Instructors: Vineet Bafna and Dr. Trey Ideker
Lectures: MW 9:30-10:50am, BMRF 1104
Office hours
TA: Ryan O' Neil: Thursday 11-12pm, Leichtag Lobby
Dr. Vineet Bafna Monday 11-12pm, CSE 4218
Dr. Trey Ideker Wednesday 11-12pm, BRF2 3A13
| Assignment | Due date | Data | ||
|---|---|---|---|---|
| Problem set 2 | 4/18/14 | |||
| Problem set 3 | 4/25/14 | Arabidopsis | New Website | |
| Problem set 4 | 5/2/14 | yeast_aaseqs.txt | yeast_microarraydata2.txt | yeast_phyloprofiles2.txt |
| Problem set 5 | 5/12/14 | Arabidopsis | A.txt | b.txt |
| Problem set 6 | 5/30/14 | |||
| Practice Midterm | ||||
| Projects | 6/13/14 | |||
| PHS398 Instructions and Forms | ||||
| Example successful bioinformatics R01 application |
Lectures
| Lecture | Topic | Slides | Suggested Reading |
|---|---|---|---|
| Week 1: 3/31, 1/2 (No Class) | Functional genomics data sources
|
Lecture slides |
Ideker T, Dutkowski J, Hood L. Metzker ML. Segrè AV >/a> |
| Week 2 (4/7, 4/9) |
Data sources: processing NGS data
Indexing databases: BW Transform Indexing queries: Aho-Corasick tries |
Lecture slides |
Jay Shendure (RNA-seq commentary) Li H, Durbin R (BWA). FM index (based on BW transform) Wiki Aho Corasick Trie Wiki Roberts et al. (TopHat/CuffLinks) iReckon |
| Week 3 (4/14, 4/16) |
Introduction to Mass spectrometry
Peptide identification Isotopic analysis MS based quantification Other applications |
Lecture slides |
Introductory notes
De novo identification Validation of peptides MaxQuant for quantification Protein Prospector tools |
| Week 4 (4/21, 4/23) | Clustering methods | Lecture slides | |
| Week 5,6 (4/28, 4/30, 5/5, 5/7) |
Supervised classification
Geometry basics, hyperplane separation LDA ML discrimination Linear programming |
Classification | LP wiki |
| Week 6 (5/5, 5/7) |
Support vector machines Kernel methods Dimensionality reduction |
Classification 2 |
SVM Wiki
|
| Week 7 | Inferring gene regulatory networks | Lecture slides | |
| Week 8 | Protein Network Anaylsis | Lecture slides | |
| Week 9 | |||
| Week 10 |