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| Riadok 1: |
Riadok 1: |
| − | 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 na 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 cvicenia pre biologov v 2020 netradicne rozdelene, lebo chaos prve dva tyzdne!!
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| − | -->
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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. 23||1}}
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| − | {{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro-en}}, {{pdf|p-seq-en}} | }}
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| − | {{Lit2 | BV chapter 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs SK video 1] [https://www.youtube.com/watch?v=iHt5WPVFd7E SK video 2]
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| − | {{R | TI| Introduction to biology | {{pdf|ci-introbio-en}} | [[CI01|SK notes]] }}
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| − | {{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 SK video]
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| − | {{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} | [[CB01|SK notes]] }}
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| − | {{T|Sept. 30||2}}
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| − | {{R | L| Genome assembly 2 | {{pdf|p-seq2-en}} | }}
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| − | {{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
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| − | {{R | TI| Introduction to probability, genome coverage by sequencing reads | {{pdf|ci-coverage}} (SK) | [[CI02|SK notes]] }}
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| − | {{R | TB| Introduction to dynamic programming, introduction to probability | {{pdf|cb-dp}} | [[CB02|SK notes]] }}
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| − | {{T|Oct. 7||3}}
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| − | {{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring | {{pdf|p-aln1-en}} | }}
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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 SK video]
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| − | {{R | TI|Introduction to dynamic programming, proteomics | {{pdf|ci-msms}} (SK) | [[CI03|notes]] }}
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| − | {{R | TB|Dynamic programming for sequence alignment, dotplots | {{pdf|cb-dotplots}} | [[CB03|notes]] }}
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| − | {{T|Oct. 14||4}}
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| − | {{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | {{pdf|p-aln2-en}} | }}
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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 SK video]
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| − | {{R | TI|Advanced algorithms for sequence alignment | | [[CI04|SK notes]] }}
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| − | {{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|SK notes]] }}
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| − | {{T|Oct. 21||5}}
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| − | {{R | L| Gene finding, hidden Markov models | {{pdf|p-gene-en}} | }}
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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 SK video]
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| − | {{R | TI|Fast similarity search, BLAST, MinHash | | [[CI05|SK notes]] }}
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| − | {{R | TB|Hidden Markov models, E-value | {{pdf|cb-evalue}} | [[CB05|SK notes]] }}
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| − | {{T|Oct. 28||6}}
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| − | {{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | {{pdf|p-phylo-en}} | }}
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| − | {{Lit2 | BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2}}, [https://youtu.be/RzfNHvZH4l8 SK video]
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| − | {{R | TI|Algorithms for HMM | {{pdf|ci-hmm-en}} | [[CI06|SK notes]] }}
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| − | {{R | TB|Substitution models, bootstrap, tree rooting| {{pdf|cb-phylo}} <!--{{pdf|cb-phylo-en}}--> | [[CB06|SK notes]] }}
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| − | {{T|Nov. 4||7}}
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| − | {{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs | {{pdf|p-compgen-en}} | }}
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| − | {{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK video]
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| − | {{R | TI|Substitution models | {{pdf|ci-matice-en}} | [[CI07|SK notes]] }}
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| − | {{R | TB|Phylogenetic trees | {{pdf|cb-compgen}}, {{pdf|cb-gene}} | [[CB07|SK notes]] }}
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| − | {{T|Nov. 11||8}}
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| − | {{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr-en}} | }}
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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|Felsenstein algorithm, algorithms for HMM and phyloHMM, HW1 model solutions | {{pdf|ci-hmm}} | [[CI08|SK notes]] }}
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| − | {{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} | [[CB08|SK notes]] }}
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| − | {{T|Nov. 18||9}}
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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|Motif finding by EM and Gibbs sampling | | <!--[[CI09|notes]]--> }}
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| − | {{R | TB|Introduction to context-free grammars, Uniprot | | <!--[[CB09|notes]]--> }}
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| − | {{T|Nov. 25||10}}
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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| Examples of biological databases, introduction to context-free grammars | | <!--[[CI10|notes]]--> | }}
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| − | {{R | TB| Nussinov algorithm | | <!--[[CB10|notes]]--> }}
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| − | {{T|Dec. 2||11}}
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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| Microarray data, RNA structure, MEME, transcription factors in SGD, population genetics | | <!--[[CB11|notes]]--> }}
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| − | {{T|Dec. 9||12}}
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| − | {{R | L| No lecture | | }}
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| − | {{R | TI| Course summary, protein threading via integer linear programming | <!--{{pdf|ci-summary}}, {{pdf|ci-ilp}}--> | <!--[[CI12|notes]]--> }}
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| − | {{R | TB| Course summary, graphs, PSI-BLAST, Pfam, genes, comparative genomics, example of command-line tools | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
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| − | {{T|Dec. 16||13}}
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| − | {{R | L| Optional journal club presentations | | }}
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| − | |}
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