This page develops the application of information theory to biology by topic and roughly in historical order. You can read every paper in the given order. Most papers, including not ones listed here, can be found on the page Molecular Information Theory Papers. If you need to look up terms, you can use the glossary.

All papers will open in a separate window. The glossary also has its own window.

Basics

• primer Basic information theory in a nutshell
• zen What's wrong with consensus sequences?

Information in Nucleic Acid Binding Sites

• schneider1986 The information in a binding site is just enough for it to be found in the genome.
• logopaper Sequence logos, a graphical display of binding sites.
• ev Evolution of binding sites, be sure to run the Evj program!
• ri Theory of individual information
• walker Graphical display of individual information
• correlogo 3D sequence logos

Basic discoveries

• Flipping Bases out of DNA
  • baseflip Evidence for base flipping from sequence logos.
  • repan3 Testing the baseflip hypothesis.
• Fis sites and Molecular Computers
  • fisinfo Analysis of Fis binding sites
  • fisflipflop Discovery that Fis binding overlap
  • moco Pushing the discovery of overlapping Fis binding sites to create a molecular computer.

• Flexible binding site models
  • flexrbs E. coli ribosome binding sites can be described by a flexible model.
  • flexprom Applying the flexible model to E. coli sigma⁷⁰ promoters

• T7 promoters and islands
  • t7like Discovering promoters of T7-like bacteriophages
  • t7island Discovering bacterial genetic islands that use T7 promoters

• Clusters
  • fur Discovery that Fur sites come in clusters

Analysis of Diseases

• rfs Analysis of splice junction mutations that cause diseases
• abcr Medical Applications of Sequence Walkers
• splice server citations (PDF) Papers that cite the splice analysis server for understanding genetic diseases
• more papers could be listed here

Advanced Theory

• ccmm Channel capacity, introducing energy.
• edmm The Second law of Thermodynamics is the relationship between energy and information
• nano2 Review of ccmm and edmm.
• shannonbiologist Why information theory is a theory about biology.
• fisbc More about Fis binding sites and the first experimental evidence showing that information theory is a theory about biology because it correctly predicts a breakpoint in the DNA binding versus information curve.