1-BIN-301, 2-AIN-501 Methods in Bioinformatics

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MBI 2023/2024: Rozdiel medzi revíziami

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(Vytvorená stránka „'''Literature:''' * '''BV''': Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures) {{pdf|skripta-2015-10-...“)
 
Riadok 1: Riadok 1:
 
'''Literature:'''
 
'''Literature:'''
  
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* '''BV''': Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures) {{pdf|skripta-2015-10-01}}
+
* '''BV''': Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures)
 
* '''DEKM''': Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998. Can be studied in the FMFI library under code I-INF-D-21  
 
* '''DEKM''': Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998. Can be studied in the FMFI library under code I-INF-D-21  
 
* '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI  library under code I-INF-Z-2
 
* '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI  library under code I-INF-Z-2
Riadok 18: Riadok 18:
 
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POZOR 2023 prehodene proteiny a expresia, kvoli tomu trochu chaos v cvikach, potencialne pouzi 2022
 
POZOR 2023 prehodene proteiny a expresia, kvoli tomu trochu chaos v cvikach, potencialne pouzi 2022
 
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{{W|1}}, {{W|2}}, {{W|3}}, {{W|4}}, {{W|5}}, {{W|6}}, {{W|7}}, {{W|8}}, {{W|9}}, {{W|10}}, {{W|11}}, {{W|12}}, {{W|13}}
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[[#w1|Week 1]], [[#w2|Week 2]], [[#w3|Week 3]], [[#w4|Week 4]], [[#w5|Week 5]], [[#w6|Week 6]], [[#w7|Week 7]], [[#w8|Week 8]], [[#w9|Week 9]], [[#w10|Week 10]], [[#w11|Week 11]], [[#w12|Week 12]], [[#w13|Week 13]]
  
 
{|
 
{|
 
|-
 
|-
−
{{T|Sept. 21||1}}
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|- style="background:#f0f0f0"
−
{{R | L| Introduction, course rules, sequencing and genome assembly |  {{pdf|p-intro}}, {{pdf|p-seq}} | }}
+
| colspan="4" | '''Sept. 21''' <span id="w1"></span>
−
{{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
+
−
{{R | TI| Introduction to biology | {{pdf|ci-introbio}} | [[CI01|notes]] }}
+
−
{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 video]
+
−
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
+
 
|-
 
|-
−
{{T|Sept. 28||2}}
 
−
{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
 
−
{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
 
−
{{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} | [[CI02|notes]]  }}
 
−
{{Lit2 | Python simulations and approximations}} [https://colab.research.google.com/drive/12TdzUdwTB03Y8xJbgvHTWYIwdmlBaYZY?usp=sharing colab]
 
−
{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|notes]] }}
 
 
|-
 
|-
−
{{T|Oct. 5||3}}
+
| ''' L:''' ||  Introduction, course rules, sequencing and genome assembly  ||     ||
−
{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1}} | }}
+
−
{{Lit2 | BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2}}, [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]
+
−
{{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} | [[CI03|notes]] }}
+
−
{{Lit2 | Python implementation of DP and visualisations}} [https://colab.research.google.com/drive/14QB903XpAsUFsqfls3rYoSaYRhyNX-So?usp=sharing colab]
+
−
{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }}
+
 
|-
 
|-
−
{{T|Oct. 12||4}}
+
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
−
{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
+
|- style="color:#606060;"
−
{{Lit2 | BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
+
| || colspan="3" | '' BV chapter 1'', [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
−
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|notes]] }}
+
−
{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
+
 
|-
 
|-
−
{{T|Oct. 19||5}}
+
| ''' TI:''' || Introduction to biology  ||   || [[CI01|notes]]  
−
{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene}}| }}
+
−
{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
+
−
{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | <!-- [[CI05|notes]]--> }}
+
−
{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|notes]] }}
+
 
|-
 
|-
−
{{T|Oct. 26||6}}
+
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
−
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo}} | }}
+
|- style="color:#606060;"
−
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
+
| || colspan="3" | '' ZB chapter 1'', [https://www.youtube.com/watch?v=EtPqUOHTJD4 video]
−
{{R | TI|Algorithms for HMM | {{pdf|ci-hmm}}  | [[CI06|notes]] }}
+
−
{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
+
 
|-
 
|-
−
{{T|Nov. 2|No lecture, no tutorials|7}}
+
| ''' TB:''' ||  Introduction to computer science, UCSC genome browser  ||    ||  [[CB01|notes]]
 
|-
 
|-
−
{{T|Nov. 9||8}}
 
−
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen}} | }}
 
−
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video]
 
−
{{R | TI|Substitution models | <!-- {{pdf|ci-matice-en}}--> {{pdf|Ci-substitution-models}} |  [[CI07|notes]] }}
 
−
{{R | TB|Practical phylogenetic trees |  | [[CB07|notes]] }}
 
 
|-
 
|-
−
{{T|Nov. 16||10}}
+
|- style="background:#f0f0f0"
−
{{R | L| Protein structure and function |  {{pdf|p-prot}} | }}
+
| colspan="4" | '''Sept. 28'''  <span id="w2"></span>
−
{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
+
−
{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}}--> | <!-- [[CI08|notes]] -->}}
+
−
{{R | TB| Pfam, PSI-blast, Example of command-line tools  | | [[CB10|notes1]], [[CB11|notes2]] }}
+
 
|-
 
|-
−
{{T|Nov. 23||9}}
 
−
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}}| }}
 
−
{{Lit2 | DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1}}, [https://youtu.be/GFJ_oDV1KGU SK video]
 
−
{{R | TI|Examples of biological databases, introduction to context-free grammars |  |  [[CI10|notes]] }}
 
−
{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
 
 
|-
 
|-
−
{{T|Nov. 30||11}}
+
| ''' L:''' ||  Genome assembly 2  ||   ||   
−
{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna}} | }}
+
−
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
+
−
{{R | TI|Motif finding by EM and Gibbs sampling | {{pdf|ci-motifs}} |  <!--[[CI09|notes]]--> }}
+
−
{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} |  [[CB08|notes]]}}
+
 
|-
 
|-
−
{{T|Dec. 7||12}}
+
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
−
{{R | L| Population genetics | {{pdf|p-popgen}} | }}
+
|- style="color:#606060;"
−
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
+
| || colspan="3" | '' '' [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
−
{{R | TI| RNA structure  |  | <!-- [[CI11|notes]]--> }}
+
|-
−
{{R | TB|  Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }}
+
| ''' TI:''' ||  Introduction to probability, genome coverage by sequencing reads  ||    ||  [[CI02|notes]] 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' Python simulations and approximations'' [https://colab.research.google.com/drive/12TdzUdwTB03Y8xJbgvHTWYIwdmlBaYZY?usp=sharing colab]
 +
|-
 +
| ''' TB:''' ||  Introduction to dynamic programming, introduction to probability  ||    ||  [[CB02|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Oct. 5'''  <span id="w3"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2'', [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]
 +
|-
 +
| ''' TI:''' || Introduction to dynamic programming, proteomics  ||    ||  [[CI03|notes]]
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' Python implementation of DP and visualisations'' [https://colab.research.google.com/drive/14QB903XpAsUFsqfls3rYoSaYRhyNX-So?usp=sharing colab]
 +
|-
 +
| ''' TB:''' || Dynamic programming for sequence alignment, dotplots  ||    ||  [[CB03|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Oct. 12'''  <span id="w4"></span>
 +
|-
 +
|-
 +
| ''' L:''' || Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5'', [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 +
|-
 +
| ''' TI:''' || Advanced algorithms for sequence alignment  ||  ||  [[CI04|notes]]
 +
|-
 +
|-
 +
| ''' TB:''' || Programs for sequence alignment, scoring schemes ||  ||  [[CB04|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Oct. 19'''  <span id="w5"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Gene finding, hidden Markov models  ||  || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7'', [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
 +
|-
 +
| ''' TI:''' || Fast similarity search, BLAST, MinHash  ||    || 
 +
|-
 +
|-
 +
| ''' TB:''' || Hidden Markov models, E-value  ||      ||  [[CB05|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Oct. 26'''  <span id="w6"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2'', [https://youtu.be/RzfNHvZH4l8 video]
 +
|-
 +
| ''' TI:''' || Algorithms for HMM  ||    ||  [[CI06|notes]]
 +
|-
 +
|-
 +
| ''' TB:''' || Substitution models, bootstrap, tree rooting ||    ||  [[CB06|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Nov. 2''' No lecture, no tutorials <span id="w7"></span>
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Nov. 9'''  <span id="w8"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' BV chapter 5, ZB chapter 9.8, 10.8'', [https://youtu.be/1WM4QI2qx8A video]
 +
|-
 +
| ''' TI:''' || Substitution models  ||    ||  [[CI07|notes]]
 +
|-
 +
|-
 +
| ''' TB:''' || Practical phylogenetic trees  ||    ||  [[CB07|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Nov. 16'''  <span id="w10"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Protein structure and function  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2'', [https://youtu.be/ugMM81jZRpc SK video]
 +
|-
 +
| ''' TI:''' || Felsenstein algorithm, algorithms for HMM and phyloHMM  ||    || 
 +
|-
 +
|-
 +
| ''' TB:''' ||  Pfam, PSI-blast, Example of command-line tools  ||  ||  [[CB10|notes1]], [[CB11|notes2]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Nov. 23'''  <span id="w9"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs  ||  || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1'', [https://youtu.be/GFJ_oDV1KGU SK video]
 +
|-
 +
| ''' TI:''' || Examples of biological databases, introduction to context-free grammars  ||    ||  [[CI10|notes]]
 +
|-
 +
|-
 +
| ''' TB:''' || Introduction to context-free grammars  ||  ||  [[CB09|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Nov. 30'''  <span id="w11"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles ||    ||   
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' DEKM chapter 10, ZB chapter 11.9'', [https://youtu.be/_Hh03Khsr9k SK video]
 +
|-
 +
| ''' TI:''' || Motif finding by EM and Gibbs sampling  ||    ||   
 +
|-
 +
|-
 +
| ''' TB:''' || K-means clustering, enrichment, multiple testing correction ||    ||  [[CB08|notes]]
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Dec. 7'''  <span id="w12"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Population genetics  ||    || 
 +
|-
 +
<!--za sablonu sa da pridat linka na video, ktory nie je parameter a tym padom nema problem s = -->
 +
|- style="color:#606060;"
 +
| || colspan="3" | '' '' [https://youtu.be/7vPt1vQX21M SK video]
 +
|-
 +
| ''' TI:''' ||  RNA structure  ||    || 
 +
|-
 +
|-
 +
| ''' TB:''' ||  Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics ||     || [[CB12|notes]]  
 +
|-
 +
|-
 +
|- style="background:#f0f0f0"
 +
| colspan="4" | '''Dec. 14'''  <span id="w13"></span>
 +
|-
 +
|-
 +
| ''' L:''' ||  Optional journal club presentations  ||  || 
 +
|-
 +
|-
 +
| ''' TI:''' ||  Protein threading via integer linear programming, course summary  ||    ||   
 +
|-
 +
|-
 +
| ''' TB:''' ||  Project consultations  ||  || 
 
|-
 
|-
−
{{T|Dec. 14||13}}
 
−
{{R | L| Optional journal club presentations | | }}
 
−
{{R | TI| Protein threading via integer linear programming, course summary | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}}-->  |  <!-- [[CI12|notes]]--> }}
 
−
{{R | TB| Project consultations | | }}
 
 
|-
 
|-
 
|}
 
|}

Verzia zo dňa a času 14:41, 25. september 2024

Literature:

  • BV: Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures)
  • DEKM: Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998. Can be studied in the FMFI library under code I-INF-D-21
  • ZB: Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI library under code I-INF-Z-2

For each lecture, we list book chapters best corresponding to the covered material. However, the lecture may differ substantially from the listed chapters which serve as the source of additional information.

Recordings of lectures in Slovak from 2018/19


Notes and presentations

L: lecture (everybody), TI: tutorial for computer science/informatics students, TB: tutorial for biology/chemistry/physics students


Week 1, Week 2, Week 3, Week 4, Week 5, Week 6, Week 7, Week 8, Week 9, Week 10, Week 11, Week 12, Week 13

Sept. 21
L: Introduction, course rules, sequencing and genome assembly
BV chapter 1, video 1 video 2
TI: Introduction to biology notes
ZB chapter 1, video
TB: Introduction to computer science, UCSC genome browser notes
Sept. 28
L: Genome assembly 2
video
TI: Introduction to probability, genome coverage by sequencing reads notes
Python simulations and approximations colab
TB: Introduction to dynamic programming, introduction to probability notes
Oct. 5
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring
BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2, video
TI: Introduction to dynamic programming, proteomics notes
Python implementation of DP and visualisations colab
TB: Dynamic programming for sequence alignment, dotplots notes
Oct. 12
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments
BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5, video
TI: Advanced algorithms for sequence alignment notes
TB: Programs for sequence alignment, scoring schemes notes
Oct. 19
L: Gene finding, hidden Markov models
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video
TI: Fast similarity search, BLAST, MinHash
TB: Hidden Markov models, E-value notes
Oct. 26
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video
TI: Algorithms for HMM notes
TB: Substitution models, bootstrap, tree rooting notes
Nov. 2 No lecture, no tutorials
Nov. 9
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
BV chapter 5, ZB chapter 9.8, 10.8, video
TI: Substitution models notes
TB: Practical phylogenetic trees notes
Nov. 16
L: Protein structure and function
DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2, SK video
TI: Felsenstein algorithm, algorithms for HMM and phyloHMM
TB: Pfam, PSI-blast, Example of command-line tools notes1, notes2
Nov. 23
L: Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs
DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1, SK video
TI: Examples of biological databases, introduction to context-free grammars notes
TB: Introduction to context-free grammars notes
Nov. 30
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Motif finding by EM and Gibbs sampling
TB: K-means clustering, enrichment, multiple testing correction notes
Dec. 7
L: Population genetics
SK video
TI: RNA structure
TB: Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics notes
Dec. 14
L: Optional journal club presentations
TI: Protein threading via integer linear programming, course summary
TB: Project consultations
Zdroj: „http://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=MBI_2023/2024&oldid=3064“