1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2022/23

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Groups for journal club have each their own channel in MS Teams.


Materials: Rozdiel medzi revíziami

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Na tejto stránke nájdete '''orientačný rozvrh semestra''', ktorý budeme priebežne aktualizovať. Poznámky z prednášok a ďalšie rozširujúce materiály budú pribúdať po skončení príslušných prednášok.
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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.
  
'''Literatúra:'''
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'''Literature:'''
  
* '''BV''': Brejová, Vinař: Metódy v bioinformatike. (predbežná verzia skrípt, iba niektoré prednášky)  
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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}}  
** Verzia z 1.10.2015: {{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  
* '''DEKM''': Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998.<br>K dispozícii v knižnici FMFI k prezenčnému používaniu, signatúra 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
* '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008.<br>K dispozícii v knižnici FMFI k prezenčnému používaniu, signatúra I-INF-Z-2
+
  
Pri prednáškach uvádzame kapitoly najviac pokrývajúce učivo, ktoré plánujeme prebrať. Prezentácia materiálu v rámci prednášok sa obvykle nezhoduje s prezentáciou v učebniciach. Uvedené kapitoly by mali hlavne slúžiť ako doplňujúci materiál pre samoštúdium.
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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.  
  
'''Videozáznamy prednášok zo školského roku 2018/19'''
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'''Recordings of lectures in Slovak from 2018/19'''
* [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist na youtube]
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* [https://www.youtube.com/playlist?list=PLU2XVjShDFwVeTDmo9Uv2NHWz3ijUjy5p playlist on youtube]
  
  
'''Poznámky a prezentácie'''
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'''Notes and presentations'''
  
PR: spoločná prednáška, CI: cvičenia pre informatikov, CB: cvičenia pre biológov
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L: lecture (everybody), TI: tutorial for computer science/informatics students,
 +
TB: tutorial for biology/chemistry/physics students
  
 
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Pouzitie sablon:
 
Pouzitie sablon:
tyzden: {{T|datumy od-do|nepovinny dalsi text}}
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tyzden: {{T|datumy od-do|nepovinny dalsi text|cislo tyzdna}}
riadok (hodina): {{R| aka hodina, t.j. PR alebo CI alebo CB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
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riadok (hodina): {{R| aka hodina, t.j. L alebo TI alebo TB| popis | {{pdf|meno pdf suboru}} | [[wiki poznamky|poznamky]] }}
 
literatura: {{Lit | cisla kapitol}}
 
literatura: {{Lit | cisla kapitol}}
v url prepis = na %3D
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pozor cvicenia pre biologov v 2020 netradicne rozdelene, lebo chaos prve dva tyzdne!!
 
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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}}
  
 
{|
 
{|
 
|-
 
|-
{{T|21.-27.9.|}}
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{{T|Sept. 22||1}}
{{R | PR| Úvod, administratíva, sekvenovanie a zostavovanie genómov | {{pdf|p-intro}}, {{pdf|p-seq}} | }}
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{{R | L| Introduction, course rules, sequencing and genome assembly | {{pdf|p-intro}}, {{pdf|p-seq}} | }}
{{Lit2 | BV kap. 1}}, [https://www.youtube.com/watch?v=3HI-wKmTuSs video 1] [https://www.youtube.com/watch?v%3DiHt5WPVFd7E video 2]
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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]
{{R | CI| Úvod do biológie | {{pdf|ci-introbio}} | [[CI01|poznámky]] }}
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{{R | TI| Introduction to biology | {{pdf|ci-introbio}} | [[CI01|SK notes]] }}
{{Lit2 | ZB kap. 1}}, [https://www.youtube.com/watch?v%3DEtPqUOHTJD4 video]
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{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 SK video]
{{R | CB| Úvod do informatiky, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|poznámky]] }}
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{{R | TB| Introduction to computer science, UCSC genome browser | {{pdf|cb-introcs}} |  [[CB01|SK notes]] }}
 
|-
 
|-
{{T|28.9.-4.10.|}}
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{{T|Sept. 29||2}}
{{R | PR| Zostavovanie genómov 2 | {{pdf|p-seq2}} | }}
+
{{R | L| Genome assembly 2 | <!-- {{pdf|p-seq2-en}} --> | }}
{{Lit2 | }} [https://www.youtube.com/watch?v%3DYvZlTL1qyUg video]
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{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg SK video]
{{R | CI| Úvod do pravdepodobnosti, pokrytie pri sekvenovaní | <!-- {{pdf|ci-coverage}} --> | [[CI02|poznámky]] }}
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{{R | TI| Introduction to probability, genome coverage by sequencing reads | <!-- {{pdf|ci-coverage}} (SK) --> | <!-- [[CI02|SK notes]] --> }}
{{R | CB| Úvod do dynamického programovania, úvod do pravdepodobnosti | {{pdf|cb-dp}} | [[CB02|poznámky]] }}
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{{R | TB| Introduction to dynamic programming, introduction to probability | <!-- {{pdf|cb-dp}} --> | <!--[[CB02|SK notes]] --> }}
 
|-
 
|-
{{T|5.-11.10.|}}
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{{T|Oct. 6||3}}  
{{R | PR| Zarovnávanie sekvencií: Smith-Waterman, Needleman-Wunsch, skórovanie |  {{pdf|p-aln1}} | }}
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{{R | L| Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring <!-- {{pdf|p-aln1-en}} --> | }}
{{Lit2 | BV kap. 2, DEKM kap. 2.1-2.4, 2.8, ZB kap. 4.1-4.4, 5.1-5.2}}, [https://www.youtube.com/watch?v=0GkhkRiqbl4 video]
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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]
{{R | CI|Úvod do dynamického programovania, proteomika | <!-- {{pdf|ci-msms}} --> |  [[CI03|poznámky]] }}
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{{R | TI|Introduction to dynamic programming, proteomics | <!-- {{pdf|ci-msms}} (SK) --> |  <!-- [[CI03|SK notes]] --> }}
{{R | CB|Dynamické programovanie pre zarovnávanie sekvencií, dotploty | {{pdf|cb-dotplots}} |  [[CB03|poznámky]] }}
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{{R | TB|Dynamic programming for sequence alignment, dotplots | <!-- {{pdf|cb-dotplots}} --> <!-- [[CB03|SK notes]] --> }}
 
|-
 
|-
{{T|12.-18.10.|}}
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{{T|Oct. 13||4}}
{{R | PR| Zarovnávanie sekvencií: heuristické zarovnávanie (BLAST), štatistická významnosť zarovnaní, zarovnávanie genómov, viacnásobné zarovnanie | {{pdf|p-aln2}}  
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{{R | L| Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments | <!-- {{pdf|p-aln2-en}} --> | }}
{{Lit2 | BV kap. 2, DEKM kap. 2.5, 2.7, 6.1-6.3; ZB kap. 4.5-4.7, 5.3-5.5}}, [https://www.youtube.com/watch?v=jkQGXiqKbxM video]| }}
+
{{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]
{{R | CI|Pokročilé algoritmy pre zarovnávanie sekvencií | |  [[CI04|poznámky]] }}
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{{R | TI|Advanced algorithms for sequence alignment | |  <!-- [[CI04|SK notes]] --> }}
{{R | CB|Programy na zarovnávanie sekvencií, skórovacie schémy| | [[CB04|poznámky]] }}
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{{R | TB|Programs for sequence alignment, scoring schemes| | <!-- [[CB04|SK notes]] --> }}
 
|-
 
|-
{{T|19.-25.10.|}}
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{{T|Oct. 20||5}}
{{R | PR| Hľadanie génov, skryté Markovove modely | <!-- {{pdf|p-gene}} --> | }}
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{{R | L| Gene finding, hidden Markov models | <!-- {{pdf|p-gene-en}} --> | }}
{{Lit | BV kap. 4, DEKM kap. 3; ZB kap. 9.3, 10.4-10.7}}
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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]
{{R | CI|Rýchle hľadanie podobnosti, BLAST, MinHash |  | <!-- [[CI05|poznámky]] --> }}
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{{R | TI|Fast similarity search, BLAST, MinHash |  | <!-- [[CI05|SK notes]] --> }}
{{R | CB|Skryté Markovove modely, E-value | <!-- {{pdf|cb-evalue}} --> | <!-- [[CB05|poznámky]] --> }}
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{{R | TB|Hidden Markov models, E-value |   <!-- {{pdf|cb-evalue}} --> | <!-- [[CB05|SK notes]] --> }}
<!-- {{pdf|ci-seeds}} -->
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|-
 
|-
{{T|27.10.-1.11.|}}
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{{T|Oct. 27||6}}
{{R | PR| Rekonštrukcia fylogenetických stromov (úspornosť, metóda spájania susedov, modely evolúcie) | <!-- {{pdf|p-phylo}} --> | }}
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{{R | L| Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) | <!-- {{pdf|p-phylo-en}} --> | }}
{{Lit | BV kap. 3, DEKM kap. 7,8; ZB kap. 7, 8.1-8.2}}
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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]
{{R | CI|Algoritmy pre HMM | <!-- {{pdf|ci-hmm}} -->  | <!-- [[CI06|poznámky]] --> }}
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{{R | TI|Algorithms for HMM | <!-- {{pdf|ci-hmm-en}} -->  | <!-- [[CI06|SK notes]] --> }}
{{R | CB|Substitučné modely, bootstrap, zakorenenie stromu <!-- Fitchov algoritmus --> | <!-- {{pdf|cb-phylo}} --> | <!-- [[CB06|poznámky]] -->   }}
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{{R | TB|Substitution models, bootstrap, tree rooting| <!-- {{pdf|cb-phylo}} --> | <!-- [[CB06|SK notes]] --> }}
 
|-
 
|-
{{T|2.-8.11.|}}
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{{T|Nov. 3||7}}
{{R | PR| Komparatívna genomika, detekcia pozitívneho a purifikačného výberu, komparatívne hľadanie génov, fylogenetické HMM |  <!-- {{pdf|p-compgen}} --> | }}
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{{R | L| Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs |  <!-- {{pdf|p-compgen-en}} --> | }}
{{Lit | BV kap. 5, ZB kap. 9.8, 10.8}}
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{{Lit2 | BV chapter 5, ZB chapter 9.8, 10.8}}, [https://youtu.be/1WM4QI2qx8A SK video]
{{R | CI|Substitučné modely |  <!-- {{pdf|ci-matice}} --> | <!-- [[CI07|poznámky]] --> }}
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{{R | TI|Substitution models |  <!-- {{pdf|ci-matice-en}} --> | <!-- [[CI07|SK notes]] --> }}
{{R | CB|Gény v UCSC browseri, komparatívna genomika, fylogenetické stromy | <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}} --> | <!-- [[CB07|poznámky]] --> }}
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{{R | TB|Phylogenetic trees | | <!-- [[CB07|SK notes]] --> }}
 
|-
 
|-
{{T|9.-15.11.|}}
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{{T|Nov. 10||8}}
{{R | PR| Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách | <!-- {{pdf|p-expr}} --> | }}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | <!-- {{pdf|p-expr-en}} --> | }}
{{Lit | DEKM kap. 5.1, 11.5, ZB kap. 6.6,15.1,16.1-16.5,17.1}}
+
{{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 | CI|Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM, vzorové riešenia DÚ1 | <!-- {{pdf|ci-hmm}} --> | <!-- [[CI08|poznámky]] --> }}
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{{R | TI|Felsenstein algorithm, algorithms for HMM and phyloHMM | <!-- {{pdf|ci-hmm}} --> | <!-- [[CI08|SK notes]] --> }}
{{R | CB|Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction| <!-- {{pdf|cb-kmeans}} --> | <!-- [[CB08|poznámky]] --> }}
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{{R | TB|K-means clustering, enrichment, multiple testing correction| <!-- {{pdf|cb-kmeans}} <!-- {{pdf|cb-enrichment-en}} | <!-- [[CB08|SK notes]] }}
 
|-
 
|-
{{T|16.-22.11.|}}
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{{T|Nov. 17||9}}
{{R | PR| Štruktúra a funkcia proteínov |  <!-- {{pdf|p-prot}} --> | }}
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{{R | L| Protein structure and function |  <!-- {{pdf|p-prot-en}} --> | }}
{{Lit | DEKM kap. 5; ZB kap. 4.8-4.10, 6.1-6.2, 13.1-13.2}}
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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]
{{R | CI|Hľadanie motívov EM a Gibbsovým vzorkovaním |  |  <!-- [[CI09|poznámky]] --> }}
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{{R | TI|Motif finding by EM and Gibbs sampling |  |  <!-- [[CI09|SK notes]] --> }}
{{R | CB|Úvod do bezkontextových gramatík, Uniprot | | <!-- [[CB09|poznámky]] --> }}
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{{R | TB|Introduction to context-free grammars | | <!-- [[CB09|SK notes]] --> }}
 
|-
 
|-
{{T|23.-29.11.|}}
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{{T|Nov. 24||10}}
{{R | PR| RNA, sekundárna štruktúra, Nussinovovej algoritmus, stochastické bezkontextové gramatiky, profily RNA rodín | <!-- {{pdf|p-rna}} --> | }}
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{{R | L| RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles | <!-- {{pdf|p-rna-en}} --> | }}
{{Lit | DEKM kap. 10, ZB kap. 11.9}}
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{{Lit2 | DEKM chapter 10, ZB chapter 11.9}}, [https://youtu.be/_Hh03Khsr9k SK video]
{{R | CI| Ukážky biologických databáz, úvod do bezkontextových gramatík |  | <!-- [[CI10|poznámky]] --> |  }}
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{{R | TI| Examples of biological databases, HW1 model solutions, introduction to context-free grammars <!-- {{pdf|cb-compgen}}, {{pdf|cb-gene}} --> | <!-- [[CI10|SK notes]] --> |  }}
{{R | CB| Nussinovovej algoritmus | | <!-- [[CB10|poznámky]] --> }}
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{{R | TB| Genes, comparative genomics, Pfam  | | <!-- [[CB10|SK notes]] --> }}
 
|-
 
|-
{{T|30.11.-6.12.|}}
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{{T|Dec. 1||11}}
{{R | PR| Populačná genetika | <!-- {{pdf|p-popgen}} --> | }}
+
{{R | L| No lecture, no tutorials | | }}
{{Lit | }}
+
{{R | CI| RNA štruktúra  |  | <!-- [[CI11|poznámky]] --> }}
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{{R | CB| Microarray dáta, PSI-BLAST, Pfam, RNA štruktúra, MEME, transkripčné faktory v SGD, populačná genetika | | <!-- [[CB11|poznámky]] -->  }}
+
 
|-
 
|-
{{T|7.-13.12.|}}
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{{T|Dec. 8||12}}
{{R | PR| Nepovinné prezentácie | | }}
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{{R | L| Population genetics | <!-- {{pdf|p-popgen-en}} --> | }}
{{R | CI| Zhrnutie semestra, Protein threading pomocou celočíselného lineárneho programovania | <!-- {{pdf|ci-summary}} --> | <!-- [[CI12|poznámky]] --> }}
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{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
{{R | CB| Zhrnutie semestra, grafy, ukážka práce na príkazovom riadku | <!-- {{pdf|cb-summary}}, {{pdf|cb-graphs}} --> | <!-- [[CB12|poznámky]] --> }}
+
{{R | TI| RNA structure  |  | <!-- [[CI11|SK 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}} --> | <!-- [[CB11|SK notes]] --> }}
 
|-
 
|-
{{T|14.-20.12.|Rezerva}}
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{{T|Dec. 15||13}}
 +
{{R | L| Optional journal club presentations | | }}
 +
{{R | TI| Course summary, protein threading via integer linear programming | <!-- {{pdf|ci-summary-en}}, {{pdf|ci-ilp-en}} --> | <!-- [[CI12|SK notes]] --> }}
 +
{{R | TB| Cancelled <!-- example of command-line tools--> | <!--{{pdf|cb-summary}}, {{pdf|cb-graphs}}--> | <!--[[CB12|notes]]--> }}
 
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Verzia zo dňa a času 13:21, 22. september 2022

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. 22
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, SK video 1 SK video 2
TI: Introduction to biology pdf SK notes
ZB chapter 1, SK video
TB: Introduction to computer science, UCSC genome browser pdf SK notes
Sept. 29
L: Genome assembly 2
SK video
TI: Introduction to probability, genome coverage by sequencing reads
TB: Introduction to dynamic programming, introduction to probability
Oct. 6
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, SK video
TI: Introduction to dynamic programming, proteomics
TB: Dynamic programming for sequence alignment, dotplots
Oct. 13
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, SK video
TI: Advanced algorithms for sequence alignment
TB: Programs for sequence alignment, scoring schemes
Oct. 20
L: Gene finding, hidden Markov models
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, SK video
TI: Fast similarity search, BLAST, MinHash
TB: Hidden Markov models, E-value
Oct. 27
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution)
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, SK video
TI: Algorithms for HMM
TB: Substitution models, bootstrap, tree rooting
Nov. 3
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs
BV chapter 5, ZB chapter 9.8, 10.8, SK video
TI: Substitution models
TB: Phylogenetic trees
Nov. 10
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: Felsenstein algorithm, algorithms for HMM and phyloHMM
TB: K-means clustering, enrichment, multiple testing correction
DEKM chapter 5; ZB chapter 4.8-4.10, 6.1-6.2, 13.1-13.2, SK video
TI: Motif finding by EM and Gibbs sampling
TB: Introduction to context-free grammars
Nov. 24
L: RNA, secondary structure, Nussinov algorithm, stochastic context-free grammars, RNA family profiles
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Examples of biological databases, HW1 model solutions, introduction to context-free grammars
TB: Genes, comparative genomics, Pfam
Dec. 1
L: No lecture, no tutorials
Dec. 8
L: Population genetics
SK video
TI: RNA structure
TB: PSI-BLAST, microarray data, RNA structure, MEME, transcription factors in SGD, population genetics, course summary, graphs
Dec. 15
L: Optional journal club presentations
TI: Course summary, protein threading via integer linear programming
TB: Cancelled