Term: Fall 2006
Time:
- Tuesdays 1:30-3:20 pm (Lectures)
- Wednesdays 1:30-3:30 pm (Graduate Labs)
- Wednesdays 3:30-5:20 pm (Undergrate Labs)
- Thursdays 1:30-3:20 pm (Undergrate Labs)
Instructor: Jack Chen
TA: Amber Fedynak
Note: Lab attendance mandatory!
| Lectures | Date (2006) | Topic | Slides | Labs |
|---|
| 1 | Sep 5 | What is bioinformatics? History of Bioinformatics | Slides | 1 |
| Gene, molecular genetics, epigenetics, molecular cloning, the Human Genome Project, comparative genomics, functional genomics, structural genomics, metagenomics, cancer genomics, brain genomics, interactome, transcriptome, proteomics, SNPs & HapMap, personalized medicine, computational biology, systems biology, bioinformatics, beyond bioinformatics |
References
|
| 2 | Sep 12 | Biological databases and data models | Slides | 2 |
| GenBank, Ensembl, UCSC browser, MODs, FASTA, GFF, DBMS |
References
|
| 3 | Sep 19 | Pair-wise sequence alignment and database searching | Slides | 3 |
| Dynamic programming, Smith-Waterman algorithm, Needleman-Wunsch algorithm, BLAST |
References
|
| 4 | Sep 26 | Perl programming and bioinformatics - basics | Slides | 4 |
| UNIX, regular expressions, operators, I/O, control structures, arrays, hashes, file handle, subroutines |
References
|
| 5 | Oct 3 | Perl programming and bioinformatics - advanced | Slides | 5 |
| Modules, OO Perl, CPAN, BioPerl, CGI, DBI, GD |
References
|
| 6 | Oct 10 | Multiple-sequence alignment and molecular evolution | Slides | 6 |
| BLASTZ, WABA, Clustal, Phylip |
References
|
| 7 | Oct 17 | Protein analysis - structure and function | Slides | 7 |
| PFAM, TMHMM |
References
|
| 8 | Oct 24 | Introduction to genome analysis | Slides | 8 |
| WGS, RepeatMasker, Gene finding, RFAM, TreeFAM |
References
|
| 9 | Oct 31 | Gene prediction | Slides | 9 |
| HMM, GenScan, GeneWise, Exonerate, GLEAN |
References
|
| 10 | Nov 7 | Data visualization and GMOD | Slides | 10 |
| GD, Bio::Graphics, SO, GFF3, Gbrowse,
GenePattern |
References
|
| 11 | Nov 14 | Current topics in bioinformatics: comparative genomics | Slides | No Lab |
| Phylogenetic analysis, molecular evolution, ultraconserved elements, gene family evolution, ENCODE, modENCODE |
References
|
| 12 | Nov 21 | Current topics in bioinformatics: functional genomics | Slides | No Lab |
| EST, microarray, SAGE, CAGE, GIS, ChIP-Chip, ChIP-PET |
References
|
| 13 | Nov 28 | Current topics in bioinformatics: RNAs | Slides | No Lab |
| mRNA, tRNA, rRNA, microRNA, siRNA |
References
|
