麻省理工大学：《Systems Biology》Systems Biology

7.81J/8.591J/9.531J Systems Biology

7.81J/8.591J/9.531J Systems Biology

ntroducing… ecture Recitations TR1:00-2:30PM W4:00-5:00PM Alexander van Oudenaarden juan pedraza

Introducing ... Lectures: Recitations: TR 1:00 -2:30 PM W 4:00 - 5:00 PM Alexander van Oudenaarden Juan Pedraza

Text books: none Handouts will be available on -line Good reference(biology textbook) Molecular biology of the cell Alberts et al Matlab will be used intensively during the course, make sure you known(or learn) how to use it(necessary for problem sets)

Text books: none Handouts will be available on-line Good reference (biology textbook): Molecular biology of the cell Alberts et al. Matlab will be used intensively during the course, make sure you known (or learn) how to use it (necessary for problem sets)

Intrinsic challenge of this class mixed audience with wildly different backgrounds read up on your biology or math if needed recitations(W 4PM, are intended to close the gaps and prepare for homework

Intrinsic challenge of this class: mixed audience with wildly different backgrounds ⇒ read up on your biology or math if needed ⇒ recitations (W 4PM,) are intended to close the gaps and prepare for homework

Systems Biology

Systems Biology ?

Systems Biology x Network Biology GOAL: develop a quantitative understanding of the biological function of genetic and biochemical networks INPUT gene gene B gene C gene D gene E gene F OUTPUT function of gene product A-F can be known in detail but this is not sufficient to reveal the biological function of the inPUt-oUTPUt relation a system approach ( looking beyond one gene/protein) is necessary to reveal the biological function of this whole network what is the function of the individual interactions(feedbacks and feedforwards)in the context of the entire network?

Systems Biology ≈ Network Biology GOAL: develop a quantitative understanding of the biological function of genetic and biochemical networks gene A gene C gene E gene B gene D gene F INPUT OUTPUT - function of gene product A-F can be known in detail but this is not sufficient to reveal the biological function of the INPUT-OUTPUT relation - a system approach (looking beyond one gene/protein) is necessary to reveal the biological function of this whole network - what is the function of the individual interactions (feedbacks and feedforwards) in the context of the entire network ?

Three levels of complexity I Systems Microbiology(14 Lectures) The cell as a we/l-stirred biochemica/ reactor II Systems Cell Biology(8 Lectures) The cell as a compartmentalized system with concentration gradients Ill Systems Developmental Biology (3 Lectures The cell in a social context communicating with neighboring cells

Three levels of complexity I Systems Microbiology (14 Lectures) ‘The cell as a well-stirred biochemical reactor’ II Systems Cell Biology (8 Lectures) ‘The cell as a compartmentalized system with concentration gradients’ III Systems Developmental Biology (3 Lectures) ‘The cell in a social context communicating with neighboring cells’

I Systems Microbiology(14 Lectures 7hece∥ as a we∥}- stirred boc/ nem/ca/ reactor Introduction 2 Chemical kinetics, Equilibrium binding, cooperativity L3 Lambda phage L4 Stability analysis L5-6 Genetic switches L7 E coli chemotaxis L8 Fine -tuned versus robust models L9 Receptor clustering L10-11 Stochastic chemical kinetics L12-13 Genetic oscillators L14 Circadian rhythms

I Systems Microbiology (14 Lectures) ‘The cell as a well-stirred biochemical reactor’ L1 Introduction L2 Chemical kinetics, Equilibrium binding, cooperativity L3 Lambda phage L4 Stability analysis L5-6 Genetic switches L7 E. coli chemotaxis L8 Fine-tuned versus robust models L9 Receptor clustering L10-11 Stochastic chemical kinetics L12-13 Genetic oscillators L14 Circadian rhythms

I Systems Microbiology(14 Lectures 7hece∥ as a we∥}- stirred boc/ nem/ca/ reactor Introduction L2 Chemical kinetics, Equilibrium binding, cooperativity Lambda phage L4 Stability analysis L5-6 Genetic switches L7 E coli chemotaxis L8 Fine -tuned versus robust models L9 Receptor clustering L10-11 Stochastic chemical kinetics L12-13 Genetic oscillators L14 Circadian rhythms

I Systems Microbiology (14 Lectures) ‘The cell as a well-stirred biochemical reactor’ L1 Introduction L2 Chemical kinetics, Equilibrium binding, cooperativity L3 Lambda phage L4 Stability analysis L5-6 Genetic switches L7 E. coli chemotaxis L8 Fine-tuned versus robust models L9 Receptor clustering L10-11 Stochastic chemical kinetics L12-13 Genetic oscillators L14 Circadian rhythms

Introduction phage biology Phage genome 48512 base pairs- 12 kB phage. jpg 10 kB Image removed due to copyright considerations See Ptashne, Mark. a genetic switch: phage lambda. 3rd ed. Cold Spring Harbor, NY. Cold Spring Harbor Laboratory Press, 2004

Introduction phage biology Phage genome: 48512 base pairs ~ 12 kB ‘phage.jpg’ ~ 10 kB Image removed due to copyright considerations. See Ptashne, Mark. A genetic switch: phage lambda. 3rd ed. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004