Statistische Mechanik in biologischen Systemen: Themenliste

1. Thermodynamik der Genregulierung
   • U. Gerland, J.D. Moroz and T. Hwa, Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction, PNAS 99: 12015-12020 (2002)
   • N. Buchler, U. Gerland and T. Hwa, On Schemes of Combinatorial Transcription Control, PNAS 100: 5136-5141 (2003)

2. Motive in biologischen Netzwerken
   • S. Shen-Orr, R. Milo, S. Mangan and U. Alon, Network motifs in the transcriptional regulation network of Escherichia coli., Nature Genetics 31: 64-68 (2002)
   • J. Berg and M. Lässig, Local graph alignment and motif search in biological networks, PNAS 101(41), 14689-14694 (2004)

3. Boolesche Netzwerke als einfachste Modelle für Genregulation
   • L. Correale, M. Leone, A. Pagnani, M. Weigt, R. Zecchina, Core percolation and onset of complexity in Boolean networks , Phys. Rev. Lett. 96, 018101 (2006)
   • L. Correale, M. Leone, A. Pagnani, M. Weigt, R. Zecchina, Computational core and fixed-point organization in Boolean networks J. Stat. Mech. P03002 (2006)

4. Inferenz von Genregulierungsnetzwerken aus Expressionsdaten
   • A.A. Margolin, I. Nemenman, K. Basso, U. Klein, C. Wiggins, G. Stolovitzky, R. Dalla-Favera, and A. Califano, ARACNE: An algorithm for reconstruction of genetic networks in a mammalian cellular context, BMC Bioinformatics 7 (Suppl. 1):S7 (2006)

   • K. Basso, A.A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, A. Califano, Reverse engineering of regulatory networks in human B cells, Nat. Genet. 37:382-90 (2005)

5. Hidden Markov Modelle (oft zur Analyse von Gen Sequenzen verwendet)
   • I. Kanter, A. Frydman and A. Ater, Utilizing hidden Markov processes as a tool for experimental physics, Europhys. Lett. 69, 798 (2005)
   • O. Zuk, I. Kanter, E. Domany, The Entropy of a Binary Hidden Markov Process, preprint cs.IT/0507060 (2005)

6. Sequenz Alignments
   • T. Hwa and M. Lässig, Similarity Detection and Localization, Phys. Rev. Lett. 76 (14), 2591 (1996)

   • T. Hwa and M. Lässig, Optimal Detection of Sequence Similarity by Local Alignment RECOMB '98: Proceedings of the second annual international conference on Computational molecular biology, pages 109-116 (1998)

7. RNA Sekundärstrukturen
   • P. G. Higgs, Overlaps between secondary structures, Phys. Rev. Lett. 76, 704 (1996)
   • A. Pagnani, G. Parisi, and F. Ricci-Tersenghi, Glassy Transition in a Disordered Model for the RNA Secondary Structure, Phys. Rev. Lett. 84, 2026-2029 (2000)
   • P.G. Higgs, RNA secondary structure: physical and computational aspects, Quarterly Review of Biophysics, 33(3):199-253, (2000)

8. Proteinfaltung
   • P. Grassberger, Pruned-enriched rosenbluth method: Simulations of theta-polymers of chain length up to 1 000 000., Phys. Rev. E 56(3):3682-3693, (1997)

   • H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, and W. Nadler, New Monte Carlo algorithm for protein folding, Phys. Rev. Lett. 80, 3149 (1998)

Allen Vortragenden wird empfohlen auch in der Datenbank INSPEC (nur lokal zugänglich) zu recherchieren. Eine sehr aktuelle Quelle stellt der Preprint-Server dar. Alle dort gespeicherten Artikel lassen sich direkt herunterladen.

• R. Blossey
  Computational Biology: A Statistical Mechanics Perspective
  Chapman and Hall/CRC, 2006
• P. Clote and R. Backofen
  Computational Molecular Biology Wiley Series in Mathematical and Computational Biology
  John Wiley and Sons, Chichester 2001
  
• K. A. Dill
  Molecular Driving Forces
  Garland Science, 2002
• R. Durbin, S. R. Eddy, A. Krogh, und G. Mitchison
  Biological sequence analysis
  Cambridge University Press, Cambridge 1998
  
• A.K. Hartmann und H. Rieger (eds.)
  New Optimization Algorithms in Physics
  Wiley-VCH, Berlin 2004
• K. Huang
  Lectures on Statistical Physics and Protein Folding
  World Scientific Publishing Company, Singapore 2005
• M. Lässig und A. Valleriani
  Biological Evolution and Statistical Physics
  Springer, Berlin 2002
• D. Reguera, J. M. G. Vilar, und J. M. Rubi
  Statistical Mechanics of Biocomplexity
  Springer, Berlin 1999