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courses:bin:program [2024/02/19 10:19]
klema
courses:bin:program [2024/02/26 17:31] (current)
klema
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 ^  Lecture ​ ^  Date    ^  Lecturer ​ ^  Topics ​ ^  Slides ​  ​^ ​ References ​ ^ ^  Lecture ​ ^  Date    ^  Lecturer ​ ^  Topics ​ ^  Slides ​  ​^ ​ References ​ ^
 |  1         ​| ​ 19.2.   ​| ​ JK  | Intro, sample bioinformatics tasks. | {{bin_intro.pdf|intro}} | |  1         ​| ​ 19.2.   ​| ​ JK  | Intro, sample bioinformatics tasks. | {{bin_intro.pdf|intro}} |
-|  2         ​| ​ 26.2.  |  JK  | Sequencing algorithms, fragment assembly. | {{bin_assembly.pdf|assembly}} | [[https://makarich.fbb.msu.ru/snaumenko/ngs_lecture/sequence_assembly_demistified2013.pdf|Nagarajan13]],​ [[http://​profs.scienze.univr.it/​~liptak/​MBD/​files/​nbt.2023.pdf|Compeau11]] |+|  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 |  |  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]] | |  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]] |
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 |  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}} |  ​ |  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]] | |  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        |  ​9.5.  |  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]] | +|  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        |  ​14.5.  |   ​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 | +|  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        |  ​21.5.  |  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}} |+|  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}} |
  
  
courses/bin/program.1708334396.txt.gz · Last modified: 2024/02/19 10:19 by klema