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

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


Materials

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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. 21
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, video 1 video 2
TI: Introduction to biology pdf notes
ZB chapter 1, video
TB: Introduction to computer science, UCSC genome browser pdf notes
Sept. 28
L: Genome assembly 2 pdf
video
TI: Introduction to probability, genome coverage by sequencing reads pdf notes
Python simulations and approximations colab
TB: Introduction to dynamic programming, introduction to probability pdf notes
Oct. 5
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, video
TI: Introduction to dynamic programming, proteomics pdf notes
Python implementation of DP and visualisations colab
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 12
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, video
TI: Advanced algorithms for sequence alignment notes
TB: Programs for sequence alignment, scoring schemes notes
Oct. 19
L: Gene finding, hidden Markov models pdf
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video
TI: Fast similarity search, BLAST, MinHash pdf
TB: Hidden Markov models, E-value pdf notes
Oct. 26
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) pdf
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video
TI: Algorithms for HMM pdf notes
TB: Substitution models, bootstrap, tree rooting pdf notes
Nov. 2 No lecture, no tutorials
Nov. 9
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
TI: Substitution models
TB: Phylogenetic trees
Nov. 16
L: Protein structure and function
TI: Felsenstein algorithm, algorithms for HMM and phyloHMM
TB: Genes, comparative genomics, Pfam
Nov. 23
L: Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs
TI: Protein threading via integer linear programming pdf notes
TB: Introduction to context-free grammars
Nov. 30
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
TB: K-means clustering, enrichment, multiple testing correction
Dec. 7
L: Population genetics
Dec. 14
L: Optional journal club presentations