Computational Modelling Of Gene Regulatory Networks -- A Primer

Contents: Introduction; What Is a System, and Why Should We Care?; What Models Can and Cannot Predict; Why Make Computational Models of Gene Regulatory Networks?; Graphical Representations of Gene Regulatory Networks; Implicit Modeling via Interaction Network Maps; The Biochemical Basis of Gene Regulation; A Single-Cell Model of Transcriptional Regulation; Simplified Models: Mass-Action Kinetics; Simplified Models: Boolean and Multi-valued Logic; Simplified Models: Bayesian Networks; The Relationship between Logic and Bayesian Networks; Network Inference in Practice; Searching DNA Sequences for Transcription Factor Binding Sites; Model Selection Theory; Simplified Models -- GRN State Signatures in Data; System Dynamics; Robustness Analysis; GRN Modules and Building Blocks; Notes on Data Processing for GRN Modeling; Applications of Computational GRN Modeling; Quo Vadis.