Lecture | Date | Lecturer | Topics | Slides | References |
1 | 15.2. | JK | Intro, sample bioinformatics tasks. | intro | |
2 | 22.2. | JK | Sequencing algorithms, fragment assembly. | assembly | Nagarajan13, Compeau11 |
3 | 1.3. | JK | Biological sequence alignment. | alignment | Durbin's book, ch 2,6 |
4 | 8.3. | JK | BLAST algorithm and its modifications. | multi align, BLAST | Altschul97 |
5 | 15.3. | JK | Phylogenetic trees, hierarchical clustering. | phylogeny | Durbin's book, ch 7 |
6 | 22.3. | JK | Phylogenetic trees, parsimony and probabilistic methods. | see the previous lecture | Durbin's book, ch 8 |
7 | 29.3. | JK | Markov models, Markov chains. | Markov chains | Durbin's book, ch 3 |
- | 5.4. | - | Easter Monday | | |
8 | 12.4. | JK | Hidden Markov models, profile HMMs, gene finidng. | HMMs | Burge97, HMM_algs |
9 | 19.4. | JK | Gene expression profiling. | DGE | Love14 |
10 | 26.4. | JK | RNA secondary structure prediction | RNA secondary | Eddy04, Durbin's book, ch 9,10 |
11 | 3.5. | JK | Modeling of higher protein structures, protein databases. | Protein folding | AlphaFold, Dill12, Rost98, Lathorp96, Threading |
12 | 10.5. | JK | Gene ontology, gene/protein function prediction. | Gene ontology | GOingStrong19, GOLabeler, GSEA |
13 | 17.5. | JK | Network inference and modeling. | Network inference | Sachs05 |