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

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This webpage contains a '''preliminary schedule of lectures and tutorials for the semester''' which will be updated as needed. Notes and presentations will be published after each class.
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<tr><td>
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'''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}}
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* '''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
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* '''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'''
 +
* [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist on youtube]
 +
 
 +
 
 +
'''Notes and presentations'''
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L: lecture (everybody), TI: tutorial for computer science/informatics students,
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TB: tutorial for biology/chemistry/physics students
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 +
<!--
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Pouzitie sablon:
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tyzden: {{T|datumy od-do|nepovinny dalsi text|cislo tyzdna}}
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riadok (hodina): {{R| aka hodina, t.j. L alebo TI alebo TB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
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literatura: {{Lit | cisla kapitol}}
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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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{|
 
{|
 
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|-
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{{T|22.-28.9.|}}
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{{T|Sept. 21||1}}
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{{R | PR | Úvod, administratíva, ukážky bioinformatických problémov | {{pdf|p01}} | }}
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{{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro}}, {{pdf|p-seq}} | }}
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{{R | CI | Úvod do biológie | {{pdf|ci01}} | [[CI01]] }}
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{{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
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{{R | CB | Úvod do informatiky | {{pdf|cb01}} | }}
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{{R | TI| Introduction to biology  | {{pdf|ci-introbio}} | [[CI01|notes]] }}
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{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 video]
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{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} | [[CB01|notes]] }}
 
|-
 
|-
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{{T|29.9.-5.10|}}
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{{T|Sept. 28||2}}
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{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
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{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
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{{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]
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{{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|notes]] }}  
 
|-
 
|-
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{{T|6.-12.10.|}}
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{{T|Oct. 5||3}}
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1}} | }}
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{{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]] }}  
 
|-
 
|-
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{{T|13.-19.10.|}}
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{{T|Oct. 12||4}}
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
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{{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]
 +
{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|notes]] }}
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{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
 
|-
 
|-
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{{T|20.-26.10.|}}
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{{T|Oct. 19||5}}
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{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene}}| }}
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{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
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{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | <!-- [[CI05|notes]]--> }}
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{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|notes]] }}
 
|-
 
|-
−
{{T|27.10.-2.11.|}}
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{{T|Oct. 26||6}}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo}} | }}
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{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
 +
{{R | TI|Algorithms for HMM | {{pdf|ci-hmm}}  | [[CI06|notes]] }}
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{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
 
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|-
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{{T|3.-9.11.|}}
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{{T|Nov. 2|No lecture, no tutorials|7}}
 
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|-
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{{T|10.-16.11.|}}
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{{T|Nov. 9||8}}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen}} | }}
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{{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]] }}
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{{R | TB|Practical phylogenetic trees |  | [[CB07|notes]] }}
 
|-
 
|-
−
{{T|17.-23.11.|}}
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{{T|Nov. 16||10}}
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{{R | L| Protein structure and function |  {{pdf|p-prot}} | }}
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{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
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{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}}--> | <!-- [[CI08|notes]] -->}}
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{{R | TB| Pfam, PSI-blast, Example of command-line tools  | | [[CB10|notes1]], [[CB11|notes2]] }}
 
|-
 
|-
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{{T|24.-30.11.|}}
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{{T|Nov. 23||9}}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}}| }}
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{{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]] }}
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{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
 
|-
 
|-
−
{{T|1.-7.12.|}}
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{{T|Nov. 30||11}}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna}} | }}
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{{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|8.-14.12.|}}
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{{T|Dec. 7||12}}
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{{R | L| Population genetics | {{pdf|p-popgen}} | }}
 +
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
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{{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]] }}
 
|-
 
|-
−
{{T|15.-21.12.|}}
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{{T|Dec. 14||13}}
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{{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 | | }}
 
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Verzia zo dňa a času 09:51, 7. december 2023

This webpage contains a preliminary schedule of lectures and tutorials for the semester which will be updated as needed. Notes and presentations will be published after each class.

Literature:

  • BV: Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures) pdf
  • 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 pdf, pdf
BV chapter 1, video 1 video 2
TI: Introduction to biology pdf notes
ZB chapter 1, video
TB: Introduction to computer science, UCSC genome browser pdf notes
Sept. 28
L: Genome assembly 2 pdf
video
TI: Introduction to probability, genome coverage by sequencing reads pdf notes
Python simulations and approximations colab
TB: Introduction to dynamic programming, introduction to probability pdf notes
Oct. 5
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring pdf
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 pdf notes
Python implementation of DP and visualisations colab
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 12
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments pdf
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 pdf
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video
TI: Fast similarity search, BLAST, MinHash pdf
TB: Hidden Markov models, E-value pdf notes
Oct. 26
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) pdf
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video
TI: Algorithms for HMM pdf notes
TB: Substitution models, bootstrap, tree rooting pdf notes
Nov. 2 No lecture, no tutorials
Nov. 9
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs pdf
BV chapter 5, ZB chapter 9.8, 10.8, video
TI: Substitution models pdf notes
TB: Practical phylogenetic trees notes
Nov. 16
L: Protein structure and function pdf
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 pdf
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 pdf
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Motif finding by EM and Gibbs sampling pdf
TB: K-means clustering, enrichment, multiple testing correction pdf pdf notes
Dec. 7
L: Population genetics pdf
SK video
TI: RNA structure
TB: Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics pdf, pdf 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=Materials&oldid=3041“