Gene and Protein Evolution - Spring 2018

Instructors: Hue Sun Chan, Zhaolei Zhang
Time: Weekly Friday 2-4 pm, February 09 - March 16, 2018
Location: MSB 4174
Course description: see here

Student activities and grading:
The final grade will consist of the following four parts.
(1) Attendance of each lecture on time. (10%)
(2) Journal club presentation. (25%)
(3) Class participation. Students will be quizzed randomly on the papers being discussed. (15%)
(4) Final project - a mock grant LOI. (50%)

Week 1, Feb 09, 2-4 PM, Friday
Instructor: Zhaolei Zhang
Topic: introduction to molecular evolution, mutation and selection, phylogenetic trees

Paper for discussion :
Lek et al, Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016
Cassa et al. Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nature Genetics 2017

Week 2, Feb 16, 2-4 PM, Friday
Instructor: Zhaolei Zhang
Topic: Population genetics techniques in finding selection in genes.

Paper for discussion :
Samocha et al A framework for the interpretation of de novo mutation in human disease. Nature Genetics 2014
Drummond and Wilkes Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008

Week 3, Feb 23, 2-4 PM, Friday
Instructor: Zhaolei Zhang
Topic: Evolution of gene expression and gene regulation

Paper for discussion :
Lachance et al, Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 2012
Kachroo et al, Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science 2015

Week 4, Marcg 02 2-4 PM, Friday
Instructor: Gary Bader
Topic: Gene Families, Protein Domains, Sequence Motifs

Paper for discussion :
Villar et al Enhancer Evolution across 20 Mammalian Species, Cell 2015
Kalinka et al Gene expression divergence recapitulates the developmental hourglass model, Nature 2010

Week 5, Marcg 09 2-4 PM, Friday
Instructor: Hue Sun Chan
Topic: Biophysics of protein evolution and Evolutionary protein biophysics (I)

Week 4, Marcg 16 2-4 PM, Friday
Instructor: Hue Sun Chan
Topic: Biophysics of protein evolution and Evolutionary protein biophysics (II