Schedule
|
Date |
Topic |
Assignments |
|
I: Functional inference - Babbitt |
||
|
9/26 |
Course Intro Molecular evolution and the emergence of new molecular functions |
- |
|
9/27 (Fri) |
- |
|
|
10/1 |
Protein similarity networks: A large-scale context for inference of functional properties in proteins |
Papers assigned |
|
10/3 |
Using the superfamily context for prediction of molecular function |
- |
|
10/4 (Fri) LAB |
Cytoscape Lab & Projects assigned |
|
|
10/8 |
Annotation, misannotation, and bias in annotation in public databases |
- |
|
10/10 |
Critical Assessment of Genome Interpretation, CAGI 2013, a community experiment to evaluate phenotype prediction - Steven Brenner |
- |
|
10/11 (Fri.) |
Paper presentations - students Teams meet with TA to approve project strategy; help session for using computational databases and tools |
Cytoscape Lab Due |
|
10/15 |
in silico docking for prediction of function - Matt Jacobson |
- |
|
10/17 |
PROJECT PRESENTATIONS(plus another time TBA) |
|
|
II: Protein structure, modeling & design - Kortemme |
||
|
10/22 |
Protein structure modeling fundamentals - Kortemme |
Papers assigned |
|
10/24 |
Protein structure prediction & refinement - Kortemme |
|
|
10/25 (Fri.) LAB |
Introduction of team projects & Rosetta Lab (Noah Ollikainen) |
Rosetta Lab & Projects assigned |
|
10/29 |
Protein design I - Kortemme |
|
|
10/31 |
Comparative Modeling (Andrej Sali) |
|
|
11/1 (Fri) |
3:00-4:30 Protein Assemblies (Andrej Sali) Teams meet with TA/Noah to approve project strategy; help session for using Rosetta |
|
|
11/5 |
Paper presentations - students |
|
|
11/7 |
Protein design II - Kortemme |
|
|
11/8 (Fri) |
TEAM PROJECT PRESENTATIONS (students) |
|
|
III: Comparative Genomics & Metagenomics - Pollard |
||
|
11/12 |
Introduction to comparative genomics |
|
|
11/14 |
Bioinformatics, statistics and probability models for comparative genomics |
- |
|
10/15 (Fri) LAB |
Analyzing substitution patterns in multiple sequence alignments with RPHAST |
Lab |
|
11/19 |
Population genomics & medical genetics – Noah Zaitlen |
- |
|
11/21 |
Genome browser demo & lecture – Nadav Ahituv |
|
|
11/22 (Fri) |
Paper presentations - students |
Lab |
|
11/26 |
Functional genomics: data exploration and integration |
- |
|
11/28 |
NO CLASS - THANKSGIVING |
- |
|
11/29 (Fri) |
NO CLASS - HOLIDAY |
- |
|
12/3 |
Phylogenetic methods for metagenomics |
- |
|
12/5 |
Ecological and medical applications of metagenomics |
- |
|
12/6 (Fri) |
PROJECT PRESENTATIONS (plus another time if needed) |
Lab |
Grading:
The class must be taken for a letter grade for BMI track students; other students can take the class for either a letter grade or pass/fail.
100 points are assigned for each unit, for a point total of 300 points for the class and grading will be done separately for each unit. The presentation assignment for each unit requires working in teams students to solve the assigned problem(s) and presenting the results to the rest of the class. Presentations will be graded by the faculty/TA, and all members of the team will receive the same grade. Instructions for the presentation format, other presentation materials, and for lab assignments to be submitted will be posted on the online website for the course.
Discussions for assigned papers will be held as shown in the syllabus. Each student will act as a discussion leader for specific features of assigned discussion papers in the three units and participation is required to pass the course. Instructions for discussion leaders will also be posted on the course website.
Reading assignments, the presentation schedule, and other relevant information will be updated as needed at the online syllabus. Lectures slides will also be available on the course web site, along with past lectures presenting basic information that you may find useful.