1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2023/24

Introduction · Rules · Tasks and dates · Materials · Moodle
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Exam rules, example questions and syllabus
Groups for journal club have each their own group in Moodle.


Materials: Rozdiel medzi revíziami

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Riadok 1: Riadok 1:
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.
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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.
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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.  
  
PR: spoločná prednáška, CI: cvičenia pre informatikov, CB: cvičenia pre biológov
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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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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}}
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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}}
  
 
{|
 
{|
 
|-
 
|-
{{T|24.-30.9.|}}
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{{T|Sept. 21||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}} | }}
{{Lit | BV kap. 1}}
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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]
{{R | CI| Úvod do biológie | {{pdf|ci-introbio}} | [[CI01|poznámky]] }}
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{{R | TI| Introduction to biology | {{pdf|ci-introbio}} | [[CI01|notes]] }}
{{Lit | ZB kap. 1}}
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{{Lit2 | ZB chapter 1}}, [https://www.youtube.com/watch?v=EtPqUOHTJD4 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|notes]] }}
 
|-
 
|-
{{T|1.-7.10.|}}
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{{T|Sept. 28||2}}
{{R | PR| Zostavovanie genómov 2 | | }}
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{{R | L| Genome assembly 2 | {{pdf|p-seq2}} | }}
{{R | CI| Úvod do pravdepodobnosti, pokrytie pri sekvenovaní | <!-- {{pdf|ci-coverage}} --> | <!-- [[CI02|poznámky]] --> }}
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{{Lit2 | }} [https://www.youtube.com/watch?v=YvZlTL1qyUg video]
{{R | CB| Úvod do dynamického programovania, úvod do pravdepodobnosti | <!-- {{pdf|cb-dp}} --> | <!-- [[CB02|poznámky]] --> }}
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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]] }}  
 
|-
 
|-
{{T|8.-14.10.|}}
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{{T|Oct. 5||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}} | }}
{{Lit | BV kap. 2, DEKM kap. 2.1-2.4, 2.8, ZB kap. 4.1-4.4, 5.1-5.2}}
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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]] }}
{{R | CI|Úvod do dynamického programovania, proteomika | {{pdf|ci-msms}} | [[CI03|poznámky]] }}
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{{Lit2 | Python implementation of DP and visualisations}} [https://colab.research.google.com/drive/14QB903XpAsUFsqfls3rYoSaYRhyNX-So?usp=sharing colab]
{{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|notes]] }}  
-->
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|-
 
|-
{{T|15.-21.10.|}}
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{{T|Oct. 12||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}} | }}
{{Lit | BV kap. 2, DEKM kap. 2.5, 2.7, 6.1-6.3; ZB kap. 4.5-4.7, 5.3-5.5}}
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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]] }}
{{R | CI|Pokročilé algoritmy pre zarovnávanie sekvencií | |  [[CI04|poznámky]] }}
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{{R | TB|Programs for sequence alignment, scoring schemes| | [[CB04|notes]] }}
{{R | CB|Programy na zarovnávanie sekvencií, skórovacie schémy| | [[CB04|poznámky]] }}
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-->
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|-
 
|-
{{T|22.-28.10.|}}
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{{T|Oct. 19||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}}| }}
{{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 video]
<!--
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{{R | TI|Fast similarity search, BLAST, MinHash | {{pdf|ci-seeds}} | <!-- [[CI05|notes]]--> }}
{{R | CI|BLAST, rýchle hľadanie podobnosti | | [[CI05|poznámky]] }}
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{{R | TB|Hidden Markov models, E-value |   {{pdf|cb-evalue}} | [[CB05|notes]] }}
{{R | CB|Skryté Markovove modely, E-value | {{pdf|cb-evalue}} | [[CB05|poznámky]] }}
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-->
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<!-- {{pdf|ci-seeds}} -->
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|-
 
|-
{{T|29.10.-4.11.|sviatky}}
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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|5.-11.11.|}}
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{{T|Nov. 2|No lecture, no tutorials|7}}
{{R | PR| Rekonštrukcia fylogenetických stromov (úspornosť, metóda spájania susedov, modely evolúcie) | <!-- {{pdf|p-phylo}}--> | }}
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{{Lit | BV kap. 3, DEKM kap. 7,8; ZB kap. 7, 8.1-8.2}}
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<!--
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{{R | CI|Algoritmy pre HMM | {{pdf|ci-hmm}}  | [[CI06|poznámky]] }}
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{{R | CB|Substitučné modely, bootstrap| {{pdf|cb-phylo}} | [[CB06|poznámky]]  }}
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-->
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{{T|12.-18.11.|}}
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{{T|Nov. 9||8}}
{{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}} | }}
{{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 video]
<!--
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{{R | TI|Substitution models | <!-- {{pdf|ci-matice-en}}--> {{pdf|Ci-substitution-models}} |  [[CI07|notes]] }}
{{R | CI|Substitučné modely | {{pdf|ci-matice}} | [[CI07|poznámky]] }}
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{{R | TB|Practical phylogenetic trees | | [[CB07|notes]] }}
{{R | CB|Gény v UCSC browseri, komparatívna genomika, fylogenetické stromy, Fitchov aloritmus| {{pdf|cb-compgen}}, {{pdf|cb-gene}} | [[CB07|poznámky]] }}
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{{T|19.-25.11.|}}
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{{T|Nov. 16||10}}
{{R | PR| Expresia génov, zhlukovanie, klasifikácia, regulačné siete, transkripčné faktory, motívy v sekvenciách | <!-- {{pdf|p-expr}} --> | }}
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{{R | L| Protein structure and function | {{pdf|p-prot}} | }}
{{Lit | DEKM kap. 5.1, 11.5, ZB kap. 6.6,15.1,16.1-16.5,17.1}}
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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]] -->}}
{{R | CI|Felsensteinov algoritmus, algoritmy pre HMM a phyloHMM | {{pdf|ci-hmm}} | [[CI08|poznámky]] }}
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{{R | TB| Pfam, PSI-blast, Example of command-line tools  | | [[CB10|notes1]], [[CB11|notes2]] }}
{{R | CB|Zhlukovanie algoritmom k-means, nadreprezentácia, multiple testing correction| {{pdf|cb-kmeans}} | [[CB08|poznámky]] }}
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-->
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|-
{{T|26.11.-2.12.|}}
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{{T|Nov. 23||9}}
{{R | PR| Štruktúra a funkcia proteínov | <!-- {{pdf|p-prot}} --> | }}
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{{R | L| Gene expression, clustering, classification, regulatory networks, transcription factors, sequence motifs | {{pdf|p-expr}}| }}
{{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 5.1, 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]] }}
{{R | CI|Hľadanie motívov EM a Gibbsovým vzorkovaním |  |  [[CI09|poznámky]] }}
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{{R | TB|Introduction to context-free grammars | | [[CB09|notes]] }}
{{R | CB|Úvod do bezkontextových gramatík, microarray dáta, Uniprot, Pfam | | [[CB09|poznámky]] }}
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-->
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|-
{{T|3.-9.12.|}}
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{{T|Nov. 30||11}}
{{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}} | }}
{{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]
<!--
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{{R | TI|Motif finding by EM and Gibbs sampling | {{pdf|ci-motifs}} |  <!--[[CI09|notes]]--> }}
{{R | CI| Ukážky biologických databáz, úvod do bezkontextových gramatík | | [[CI10|poznámky]] }}
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{{R | TB|K-means clustering, enrichment, multiple testing correction| {{pdf|cb-kmeans}} {{pdf|cb-enrichment-en}} |  [[CB08|notes]]}}
{{R | CB| Nussinovovej algoritmus | | [[CB10|poznámky]] }}
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{{T|10.-16.12.|}}
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{{T|Dec. 7||12}}
{{R | PR| Populačná genetika | <!-- {{pdf|p-popgen}} --> | }}
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{{R | L| Population genetics | {{pdf|p-popgen}} | }}
{{Lit | }}
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{{Lit2 | }} [https://youtu.be/7vPt1vQX21M SK video]
<!--
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{{R | TI| RNA structure |  | <!-- [[CI11|notes]]--> }}
{{R | CI| Protein threading pomocou celočíselného lineárneho programovania, RNA štruktúra |  | [[CI11|poznámky]] }}
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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]] }}
{{R | CB| Microarray dáta, PSI-BLAST, RNA štruktúra, MEME, transkripčné faktory v SGD | | [[CB11|poznámky]] }}
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|-
{{T|17.-23.12.|}}
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{{T|Dec. 14||13}}
{{R | CI| Zhrnutie semestra, štruktúra populácie | <!-- {{pdf|ci-summary}} --> | [[CI12|poznámky]] }}
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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]]--> }}
{{R | PR| Nepovinné prezentácie | | }}
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{{R | TB| Project consultations | | }}
{{R | CB| Zhrnutie semestra, grafy, populačná genetika | {{pdf|cb-summary}}, {{pdf|cb-graphs}} | [[CB12|poznámky]]  }}
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Aktuálna revízia z 09:51, 7. december 2023

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. 21
L: Introduction, course rules, sequencing and genome assembly pdf, pdf
BV chapter 1, video 1 video 2
TI: Introduction to biology pdf notes
ZB chapter 1, video
TB: Introduction to computer science, UCSC genome browser pdf notes
Sept. 28
L: Genome assembly 2 pdf
video
TI: Introduction to probability, genome coverage by sequencing reads pdf notes
Python simulations and approximations colab
TB: Introduction to dynamic programming, introduction to probability pdf notes
Oct. 5
L: Sequence alignment: Smith-Waterman, Needleman-Wunsch, scoring pdf
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 pdf notes
Python implementation of DP and visualisations colab
TB: Dynamic programming for sequence alignment, dotplots pdf notes
Oct. 12
L: Sequence alignment: heuristic alignment (BLAST), statistical significance of alignments, whole genome alignments, multiple alignments pdf
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 pdf
BV chapter 4, DEKM chapter 3; ZB chapter 9.3, 10.4-10.7, video
TI: Fast similarity search, BLAST, MinHash pdf
TB: Hidden Markov models, E-value pdf notes
Oct. 26
L: Phylogenetic tree reconstruction (parsimony, neighbor joining, models of evolution) pdf
BV chapter 3, DEKM chapter 7,8; ZB chapter 7, 8.1-8.2, video
TI: Algorithms for HMM pdf notes
TB: Substitution models, bootstrap, tree rooting pdf notes
Nov. 2 No lecture, no tutorials
Nov. 9
L: Comparative genomics, detection of positive and purification selection, comparative gene finding, phylogenetic HMMs pdf
BV chapter 5, ZB chapter 9.8, 10.8, video
TI: Substitution models pdf notes
TB: Practical phylogenetic trees notes
Nov. 16
L: Protein structure and function pdf
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 pdf
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 pdf
DEKM chapter 10, ZB chapter 11.9, SK video
TI: Motif finding by EM and Gibbs sampling pdf
TB: K-means clustering, enrichment, multiple testing correction pdf pdf notes
Dec. 7
L: Population genetics pdf
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