Schedule

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)

01 CancerSystemsPharmacology (intro lecture slides)

01 CancerSystemsPharmacology (intro lecture presentation)

Good online reference:

• Introduction to Bioimage Analysis by Pete Bankhead.

Download FIJI (FIJI is just ImageJ)

• Get FIJI here

Lecture slides (PDF)

02 Digital Image Analysis (slides)

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)

Lecture notebook (ipynb) and recordings (MP4)

Image processing in Python - Jupyter notebook
Image processing in Python - lecture video

Lecture notebook (ipynb) and recordings (MP4)

Dose-response relationships - Jupyter notebook
Dose-response using Thunor - Jupyter notebook
Dose-response relationships - lecture recording

Lecture recording (MP4)