"Algorithms for Genomic Data"
Fall 2015
| No. | Date | Topics | Notes | Homework |
|---|---|---|---|---|
| 1 | Wed, Sept 9 | Goals of computational biology Genetics overview |
lec1.pdf | |
| 2 | Fri, Sept 11 | Next-generation sequencing overview String alignment |
lec2.pdf Board photos 2 handout1.pdf |
|
| 3 | Mon, Sept 14 | String alignment (back-tracing) Research papers intro |
Board photos 3
handout2.pdf handout3.pdf Interactive string matching demo |
Velvet Assembler Paper |
| 4 | Wed, Sept 16 | Genome assembly | lec4.pdf Board photos 4 handout4.pdf |
Homework 1: String Alignment |
| 5 | Fri, Sept 18 | Genome assembly (Velvet) | lec5.pdf Board photos 5 |
|
| 6 | Mon, Sept 21 | Burrows Wheeler Transform (BWT) | Board photos 6 handout5.pdf handout6.pdf |
Bowtie Aligner Paper |
| 7 | Wed, Sept 23 | Pattern matching with BWT | Board photos 7 handout7.pdf |
Homework 2: Genome Assembly |
| 8 | Fri, Sept 25 | Alignment with BWT (Bowtie) | lec8.pdf | |
| 9 | Mon, Sept 28 | Phylogenetics (UPGMA) | Board photos 9 | |
| 10 | Wed, Sept 30 | UPGMA (cont) | Board photos 10 handout8.pdf handout9.pdf |
Neighbor-Joining Paper |
| 11 | Fri, Oct 2 | Neighbor-Joining | Board photos 11 | Homework 3: BWT |
| 12 | Mon, Oct 5 | Neighbor-Joining (paper) | lec12.pdf | |
| - | Wed, Oct 7 | MOUNTAIN DAY | 13 | Fri, Oct 9 | Perfect Phylogeny | Numpy Notes
Board photos 13 handout10.pdf handout11.pdf |
Homework 4: Phylogenetic Trees |
| - | Mon, Oct 12 | AUTUMN RECESS | ||
| 14 | Wed, Oct 14 | Perfect Phylogeny (cont) | Board photos 14 | 15 | Fri, Oct 16 | Fitch's Algorithm Sankoff's Algorithm |
lec15_board1.jpg lec15_board2.jpg lec15_board3.jpg handout12.pdf |
Ancestral
Reconstruction Paper handout13.pdf |
| 16 | Mon, Oct 19 | Population Genetics overview | lec16.pdf Board photos 16 |
Homework 5: In-class presentation |
| 17 | Wed, Oct 21 | Ancestral Genome paper (Black Death agent) | lec17.pdf | 18 | Fri, Oct 23 | Measures of sequence diversity | lec18_board1.jpg lec18_board2.jpg |
| 19 | Mon, Oct 26 | SFS exercises Start PCA |
Board photos 19 PCA Tutorial handout14.pdf |
|
| 20 | Wed, Oct 28 | PCA in genomics | Board photos 20 | midterm.pdf midterm.py midterm_sol.pdf midterm_sol.py rubric.txt |
21 | Fri, Oct 30 | Modeling recombination | Board photos 21 Recombination notes Recombination video |
| 22 | Mon, Nov 2 | Finish recombination Natural selection |
lec22.pdf Board photos 22 |
|
| 23 | Wed, Nov 4 | Finish natural selection | Board photos 23 handout15.pdf |
|
| 24 | Fri, Nov 6 | Student presentations: Chloe and Karen | Selection slides GWAS slides |
Papers to read: (1) Selection (2) GWAS |
| 25 | Mon, Nov 9 | Student presentations: Arcadia and Hee | NJ slides PCA slides |
Papers to read: (1) NJ for proteins (2) PCA in Europe |
| 26 | Wed, Nov 11 | Student presentations: Em and Mara | Genome comparison slides | Papers to read: (1) Neanderthal (2) Genome Comparison |
| 27 | Fri, Nov 13 | Population size changes, PSMC, HMMs | lec27.pdf Board photos 27 |
Homework 6: Project proposal |
| 28 | Mon, Nov 16 | HMMs (cont) Viterbi algorithm |
Board photos 28 | |
| 29 | Wed, Nov 18 | Population sizes: PSMC | Board photos 29 | 30 | Fri, Nov 20 | Genome-wide association studies (GWAS) | lec30.pdf Board photos 30 |
| 31 | Mon, Nov 23 | Prenatal testing with next-generation sequencing | lec31.pdf Board photos 31 |
Homework 7: Sequence diversity |
| - | Wed, Nov 25 | THANKSGIVING RECESS | ||
| - | Fri, Oct 2 | THANKSGIVING RECESS | ||
| 32 | Mon, Nov 30 | Ethics and the genome: prenatal testing | Class discussion |
Methods article Opinion 1 Opinion 2 |
| 33 | Wed, Dec 2 | Project check-in | Individual meetings | Homework 8: Hidden Markov Models |
| 34 | Fri, Dec 4 | Measuring the fetal genome | Board photos 34 | |
| 35 | Mon, Dec 7 | Special topic: RNA folding | lec35.pdf Board photos 35 Infectious Disease Modeling |
Redo Homework |
| 36 | Wed, Dec 9 | Final presentations: Em and Mara | Em slides Mara slides |
Final Presentations |
| 37 | Fri, Dec 11 | Final presentations: Arcadia and Hee | Arcadia slides Hee slides |
|
| 38 | Mon, Dec 14 | Final presentations: Karen and Chloe | Karen slides Chloe slides |
|
| - | Sun, Dec 20 | Final project writeup due | Final Project Figures | Final Project Writeup |
