==== Lectures =====

^  Lecture  ^  Date    ^  Lecturer  ^  Topics  ^  Slides   ^  References  ^
|  1         |  19.2.   |  JK  | Intro, sample bioinformatics tasks. | {{bin_intro.pdf|intro}} |
|  2         |  26.2.  |  JK  | Sequencing algorithms, fragment assembly. | {{bin_assembly.pdf|assembly}} | [[http://bioinformatics.hgen.slu.se/SLUBIOINFO2015/SLUBIOINFO2015/Literature_files/assembly_review.PDF|Nagarajan13]], [[http://profs.scienze.univr.it/~liptak/MBD/files/nbt.2023.pdf|Compeau11]] |
|  3         |   4.3.  |  JK  | Biological sequence alignment. | {{bin_align.pdf |alignment}} | Durbin's book, ch 2,6 | 
|  4         |  11.3.  |  JK  | BLAST algorithm and its modifications. | {{bin_malign.pdf|multi align}}, {{bin_blast.pdf|BLAST}} |[[http://users.cis.fiu.edu/~giri/teach/Bioinf/Papers/GappedBLASTPaperNAR97.pdf|Altschul97]] |
|  5         |  18.3.  |  JK  | Motif discovery. | {{ :courses:bin:bin_motif.pdf|Motif discovery}} | {{http://146.6.100.192/users/BCH339N_2018/nbt0806-959-primer-howdoesmotifdiscoverywork.pdf|Dhaeseleer06}} |
|  6         |  25.3.  |   JK  | Phylogenetic trees, hierarchical clustering. | {{ :courses:bin:bin_phylo.pdf |phylogeny}} | Durbin's book, ch 7 |
|  -         |  1.4.   |  -  | //Easter Monday// |
|  7        |   8.4.  |   JK  | Phylogenetic trees, parsimony and probabilistic methods. | see the previous lecture | Durbin's book, ch 8 |
|  8         |  15.4.  |  JK  | Markov models, Markov chains. | {{bin_markov.pdf|Markov chains}}| Durbin's book, ch 3 |  
|  9         |  22.4.  |  JK  | Hidden Markov models, profile HMMs, gene finidng. | {{bin_hmm.pdf|HMMs}} | [[https://www.cs.princeton.edu/~bee/courses/read/burge-jmb-1997.pdf|Burge97]], {{ :courses:bin:hmms-1.pdf |HMM_algs}} |  
|  10        |  29.4.  |  JK  | Gene expression profiling. | {{:courses:bin:bin_dge.pdf |DGE}} | [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8|Love14]] |
|  11        |  6.5.  |  JK  | Gene ontology, gene/protein function prediction. | {{ :courses:bin:bin_go.pdf |Gene ontology}} | [[https://www.repository.cam.ac.uk/bitstream/handle/1810/289177/gky1055.pdf?sequence=1|GOingStrong19]], [[https://academic.oup.com/bioinformatics/article/34/14/2465/4924212?login=true|GOLabeler]], [[https://www.pnas.org/content/102/43/15545|GSEA]] |
|  12        |  13.5.  |   JK  | RNA secondary structure prediction | {{bin_strucrna.pdf|RNA secondary}} | [[https://www.molgen.mpg.de/3710236/eddy2004.pdf|Eddy04]], [[https://www.pnas.org/doi/epdf/10.1073/pnas.2112677119|Vicens22]], Durbin's book, ch 9,10 |
|  13        |  20.5.  |  JK   | Modeling of higher protein structures, protein databases. | {{ :courses:bin:bin_folding.pdf |Protein folding}}   | [[https://www.nature.com/articles/s41586-021-03819-2|AlphaFold2]], [[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]], {{threading-2p.pdf|Threading}} |