Skip to main content
SpringerLink
Log in

From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation

  • Chapter
Structural Approaches to Sequence Evolution

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

  • 899 Accesses

Genomic functions often cannot be understood at the level of single genes but require the study of gene networks. This systems biology credo is nearly commonplace by now. Evidence comes from the comparative analysis of entire genomes: current estimates put, for example, the number of human genes at around 22,000, hardly more than the 14,000 of the fruit fly, and not even an order of magnitude higher than the 6,000 of baker's yeast. The complexity and diversity of higher animals, therefore, cannot be explained in terms of their gene numbers. If, however, a biological function requires the concerted action of several genes, and conversely, a gene takes part in several functional contexts, an organism may be defined less by its individual genes but by their interactions. The emerging picture of the genome as a strongly interacting system with many degrees of freedom brings new challenges for experiment and theory, many of which are of a statistical nature. And indeed, this picture continues to make the subject attractive to a growing number of statistical physicists.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. M. Ptashne, A. Gann, in Genes and Signals (Cold Spring Harbour Laboratory Press, Cold Spring Habor, 2002)

    Google Scholar 

  2. D. Tautz, Curr. Opin. Genet. Dev. 10, 575 (2000)

    Article  Google Scholar 

  3. G.A. Wray, M.W. Hahn, H. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, R.A. Romano, Mol. Biol. Evol. 20, 1377 (2003)

    Article  Google Scholar 

  4. O.G. Berg, R.B. Winter, P.H. von Hippel, Biochemistry 20, 6929 (1981)

    Article  Google Scholar 

  5. R.B. Winter, P.H. von Hippel, Biochemistry 20, 6948 (1981)

    Article  Google Scholar 

  6. R.B. Winter, O.G. Berg, P.H. von Hippel, Biochemistry 20, 6961 (1981)

    Article  Google Scholar 

  7. P.H. von Hippel, O.G. Berg, Proc. Natl. Acad. Sci. USA 83, 1608 (1986)

    Article  ADS  Google Scholar 

  8. A. Sarai, Y. Takeda, Proc. Natl. Acad. Sci. USA 86, 6513 (1989)

    Article  ADS  Google Scholar 

  9. D. Fields, Y. He, A. Al-Uzri, G. Stormo, J. Mol. Biol. 271, 178 (1997)

    Article  Google Scholar 

  10. G.D. Stormo, D.S. Fields, Trends Biochem. Sci. 23, 109 (1998)

    Article  Google Scholar 

  11. M. Oda, K. Furukawa, K. Ogata, A. Sarai, N. Nakamura, J. Mol. Biol. 276, 571 (1998)

    Article  Google Scholar 

  12. K. Omagari et al., FEBS Lett. 563, 55 (2004)

    Article  Google Scholar 

  13. U. Gerland, D. Moroz, T. Hwa, Proc. Natl. Acad. Sci. USA 99, 12015 (2002)

    Article  ADS  Google Scholar 

  14. M. Djordjevic, A.M. Sengupta, B.I. Shraiman, Genome Res. 13, 2381 (2003)

    Article  Google Scholar 

  15. V. Mustonen, M. Lässig, Proc. Natl. Acad. Sci. USA 15, 15936 (2005)

    Article  ADS  Google Scholar 

  16. M. Slutsky, L.A. Mirny, Bioinformatics 15, 2539 (2002)

    Google Scholar 

  17. J. Berg, S. Willmann, M. Lässig, BMC Evol. Biol. 4, 42 (2004)

    Google Scholar 

  18. R. Durbin, S.R. Eddy, A. Krogh, G. Mitchison, in Biological Sequence Analysis (Cambridge University Press, Cambridge, 1998)

    Book  MATH  Google Scholar 

  19. G. Stormo, G.W. Hartzell, Proc. Natl. Acad. Sci. USA 86, 1183 (1989)

    Article  ADS  Google Scholar 

  20. G. Hertz, G. Stormo, Bioinformatics 15, 563 (1999)

    Article  Google Scholar 

  21. N. Rajewsky, N.D. Socci, M. Zapotocky, E.D. Siggia, Genome Res. 12, 298 (2002)

    Article  Google Scholar 

  22. E. van Nimwegen, M. Zavolan, N. Rajewsky, E.D. Siggia, Proc. Natl. Acad. Sci. USA 99, 7323 (2002)

    Article  MATH  MathSciNet  ADS  Google Scholar 

  23. B. Lenhard, A. Sandelin, L. Mendoza, P. Engström, N. Jareborg, W.W. Wasserman, J. Biol. 2, 13 (2003)

    Article  Google Scholar 

  24. U. Gerland, T. Hwa, J. Mol. Evol. 55, 386 (2002)

    Article  Google Scholar 

  25. A.M. Moses, D.Y. Chiang, M. Kellis, E.S. Lander, M.B. Eisen, BMC Evol. Biol. 3, 19 (2003)

    Google Scholar 

  26. C.T. Brown, C.G. Callan, Proc. Natl. Acad. Sci. USA 101, 2404 (2003)

    Article  ADS  Google Scholar 

  27. J. Hofbauer, K. Sigmund, in The Theory of Evolution and Dynamical Systems (Cambridge University Press, Cambridge, 1988)

    MATH  Google Scholar 

  28. M. Kimura, J.F. Crow, in An Introduction to Population Genetics Theory (Harper & Row, New York, 1973)

    Google Scholar 

  29. M. Kimura, in The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983)

    Book  Google Scholar 

  30. M. Kimura, Genetics 47, 713 (1962)

    Google Scholar 

  31. M. Kimura, T. Ohta, Genetics 61, 763 (1969)

    Google Scholar 

  32. M. Rouzine, A. Rodrigo, J.M. Coffin, Microbiol. Mol. Biol. Rev. 65, 151 (2001)

    Article  Google Scholar 

  33. . D. Grün, M. Lässig, to be published.

    Google Scholar 

  34. P. Arndt, T. Hwa, Bioinformatics 21, 2322 (2005)

    Article  Google Scholar 

  35. L. Peliti, Europhys. Lett. 57, 745 (2002)

    Article  ADS  Google Scholar 

  36. J. Berg, M. Lässig, Biophysics (Moscow) 48(Suppl. 1), 36 (2003)

    Google Scholar 

  37. A.L. Halpern, W.J. Bruno, Mol. Biol. Evol. 15, 910 (1998)

    Google Scholar 

  38. G. Sella, A. Hirsh, Proc. Natl. Acad. Sci. USA 102, 9541 (2005)

    Article  ADS  Google Scholar 

  39. K. Robison, A.M. McGuire, G.M. Church, J. Mol. Biol. 284, 241 (1998)

    Article  Google Scholar 

  40. V. Mustonen, M. Lässig, Proc. Natl. Acad. Sci. USA 104, 2277 (2007)

    Article  ADS  Google Scholar 

  41. A.M. Moses, D.Y. Chiang, A.P. Pollard, N.I. Iyer, M.B. Eisen, Genome Biol. 5, R98 (2004)

    Article  Google Scholar 

  42. S. MacArthur, J. Brookfield, Mol. Biol. Evol. 21, 1064 (2004)

    Article  Google Scholar 

  43. D. Arnosti, Annu. Rev. Entomol. 48, 579 (2003)

    Article  Google Scholar 

  44. N. Buchler, U. Gerland, T. Hwa, Proc. Natl. Acad. Sci. USA 100, 5136 (2003)

    Article  ADS  Google Scholar 

  45. M. Ludwig, C. Bergman, N. Patel, M. Kreitman, Nature 403, 564 (2000)

    Article  ADS  Google Scholar 

  46. M. Ludwig, N. Patel, M. Kreitman, Development 125, 949 (1998)

    Google Scholar 

  47. A. McGregor, P. Shaw, J. Hancock, D. Bopp, M. Hediger, N. Wratten, G. Dover, Evol. Dev. 3, 397 (2001)

    Article  Google Scholar 

  48. E. Dermitzakis, C. Bergman, A. Clark, Mol. Biol. Evol. 20, 703 (2002)

    Article  Google Scholar 

  49. J. Scemama, M. Hunter, J. McCallum, V. Prince, E. Stellwag, J. Exp. Zool. 294, 285(2002)

    Article  Google Scholar 

  50. J. Costas, F. Casares, J. Vieira, Gene 310, 215 (2003)

    Google Scholar 

  51. A. Wagner, Genome Biol. 3, 1012 (2002)

    Article  Google Scholar 

  52. M. Lynch, J.S. Conery, J. Struct. Funct. Genomics 3, 35 (2003)

    Article  Google Scholar 

  53. M. Lynch, J.S. Conery, Science 302, 1401 (2003)

    Article  ADS  Google Scholar 

  54. E. Davidson, Curr. Opin. Genet. Dev. 9, 530 (1999)

    Article  Google Scholar 

  55. A.P Gasch, A.M. Moses, D.Y. Chiang, H.B. Fraser, M. Berardini, M.B. Eisen, PLoS Biol. 2, E398 (2004)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut für Theoretische Physik, Universität zu Köln, Zülpicher Str. 77, 50937, Köln, Germany

    Michael Lässig

Authors
  1. Michael Lässig
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Fac. de Ciencias, Universidad Autonoma Madrid, Cantoblanco, 28049, Madrid, Spain

    Ugo Bastolla

  2. Institut für Festkörperphysik, TU Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany

    Markus Porto

  3. Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza 3, 29126, Milano, Italy

    H. Eduardo Roman

  4. Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK

    Michele Vendruscolo

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Lässig, M. (2007). From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_12

Download citation

Publish with us

Policies and ethics

Search

Navigation