Schedule and Readings
Due Tuesday, 8 February (4:59pm): Project 1
Before Wednesday, 9 February:
- Read Chapter 19 – 26 of Hubert’s The DNA Book. (Chapter 26 on Mutations and Changes is the one most relevant to today’s class.)
- Read Chapter 5 of the Bioinformatics Algorithms: How do we compare biological sequences?.
Before Monday, 14 Feb:
- Chapter 26 of Manolis Kellis et al., Computational Biology - Genomes, Networks, and Evolution: Molecular Evolution and Phylogenetics (also available as [PDF]) (if you prefer to watch a video lecture that this chapter is based on, you can watch MIT CompBio Lecture 19 - Phylogenetics).
Slides
The slides from the 7 February class are here: class6.pdf
Some links to materials for the class:
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R. Peto, F. J. Roe, P. N. Lee, L. Levy, and J. Clack. Cancer and ageing in mice and men, British Journal of Cancer, October 1975. (“Peto’s Paradox”).
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Orsolya Vincze, et al. Cancer risk across mammals, Nature, 22 December 2021. This is the paper with the diagram showing the cancer mortality risk variation across different orders of mammals (an “order” is taxonomic rank above a family).
- See also this video (thanks Grant!): Why Blue Whales Don’t Get Cancer - Peto’s Paradox (which is based on this paper: John D. Nagy, Erin M. Victor, Jenese H. Cropper, Why don’t all whales have cancer? A novel hypothesis resolving Peto’s paradox, 2007.
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Temple Smith and Michael S. Waterman, Identification of Common Molecular Subsequences, 1981.
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The notebook I used is: class6.ipynb.