Chapter 1: Modeling the Activity of Single Genes

Chapter 2: A Probabilistic Model of a Prokaryotic Gene and Its Regulation

Chapter 3: A Logical Model of cis-Regulatory Control in a Eukaryotic System

Chapter 4: Trainable Gene Regulation Networks with Applications to Drosophila Pattern Formation

Chapter 5: Genetic Network Inference in Computational Models and Applications to Large-Scale Gene Expression Data

1.1.1 Motivation The Challenge of Understanding Gene Regulation

The central dogma of molecular biology states that information is stored in DNA, transcribed to messenger RNA (mRNA), and then translated into proteins. This picture is significantly augmented when we consider the action of certain proteins in regulating transcription. These transcription factors provide a feedback pathway by which genes can regulate one another's expression as mRNA and then as protein.

To review: DNA, RNA, and proteins have different functions. DNA is the molecular storehouse of genetic information. When cells divide, the DNA is replicated, so that each daughter cell maintains the same genetic information as the mother cell. RNA acts as a gobetween from DNA to proteins. Only a single copy of DNA is present, but multiple copies of the same piece of RNA may be present, allowing cells to make huge amounts of protein. In eukaryotes (organisms with a nucleus), DNA is found in the nucleus only. RNA is copied in the nucleus and then translocates (moves) outside the nucleus, where it is transcribed into proteins. Along the way, the RNA...