==== Lectures =====

^  Lecture  ^  Date    ^  Lecturer  ^  Topics  ^  Slides   ^  References  ^
|  1         |  18.2.   |  JK  | Intro, sample bioinformatics tasks. | {{intro_2019.pdf|intro}} |
|  2         |  25.2.  |  JS  | Biological sequence alignment. | {{pairwise_alignment_jk_ms.pdf|alignment}}, {{{{pairwise_alignment_jk_2017_2p.pdf |alignment_2p}}, {{linear-space-alignment.pdf|linear space}} | Durbin's book, ch 2,6 | 
|  3         |  4.3.  |  JK  | BLAST algorithm and its modifications. | {{multiple_alignment_mod.pdf|multi align}}, {{blast_jk_2017_2p.pdf|BLAST}} |[[http://users.cis.fiu.edu/~giri/teach/Bioinf/Papers/GappedBLASTPaperNAR97.pdf|Altschul97]] |
|  4         |  11.3.  |  JK  | Sequencing algorithms, fragment assembly. | {{assembly_jk_2017_2p.pdf|assembly}} | [[http://vps.fmvz.usp.br/labmas/wp-content/uploads/2014/04/Artigo_3.2.pdf|Nagarajan13]], [[http://profs.scienze.univr.it/~liptak/MBD/files/nbt.2023.pdf|Compeau11]] |
|  5         |  18.3.  |   JK  | Phylogenetic trees, hierarchical clustering. | {{intro_phylogeny_2017_2p.pdf|phylogeny}},{{distance_phylogeny_2017_2p.pdf|dist_based}}| Durbin's book, ch 7 |
|  6         |  25.3.  |   JK  | Phylogenetic trees, parsimony and probabilistic methods. | {{parsimony_phylogeny_2017_2p.pdf|parsimony}}, {{prob_phylogeny_2017_2p.pdf|probablistic}}| Durbin's book, ch 8 |
|  7         |  1.4.  |  JK  | Markov models. | {{markov-models-jk-2019.pdf|Markov chains}}| Durbin's book, ch 3 |  
|  8         |  8.4.  |   JK  | Markov models of genomic sequences, gene finidng, profile HMMs. | {{HMMs-1.pdf|HMM}},{{hmm_applications_jk_2p.pdf|applications}} | [[https://www.cs.princeton.edu/~bee/courses/read/burge-jmb-1997.pdf|Burge97]] | 
|  9        |  15.4.  |  JS  | High-throughput data analysis, marker detection, predictive modeling. | {{high-throughput-jk-ms-2p.pdf |microarray}}, {{ :courses:bin:deseq2-2p.pdf |DeSEQ}} | [[https://academic.oup.com/bioinformatics/article/23/8/980/198511/Analyzing-gene-expression-data-in-terms-of-gene|Goeman07]] | 
|  -         |  22.4. |  -  | //Easter Monday// |
|  10        |  29.4.  |   JK  | RNA secondary structure prediction | {{rna-secondary-jk-2p.pdf|RNA secondary}} | [[http://www.cs.utsa.edu/~jruan/teaching/cs5263_fall_2007/papers/how_to_predict_rna_structure.pdf|Eddy04]], Durbin's book, ch 9,10 |
|  11        |  6.5.  |  JK   | Modeling of higher protein structures, protein databases. | {{protein-structure-2p.pdf|Protein structure prediction}}, {{threading-2p.pdf|Threading}}  | [[https://www.academia.edu/5023856/The_Protein-Folding_Problem_50_Years_On|Dill12]], {{rost.pdf|Rost98}}, [[https://www.biostat.wisc.edu/bmi776/spring-17/papers/lathrop.pdf|Lathorp96]] |
|  12        |  13.5.  |  JK  | Gene ontology, gene/protein function prediction. | {{GFP-Intro.pdf}} |
|  13        |  20.5.   |  JS  | Network inference and modeling. | {{networkinference_2p.pdf|Network inference}} | {{science-2005-sachs-523-9.pdf|Sachs05}} |