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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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 | pmid=17646308 | doi=10.1093/bioinformatics/btm185 }} '''Čítajú:''' Hajkovský, Mihál, Miklošovič, Poliak, Schichman
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A detailed description of the journal club activity is included in the [[Rules#Journal club|course rules]].
  
3. {{cite journal| author=Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D| title=Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. | journal=Proc Natl Acad Sci U S A | year= 2003 | volume= 100 | issue= 20 | pages= 11484-9 | pmid=14500911 | doi=10.1073/pnas.1932072100 }} '''Čítajú:''' Danko, Dávid_Dobiáš, Gunčaga, Masaryk, Slavkovský, Vetrík
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<!-- Please submit your preferences regarding these papers using '''[https://forms.gle/K7BZJD5fA3wRmmXk8 this form]''' until Wednesday  '''20.10.2021, 22:00'''. In the form, include '''numbers of three papers from this list''' in the order of preference. -->
  
4. {{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 | pmid=17805289 | doi=10.1038/nature06107 | url=http://www.eecs.ucf.edu/~shzhang/CAP6938/p7_nature06107_aviv_duplication.pdf}} '''Čítajú:''' Karlubík, Mrózek, Seč, Šinský, Vajdová
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Groups:
  
5. {{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 | pmid=18040051 | doi=10.1073/pnas.0709013104}} '''Čítajú:''' Dominik_Dobiáš, Filip, Kolková, Krampl, Pisarčíková, Rabatin
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* '''Group 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]) '''Read by Sekerka, Babinská, Sládečková, Detko, Melicherčík, Magát'''
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* '''Group 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://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab397/6377518] '''Read by Kunzo, Černíková, Agarský, Strečanský, Cartes, Petescia, Rizzo, Mwaniki'''
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* '''Group 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]) '''Read by Peričková, Trizna, Korbeľ, Botlová, Struharňanský, Kohár'''
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* '''Group 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] '''Read by Charna, Pisoňová, Zubčák, Šoucová, Neográdyová, Slávik'''
  
6. {{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 | pmid=15343339  | doi=10.1038/nature02800 | url=http://www.psrg.csail.mit.edu/pubs/nature-2004.pdf }} '''Čítajú:''' Jamrichová, Kmeťová, Kubica, Lukáč, Metohajrova, Scholtzová
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Unused papers:
  
8. {{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 | pmid=15095976 | doi=10.1016/j.jmb.2003.12.041 | url=http://people.cs.ubc.ca/~hutter/papers/jmb04-rna-ssd.pdf }} '''Čítajú:''' Fikar, Gahurová, Holas, Šešerová, Szabo
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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]
  
9. {{cite journal| author=Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J et al.| title=Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. | journal=Science | year= 2007 | volume= 316 | issue= 5822 | pages= 240-3 | pmid=17431170 | url=http://www.sciencemag.org/cgi/content/full/316/5822/240 |  doi=10.1126/science.1140462 }} '''Čítajú:''' Greššák, Klembarová, Krajčovič, Kunertová, Marčanová
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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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==Nepoužité články==
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1. {{cite journal| author=Valouev, A., Schwartz, D. C., Zhou, S., & Waterman, M. S|title=An algorithm for assembly of ordered restriction maps from single DNA molecules | journal = Proceedings of the National Academy of Sciences| volume= 03 | issue=43 (2006) | pages= 15770-15775| url=http://www.pnas.org/content/103/43/15770.full}}
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7. {{cite journal| author=Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P et al.| title=Conserved patterns of protein interaction in multiple species. | journal=Proc Natl Acad Sci U S A | year= 2005 | volume= 102 | issue= 6 | pages= 1974-9 | pmid=15687504 | doi=10.1073/pnas.0409522102 }}
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Verzia zo dňa a času 09:43, 26. október 2021

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


Groups:

  • Group 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. [1] or [2] (application to SARS-CoV-2 [3]) Read by Sekerka, Babinská, Sládečková, Detko, Melicherčík, Magát
  • Group 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. [4] Read by Kunzo, Černíková, Agarský, Strečanský, Cartes, Petescia, Rizzo, Mwaniki
  • Group 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. [5] (comment on the paper from different authors [6]) Read by Peričková, Trizna, Korbeľ, Botlová, Struharňanský, Kohár
  • Group 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). [7] Read by Charna, Pisoňová, Zubčák, Šoucová, Neográdyová, Slávik

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. [8]
  • 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. [9]