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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 the 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. 24

L: Introduction, course rules, sequencing and genome assembly

pdf 1 · pdf 2 · video 1 · video 2 · BV chapter 1

TI: Introduction to biology

pdf · notes · video · ZB chapter 1

TB: Introduction to computer science, UCSC genome browser

pdf · notes

Oct. 1

L: Genome assembly 2

pdf · video

TI: Introduction to probability, genome coverage by sequencing reads

notes (en, current) · notes (sk, older) · colab ⤓

TB: Introduction to dynamic programming, introduction to probability

notes 1 · notes 2

Oct. 8

L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring

pdf · video ·

TI: Burrows-Wheeler transform

pdf

TB: Dynamic programming for sequence alignment, dotplots

notes · pdf · dyn. prog. in colab ⤓

Oct. 15

L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments

pdf · video · Biology is messy (video by Phy the Neutrophil) ·

TI: Advanced algorithms for sequence alignment

notes (en, current) · notes (sk, older)

TB: Programs for sequence alignment, scoring schemes, introduction to projects

notes · Projects

Oct. 22

L: Gene finding, hidden Markov models

pdf · video · What is a Dark Protein (video by Phy the Neutrophil)

TI: Fast similarity search, BLAST, MinHash

notes · pdf

TB: Hidden Markov models, E-value

notes · pdf

Oct. 29

L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)

TI: Algorithms for HMM

TB: Substitution models, bootstrap, tree rooting

Nov. 5

L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs

TI: Substitution models

TB: Project proposals, practical phylogenetic trees

Nov. 12

L: Gene expression, differential expression, clustering, transcription factors, sequence motifs

TI: Felsenstein algorithm, algorithms for HMM and phyloHMM

TB: K-means clustering, enrichment, introduction do Uniprot for projects

Nov. 19

L: Protein structure and function

TI: Motif finding by EM and Gibbs sampling

TB: Introduction to context-free grammars, expression data

Nov. 26

L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles

TI: Examples of biological databases, HMM topology, introduction to context-free grammars

TB: Proteins, RNA structure, sequence motifs

Dec. 3

L: Population genetics

TI: RNA structure

TB: Course summary, graphs, population genetics, example of command-line tools

Dec. 10

L: (no lecture)

TI: Integer linear programming, course summary

TB: no tutorial

Dec. 17

L: Mandatory journal club presentations (no lecture)

TI: Consultations for the exam in F1-109

TB: Project consultations, starting sooner