Course: BBS705 - Molecular Evolution

Spring 2016 (February through May)

Classes are held Tuesdays 9:00 - 11:00 am in AS4-1073.

Instructors: Jeffrey Bailey, Daniel Caffrey, Evgeny Rogaev, Zhiping Weng, Konstantin Zeldovich

Syllabus: The course will focus on the quantitative study of molecular evolution using sequence and structural data, showing how both classical and novel methods in population genetics, bioinformatics and computational biology can be used to assess the variability in the genomic sequences and make inferences about the underlying processes of natural selection and evolution. The course is primarily aimed at the students interested in quantitative aspects of biology, and may be useful to practicing biologists desiring a deeper understanding of the computational and statistical techniques.

Specific topics will include:

Populations, variation, and evolution. Population genetics and the site frequency spectrum. Expected patterns of genomic variation. Finding and describing selection in the genome.

Gene evolution through segmental duplication, exon shuffling and concerted evolution. Large-scale genome evolution: synteny and chromosomal morphology.
Using evolutionary theory to identify transcription factor binding sites and miRNA target sites.

Evolution of protein structures and sequences from biophysics and systems biology perspective. Evolvability, robustness, and rates of evolution in proteins.

Evolution of protein subfamilies (and their binding sites) following gene duplication, algorithmic aspects of homology searching, multiple sequence alignment, and tree reconstruction.

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