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courses:bin:program [2024/02/19 10:19]
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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}} |
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| 2 | 26.2. | JK | Sequencing algorithms, fragment assembly. | {{bin_assembly.pdf|assembly}} | [[
https
://
makarich
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fbb
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msu
.
ru
/
snaumenko
/
ngs_lecture
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sequence_assembly_demistified2013
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pdf
|Nagarajan13]], [[http://profs.scienze.univr.it/~liptak/MBD/files/nbt.2023.pdf|Compeau11]] |
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| 2 | 26.2. | JK | Sequencing algorithms, fragment assembly. | {{bin_assembly.pdf|assembly}} | [[
http
://
bioinformatics
.
hgen
.
slu
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se
/
SLUBIOINFO2015
/
SLUBIOINFO2015
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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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| 8 | 15.4. | JK | Markov models, Markov chains. | {{bin_markov.pdf|Markov chains}}| Durbin's book, ch 3 |
| 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}} |
| 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}} |
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| 10 |
2
.
5
. | JK | Gene expression profiling. | {{:courses:bin:bin_dge.pdf |DGE}} | [[https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8|Love14]] |
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| 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]] |
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| 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]] |
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| 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]] |
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| 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 |
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| 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 |
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| 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}} |
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| 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.txt
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