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

Website moved to https://fmfi-compbio.github.io/mbi/


Materials: Rozdiel medzi revíziami

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Riadok 40: Riadok 40:
 
{{T|Sept. 29||2}}
 
{{T|Sept. 29||2}}
 
{{R | L| Genome assembly 2 | <!-- {{pdf|p-seq2-en}} --> | }}
 
{{R | L| Genome assembly 2 | <!-- {{pdf|p-seq2-en}} --> | }}
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<!--  {{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video] -->
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{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
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{{R | TI| Introduction to probability, genome coverage by sequencing reads | <!-- {{pdf|ci-coverage}} (SK) | [[CI02|SK notes]] --> }}
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{{R | TI| Introduction to probability, genome coverage by sequencing reads | <!-- {{pdf|ci-coverage}} (SK) --> | <!-- [[CI02|SK notes]] --> }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | <!-- {{pdf|cb-dp}} |  [[CB02|SK notes]] --> }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | <!-- {{pdf|cb-dp}} --> |  <!--[[CB02|SK notes]] --> }}
 
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{{T|Oct. 6||3}}  
 
{{T|Oct. 6||3}}  
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  {{pdf|p-aln1-en}} | }}
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring |  <!-- {{pdf|p-aln1-en}} --> | }}
 
{{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 SK video]
 
{{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 SK video]
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{{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} (SK) |  [[CI03|notes]] }}
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{{R | TI|Introduction to dynamic programming, proteomics | <!-- {{pdf|ci-msms}} (SK) --> |  <!-- [[CI03|notes]] --> }}
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{{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} |  [[CB03|notes]] }}
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{{R | TB|Dynamic programming for sequence alignment, dotplots | <!-- {{pdf|cb-dotplots}} --> |  <!-- [[CB03|notes]] --> }}
 
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{{T|Oct. 13||4}}
 
{{T|Oct. 13||4}}
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2-en}} | }}
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | <!-- {{pdf|p-aln2-en}} --> | }}
 
{{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 SK video]
 
{{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 SK video]
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{{R | TI|Advanced algorithms for sequence alignment | |  [[CI04|SK notes]] }}
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{{R | TI|Advanced algorithms for sequence alignment | |  <!-- [[CI04|SK notes]] --> }}
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{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|SK notes]] }}
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{{R | TB|Programs for sequence alignment, scoring schemes| | <!-- [[CB04|SK notes]] --> }}
 
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{{T|Oct. 20||5}}
 
{{T|Oct. 20||5}}
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{{R | L| Gene finding, hidden Markov models | {{pdf|p-gene-en}} | }}
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{{R | L| Gene finding, hidden Markov models | <!-- {{pdf|p-gene-en}} --> | }}
 
{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM SK video]
 
{{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM SK video]
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{{R | TI|Fast similarity search, BLAST, MinHash |  | [[CI05|SK notes]] }}
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{{R | TI|Fast similarity search, BLAST, MinHash |  | <!-- [[CI05|SK notes]] --> }}
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{{R | TB|Hidden Markov models, E-value |  {{pdf|cb-evalue}} | [[CB05|SK notes]] }}
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{{R | TB|Hidden Markov models, E-value |  <!-- {{pdf|cb-evalue}} --> | <!-- [[CB05|SK notes]] --> }}
 
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{{T|Oct. 27||6}}
 
{{T|Oct. 27||6}}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo-en}} | }}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!-- {{pdf|p-phylo-en}} --> | }}
 
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 SK video]
 
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 SK video]
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{{R | TI|Algorithms for HMM | {{pdf|ci-hmm-en}}  | [[CI06|SK notes]] }}
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{{R | TI|Algorithms for HMM | <!-- {{pdf|ci-hmm-en}} --> | <!-- [[CI06|SK notes]] --> }}
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{{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}}  <!--{{pdf|cb-phylo-en}}--> | [[CB06|SK notes]] }}
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{{R | TB|Substitution models, bootstrap, tree rooting| <!-- {{pdf|cb-phylo}} --> | <!-- [[CB06|SK notes]] --> }}
 
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{{T|Nov. 3||7}}
 
{{T|Nov. 3||7}}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  {{pdf|p-compgen-en}} | }}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  <!-- {{pdf|p-compgen-en}} --> | }}
 
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK video]
 
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK video]
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{{R | TI|Substitution models |  {{pdf|ci-matice-en}} |  [[CI07|SK notes]] }}
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{{R | TI|Substitution models |  <!-- {{pdf|ci-matice-en}} --> | <!-- [[CI07|SK notes]] --> }}
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{{R | TB|Phylogenetic trees |  | [[CB07|SK notes]] }}
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{{R | TB|Phylogenetic trees |  | <!-- [[CB07|SK notes]] --> }}
 
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{{T|Nov. 10||8}}
 
{{T|Nov. 10||8}}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr-en}} | }}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr-en}} --> | }}
 
{{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]
 
{{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]
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{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | {{pdf|ci-hmm}} | [[CI08|SK notes]] }}
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{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}} --> | <!-- [[CI08|SK notes]] --> }}
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{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|SK notes]] }}
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{{R | TB|K-means clustering, enrichment, multiple testing correction| <!-- {{pdf|cb-kmeans}} <!-- {{pdf|cb-enrichment-en}} | <!-- [[CB08|SK notes]] }}
 
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{{T|Nov. 17||9}}
 
{{T|Nov. 17||9}}
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{{R | L| Protein structure and function |  {{pdf|p-prot-en}} | }}
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{{R | L| Protein structure and function |  <!-- {{pdf|p-prot-en}} --> | }}
 
{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
 
{{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|Motif finding by EM and Gibbs sampling |  |  [[CI09|SK notes]] }}
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{{R | TI|Motif finding by EM and Gibbs sampling |  |  <!-- [[CI09|SK notes]] --> }}
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{{R | TB|Introduction to context-free grammars | | [[CB09|SK notes]] }}
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{{R | TB|Introduction to context-free grammars | | <!-- [[CB09|SK notes]] --> }}
 
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{{T|Nov. 24||10}}
 
{{T|Nov. 24||10}}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna-en}} | }}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna-en}} --> | }}
 
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
 
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
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{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars |  {{pdf|cb-compgen}}, {{pdf|cb-gene}} | [[CI10|SK notes]] |  }}
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{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars |  <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}} --> | <!-- [[CI10|SK notes]] --> |  }}
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{{R | TB| Genes, comparative genomics, Pfam  | | [[CB10|SK notes]] }}
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{{R | TB| Genes, comparative genomics, Pfam  | | <!-- [[CB10|SK notes]] --> }}
 
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{{T|Dec. 1||11}}
 
{{T|Dec. 1||11}}
Riadok 96: Riadok 96:
 
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{{T|Dec. 8||12}}
 
{{T|Dec. 8||12}}
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{{R | L| Population genetics | {{pdf|p-popgen-en}} | }}
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{{R | L| Population genetics | <!-- {{pdf|p-popgen-en}} --> | }}
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
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{{R | TI| RNA structure  |  | [[CI11|SK notes]] }}
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{{R | TI| RNA structure  |  | <!-- [[CI11|SK notes]] --> }}
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{{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs  |{{pdf|cb-summary}}, {{pdf|cb-graphs}}  | [[CB11|SK notes]]  }}
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{{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs  | <!-- {{pdf|cb-summary}}, {{pdf|cb-graphs}} --> | <!-- [[CB11|SK notes]] --> }}
 
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{{T|Dec. 15||13}}
 
{{T|Dec. 15||13}}
 
{{R | L| Optional journal club presentations | | }}
 
{{R | L| Optional journal club presentations | | }}
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{{R | TI| Course summary, protein threading via integer linear programming | {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} | [[CI12|SK notes]] }}
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{{R | TI| Course summary, protein threading via integer linear programming | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} --> | <!-- [[CI12|SK notes]] --> }}
 
{{R | TB| Cancelled <!-- example of command-line tools--> | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
{{R | TB| Cancelled <!-- example of command-line tools--> | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
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Verzia zo dňa a času 13:26, 21. september 2022

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. 22
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, SK video 1 SK video 2
TI: Introduction to biology pdf SK notes
ZB chapter 1, SK video
TB: Introduction to computer science, UCSC genome browser pdf SK notes
Sept. 29
L: Genome assembly 2
SK video
TI: Introduction to probability, genome coverage by sequencing reads
TB: Introduction to dynamic programming, introduction to probability
Oct. 6
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, SK video
TI: Introduction to dynamic programming, proteomics
TB: Dynamic programming for sequence alignment, dotplots
Oct. 13
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, SK video
TI: Advanced algorithms for sequence alignment
TB: Programs for sequence alignment, scoring schemes
Oct. 20
L: Gene finding, hidden Markov models
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, SK video
TI: Fast similarity search, BLAST, MinHash
TB: Hidden Markov models, E-value
Oct. 27
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, SK video
TI: Algorithms for HMM
TB: Substitution models, bootstrap, tree rooting
Nov. 3
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
BV chapter 5, ZB chapter 9.8, 10.8, SK video
TI: Substitution models
TB: Phylogenetic trees
Nov. 10
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: Felsenstein algorithm, algorithms for HMM and phyloHMM
TB: K-means clustering, enrichment, multiple testing correction
DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2, SK video
TI: Motif finding by EM and Gibbs sampling
TB: Introduction to context-free grammars
Nov. 24
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Examples of biological databases, HW1 model solutions, introduction to context-free grammars
TB: Genes, comparative genomics, Pfam
Dec. 1
L: No lecture, no tutorials
Dec. 8
L: Population genetics
SK video
TI: RNA structure
TB: PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs
Dec. 15
L: Optional journal club presentations
TI: Course summary, protein threading via integer linear programming
TB: Cancelled
Zdroj: „https://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Materials&oldid=2743“