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Course Date: 02 September 2014 to 11 November 2014 (10 weeks)
An introduction to current concepts of how cellular molecules come together to form systems, how these systems exhibit emergent properties, and how these properties are used to make cellular decisions.
course will introduce the student to contemporary Systems Biology focused on
mammalian cells, their constituents and their functions. Biology is moving from molecular to modular.
As our knowledge of our genome and gene expression deepens and we develop lists
of molecules (proteins, lipids, ions) involved in cellular processes, we need
to understand how these molecules interact with each other to form modules that
act as discrete functional systems. These systems underlie core subcellular processes such as signal
transduction, transcription, motility and electrical excitability. In turn
these processes come together to exhibit cellular behaviors such as secretion,
proliferation and action potentials. What are the properties of such subcellular
and cellular systems? What are the
mechanisms by which emergent behaviors of systems arise? What types of experiments inform systems-level
thinking? Why do we need computation and simulations to understand these
The course will develop multiple lines of
reasoning to answer the questions listed above. Two major reasoning threads
are: the design, execution and interpretation of multivariable experiments that
produce large data sets; quantitative reasoning, models and simulations. Examples will be discussed to demonstrate
“how” cell- level functions arise and “why” mechanistic knowledge allows us to
predict cellular behaviors leading to disease states and drug responses.
Will I get a Statement of Accomplishment after completing this class?
Yes. Students who successfully complete the class will receive a Statement of Accomplishment signed by the Course Director.
Topics covered include:
Systems Level Reasoning: Bottom-Up and Top-Down Approaches for Complex Systems
Cell Signaling Pathways: Molecules to Pathways, cAMP and MAP-kinase Pathways
Signal Flow: Pathways to Networks
The Actin Cytoskeleton: The Cell Motility Machine
Mathematical Representations of Cell Biological Systems Time and Space
Gathering Large Data Sets in Genomics and Proteomics
Inferring Modules: Computational Analysis of Large Data Sets; Building Networks
Small Scale Systems Biology Experiments
Identifying Emergent Properties by Computation: Dynamical Models
Emergent Properties: Ultrasensitivity, Bistability, Robustness and Fragility
Modules to Functions: Control Systems
Module-Boundaries: Sharp and Fuzzy, Interactions between Subcellular Modules
Emergence of Cellular Functions from Subcellular Modules
Systems Analysis of Complex Diseases
Systems Pharmacology: Understanding Drug Action from a Systems Perspective
class session will consist of an approximately one hour lecture, divided into
multiple shorter segments.
For evaluation, students will be given homework assignments
that will require critical reasoning and problem solving skills. Questions may
be multiple choice or short (100 -300 word) essays.
Review articles and
selected original research articles are discussed in the lectures. A set of
review articles will be required reading. Reading primary articles is not
required to complete the course, but can be quite useful. All materials will be from open access journals or will be provided as links to
e-reprints, so there will be no cost to the student.