Introduction to Bioinformatics (Fall 2015; 3 CR)
Schedule
- Week 1
- Mon (24th Aug): Course overview (notes)
- Wed (26th Aug): Python basics (notes)
- Lab: Linux basics & Python
- Week 2
- Week 3
- Mon (7th Sep): No class (Labor day)
- Wed (9th Sep): Sequence comparison (slides-1 slides-2)
- Lab: Genebank & BLAST (optional: Github)
- Week 4
- Mon (14th Sep): Sequence comparison (Cont.)
- Wed (16th Sep): Sequence database searching (slides)
- Lab: Cluster Analysis (in R), CD-HIT, and usearch
- Week 5
- Mon (21st Sep): Clustering algorithms (UPGMA and others) (slides/2013; Cluster analysis in R)
- Wed (23rd Sep): Multiple sequence alignment (slides)
- Lab: Multiple alignment tools (ClustalW, Muscle, and Jalview) & Phylogeny tools (PHYLIP and MEGA)
- Week 6
- Week 7
- Week 8
- Mon (12th Oct): Gene finding (slides)
- Wed (14th Oct):
- Lab: Assemblers (Phrap & Velvet) & Genome browsers (UCSC genome browser)
- Week 9
- Mon (19th Oct): Review
- Wed (21st Oct): Midterm
- Lab: samtools & VCFtools
- Week 10
- Week 11
- Mon (2nd Nov): Indexing (hashing, suffix array & BWT) (slides; notes)
- Wed (4th Nov): RNA-seq & ncRNA (slides; notes)
- Lab: edgeR
- Week 12
- Mon (9th Nov): Epigenomics (ChIP-seq) (notes) & Gene regulatory network (notes)
- Wed (11th Nov): Metagenomics (slides)
- Lab: MEGAN
- Week 13
- Week 14
- Mon (23rd Nov): Happy Thanksgiving!
- Wed (25th Nov):
- Lab:
- Week 15
- Week 16
- Week 17
- Mon (14th Dec): no class
- Wed (16th Dec): no class