Lecture | Date | Lecturer | Topics | Slides | References |
1 | 18.2. | JK | Intro, sample bioinformatics tasks. | intro | |
2 | 25.2. | JS | Biological sequence alignment. | alignment, alignment_2p, linear space | Durbin's book, ch 2,6 |
3 | 4.3. | JK | BLAST algorithm and its modifications. | multi align, BLAST | Altschul97 |
4 | 11.3. | JK | Sequencing algorithms, fragment assembly. | assembly | Nagarajan13, Compeau11 |
5 | 18.3. | JK | Phylogenetic trees, hierarchical clustering. | phylogeny,dist_based | Durbin's book, ch 7 |
6 | 25.3. | JK | Phylogenetic trees, parsimony and probabilistic methods. | parsimony, probablistic | Durbin's book, ch 8 |
7 | 1.4. | JK | Markov models. | Markov chains | Durbin's book, ch 3 |
8 | 8.4. | JK | Markov models of genomic sequences, gene finidng, profile HMMs. | HMM,applications | Burge97 |
9 | 15.4. | JS | High-throughput data analysis, marker detection, predictive modeling. | microarray, DeSEQ | Goeman07 |
- | 22.4. | - | Easter Monday | | |
10 | 29.4. | JK | RNA secondary structure prediction | RNA secondary | Eddy04, Durbin's book, ch 9,10 |
11 | 6.5. | JK | Modeling of higher protein structures, protein databases. | Protein structure prediction, Threading | Dill12, Rost98, Lathorp96 |
12 | 13.5. | JK | Gene ontology, gene/protein function prediction. | gfp-intro.pdf | |
13 | 20.5. | JS | Network inference and modeling. | Network inference | Sachs05 |