| Date | | Topic | Readings and other activities
|
| 1/9 | T | What is bioinformatics, data types, and access | BFG chapter 1,2
|
| 1/11 | R | Programming I: Unix basics and programming environments | Guest lecture: Sarah Payok (ACNS). PT chapter 2, exercise 1
|
| 1/16 | T | Pairwise sequence alignment | BFG chapter 3
|
| 1/18 | R | Programming II: Data types and control flow | PT chapter 3,4, exercise 2
|
| 1/23 | T | Database search | BFG chapter 4
|
| 1/25 | R | Programming III: Data structure, modules, and IO | PT chapter 5,6,7 exercise 3
|
| 1/30 | T | Genome sequencing and assembly |
|
| 2/1 | R | Programming IV: Error handling, Biopython, database programming | PT chapter 8, exercise 4
|
| 2/6 | T | Gene prediction, annotation |
|
| 2/8 | R | Mid-term I |
|
| 2/13 | T | Gene expression and its regulation I | BFG chapter 6, selected papers
|
| 2/15 | R | Gene expression and its regulation II | Selected papers, exercise 5
|
| 2/20 | T | Gene expression and its regulation III | BFG chapter 6
|
| 2/22 | R | Microarray and array data analysis | BFG chapter 7, expercise 6
|
| 2/27 | T | The R project and bioconductor | Exercise 5
|
| 3/1 | R | Proteins, proteomics, and data analysis | BFG chapter 8, exercise 7
|
| 3/5-3/9 | | Spring break |
|
| 3/13 | T | Protein structure and pattern finding | BFG chapter 9, Project team selection
|
| 3/15 | R | Protein and genetic interaction networks | Selected papers
|
| 3/20 | T | Mid-term II |
|
| 3/22 | R | Metabolomics | Guest lecture: Yair Shachar-Hill (PLB). Project topic selection start
|
| 3/27 | T | Metabolic network analysis | Guest lecture: Yair Shachar-Hill (PLB)
|
| 3/29 | R | Metabolic flux analysis | Guest lecture: Yair Shachar-Hill (PLB). Project topic finalized, exercise 8
|
| 4/3 | T | Multiple sequence alignments | BFG chapter 10
|
| 4/5 | R | Sequence evolution and phylogeny | BFG chapter 11
|
| 4/10 | T | Genome evolution | BFG chapter 11
|
| 4/12 | R | Machine learning | Guest lecture: Rong Jin (CSE). Selected papers, Project progress report due
|
| 4/17 | T | Data mining | Guest lecture: Pan-Ning Tan (CSE).Selected papers
|
| 4/19 | R | Bioinformatics and systems biology | Selected papers
|
| 4/24 | T | Student presentation on project outcomes | ISMB meeting abstracts for discussion on 4/26
|
| 4/26 | R | Discussion the current and future impacts of genomics, bioinformatics, and systems biology | Project report due
|
| 4/30-5/4 | | Final exam |
|
