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.


Journal club papers: Rozdiel medzi revíziami

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Svoje preferencie ohľadom článkov na journal club odovzdajte pomocou '''[https://docs.google.com/forms/d/e/1FAIpQLSc_smiqzJVw0h0Gwgb1wIgEXF07CIR9Fu4s4VLNIwC96HZAxw/viewform tohto formulára]''' najneskôr do utorka '''27.10.2020, 22:00'''. Vo formulári uveďte '''čísla troch článkov z tohto zoznamu''' v poradí podľa preferencie.  
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A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].
  
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Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''19.10.2022, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference.
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* Students from the same study program will typically not be in the same group.
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* Preferences submitted earlier will be considered with higher preference.
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Detaily ohľadom požiadavok na journal club nájdete v [[Pravidlá#Journal club|pravidlách predmetu]].
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* 3 Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [https://journals.asm.org/doi/full/10.1128/mSphere.00160-20]
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** Čítajú Macko, Kajan, Daniš, Petrová
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* 4 Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings in Bioinformatics. 2021 Sep 28. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8500159/]  
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** Čítajú Sojka, Kreutzová, Šoucová, Piatrová
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* 5 Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B. and Hastie, K.M., 2020. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. [https://www.sciencedirect.com/science/article/pii/S0092867420308205] (comment on the paper from different authors  [https://www.sciencedirect.com/science/article/pii/S0092867420308175])
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** Čítajú Švorc, Jankechová, Zivák, Čačaná
  
# Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O’toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature communications. 2020 Oct 9;11(1):1-4. [https://www.nature.com/articles/s41467-020-18877-9]
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==Unused papers==
# Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols. 2017 Jun;12(6):1261. [https://www.nature.com/articles/nprot.2017.066] alebo [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902022/] (application to SARS-CoV-2 [https://artic.network/ncov-2019])
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* 1 Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O’toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature communications. 2020 Oct 9;11(1):1-4. [https://www.nature.com/articles/s41467-020-18877-9]
# Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [https://journals.asm.org/doi/full/10.1128/mSphere.00160-20]
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* 2 Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols. 2017 Jun;12(6):1261. [https://www.nature.com/articles/nprot.2017.066] or [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902022/] (application to SARS-CoV-2 [https://artic.network/ncov-2019])  
# Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings in Bioinformatics. 2021 Sep 28. [https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab397/6377518]
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* 6 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). [https://science.sciencemag.org/content/370/6521/eabe9403.abstract]
# Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B. and Hastie, K.M., 2020. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. [https://www.sciencedirect.com/science/article/pii/S0092867420308205] (comment on the paper from different authors  [https://www.sciencedirect.com/science/article/pii/S0092867420308175])
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# Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). [https://science.sciencemag.org/content/370/6521/eabe9403.abstract]
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Verzia zo dňa a času 07:57, 27. október 2022

A detailed description of the journal club activity is included in the course rules.


  • 3 Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An extensive meta-metagenomic search identifies SARS-CoV-2-homologous sequences in pangolin lung viromes. MSphere. 2020 May 6;5(3):e00160-20. [1]
    • Čítajú Macko, Kajan, Daniš, Petrová
  • 4 Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings in Bioinformatics. 2021 Sep 28. [2]
    • Čítajú Sojka, Kreutzová, Šoucová, Piatrová
  • 5 Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E.E., Bhattacharya, T., Foley, B. and Hastie, K.M., 2020. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. [3] (comment on the paper from different authors [4])
    • Čítajú Švorc, Jankechová, Zivák, Čačaná

Unused papers

  • 1 Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O’toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature communications. 2020 Oct 9;11(1):1-4. [5]
  • 2 Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols. 2017 Jun;12(6):1261. [6] or [7] (application to SARS-CoV-2 [8])
  • 6 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Dec 4;370(6521). [9]