Gene and Protein Evolution - Spring 2016

Instructors: Hue Sun Chan, Zhaolei Zhang
Time: Weekly Wednesday 3-5pm, February 24 - March 30, 2016
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 projec - a mock grant LOI. (50%)

Week 1, Feb 24, 3-5PM, Wednesday
Lecturer: Zhaolei Zhang
Topic: introduction to molecular evolution, mutation and selection, phylogenetic trees
Lecture slides are here

Week 2, March 02, 3-5PM, Wednesday
Lecturer: Zhaolei Zhang
Topic: Use Population Genetics to Detect Positive Selection
Lecture slides are here

Paper for discussion :

Science. 2013 Dec 13;342(6164):1367-72.
Exonic transcription factor binding directs codon choice and affects protein evolution.
Stergachis AB , Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA.

Cell. 2010 Apr 16;141(2):355-67.
A role for codon order in translation dynamics.
Cannarozzi G , Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y

Cell. 2015 Mar 12;160(6):1111-24.
Codon optimality is a major determinant of mRNA stability.
Presnyak V , Alhusaini N1, Chen YH , Martin S , Morris N , Kline N , Olson S, Weinberg D , Baker KE , Graveley BR , Coller J .

Week 3, March 09, 3-5PM, Wednesday
Lecturer: Zhaolei Zhang
Topic: Evolution of gene expression and gene regulation
Lecture slides are here

Paper for discussion :

Science. 2012 Jul 6;337(6090):64-9
Evolution and functional impact of rare coding variation from deep sequencing of human exomes.
Tennessen JA1, Bigham AW, O'Connor TD et al

Science. 2013 Mar 29;339(6127):1578-82.
Multiple instances of ancient balancing selection shared between humans and chimpanzees.
Leffler EM, Gao Z, Pfeifer S, ... Donnelly P, McVean G, Przeworski M.

Nature 468, 811–814 (09 December 2010)
Gene expression divergence recapitulates the developmental hourglass model
Kalinka AT1, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P.

Week 4, March 16, 3-5PM, Wednesday
Lecturer: Brandon Xia (McGill)
Topic: Evolution of protein structure, interaction, and network.
Paper Assignment:

Nature. 2015 Jul 16;523(7560):361-5.
Intersecting transcription networks constrain gene regulatory evolution
Sorrells TR, Booth LN, Tuch BB, Johnson AD

Cell. 2015 Jan 29;160(3):554-66
Enhancer Evolution across 20 Mammalian Species
Villar D, Berthelot C, … Flicek P, Odom DT

Week 5, March 23, 3-5PM, Wednesday
Lecturer: Hue Sun Chan
Topic: Synergy between the studies of protein biophysics and protein evolution
Lecture slides are here

Week 6, March 30, 3-5PM, Wednesday
Lecturer: Hue Sun Chan
Topic: Theory of protein sequence space organization and the dynamics of molecular evolution
Lecture slides are here