Materials
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
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. 25
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
Oct. 2
L: Genome assembly 2
TI: Introduction to probability, genome coverage by sequencing reads
notes (en, current) · notes (sk, older) · colab ⤓
TB: Introduction to dynamic programming, introduction to probability
Oct. 9
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring
pdf · video · BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2
TI: Burrows-Wheeler transform
TB: Dynamic programming for sequence alignment, dotplots
notes · pdf 1 · pdf 2 · dyn. prog. in colab ⤓
Oct. 16
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments
pdf · video · BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5
TI: Advanced algorithms for sequence alignment
notes (en, current) · notes (sk, older)
TB: Programs for sequence alignment, scoring schemes, introduction to projects
Oct. 23
L: Gene finding, hidden Markov models
pdf · video · BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7
TI: Fast similarity search, BLAST, MinHash
TB: Hidden Markov models, E-value
Oct. 30
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)
pdf · video · BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video
TI: Algorithms for HMM
notes (en) · notes (sk, old) · pdf
TB: Substitution models, bootstrap, tree rooting
Nov. 6
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
pdf · video · BV chapter 5, ZB chapter 9.8, 10.8,
TI: Substitution models
TB: Project proposals, practical phylogenetic trees
Nov. 13
L: Gene expression, differential expression, clustering, transcription factors, sequence motifs
pdf · video · DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1
TI: Felsenstein algorithm, algorithms for HMM and phyloHMM
TB: K-means clustering, enrichment, introduction do Uniprot for projects
notes uniprot · notes k-means, enrichment · notes enrichment2 · pdf kmeans
Nov. 20
L: Protein structure and function
pdf · video · DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2
TI: Motif finding by EM and Gibbs sampling
TB: Introduction to context-free grammars, expression data
notes grammars · notes expression · notebook expression ⤓ · notes proteins
Nov. 27
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
pdf · video · DEKM chapter 10, ZB chapter 11.9
TI: Examples of biological databases, HMM topology, introduction to context-free grammars
notes databases · notes grammar · notes HMMs
TB: Proteins, RNA structure, sequence motifs
notes proteins · notes rna · notes motifs · notes pop. genomics · notes comp. genomics