Lecture | Date | Lecturer | Topics | Slides | References |
1 | 14.2. | JK | Intro, sample bioinformatics tasks. | intro | |
2 | 21.2. | JK | Sequencing algorithms, fragment assembly. | assembly | Nagarajan13, Compeau11 |
3 | 28.2. | JK | Biological sequence alignment. | alignment | Durbin's book, ch 2,6 |
4 | 7.3. | JK | BLAST algorithm and its modifications. | multi align, BLAST | Altschul97 |
5 | 14.3. | JK | Phylogenetic trees, hierarchical clustering. | phylogeny | Durbin's book, ch 7 |
6 | 21.3. | JK | Phylogenetic trees, parsimony and probabilistic methods. | see the previous lecture | Durbin's book, ch 8 |
7 | 28.3. | JK | Markov models, Markov chains. | Markov chains | Durbin's book, ch 3 |
8 | 4.4. | JK | Hidden Markov models, profile HMMs, gene finidng. | HMMs | Burge97, HMM_algs |
9 | 11.4. | JK | Gene expression profiling. | DGE | Love14 |
- | 18.4. | - | Easter Monday | | |
10 | 25.4. | JK | Gene ontology, gene/protein function prediction. | Gene ontology | GOingStrong19, GOLabeler, GSEA |
11 | 2.5. | JK | RNA secondary structure prediction | RNA secondary | Eddy04, Durbin's book, ch 9,10 |
12 | 9.5. | JK | Modeling of higher protein structures, protein databases. | Protein folding | AlphaFold, Dill12, Rost98, Lathorp96, Threading |
13 | 16.5. | JK | Motif discovery. | Motif discovery | Dhaeseleer06 |