| Lecture | Date | Lecturer | Topics | Slides | References |
|---|---|---|---|---|---|
| 1 | 17.2. | JK | Intro, sequencing algorithms, fragment assembly. | intro, assembly | Nagarajan13, Compeau11 |
| 2 | 24.2. | JK | Biological sequence alignment. | alignment | Durbin's book, ch 2,6 |
| 3 | 3.3. | JK | BLAST algorithm and its modifications. | multi align, BLAST | Altschul97 |
| 4 | 10.3. | JK | Motif discovery. | Motif discovery | Dhaeseleer06 |
| 5 | 17.3. | JK | Phylogenetic trees, hierarchical clustering. | phylogeny | Durbin's book, ch 7 |
| 6 | 24.3. | JK | Phylogenetic trees, parsimony and probabilistic methods. | see the previous lecture | Durbin's book, ch 8 |
| 7 | 31.3. | JK | Markov models, Markov chains. | Markov chains | Durbin's book, ch 3 |
| 8 | 7.4. | JK | Hidden Markov models, profile HMMs, gene finidng. | HMMs | Burge97, HMM_algs |
| 9 | 14.4. | JK | Gene expression profiling. | DGE | Love14 |
| - | 21.4. | - | Easter Monday | ||
| 10 | 28.4. | JK | Gene ontology, gene/protein function prediction. | Gene ontology | GOingStrong19, GOLabeler, GSEA |
| 11 | 5.5. | JK | RNA secondary structure prediction. | RNA secondary | Eddy04, Vicens22, Durbin's book, ch 9,10 |
| 12 | 12.5. | JK | Modeling of higher protein structures, protein databases. | Protein folding | AlphaFold2, Dill12, Rost98, Lathorp96, Threading |
| 13 | 19.5. | JK | Protein engineering. | Protein engineering | Yang19, Jiang25 |