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

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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.


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 stredy '''24.10.2017, 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]].
  
'''Detaily ohľadom požiadavok na journal club nájdete v [[Pravidlá#Journal club|pravidlách predmetu]].'''
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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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* 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
  
1. {{cite journal| author=David M, Dursi LJ, Yao D, Boutros PC, Simpson JT | title=Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data| journal = Bioinformatics | year = 2016 | url=http://bioinformatics.oxfordjournals.org/content/early/2016/09/07/bioinformatics.btw569.abstract}}
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==Unused papers==
 
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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]
2. {{cite journal| author=Lunter G| title=Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. | journal=Bioinformatics | year= 2007 | volume= 23 | issue= 13 | pages= i289-96 | url = http://bioinformatics.oxfordjournals.org/content/23/13/i289 }}
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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])
 
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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]
3. {{cite journal| author=Wapinski I, Pfeffer A, Friedman N, Regev A| title=Natural history and evolutionary principles of gene duplication in fungi | journal=Nature | year= 2007 | volume= 449 | issue= 7158 | pages= 54-61 | doi=10.1038/nature06107 | url=http://llama.mshri.on.ca/courses/Biophysics205/Papers/Wapinski_2007.pdf}} (pozrite aj [http://www.nature.com/nature/journal/v449/n7158/suppinfo/nature06107.html Online supplement])
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4. {{cite journal| author=Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al.| title=Distinguishing protein-coding and noncoding genes in the human genome. | journal=Proc Natl Acad Sci U S A | year= 2007 | volume= 104 | issue= 49 | pages= 19428-33 | url= http://www.pnas.org/content/104/49/19428}} 
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5. {{cite journal| author=Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al.| title=Transcriptional regulatory code of a eukaryotic genome. | journal=Nature | year= 2004 | volume= 431 | issue= 7004 | pages= 99-104 |  doi=10.1038/nature02800 | url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/ }}
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6. {{cite journal| author=Heger, Andreas, and Liisa Holm | title=Exhaustive enumeration of protein domain families | journal= Journal of molecular biology | year=2003 | volume=328 | issue=3 | pages=749-67 | url= https://www.researchgate.net/profile/Liisa_Holm/publication/10794155_Exhaustive_Enumeration_of_Protein_Domain_Families/links/55d35f0608ae0b8f3ef92c1b.pdf }}
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7. {{cite journal| author=Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A| title=A new algorithm for RNA secondary structure design. | journal=J Mol Biol | year= 2004 | volume= 336 | issue= 3 | pages= 607-24 | doi=10.1016/j.jmb.2003.12.041 | url=http://people.cs.ubc.ca/~hutter/papers/jmb04-rna-ssd.pdf }} 
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8. {{cite journal| author=Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M.| title=A global protein kinase and phosphatase interaction network in yeast | journal=Science | year= 2010 | volume= 328 | issue=5981 | pages= 1043-6 | doi=10.1126/science.1176495 | url=https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20489023/ }}  (pozrite aj [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983991/bin/NIHMS345024-supplement.pdf Online supplement])
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Aktuálna revízia z 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]