Schedule and Readings
(These are duplicated from Class 7.)
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).
Thursday, 24 Feb:
Slides
The slides from the 14 February class are here: class8.pdf
Links
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The graph on Covid virus samples is from: Massachusetts Water Resrouces Authority Wastewater COVID-19 Tracking.
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Mariana Guadalupe Matus Garcia. Analysis of fecal biomarkers to impact clinical care and public health. MIT PhD Dissertation (Computational and Systems Biology), September 2018. (If you think PhD dissertations need to be intiminating, long, documents, please look at this one! Its only about 50 double-spaced sparse pages long, if you don’t count the appendices, which are mostly pictures and directions of how you sample sewage.) The company that she co-founded that produced the data for the MWRA COVID-19 Tracking graph is Biobot Analytics.
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John C Avise, Robert A Lansman, Rosemary O Shade. The use of Restriction Endonucleases to Measure Mitochondrial DNA Sequence Relatedness in Natural Populations. Genetics, May 1979.
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Joel D. Velasco. The prior probabilities of phylogenetic trees. Biology and Philosophy. 208.
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Yoshihito Niimura, Atsushi Matsui1, and Kazushige Touhara. Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Genome Research, 22 July 2014.
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Yoav Gilad, Victor Wiebe, Molly Przeworski, Doron Lancet, Svante Pääbo. Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates, PLOS Biology, January 2004. (This is the paper that establishes correlation with color vision and loss of olfactory receptor genes.)