1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2021/22

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Cvičenia vo štvrtok o 14:00 sú určené pre študentov BIN, INF, mINF, mAIN, DAV. Cvičenia vo štvrtok o 17:20 sú pre študentov z PriFUK a z fyzikálnych odborov. Obidvoje cvičenia sa budú konať už v prvom týždni semestra.


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.
  
  
 
Detaily ohľadom požiadavok na journal club nájdete v [[Pravidlá#Journal club|pravidlách predmetu]].
 
Detaily ohľadom požiadavok na journal club nájdete v [[Pravidlá#Journal club|pravidlách predmetu]].
  
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* Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O'Toole A, McCrone JT, Andersen KG, Worobey M, Nelson MI. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. bioRxiv. 2020 Jun 23 [https://www.biorxiv.org/content/biorxiv/early/2020/06/23/2020.06.22.165464.full.pdf]
  
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}}  '''Čítajú Bánovský, Batmendijn, Bažík, Jura, Korman, Urbanová, Uhrová'''
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* 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]
  
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 }}  '''Čítajú Balažovičová, Dej, Fedáková, Kantor, Klinovská, Šuba, Trizna'''
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* Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search. BioRxiv. 2020 Feb 14. [https://www.biorxiv.org/content/10.1101/2020.02.08.939660v2]
  
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])  '''Čítajú Eliaš, Fedák, Gažiová, Mihálová, Molčan, Pavlove, Šoltes'''
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* Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, Jacobson D. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. Elife. 2020 Jul 7;9:e59177. [https://doi.org/10.7554/eLife.59177]
  
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}}  '''Čítajú Čárska, Kovalčinová, Pašen, Šemelák, Sládeček, Sládek, Števaňák'''
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* 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.cell.com/cell/pdf/S0092-8674(20)30820-5.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]) '''Čítajú Behinská, Beňo, Kokavcová, Kubík, Kyselica, Porubský, Suja'''
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==Nepoužité články==
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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 }}  '''Čítajú''' Foltýn, Geisseová, Molčan, Sucháňová, Vargovčík, Váryová
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Verzia zo dňa a času 12:58, 15. október 2020

Svoje preferencie ohľadom článkov na journal club odovzdajte pomocou tohto formulára najneskôr do utorka 27.10.2020, 22:00. Vo formulári uveďte čísla troch článkov z tohto zoznamu v poradí podľa preferencie.


Detaily ohľadom požiadavok na journal club nájdete v pravidlách predmetu.

  • Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O'Toole A, McCrone JT, Andersen KG, Worobey M, Nelson MI. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. bioRxiv. 2020 Jun 23 [1]
  • 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. [2]
  • Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search. BioRxiv. 2020 Feb 14. [3]
  • Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, Jacobson D. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. Elife. 2020 Jul 7;9:e59177. [4]
  • 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]