Materials: Rozdiel medzi revíziami
Z MBI
| Riadok 74: | Riadok 74: | ||
{{T|Nov. 9||8}} | {{T|Nov. 9||8}} | ||
{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs | <!-- {{pdf|p-compgen}} --> | }} | {{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs | <!-- {{pdf|p-compgen}} --> | }} | ||
| − | <!-- | + | <!-- {{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video] --> |
| − | {{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video] | + | {{R | TI|Substitution models | <!-- {{pdf|ci-matice-en}} --> | <!-- [[CI07|notes]] -->}} |
| − | {{R | TI|Substitution models | {{pdf|ci-matice-en}} | [[CI07|notes]] }} | + | {{R | TB|Phylogenetic trees | | <!-- [[CB07|notes]] --> }} |
| − | {{R | TB|Phylogenetic trees | | [[CB07|notes]] }} | + | |- |
| − | --> | + | {{T|Nov. 16||10}} |
| + | {{R | L| Protein structure and function | <!-- {{pdf|p-prot}} --> | }} | ||
| + | <!-- {{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]--> | ||
| + | {{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}}--> | <!-- [[CI08|notes]] -->}} | ||
| + | {{R | TB| Genes, comparative genomics, Pfam | | <!-- [[CB10|notes]]--> }} | ||
|- | |- | ||
| − | {{T|Nov. | + | {{T|Nov. 23||9}} |
{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr}} -->| }} | {{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr}} -->| }} | ||
| − | <!-- | + | <!--{{Lit2 | DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1}}, [https://youtu.be/GFJ_oDV1KGU SK video] --> |
| − | {{Lit2 | DEKM chapter 5.1, 11.5, ZB chapter 6.6,15.1,16.1-16.5,17.1}}, [https://youtu.be/GFJ_oDV1KGU SK video] | + | {{R | TI|Protein threading via integer linear programming | {{pdf|ci-ilp-en}} | [[CI12|notes]] }} |
| − | + | {{R | TB|Introduction to context-free grammars | | <!-- [[CB09|notes]]--> }} | |
| − | + | ||
| − | --> | + | |
| − | + | ||
| − | + | ||
| − | {{R | | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | {{R | TB|Introduction to context-free grammars | | [[CB09|notes]] | + | |
| − | --> | + | |
|- | |- | ||
{{T|Nov. 30||11}} | {{T|Nov. 30||11}} | ||
{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna}} --> | }} | {{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna}} --> | }} | ||
| + | {{R | TB|K-means clustering, enrichment, multiple testing correction| <!-- {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}}--> | <!-- [[CB08|notes]]-->}} | ||
<!-- | <!-- | ||
{{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] | ||
{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars | | [[CI10|notes]] | }} | {{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars | | [[CI10|notes]] | }} | ||
| − | |||
--> | --> | ||
|- | |- | ||
| Riadok 108: | Riadok 102: | ||
<!-- | <!-- | ||
{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video] | {{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video] | ||
| + | {{R | TI|Motif finding by EM and Gibbs sampling | | [[CI09|notes]] }} | ||
{{R | TI| RNA structure | | [[CI11|notes]] }} | {{R | TI| RNA structure | | [[CI11|notes]] }} | ||
{{R | TB| Example of command-line tools | | [[CB11|notes]] }} | {{R | TB| Example of command-line tools | | [[CB11|notes]] }} | ||
| Riadok 115: | Riadok 110: | ||
{{R | L| Optional journal club presentations | | }} | {{R | L| Optional journal club presentations | | }} | ||
<!-- | <!-- | ||
| − | {{R | TI| Course summary | + | {{R | TI| Course summary | {{pdf|ci-summary-en}} | [[CI12|notes]] }} |
{{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }} | {{R | TB| PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }} | ||
--> | --> | ||
|- | |- | ||
|} | |} | ||
Verzia zo dňa a času 16:05, 26. október 2023
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 | notes | |
| ZB chapter 1, video | |||
| TB: | Introduction to computer science, UCSC genome browser | notes | |
| Sept. 28 | |||
| L: | Genome assembly 2 | ||
| video | |||
| TI: | Introduction to probability, genome coverage by sequencing reads | notes | |
| Python simulations and approximations colab | |||
| TB: | Introduction to dynamic programming, introduction to probability | notes | |
| Oct. 5 | |||
| 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, video | |||
| TI: | Introduction to dynamic programming, proteomics | notes | |
| Python implementation of DP and visualisations colab | |||
| TB: | Dynamic programming for sequence alignment, dotplots | notes | |
| Oct. 12 | |||
| 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, video | |||
| TI: | Advanced algorithms for sequence alignment | notes | |
| TB: | Programs for sequence alignment, scoring schemes | notes | |
| Oct. 19 | |||
| L: | Gene finding, hidden Markov models | ||
| BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video | |||
| TI: | Fast similarity search, BLAST, MinHash | ||
| TB: | Hidden Markov models, E-value | notes | |
| Oct. 26 | |||
| L: | Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | ||
| BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video | |||
| TI: | Algorithms for HMM | notes | |
| TB: | Substitution models, bootstrap, tree rooting | 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 | 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 | ||
