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

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


Materials: Rozdiel medzi revíziami

Z MBI
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Riadok 7: Riadok 7:
 
* '''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
  
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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.  
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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'''
 
'''Recordings of lectures in Slovak from 2018/19'''
Riadok 59: Riadok 59:
 
{{R | L| Gene finding, hidden Markov models | <!--{{pdf|p-gene}}--> | }}
 
{{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 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|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 |  | <!--[[CB05|notes]]--> }}
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{{R | TB|Hidden Markov models, E-value |  | [[CB05|SK notes]] }}
 
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{{T|Oct. 28||6}}
 
{{T|Oct. 28||6}}
Riadok 87: Riadok 87:
 
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{{T|Nov. 25||10}}
 
{{T|Nov. 25||10}}
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{{R | L| RNA, sekundárna štruktúra, Nussinovovej algoritmus, stochastické bezkontextové gramatiky, profily RNA rodín | <!--{{pdf|p-rna}}--> | }}
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{{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]
 
{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
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{{R | TI| Ukážky biologických databáz, úvod do bezkontextových gramatík |  | <!--[[CI10|notes]]--> |  }}
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{{R | TI| Examples of biological databases, introduction to context-free grammars |  | <!--[[CI10|notes]]--> |  }}
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{{R | TB| Nussinovovej algoritmus | | <!--[[CB10|notes]]--> }}
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{{R | TB| Nussinov algorithm | | <!--[[CB10|notes]]--> }}
 
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{{T|Dec. 2||11}}
 
{{T|Dec. 2||11}}
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{{R | L| Populačná genetika | <!--{{pdf|p-popgen}}--> | }}
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{{R | L| Population genetics | <!--{{pdf|p-popgen}}--> | }}
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
 
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
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{{R | TI| RNA štruktúra |  | <!--[[CI11|notes]]--> }}
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{{R | TI| RNA structure |  | <!--[[CI11|notes]]--> }}
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{{R | TB| Microarray dáta, RNA štruktúra, MEME, transkripčné faktory v SGD, populačná genetika | | <!--[[CB11|notes]]-->  }}
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{{R | TB| Microarray data, RNA structure, MEME, transcription factors in SGD, population genetics | | <!--[[CB11|notes]]-->  }}
 
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{{T|Dec. 9||12}}
 
{{T|Dec. 9||12}}
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{{R | L| Prednáška nebude | | }}
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{{R | L| No lecture | | }}
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{{R | TI| Zhrnutie semestra, Protein threading pomocou celočíselného lineárneho programovania | <!--{{pdf|ci-summary}}, {{pdf|ci-ilp}}--> | <!--[[CI12|notes]]--> }}
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{{R | TI| Course summary, protein threading via integer linear programming | <!--{{pdf|ci-summary}}, {{pdf|ci-ilp}}--> | <!--[[CI12|notes]]--> }}
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{{R | TB| Zhrnutie semestra, grafy, PSI-BLAST, Pfam, gény, komparatívna genomika, ukážka práce na príkazovom riadku | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
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{{R | TB| Course summary, graphs, PSI-BLAST, Pfam, genes, comparative genomics, example of command-line tools | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
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{{T|Dec. 16||13}}
 
{{T|Dec. 16||13}}
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{{R | L| Nepovinné prezentácie | | }}
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{{R | L| Optional journal club presentations | | }}
 
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Verzia zo dňa a času 07:16, 20. október 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 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. 23
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. 30
L: Genome assembly 2 pdf
SK video
TI: Introduction to probability, genome coverage by sequencing reads pdf (SK) SK notes
TB: Introduction to dynamic programming, introduction to probability pdf SK notes
Oct. 7
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, SK video
TI: Introduction to dynamic programming, proteomics pdf (SK) notes
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 14
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, SK video
TI: Advanced algorithms for sequence alignment SK notes
TB: Programs for sequence alignment, scoring schemes SK notes
Oct. 21
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 SK notes
TB: Hidden Markov models, E-value SK notes
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: 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: E-value, phylogenetic trees
Nov. 11
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, HW1 model solutions
TB: K-means clustering, enrichment, multiple testing correction
Nov. 18
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: Motif finding by EM and Gibbs sampling
TB: Introduction to context-free grammars, Uniprot
Nov. 25
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, introduction to context-free grammars
TB: Nussinov algorithm
Dec. 2
L: Population genetics
SK video
TI: RNA structure
TB: Microarray data, RNA structure, MEME, transcription factors in SGD, population genetics
Dec. 9
L: No lecture
TI: Course summary, protein threading via integer linear programming
TB: Course summary, graphs, PSI-BLAST, Pfam, genes, comparative genomics, example of command-line tools
Dec. 16
L: Optional journal club presentations
Zdroj: „https://compbio.fmph.uniba.sk/vyuka/mbi/index.php?title=Materials&oldid=2644“