Schedule overview
-----------------

The weekly schedule is below. All sessions are accessed via the `course Zoom link <http://be150.caltech.edu/2021/zoom/>`_.

- Lecture: Mondays, Wednesdays, Fridays 11–11:50 am PDT

- TA homework help sessions

	+ John: Mondays 7–8 pm PDT
	+ Ankita: Tuesdays 3:30-4:30 pm PDT

- TA-led discussion: Thursdays, 11 am-noon PDT

- Instructor office hours

	+ Justin: Fridays 2:30-3:30 PDT
	+ Michael: By appointment

Lectures are recorded and posted on `Google Drive <http://be150.caltech.edu/2021/videos/>`_.


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Homework due dates
------------------

Below are tentative homework due dates.

- :ref:`Homework 1<Homework 1>`: due 11 am PDT, April 7
- :ref:`Homework 2<Homework 2>`: due 11 am PDT, April 14
- :ref:`Homework 3<Homework 3>`: due 11 am PDT, April 21
- :ref:`Homework 4<Homework 4>`: due 11 am PDT, April 28
- :ref:`Homework 5<Homework 5>`: due 11 am PDT, May 5
- :ref:`Homework 6<Homework 6>`: due 11 am PDT, May 12
- :ref:`Homework 7<Homework 7>`: due 11 am PDT, May 19
- :ref:`Homework 8<Homework 8>`: due 11 am PDT, May 26
- :ref:`Homework 9<Homework 9>`: due 11 am PDT, June 2
- :ref:`Homework 10<Homework 10>`: due 11 am PDT, June 3


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Lecture schedule
----------------

Lectures will roughly cover one chapter in the posted materials and will proceed in order. The schedule is subject to change. Under some lectures are suggested readings.

- Before class - :ref:`Chapter 0<0. Configuring your computer to use Python for scientific computing>`: Configuring your computer to use Python for scientific computing

- M 03/29 - :ref:`Chapter 1<1. Introduction to Biological Circuit Design>`: Introduction to biological circuit design (ME)

    + Chapter 1 of Alon

- W 03/31 - :ref:`Chapter 2<2. Introduction to Python for biological circuits>`: Introduction to Python for biological circuits (JB)

- F 04/02 - :ref:`Chapter 3<3. Big functions from small circuits>`: Big functions from small circuits (ME)

    + Chapter 2 of Alon

- M 04/05 - :ref:`Chapter 4<4. Finding biological circuit motifs>`: Motifs in biological circuits (ME)

    + Chapter 4 of Alon

- W 04/07 - :ref:`Chapter 5<5. Analysis of coherent feed forward loops>`: A coherent feed-forward loop can perform dynamic signal processing (JB)

    + Chapter 3 of Alon
    + `Alon, 2007 <https://doi.org/10.1038/nrg2102>`_

- F 04/09 - :ref:`Chapter 6<6. Incoherent feed-forward loops generate pulses, speed responses, and serve as dosage compensators>`: Incoherent feed-forward loops perform pulse generation and dosage compensation (ME)

- M 04/12 - :ref:`Chapter 7<7. Molecular titration generates ultrasensitive responses in biological circuits>`: Molecular titration generates ultrasensitive responses (ME)

- W 04/14 - Guest lecture 1: Ronghui Zhu presents *MultiFate: A scalable architecture for multistability in mammalian cells*

- F 04/16 - :ref:`Chapter 8<8. Robustness in biological circuits>`: Robustness in sensory circuits (JB)

    + Chapters 8 and 9 of Alon
    + Sections 3.2 and 5.7 of Del Vecchio and Murray

- M 04/19 - :ref:`Chapter 9<9. Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition>`: Kinetic proofreading: Multi-step processes reduce error rates in molecular recognition (JB)

    + Chapter 7 of Alon
    + `Chakraborty and Weiss, 2014 <https://doi.org/10.1038/ni.2940>`_

- W 04/21 - :ref:`Chapter 10<10. Blinking bacteria: The repressilator enables self-sustaining oscillations>`: Blinking bacteria: delayed negative feedback circuits generate periodic oscillations (ME)

    + `Elowitz and Leibler, 2000 <https://doi.org/10.1038/35002125>`_
    + `Potvin-Trottier, et al., 2016 <https://doi.org/10.1038/nature19841>`_ (`News and Views <https://doi.org/doi:10.1038/nature19478>`_)

- F 04/23 - :ref:`Chapter 11<11. Oscillators, part II: Uses, simplifications, and elaborations of negative feedback oscillators>`: Oscillators II: Applications and alternative architectures (ME)

    + `Lewis, 2003 <https://doi.org/10.1016/S0960-9822(03)00534-7>`_
    + `Stricker, et al., 2008 <https://doi.org/10.1038/nature07389>`_

- M 04/26 - :ref:`Chapter 12<12. Gene expression is noisy! How stochastic effects lead to heterogeneity>`: The noise inside the cell: How stochastic gene expression produces cellular heterogeneity (JB)

    + Appendix D of Alon
    + `Elowitz, et al., 2002 <https://doi.org/10.1126/science.1070919>`_

- W 04/28 - :ref:`Chapter 13<13. Bursty gene expression>`: Bursty gene expression enables regulation of protein variability (JB)

    + Section 4.1 of Del Vecchio and Murray
    + `Cai, et al., 2006 <https://doi.org/10.1038/nature04599>`_
    + `Singer, et al., 2014 <http://dx.doi.org/10.1016/j.molcel.2014.06.029>`_

- F 04/30 - :ref:`Chapter 14<14. Stochastic simulation of biological circuits>`: Simulating stochastic circuit dynamics (JB)

    + Section 4.2 of Del Vecchio and Murray

- M 05/03 - :ref:`Chapter 15<15. Stochastic differentiation>`: Excitable circuit dynamics enable probabilistic, transient differentiation (JB)

    + `Süel, et al., 2006 <https://doi.org/10.1038/nature04588>`_
    + `Süel, et al., 2007 <https://doi.org/10.1126/science.1137455>`_
    + `Rue and Garcia-Ojalvo, 2011 <https://doi.org/10.1016/j.mbs.2011.02.013>`_

- W 05/05 - :ref:`Chapter 16<16. Cellular bet-hedging>`: Bacterial bet-hedging and antibiotic persistence (ME)

    + `Kussell and Leibler, 2005 <https://doi.org/10.1126/science.1114383>`_
    + `Rotem, et al., 2010 <https://doi.org/10.1073/pnas.1004333107>`_

- F 05/07 - :ref:`Chapter 17<17. Time-based regulation in cells>`: Time-based regulation coordinates gene expression (ME)

    + `Cai, et al., 2008 <https://doi.org/10.1038/nature07292>`_
    + `Lin, et al., 2015 <https://doi.org/10.1038/nature15710>`_

- M 05/10 - :ref:`Chapter 18<18. Paradoxical regulation in intra- and intercellular circuits>`: Paradoxical circuits enable switch-like responses and linear amplification (JB)

    + `Hart, et al., 2012 <https://doi.org/10.1073/pnas.1117475109>`_
    + `Hart, et al., 2014 <https://doi.org/10.1016/j.cell.2014.07.033>`_
    + `Karin and Alon, 2017 <https://doi.org/10.15252/msb.20177599>`_

- W 05/12: Special guest lecture 2: `Lacromioara Bintu <https://bintulab.com>`_ presents *Principles of chromatin-based regulation*

- F 05/14 - Chapter 19: Cis-interactions enable unidirectional signaling (ME)

    + `Sprinzak, et al., 2010 <https://doi.org/10.1038/nature08959>`_

- M 05/17 - Chapter 20: Promiscuous ligand-receptor interactions allow combinatorial signal processing (ME)

    + `Antebi, et al., 2017 <https://doi.org/10.1016/j.cell.2017.08.015>`_

- W 05/19 - :ref:`Chapter 21<21. Turing patterns>`: Local activation and long-ranged inhibition can generate periodic spatial (Turing) patterns (JB)

    + `Turing, 1952 <https://doi.org/10.1098/rstb.1952.0012>`_

- F 05/21 - No class; Ditch Day!

- M 05/24 - Special guest lecture 3: `Uri Alon <https://www.weizmann.ac.il/mcb/UriAlon/>`_ presents a special lecture and song on systems medicine

- W 05/26 - :ref:`Chapter 22<22. Scaling reaction-diffusion patterns>`: Feedbacks and scaling in morphogenetic patterning (JB)

    + `Ben-Zvi, et al., 2010 <https://doi.org/10.1073/pnas.0912734107>`_
    + `Werner, et al., 2015 <https://doi.org/10.1103/PhysRevLett.114.138101>`_

- F 05/28 - Course recap and the future of understanding and programming genetic circuitry (ME)