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
- Mon (31st Aug): Algorithm basics (notes)
- Wed (2nd Sep): Probability basics and elementary statistics
- Lab: R basics & statistical tests
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
- Mon (28th Sep): Phylogeny (slides)
- Wed (30th Sep): Genome sequencing (video1; video2; slides; Next-Gen Sequencing 2014 Update; MinION: a portable analysis device; The problem of the seven bridges of Konigsberg)
- Lab: MEGA, fastq & FastQC
Week 7
- Mon (5th Oct): Genome assembly (video; slides; graph basics)
- Wed (7th Oct):
- No Lab -- Fall Break
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
- Mon (26th Oct): Genome comparison (Are there fragile regions in the human genome?; slides) & Genomic variants (notes)
- Wed (28th Oct):
- Lab: bowtie2 & BWA
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
- Mon (16th Nov): Protein bioinformatics (slides | PDB | Molecular Machinery | CRISPR RNA–guided surveillance complex )
- Wed (18th Nov):
- Lab: Modeller
Week 14
- Mon (23rd Nov): Happy Thanksgiving!
- Wed (25th Nov):
- Lab:
Week 15
- Mon (30th Nov): Functional annotation (slides | slides2)
- Wed (2nd Dec): Proteomics (slides | video: Chapter 11 playlist 1-5)
- Lab: Cytoscape & KEGG
Week 16
- Mon (7th Dec): Biological networks & systems biology (slides | A definition of Systems Biology | Gene regulatory network)
- Wed (9th Dec): Group project presentation
- Lab: in-lab final exam
Week 17
- Mon (14th Dec): no class
- Wed (16th Dec): no class