Biomolecular systems and their evolution

CREATED: 200712310908 Biological systems

• sequence
• microarray
• networks
• PPI Inferred model

** Infer models for different species and apply comparative genomics

• dependent evolution of components (Yeang, Darot, Noller, Haussler RECOMB 2006)
• coevolution, idea: reward joint transitions, penalize single transitions
• relaxed evolution - duplication
• application ** predicting secondary structure interaction in 16S RNA using log odd score and coevolution model ** predicting coevolving domain pairs (pfam) (Yeang and Haussler)
• strong covariation -> function/physical coupling
• multiple positions covariant together

** Data integration (Yeang, Ideker, Jaakkda JCB 2004)

• constraint based framework
• attributes of system - causal order, up/down regulated
• associate evidence with local constraints
• build factor graph for joint probabilistic graphical model
• use max product algorithm to calculate attribute values
• select new experiments to reduce uncertainty of model
• application ** inferring combinatorial gene function ** gene regulation, metabolic network