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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.<br>Can be studied in the faculty library under code I-INF-D-21
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| − | * '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008.<br>Can be studied in the faculty 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}}
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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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| − | {{T|23.9.|}}
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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 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}} --> | [[CI01|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|notes]] }}
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| − | {{T|30.9|}}
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| − | {{R | L| Zostavovanie genómov 2 | {{pdf|p-seq2}} | }}
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| − | {{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
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| − | {{R | TI| Úvod do pravdepodobnosti, pokrytie pri sekvenovaní | <!-- {{pdf|ci-coverage}} --> | <!-- [[CI02|notes]]--> }}
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| − | {{R | TB| Úvod do dynamického programovania, úvod do pravdepodobnosti | <!-- {{pdf|cb-dp}} --> | <!-- [[CB02|notes]]--> }}
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| − | {{T|7.10.|}}
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| − | {{R | L| Zarovnávanie sekvencií: Smith-Waterman, Needleman-Wunsch, skórovanie | <!-- {{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 SK video]
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| − | {{R | TI|Úvod do dynamického programovania, proteomika | <!-- {{pdf|ci-msms}} --> | <!--[[CI03|notes]]--> }}
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| − | {{R | TB|Dynamické programovanie pre zarovnávanie sekvencií, dotploty | <!-- {{pdf|cb-dotplots}} --> | <!--[[CB03|notes]]--> }}
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| − | {{T|14.10.|}}
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| − | {{R | L| Zarovnávanie sekvencií: heuristické zarovnávanie (BLAST), štatistická významnosť zarovnaní, zarovnávanie genómov, viacnásobné zarovnanie | <!-- {{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 SK video]
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| − | {{R | TI|Pokročilé algoritmy pre zarovnávanie sekvencií | | <!-- [[CI04|notes]]--> }}
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| − | {{R | TB|Programy na zarovnávanie sekvencií, skórovacie schémy| | <!-- [[CB04|notes]]--> }}
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| − | {{T|21.10.|}}
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| − | {{R | L| Hľadanie génov, skryté Markovove modely | {{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|Rýchle hľadanie podobnosti, BLAST, MinHash | | <!--[[CI05|notes]]--> }}
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| − | {{R | TB|Skryté Markovove modely, programy na zarovnávanie sekvencií | | <!--[[CB05|notes]]--> }}
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| − | <!-- {{pdf|ci-seeds}} -->
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| − | {{T|28.10.|}}
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| − | {{R | L| Rekonštrukcia fylogenetických stromov (úspornosť, metóda spájania susedov, modely evolúcie) | <!--{{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|Algoritmy pre HMM | <!-- {{pdf|ci-hmm}} --> | <!--[[CI06|notes]]--> }}
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| − | {{R | TB|Substitučné modely, bootstrap, zakorenenie stromu, fylogenetické stromy <!-- Fitchov algoritmus --> | <!-- {{pdf|cb-phylo}} --> <!--{{pdf|cb-phylo-en}}--> | <!--[[CB06|notes]]--> }}
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| − | {{T|4.11.|}}
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| − | {{R | L| Komparatívna genomika, detekcia pozitívneho a purifikačného výberu, komparatívne hľadanie génov, fylogenetické HMM | <!--{{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|Substitučné modely | <!-- {{pdf|ci-matice}} --> | <!--[[CI07|notes]]--> }}
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| − | {{R | TB|E-hodnota, fylogenetické stromy | <!--{{pdf|cb-evalue}}--> <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}}--> | <!--[[CB07|notes]]--> }}
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| − | {{T|11.11.|}}
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| − | {{R | L| Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách | {{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 video]
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| − | {{R | TI|Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM, vzorové riešenia DÚ1 | <!-- {{pdf|ci-hmm}} --> | <!--[[CI08|notes]]--> }}
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| − | {{R | TB|Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction| <!--{{pdf|cb-kmeans}}--> {{pdf|cb-enrichment-en}} | <!--[[CB08|notes]]--> }}
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| − | {{T|18.11.|}}
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| − | {{R | L| Štruktúra a funkcia proteínov | <!--{{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 video]
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| − | {{R | TI|Hľadanie motívov EM a Gibbsovým vzorkovaním | | <!--[[CI09|notes]]--> }}
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| − | {{R | TB|Úvod do bezkontextových gramatík, Uniprot | | <!--[[CB09|notes]]--> }}
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| − | {{T|25.11.|}}
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| − | {{R | L| RNA, sekundárna štruktúra, Nussinovovej algoritmus, stochastické bezkontextové gramatiky, profily RNA rodín | {{pdf|p-rna}} | }}
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| − | {{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k video]
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| − | {{R | TI| Ukážky biologických databáz, úvod do bezkontextových gramatík | | <!--[[CI10|notes]]--> | }}
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| − | {{R | TB| Nussinovovej algoritmus | | <!--[[CB10|notes]]--> }}
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| − | {{T|2.12.|}}
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| − | {{R | L| Populačná genetika | {{pdf|p-popgen}} | }}
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| − | {{Lit2 | }} [https://youtu.be/7vPt1vQX21M video]
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| − | {{R | TI| RNA štruktúra | | <!--[[CI11|notes]]--> }}
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| − | {{R | TB| Microarray dáta, RNA štruktúra, MEME, transkripčné faktory v SGD, populačná genetika | | <!--[[CB11|notes]]--> }}
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| − | {{T|9.12.|}}
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| − | {{R | L| Prednáška nebude | | }}
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| − | {{R | TI| Zhrnutie semestra, Protein threading pomocou celočíselného lineárneho programovania | <!--{{pdf|ci-summary}}, {{pdf|ci-ilp}}--> | <!--[[CI12|notes]]--> }}
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| − | {{R | TB| Zhrnutie semestra, grafy, PSI-BLAST, Pfam, gény, komparatívna genomika, ukážka práce na príkazovom riadku | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
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| − | {{T|16.12.|}}
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| − | {{R | L| Nepovinné prezentácie | | }}
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