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Riadok 1: |
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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.
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| − | '''Literature:'''
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| − | * '''BV''': Brejová, Vinař: Metódy v bioinformatike. (preliminary version of lecture notes in Slovak, only several lectures) {{pdf|skripta-2015-10-01}}
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| − | * '''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
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| − | * '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI library under code I-INF-Z-2
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| − | 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.
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| − | '''Recordings of lectures in Slovak from 2018/19'''
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| − | * [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist on youtube]
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| − | '''Notes and presentations'''
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| − | L: lecture (everybody), TI: tutorial for computer science/informatics students,
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| − | TB: tutorial for biology/chemistry/physics students
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| − | <!--
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| − | Pouzitie sablon:
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| − | tyzden: {{T|datumy od-do|nepovinny dalsi text|cislo tyzdna}}
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| − | riadok (hodina): {{R| aka hodina, t.j. L alebo TI alebo TB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
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| − | literatura: {{Lit | cisla kapitol}}
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| − | POZOR 2023 prehodene proteiny a expresia, kvoli tomu trochu chaos v cvikach, potencialne pouzi 2022
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| − | {{W|1}}, {{W|2}}, {{W|3}}, {{W|4}}, {{W|5}}, {{W|6}}, {{W|7}}, {{W|8}}, {{W|9}}, {{W|10}}, {{W|11}}, {{W|12}}, {{W|13}}
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| − | {{T|Sept. 21||1}}
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| − | {{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro}}, {{pdf|p-seq}} | }}
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| − | {{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E video 2]
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| − | {{R | TI| Introduction to biology | {{pdf|ci-introbio}} | [[CI01|notes]] }}
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| − | {{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 video]
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| − | {{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} | [[CB01|notes]] }}
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| − | {{T|Sept. 28||2}}
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| − | {{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
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| − | {{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
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| − | {{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} | [[CI02|notes]] }}
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| − | {{Lit2 | Python simulations and approximations}} [https://colab.research.google.com/drive/12TdzUdwTB03Y8xJbgvHTWYIwdmlBaYZY?usp=sharing colab]
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| − | {{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|notes]] }}
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| − | {{T|Oct. 5||3}}
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| − | {{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring | {{pdf|p-aln1}} | }}
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| − | {{Lit2 | BV chapter 2, DEKM chapter 2.1-2.4, 2.8, ZB chapter 4.1-4.4, 5.1-5.2}}, [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]
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| − | {{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} | [[CI03|notes]] }}
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| − | {{Lit2 | Python implementation of DP and visualisations}} [https://colab.research.google.com/drive/14QB903XpAsUFsqfls3rYoSaYRhyNX-So?usp=sharing colab]
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| − | {{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }}
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| − | {{T|Oct. 12||4}}
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| − | {{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2}} | }}
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| − | {{Lit2 | BV chapter 2, DEKM chapter 2.5, 2.7, 6.1-6.3; ZB chapter 4.5-4.7, 5.3-5.5}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
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| − | {{R | TI|Advanced algorithms for sequence alignment | | [[CI04|notes]] }}
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| − | {{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
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| − | {{T|Oct. 19||5}}
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| − | {{R | L| Gene finding, hidden Markov models | {{pdf|p-gene}}| }}
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| − | {{Lit2 | BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]
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| − | {{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | <!-- [[CI05|notes]]--> }}
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| − | {{R | TB|Hidden Markov models, E-value | {{pdf|cb-evalue}} | [[CB05|notes]] }}
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| − | {{T|Oct. 26||6}}
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| − | {{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo}} | }}
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| − | {{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 video]
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| − | {{R | TI|Algorithms for HMM | {{pdf|ci-hmm}} | [[CI06|notes]] }}
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| − | {{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} | [[CB06|notes]] }}
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| − | {{T|Nov. 2|No lecture, no tutorials|7}}
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| − | {{T|Nov. 9||8}}
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| − | {{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs | {{pdf|p-compgen}} | }}
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| − | {{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A video]
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| − | {{R | TI|Substitution models | <!-- {{pdf|ci-matice-en}}--> {{pdf|Ci-substitution-models}} | [[CI07|notes]] }}
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| − | {{R | TB|Practical phylogenetic trees | | [[CB07|notes]] }}
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| − | {{T|Nov. 16||10}}
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| − | {{R | L| Protein structure and function | {{pdf|p-prot}} | }}
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| − | {{Lit2 | DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2}}, [https://youtu.be/ugMM81jZRpc SK video]
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| − | {{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}}--> | <!-- [[CI08|notes]] -->}}
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| − | {{R | TB| Pfam, PSI-blast, Example of command-line tools | | [[CB10|notes1]], [[CB11|notes2]] }}
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| − | {{T|Nov. 23||9}}
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| − | {{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}}| }}
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| − | {{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]
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| − | {{R | TI|Examples of biological databases, introduction to context-free grammars | | [[CI10|notes]] }}
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| − | {{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
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| − | {{T|Nov. 30||11}}
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| − | {{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | {{pdf|p-rna}} | }}
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| − | {{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
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| − | {{R | TI|Motif finding by EM and Gibbs sampling | {{pdf|ci-motifs}} | <!--[[CI09|notes]]--> }}
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| − | {{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|notes]]}}
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| − | {{T|Dec. 7||12}}
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| − | {{R | L| Population genetics | {{pdf|p-popgen}} | }}
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| − | {{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
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| − | {{R | TI| RNA structure | | <!-- [[CI11|notes]]--> }}
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| − | {{R | TB| Course summary, graphs, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|notes]] }}
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| − | {{T|Dec. 14||13}}
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| − | {{R | L| Optional journal club presentations | | }}
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| − | {{R | TI| Protein threading via integer linear programming, course summary | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}}--> | <!-- [[CI12|notes]]--> }}
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| − | {{R | TB| Project consultations | | }}
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