ThursSep 13 |
Introduction
to genomics & computational biology Lecturers:
Singh & Tavazoie Readings:
Genomes, chapter 1, Recombinant DNA
Ch. 1-3 |
|
Tues Sep 18 |
Sequencing
& mapping Lecturer:
Tavazoie Readings:
Genomes, chapter 2-4 |
|
Thurs Sep 20 |
Sequence
alignment & database search Lecturer:
Singh Readings:
Lecture Notes |
|
Tues Sep 25 |
Sequence
alignment & database search Lecturer:
Singh Readings:
Lecture Notes Assignment: PS1, due 10/9 |
|
Thurs Sep 27 |
Transcriptional
regulation in prokaryotes and eukaryotes Lecturer:
Tavazoie Readings:
Recombinant DNA Ch. 4,9 |
|
Tues Oct 2 |
Technologies
for monitoring transcriptional networks Lecturer:
Tavazoie Readings:
Lockhart & Winzeler |
|
Thurs Oct 4 |
Introduction
to motifs/profiles Lecturer:
Singh Readings: Lecture Notes |
|
Tues Oct 9 |
EM
& Gibbs sampling approaches to motif finding Lecturer:
Singh Readings:
Lawrence and Reilly, Lawrence et al. Assignment: PS2, due 10/23 |
|
Thurs Oct 11 |
Transcriptional
networks: analysis I Lecturer:
Tavazoie Readings:
Eisen et al, Tavazoie et al., Quackenbush |
|
Tues Oct 16 |
Transcriptional
networks: analysis II Lecturer:
Tavazoie Readings:
Tavazoie et al. |
|
Thurs Oct 18 |
Hidden
Markov models Lecturer:
Singh |
|
Tues Oct 23 |
Phylogenetic
reconstruction Lecturer:
Singh Readings: Lecture Notes Assignment: PS3, due 11/13 |
|
Thurs Oct 25 |
Transcriptional
profiling in diagnosis and prognosis of disease Guest Lecturer: D. NottermanReadings: Alon et al. |
|
Tues Oct 30 |
Fall Break |
|
Thurs Nov 1 |
Fall Break |
|
Tues Nov 6 |
Gene
finding Lecturer:
Singh |
|
Thurs Nov 8 |
Secondary
Structure Prediction Lecturer:
Singh Final project proposals due |
|
Tues Nov 13 |
Threading Lecturer:
Singh Assignment: PS4, due 11/29 |
|
Thurs Nov 15 |
Proteomics
Lecturer:
Tavazoie Readings:
Gygi et al. |
|
Tues Nov 20 |
Functional
genomics: From genotype to phenotype to fitness Lecturer:
Tavazoie Readings:
Winzeler et al. |
|
Thurs Nov 22 |
Thanksgiving |
|
Tues Nov 27 |
Experimental
analysis of bi-molecular interactions Lecturer:
Tavazoie Readings: Uetz et al., Ito et al. |
|
Thurs Nov 29 |
Networks
I Lecturer:
Tavazoie Readings:
von Dassow et al., Alon et al. |
|
Tues Dec 4 |
Predicting
Protein-Protein Interactions Lecturer:
Singh |
|
Thurs Dec 6 |
Networks
II Lecturer:
Tavazoie Readings: Jeong et al., Wagner |
|
Tues Dec 11 |
Class Presentations |
|
Thurs Dec 13 |
Class Presentations |