Lectures
You can download the lectures here. We will try to upload lectures prior to their corresponding classes.
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Quantitative Systems Pharmacology
tl;dr: An overview of the multiple steps involved in quantifying concentration-dependent drug responses at the single-cell level using live-cell microscopy.
[fracprolif] [diprate] [clonalfracprolif] [thunor]
Relevant papers:
fracprolif: Tyson DR, Garbett SP, Frick PL, Quaranta V. Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data. Nat Methods. 2012 Sep; 9 923-928. doi:10.1038/nmeth.2138. PubMed PMID: 22886092. PMCID: PMC3459330.diprate: Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR. An unbiased metric of antiproliferative drug effect in vitro. Nat Methods. 2016 06; 13(6) 497-500. doi:10.1038/nmeth.3852. PubMed PMID: 27135974. PMCID: PMC4887341.clonalfracprolif: Frick PL, Paudel BB, Tyson DR, Quaranta V. Quantifying heterogeneity and dynamics of clonal fitness in response to perturbation. J Cell Physiol. 2015 Jul; 230(7) 1403-1412. doi:10.1002/jcp.24888. PubMed PMID: 25600161. PMCID: PMC5580929.thunor: Lubbock ALR, Harris LA, Quaranta V, Tyson DR, Lopez CF. Thunor: visualization and analysis of high-throughput dose-response datasets. Nucleic Acids Res. 2021 07 02; 49(W1) W633-W640. doi:10.1093/nar/gkab424. PubMed PMID: 34038546. PMCID: PMC8265171.musyc: Meyer CT, Wooten DJ, Paudel BB, Bauer J, Hardeman KN, Westover D, Lovly CM, Harris LA, Tyson DR, Quaranta V. Quantifying Drug Combination Synergy along Potency and Efficacy Axes. Cell Syst. 2019 02 27; 8(2) 97-108.e16. doi:10.1016/j.cels.2019.01.003. PubMed PMID: 30797775. PMCID: PMC6675406.
Lecture slides (PDF) and recordings (MP4)
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Digital Image Analysis
tl;dr: Overview of digital image analysis, application to biological samples using microscopy, live-cell imaging reporters and software tools
Good online reference:
- Introduction to Bioimage Analysis by Pete Bankhead.
Download FIJI (FIJI is just ImageJ)
Lecture slides (PDF)
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Population growth models
tl;dr: Background on cell proliferation, basic mathematical models of population growth, analysis of dynamic cell count data, performing linear and nonlinear regression of models fit to cell count data, and create functions in Python to perform calcuations
[fracprolif] [diprate]
Jupyter Notebook for class:
03 Population Growth Dynamics (iPython notebook)
Lecture slides (PDF) and recordings (MP4)
03 Population Growth Dynamics (slides as PDF)
03 Population Growth Dynamics (lecture recording) -
Digital Image Analysis 2
tl;dr: Digital image analysis in Python
[improc2_notebook] [improc2_lecture]
Lecture notebook (ipynb) and recordings (MP4)
Image processing in Python - Jupyter notebook
Image processing in Python - lecture video -
Dose-Response Models
tl;dr: Log-logistic (Hill) model equations and how to fit them to drug-response data using nonlinear regression.
[doseresponse_notebook] [thunorcolab_notebook]
Lecture notebook (ipynb) and recordings (MP4)
Dose-response relationships - Jupyter notebook
Dose-response using Thunor - Jupyter notebook
Dose-response relationships - lecture recording -
Class Summary
tl;dr: Review of homework assignments and prep for final assignment.
[doseresponse_notebook] [thunorcolab_notebook]
Lecture recording (MP4)