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This is the website for BE 700/PY 895, Methods and Logic in Quantitative Biology
This website will be updated with readings.
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General course information: M 10-12 SCI 323, W 10-12 PRB 365.
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Syllabus
pdf
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WEEK 1 (9/9 and 9/14): Analysis of fluctuations: Luria-Delbruck Fluctuation Tests.
- Background: Poisson Distribution (see Wikipedia and/or You Tube videos video1 and video2).
I highly recommend spending the 25 minutes watching the videos before reading the papers if you do not have a strong intuition about Poisson distributions.
- Papers: .pdf and .pdf
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WEEK 2 (9/21 and 9/23): All-or-none phenomena (bistability and the digital paradigm) .
- Background: Tutorial on graphical methods for dynamical systems.
- Papers: 9/21 .pdf and 9/24:.pdf and SI
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WEEK 3 (9/28 and 9/30): Stochasticity in gene expression .
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WEEK 4 (10/5 and 10/7): Sensitivity, robust adaptation, and homeostasis .
- Papers: 10/5 .pdf. For good introduction
see Wikipedia page on Enzyme Kinetics.
Supplementary Reading: .pdf (engineering aspects of biochemical cascades)
10/07:.pdf and pdf. We will
also touch upon this paper .pdf
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WEEK 5 (10/13 and 10/14): Kinetic Proofreading .
- Papers: 10/13 .pdf
and 10/14:.pdf (see Wikipedia for introdcution
to microtubles)
Supplementary Reading: Review on kinetic proofread in T-cell discrimination and our review
on the role of energy consumption in biochemical networks.
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WEEK 6 (10/19 and 10/21): Hodgkin-Huxley and Hopfield. (Note papers are different from syllabus and second paer was changed 11/18)
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WEEK 7 (10/26 and 10/28): Learning in neuroscience.
- Papers: 10/26 .pdf
and 10/21:.pdf
Other reading: Introduction to reinforcement learning (13 pages with math)
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WEEK 8 (11/2 and 11/4): Information theoretic perspective of CNS.
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WEEK 9 (11/9 and 11/11): Single Molecule Biophysics.
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WEEK 9 (11/16 and 11/18): Cellular Economy.
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WEEK 10 (11/23): Microscopy I.
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WEEK 11 (11/30 and 12/2): Microscopy and Sequence/Structure.
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