MBI 2021/2022

Literature:

• BV: Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures)
• 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

• playlist on youtube

Notes and presentations

L: lecture (everybody), TI: tutorial for computer science/applied informatics/bioinformatics/data science 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
	BV chapter 1, SK video 1 SK video 2
TI:	Introduction to biology		SK notes
	ZB chapter 1, SK video
TB:	Introduction to computer science, UCSC genome browser		SK notes
Sept. 30
L:	Genome assembly 2
	SK video
TI:	Introduction to probability, genome coverage by sequencing reads		SK notes
TB:	Introduction to dynamic programming, introduction to probability		SK notes
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		notes
TB:	Dynamic programming for sequence alignment, dotplots		notes
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		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		SK notes
TB:	Substitution models, bootstrap, tree rooting		SK notes
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		SK notes
TB:	Phylogenetic trees		SK notes
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		SK notes
TB:	K-means clustering, enrichment, multiple testing correction		SK notes
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		SK notes
TB:	Introduction to context-free grammars		SK notes
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, HW1 model solutions, introduction to context-free grammars		SK notes
TB:	Genes, comparative genomics, Pfam		SK notes
Dec. 2
L:	No lecture, no tutorials
Dec. 9
L:	Population genetics
	SK video
TI:	RNA structure		SK notes
TB:	PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs		SK notes
Dec. 16
L:	Optional journal club presentations
TI:	Course summary, protein threading via integer linear programming		SK notes
TB:	Cancelled