law distributions resulting from finite resources. Physica A 329 (2003) 499-508.
  35. R. Brüggemann, T. Wilhelm, P. Kasprzak. Ansaetze zur Klärung der ‚mesotrophic maximum hypothesis’; Auf dem Wege zur Bewertung der Integrität von Ökosystemen. In “Theorie und Modellierung von Ökosystemen”, pp. 18-36, Shaker Verlag Aachen (2003).
  36. T. Wilhelm. An elementary dynamic model for nonbinary food-webs. Ecol. Model. 168 (2003) 145-152.
  37. R. Brüggemann, T. Wilhelm. Scaling laws by randomly generated networks. In “Scales, hierarchies and emergent properties in ecological models.”, pp. 61-70, Theorie in der Ökologie 6, Peter Lang, Frankfurt/M (2002).
  38. T. Wilhelm, R. Brüggemann. Information theoretic measures for the maturity of ecosystems. In: “Integrative systems approaches to natural and social sciences - Systems science 2000”, pp.263-273, Springer Berlin (2001).
  39. T. Wilhelm, R. Brüggemann. Hat die Evolution Zielfunktionen? In „Simulation in Umwelt- und Geowissenschaften“, pp. 183-193, Shaker-Verlag, Aachen (2000).
  40. T. Wilhelm, R. Brüggemann. Goal functions for the evolution of natural systems. Berichte des IGB 10 (2000) 19-28.
  41. T. Wilhelm, R. Brüggemann. Goal functions for the development of natural systems. Ecol. Model. 132 (2000) 231-246.
  42. T. Wilhelm. Chemical systems consisting only of elementary steps - a paradigma for nonlinear behavior. J. Math. Chem. 27 (2000) 71-88.
  43. K. R. Schneider, T. Wilhelm. Model reduction by extended quasi-steady-state assumption. In “International conference on differential equations” (eds. B. Fiedler, K. Groeger, J. Sprekels) Vol.2, pp.1226-1228, World Scientific Singapore (2000).
  44. K. R. Schneider, T. Wilhelm. Model reduction by extended quasi-steady-state approximation. J. Math. Biol. 40 (2000) 443-450.
  45. T. Wilhelm, P. Hänggi. What can be stated by the Glansdorff-Prigogine criterion concerning the stability of mass-action kinetic systems? J. Chem. Phys. 110 (1999) 6128-6134.
  46. T. Wilhelm, S. Schuster, R. Heinrich. Kinetic and thermodynamic analyses of the reversible version of the smallest chemical reaction system with Hopf bifurcation. Nonlinear World 4 (1997) 295-321. (now published as: Nonlinear Analysis Series B: Real World Applications)
  47. T. Wilhelm, R. Heinrich. Mathematical analysis of the smallest chemical reaction system with Hopf bifurcation. J. Math. Chem. 19 (1996) 111-130.
  48. T. Wilhelm, R. Heinrich. Smallest chemical reaction system with Hopf bifurcation. J. Math. Chem. 17 (1995) 1-14.
  49. T. Wilhelm, R. Heinrich. A chemical system with Hopf bifurcation consisting of three intermediates and mono- and bimolecular reactions. J. Biol. Syst. 3 (1995) 231-238.
  50. R. Heinrich, E. Klipp, A. Stephani, T. Wilhelm. Evolutionary optimization of enzymes on the basis of kinetic and thermodynamic principles. In: “What is Controlling Life? 50 Years after Erwin Schrödinger's What is Life?” Modern Trends in BioThermoKinetics 3, pp. 99-103, Innsbruck Univ. Press (1994).
  51. T. Wilhelm, E. Hoffmann-Klipp, R. Heinrich. An evolutionary approach to enzyme kinetics: optimization of ordered mechanisms. Bull. Math. Biol. 56 (1994) 65-106.