Evolutionary Bioinformatics: Trees, Sequences and the Comparative Method

Catalog description

An advanced introduction to the evolutionary concepts and bioinformatic skills that are central to molecular, cell, developmental, and microbiology. Proteins that share common ancestry also share functional properties. This is the guiding principle of model organism research and sequence-based bioinformatics. Evolutionary trees (phylogenies) and multiple sequence alignments provide evidence for predicting structural and functional constraints, sites of molecular interaction, and residues that confer functional specificity. In 2021, phylogenetics is emerging as an essential technique in metagenomics, cancer, and infectious disease, driven by technological advances such as high through-put sequencing and single-cell phenotyping. This course covers both the conceptual foundation and the practical skills of evolutionary bioinformatics. Students will acquire the "tree thinking" skills required for critical interpretation of phylogenetic analyses and figures in the literature and a rigorous understanding of phylogenetic inference methods. Theoretical knowledge will be complemented by hands-on experience with sequence data repositories, bioinformatic tools for database retrieval, sequence analysis, and tree building. Students will walk out of the course with the knowledge required to apply those tools correctly to messy, genuine data sets, and the ability to evaluate alternate hypotheses in light of these bioinformatic analyses. Students with a range of computational backgrounds are welcome. Prerequisites: 03-121 or 03-151 Course Website: http://www.cs.cmu.edu/~durand/Phylogenetics/