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If you would like to help us identify a good collection of papers on a specific topic that would be a good starting point for someone wanting to do research in a given area, we would very much welcome your input. Please send us an email.

 

Biology and Information Theory

 

Today, interdisciplinary research is omnipresent combining scientists from diverse fields with even more diverse background to work collectively on problems that could not be solved within a single discipline simply because the problems studied are, at least to some degree, outside of these traditional fields. This page provides a collection of links to publications, people, conferences and resources that might be useful for people interested in the application of information theory to biological problems to show its utility and power even in such remote fields. The biological problems comprise a far range of subfields of biology whereas the major fields so far are molecular biology and neuroscience.

The title of this page is information theory and biology and not applications of information theory to biological problems because the latter version would be at least misleading. Misleading because it would imply that a complete theoretical framework exists already and one just needs to apply it. Instead, information theory provides a conceptual framework that needs to be adopted to the corresponding problem under consideration properly. This makes it more challenging but also much more exciting.

We hope this page will help to give an overview about the rapidly expanding connection between information theory and biology.

 

Table of Contents:

Publications

  • C. Adami
    Information Theory in Molecular Biology
    Physics of Life Reviews 1 3-22 (2004).

  • N. Ay and D.C. Krakauer
    Geometric robustness theory and biological networks
    Theory in Biosciences 125(2) 93-121 (2007).

  • J. Avery
    Information Theory and Evolution
    World Scientific Publishing (2003).

  • G. Deco and D. Obradovic
    An Information-Theoretic Approach to Neural Computing
    Springer (1997).

  • G. Deco and B. Schürmann
    Information Dynamics: Foundations and Applications
    Springer (2000).

  • M. Dehnerta, W. E. Helmb and M.-T. Hütt
    Information theory reveals large-scale synchronisation of statistical correlations in eukaryote genomes
    Gene 345(1) 81-90 (2005).

  • R. A. Gatenby and R.B. Frieden
    Information Theory in Living Systems, Methods, Applications, and Challenges
    Bulletin of Mathematical Biology 69(2) 635-657 (2007).

  • Hazen RM, Griffin PL, Carothers JM, Szostak JW.
    Functional information and the emergence of biocomplexity
    Proc Natl Acad Sci U S A. 104 Suppl 1:8574-81 (2007).

  • A. Kocsor, A. Kertesz-Farkas, L. Kajan and S. Pongor
    Application of compression-based distance measures to protein sequence classification: a methodological study
    Bioinformatics 22(4):407-412 (2006).

  • Krasnogor, N. and Pelta, D.A.
    Measuring the similarity of protein structures by means of the universal similarity metric
    Bioinformatics, 20, 1015-1021 (2004).

  • Li, M. et al.
    An information-based sequence distance and its application to whole mitochondrial genome phylogeny
    Bioinformatics, 17, 149-154 (2001).

  • A Margolin, I Nemenman, K Basso, U Klein, C Wiggins, G Stolovitzky, Riccardo D Favera, and A Califano.
    ARACNE: An algorithm for reconstruction of genetic networks in a mammalian cellular context
    BMC Bioinformatics, 7 (Suppl. 1):S7 (2006).

  • H. Quastler
    Information Theory in Biology
    University of Illinois Press, Urbana (1953).

  • M. Rosvall and C. T. Bergstrom
    An information-theoretic framework for resolving community structure in complex networks
    Proceedings of the National Academy of Sciences USA 104:7327-7331 (2007).

  • Martin Rosvall and Kim Sneppen
    Self-Assembling of information in networks
    Europhys. Lett. 74:1109 (2006).

  • F. Rieke, D. Warland, R. deRuytervanSteveninck, W. Bialek
    Spikes: Exploring the Neural Code
    MIT Press (1999).

  • Schneider T.D., G.D. Stormo, L. Gold, and A. Ehrenfeucht
    Information content of binding sites on nucleotide sequences
    J. Mol. Biol. 188:415-431 (1986).

  • John Maynard Smith
    The Idea of Information in Biology
    The Quarterly Review of Biology, 74(4), 395-400 (1999).

  • G. Tkacik, C.G. Callan Jr. and W. Biallek
    Information flow and optimization in transcriptional control
    q-Bio.MN arXiv:0705.0313 (2007).

  • A. Trusina, M. Rosvall and K. Sneppen
    Communication Boundaries in Networks
    Phys. Rev. Lett. 94:238701 (2004).

  • Yockey, H.P.
    An application of information theory to the Central Dogma and the sequence hypothesis
    Journal of Theoretical Biology 46: 369-406 (1974).

  • Yockey, H.P.
    Information Theory and Molecular Biology
    Cambridge: Cambridge University Press (1992).

People

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Questions?

If you have some question regarding this page or want to contribute some information just send an email to Frank Emmert-Streib.