| Lecture | Date | Lecturer | Topics | Slides | References |
|---|---|---|---|---|---|
| 1 | 17.2. | JK | Intro, sample bioinformatics tasks. | intro | |
| 2 | 24.2. | JK | Biological sequence alignment. | alignment, linear space | Durbin's book, ch 2,6 |
| 3 | 2.3. | PR | BLAST algorithm and its modifications. | multi align, BLAST | Altschul97 |
| 4 | 9.3. | JK | Sequencing algorithms, fragment assembly. | assembly | Nagarajan13, Compeau11 |
| 5 | 16.3. | JK | Phylogenetic trees, hierarchical clustering. | phylogeny,dist_based | Durbin's book, ch 7 |
| 6 | 23.3. | JK | Phylogenetic trees, parsimony and probabilistic methods. | parsimony, probablistic | Durbin's book, ch 8 |
| 7 | 30.3. | JK | Markov models. | Markov chains | Durbin's book, ch 3 |
| 8 | 6.4. | JK | Markov models of genomic sequences, gene finidng, profile HMMs. | HMM,applications | Burge97 |
| - | 13.4. | - | Easter Monday | ||
| 9 | 20.4. | JK | High-throughput data analysis, marker detection, predictive modeling. | microarray, DeSEQ | Goeman07 |
| 10 | 27.4. | JK | RNA secondary structure prediction | RNA secondary | Eddy04, Durbin's book, ch 9,10 |
| 11 | 4.5. | JK | Modeling of higher protein structures, protein databases. | Protein structure prediction, Threading | Dill12, Rost98, Lathorp96 |
| 12 | 11.5. | JK | Gene ontology, gene/protein function prediction. | gfp-intro.pdf | Ashburner00, GOingStrong19 |
| 13 | 18.5. | JK | Network inference and modeling. | Network inference | Sachs05 |