MMG1016H - Comparative Genomics - 2010

Instructors: John Parkinson + Zhaolei Zhang
Time: Monday, 2-4 pm
Location: Donnelly Centre (formerly known as CCBR), 160 College Street, 2nd floor, black seminar room,

Assignment Report due
TBD

Assignment presentation
TBD

Course description:
Comparative genomics is the analysis and comparison of genomes from different species. With over 400 genomes now sequenced, comparative genomics offers a powerful tool to provide unique insights into the functional and evolutionary relationships. This course is aimed at teaching some of the fundamental concepts, algorithms and programs that may be applied to the comparative study of genomes. Each class consists of a 1-hour of expert lecture and a 1-hour journal club. In the first hour, an expert faculty will give a guest lecture on a particular topic. In the second hour, two students will give summary presentation (15 minutes) and critique on two pre-assigned papers, followed by class discussions.

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) An analysis project, to be submitted during the last week of class, demonstrating knowledge of the conceptual issues and command of basic techniques. (50%)

Week 1, Monday, 04/26
Course overview and objectives, student activities and grading
Lecture: Dr. Gary Bader
Topic: Protein domains, peptides, motifs, pathways
Paper Assignment:
The dynamic genome of Hydra. Chapman et al Nature 2010, Mar 25
Presenter: Chenyi L.

Week 2. Monday 05/03
Lecture: Dr. Leah Cowen
Topic: Basic concepts and methods in evolutionary biology and comparative genomics
Paper Assignment:
Oxygen content of transmembrane proteins over macroevolutionary time scales
The Human and Mouse Complement of SH2 Domain Proteinsâ Establishing the Boundaries of Phosphotyrosine Signaling
Presenter:Epshita I., Anna S.

Week 3. Monday 05/10
Lecture: Dr. Gabriel (Gabo) Moreno-Hagelsieb
Topic: Comparative genomics of prokaryotes
Paper Assignment:
Chromosomal periodicity of evolutionarily conserved gene pairs
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species
Presenter: Jingjing L., Gavin W.

Week 4. Monday 05/17
Lecture: Dr. Alan Moses
Topic: Evolution of gene regulation
Paper Assignment:
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
Evolutionary tinkering with conserved components of a transcriptional regulatory network.
Presenter: Stephen M., Eniko P.

Week 5. Monday 05/24
Lecturer: Dr. John Parkinson
Topic: Comparative genomics from the perspective of network
Paper Assignment:
A global network of coexisting microbes from environmental and whole-genome sequence data.
Genetic properties influencing the evolvability of gene expression
Presenter: Brad, Elena

Week 6. Monday 05/31
Lecturer: Dr. Zhaolei Zhang
Topic: Mammalian comparative genomics
Paper Assignment:
A Draft Sequence of the Neandertal Genome
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
Presenter: Vincent, Payman