7.91 Amy Keating The protein interactome a critical framework underlying systems biology Overview-the many levels of systems biology 2. Experimental methods for measuring protein-protein interactions and their limitations 3. Data sources for information about proteins and their interactions 4. Computational methods for assessing and predicting protein-protein interactions
The Protein Interactome A critical framework underlying systems biology 1. Overview - the many levels of systems biology 2. Experimental methods for measuring protein-protein interactions, and their limitations 3. Data sources for information about proteins and their interactions 4. Computational methods for assessing and predicting protein-protein interactions. 7.91 Amy Keating
Spectrum of Systems Biology detailed models-describe rates concentrations structure low-resolution models-describe information flow, logic, mechanism circuitry logic/controI-positive and negative regulation connectivity/topology-who talks to who? interaction scaffold parts list- protein and DNA sequences( structures) Recommended reading: Ideker Lauffenburger, TRENDS in Biotechnology(2003)21, 255-262
Spectrum of Systems Biology detailed models - describe rates, concentrations, structure low-resolution models - describe information flow, logic, mechanism circuitry logic/control - positive and negative regulation connectivity/topology - who talks to who? interaction scaffold parts list - protein and DNA sequences (& structures) Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
Spectrum of Systems Biology allow simulation detailed models- differential equations comparison with data loW-resolution models boolean markov models circuitry logic/control- Bayesian networks connectivity/topology -graph theory parts list-databases Recommended reading: Ideker Lauffenburger, TRENDS in Biotechnology(2003)21, 255-262
Spectrum of Systems Biology allow simulation & detailed models - differential equations comparison with data low-resolution models - Boolean & Markov models circuitry logic/control - Bayesian networks connectivity/topology - graph theory parts list - databases Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
Spectrum of Systems Biology detailed models- rates of individual reactions, protein concentrations in the cell, extent of phosphorylation, diffusion rates low-resolution models-which elements are most crucial? combinatorial dependencies. circuitry logic/control-Expression profiling, post-translational modifications in response to different stimuli. Identify pathways and clusters; does an interaction activate or repress; are multiple components required? connectivity/topology-protein-protein, protein-DNA and protein-small molecule interactions parts list- genome sequencing projects, gene finding algorithms EST libraries Recommended reading: Ideker Lauffenburger, TRENDS in Biotechnology(2003)21, 255-262
Spectrum of Systems Biology detailed models - rates of individual reactions, protein concentrations in the cell, extent of phosphorylation, diffusion rates low-resolution models - which elements are most crucial? combinatorial dependencies. circuitry logic/control - Expression profiling, post-translational modifications in response to different stimuli. Identify pathways and clusters; does an interaction activate or repress; are multiple components required? connectivity/topology - protein-protein, protein-DNA and protein-small molecule interactions parts list - genome sequencing projects, gene finding algorithms, EST libraries Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262
Spectrum of Systems Biology detailed models YAFFE low-resolution models-not covering this topic much this year circuitry logic/control- BURGE connectivity/topology -KEATING (today) parts list BURGE Recommended reading: Ideker Lauffenburger, TRENDS in Biotechnology(2003)21, 255-262
Spectrum of Systems Biology detailed models YAFFE low-resolution models - not covering this topic much this year circuitry logic/control - BURGE connectivity/topology - KEATING (today) parts list BURGE Recommended reading: Ideker & Lauffenburger, TRENDS in Biotechnology (2003) 21, 255-262