Materials: Rozdiel medzi revíziami
Z MBI
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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. | 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. | ||
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Verzia zo dňa a času 13:52, 25. september 2024
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 | ||
| BV chapter 5, ZB chapter 9.8, 10.8, video | |||
| TI: | Substitution models | notes | |
| TB: | Practical phylogenetic trees | notes | |
| Nov. 16 | |||
| 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: | Felsenstein algorithm, algorithms for HMM and phyloHMM | ||
| TB: | Pfam, PSI-blast, Example of command-line tools | notes1, notes2 | |
| Nov. 23 | |||
| 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: | Examples of biological databases, introduction to context-free grammars | notes | |
| TB: | Introduction to context-free grammars | notes | |
| Nov. 30 | |||
| L: | RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | ||
| DEKM chapter 10, ZB chapter 11.9, SK video | |||
| TI: | Motif finding by EM and Gibbs sampling | ||
| TB: | K-means clustering, enrichment, multiple testing correction | pdf pdf | notes |
| Dec. 7 | |||
| L: | Population genetics | ||
| SK video | |||
| TI: | RNA structure | ||
| TB: | Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics | pdf, pdf | notes |
| Dec. 14 | |||
| L: | Optional journal club presentations | ||
| TI: | Protein threading via integer linear programming, course summary | ||
| TB: | Project consultations | ||
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