1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2022/23

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Groups for journal club have each their own channel in MS Teams.


Materials: Rozdiel medzi revíziami

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Riadok 36: Riadok 36:
 
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
 
{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|notes]] }}
 
|-
 
|-
{{T|Sept 30|}}
+
{{T|Sept. 30|}}
{{R | L| Zostavovanie genómov 2 | {{pdf|p-seq2}} | }}
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{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
 
{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
 
{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
{{R | TI| Úvod do pravdepodobnosti, pokrytie pri sekvenovaní | <!-- {{pdf|ci-coverage}}  --> | <!-- [[CI02|notes]]--> }}
+
{{R | TI| Introduction to probability, genome coverage by sequencing reads | <!-- {{pdf|ci-coverage}}  --> | <!-- [[CI02|notes]]--> }}
{{R | TB| Úvod do dynamického programovania, úvod do pravdepodobnosti | <!-- {{pdf|cb-dp}} --> | <!-- [[CB02|notes]]--> }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | <!-- {{pdf|cb-dp}} --> | <!-- [[CB02|notes]]--> }}
 
|-
 
|-
{{T|Oct 7|}}
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{{T|Oct. 7|}}
{{R | L| Zarovnávanie sekvencií: Smith-Waterman, Needleman-Wunsch, skórovanie |  <!-- {{pdf|p-aln1}}--> | }}
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{{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 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]
{{R | TI|Úvod do dynamického programovania, proteomika | <!-- {{pdf|ci-msms}} --> |  <!--[[CI03|notes]]--> }}
+
{{R | TI|Introduction to dynamic programming, proteomics | <!-- {{pdf|ci-msms}} --> |  <!--[[CI03|notes]]--> }}
{{R | TB|Dynamické programovanie pre zarovnávanie sekvencií, dotploty | <!-- {{pdf|cb-dotplots}} --> |  <!--[[CB03|notes]]--> }}
+
{{R | TB|Dynamic programming for sequence alignment, dotplots | <!-- {{pdf|cb-dotplots}} --> |  <!--[[CB03|notes]]--> }}
 
|-
 
|-
{{T|Oct 14|}}
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{{T|Oct. 14|}}
{{R | L| Zarovnávanie sekvencií: heuristické zarovnávanie (BLAST), štatistická významnosť zarovnaní, zarovnávanie genómov, viacnásobné zarovnanie | <!-- {{pdf|p-aln2}} --> | }}
+
{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | <!-- {{pdf|p-aln2}} --> | }}
 
{{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]
{{R | TI|Pokročilé algoritmy pre zarovnávanie sekvencií | |  <!-- [[CI04|notes]]--> }}
+
{{R | TI|Advanced algorithms for sequence alignment | |  <!-- [[CI04|notes]]--> }}
{{R | TB|Programy na zarovnávanie sekvencií, skórovacie schémy| | <!-- [[CB04|notes]]--> }}
+
{{R | TB|Programs for sequence alignment, scoring schemes| | <!-- [[CB04|notes]]--> }}
 
|-
 
|-
{{T|Oct 21|}}
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{{T|Oct. 21|}}
{{R | L| Hľadanie génov, skryté Markovove modely | {{pdf|p-gene}} | }}
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{{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]
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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 Sk video]
{{R | TI|Rýchle hľadanie podobnosti, BLAST, MinHash |  | <!--[[CI05|notes]]--> }}
+
{{R | TI|Fast similarity search, BLAST, MinHash |  | <!--[[CI05|notes]]--> }}
{{R | TB|Skryté Markovove modely, programy na zarovnávanie sekvencií |  | <!--[[CB05|notes]]--> }}
+
{{R | TB|Hidden Markov models, E-value |  | <!--[[CB05|notes]]--> }}
<!-- {{pdf|ci-seeds}} -->
+
 
|-
 
|-
{{T|Oct 28|}}
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{{T|Oct. 28|}}
{{R | L| Rekonštrukcia fylogenetických stromov (úspornosť, metóda spájania susedov, modely evolúcie) | <!--{{pdf|p-phylo}}--> | }}
+
{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!--{{pdf|p-phylo}}--> | }}
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
+
{{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 SK video]
{{R | TI|Algoritmy pre HMM | <!-- {{pdf|ci-hmm}} -->  | <!--[[CI06|notes]]--> }}
+
{{R | TI|Algorithms for HMM | <!-- {{pdf|ci-hmm}} -->  | <!--[[CI06|notes]]--> }}
{{R | TB|Substitučné modely, bootstrap, zakorenenie stromu, fylogenetické stromy <!-- Fitchov algoritmus --> | <!-- {{pdf|cb-phylo}} --> <!--{{pdf|cb-phylo-en}}--> | <!--[[CB06|notes]]--> }}
+
{{R | TB|Substitution models, bootstrap, tree rooting, Fitch's algorithm| <!-- {{pdf|cb-phylo}} --> <!--{{pdf|cb-phylo-en}}--> | <!--[[CB06|notes]]--> }}
 
|-
 
|-
{{T|Nov 4|}}
+
{{T|Nov. 4|}}
 
{{R | L| Komparatívna genomika, detekcia pozitívneho a purifikačného výberu, komparatívne hľadanie génov, fylogenetické HMM |  <!--{{pdf|p-compgen}}-->  | }}
 
{{R | L| Komparatívna genomika, detekcia pozitívneho a purifikačného výberu, komparatívne hľadanie génov, fylogenetické HMM |  <!--{{pdf|p-compgen}}-->  | }}
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video]
+
{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK video]
 
{{R | TI|Substitučné modely |  <!-- {{pdf|ci-matice}} --> |  <!--[[CI07|notes]]--> }}
 
{{R | TI|Substitučné modely |  <!-- {{pdf|ci-matice}} --> |  <!--[[CI07|notes]]--> }}
 
{{R | TB|E-hodnota, fylogenetické stromy | <!--{{pdf|cb-evalue}}--> <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}}--> | <!--[[CB07|notes]]--> }}
 
{{R | TB|E-hodnota, fylogenetické stromy | <!--{{pdf|cb-evalue}}--> <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}}--> | <!--[[CB07|notes]]--> }}
Riadok 75: Riadok 74:
 
{{T|Nov 11|}}
 
{{T|Nov 11|}}
 
{{R | L| Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách | {{pdf|p-expr}} | }}
 
{{R | L| Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách | {{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 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]
 
{{R | TI|Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM, vzorové riešenia DÚ1 | <!-- {{pdf|ci-hmm}} --> | <!--[[CI08|notes]]--> }}
 
{{R | TI|Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM, vzorové riešenia DÚ1 | <!-- {{pdf|ci-hmm}} --> | <!--[[CI08|notes]]--> }}
 
{{R | TB|Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction| <!--{{pdf|cb-kmeans}}--> {{pdf|cb-enrichment-en}} | <!--[[CB08|notes]]--> }}
 
{{R | TB|Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction| <!--{{pdf|cb-kmeans}}--> {{pdf|cb-enrichment-en}} | <!--[[CB08|notes]]--> }}
Riadok 81: Riadok 80:
 
{{T|Nov 18|}}
 
{{T|Nov 18|}}
 
{{R | L| Štruktúra a funkcia proteínov |  <!--{{pdf|p-prot}} | }}
 
{{R | L| Štruktúra a funkcia proteínov |  <!--{{pdf|p-prot}} | }}
{{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc 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]
 
{{R | TI|Hľadanie motívov EM a Gibbsovým vzorkovaním |  |  <!--[[CI09|notes]]--> }}
 
{{R | TI|Hľadanie motívov EM a Gibbsovým vzorkovaním |  |  <!--[[CI09|notes]]--> }}
 
{{R | TB|Úvod do bezkontextových gramatík, Uniprot | | <!--[[CB09|notes]]--> }}
 
{{R | TB|Úvod do bezkontextových gramatík, Uniprot | | <!--[[CB09|notes]]--> }}

Verzia zo dňa a času 21:15, 22. september 2021

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 faculty library under code I-INF-D-21
  • ZB: Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008.
    Can be studied in the faculty 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


Sept. 23
L: Introduction, course rules, sequencing and genome assembly
BV chapter 1, SK video 1 SK video 2
TI: Introduction to biology notes
ZB chapter 1, SK video
TB: Introduction to computer science, UCSC genome browser pdf notes
Sept. 30
L: Genome assembly 2 pdf
SK video
TI: Introduction to probability, genome coverage by sequencing reads
TB: Introduction to dynamic programming, introduction to probability
Oct. 7
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. 14
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. 21
L: Gene finding, hidden Markov models pdf
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. 28
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, Fitch's algorithm
Nov. 4
L: Komparatívna genomika, detekcia pozitívneho a purifikačného výberu, komparatívne hľadanie génov, fylogenetické HMM
BV chapter 5, ZB chapter 9.8, 10.8, SK video
TI: Substitučné modely
TB: E-hodnota, fylogenetické stromy
Nov 11
L: Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách pdf
DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1, SK video
TI: Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM, vzorové riešenia DÚ1
TB: Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction pdf
Nov 18
L: Štruktúra a funkcia proteínov {{{4}}}
TB: Úvod do bezkontextových gramatík, Uniprot
Nov 25
L: RNA, sekundárna štruktúra, Nussinovovej algoritmus, stochastické bezkontextové gramatiky, profily RNA rodín pdf
DEKM chapter 10, ZB chapter 11.9, video
TI: Ukážky biologických databáz, úvod do bezkontextových gramatík
TB: Nussinovovej algoritmus
Dec 2
L: Populačná genetika pdf
video
TI: RNA štruktúra
TB: Microarray dáta, RNA štruktúra, MEME, transkripčné faktory v SGD, populačná genetika
Dec 9
L: Prednáška nebude
TI: Zhrnutie semestra, Protein threading pomocou celočíselného lineárneho programovania
TB: Zhrnutie semestra, grafy, PSI-BLAST, Pfam, gény, komparatívna genomika, ukážka práce na príkazovom riadku
Dec 16
L: Nepovinné prezentácie