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 stredy '''24.10.2017, 22:00'''. Vo formulári uveďte '''čísla troch článkov z tohto zoznamu''' v poradí podľa preferencie.  -->
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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 '''23.10.2018, 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]].
  
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''' Baláž, Bérešová, Kováč, Psota, Smoľak, Szelleová
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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}}  
  
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''' Fabianová, Forbak, Husár, Mišíková, Šomodi, Szendy
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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 | url = http://bioinformatics.oxfordjournals.org/content/23/13/i289 }}  
  
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''' Bakoš, Bilisics, Heinz, Kačír, Kolková, Kotrlová, Százová
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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])  
  
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''' Jamrichová, Koza, Mašlej, Ondriašová, Trubač, Zeman
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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}}   
  
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/ }} '''Čítajú''' Borbová, Brojo, Bujna, Búran, Hadžega, Hoľa, Kellner
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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/ }}  
  
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''' Adamec, Harmanová, Ištok, Krajčiová, Kvačkay, Mayerová, Mudroch
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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 }}
==Nepoužité články==
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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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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])
 
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])

Verzia zo dňa a času 10:35, 11. október 2018

Svoje preferencie ohľadom článkov na journal club odovzdajte pomocou tohto formulára najneskôr do utorka 23.10.2018, 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.

1. David M, Dursi LJ, Yao D, Boutros PC, Simpson JT (2016). "Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data". Bioinformatics.

2. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.". Bioinformatics 23 (13): i289-96.

3. Wapinski I, Pfeffer A, Friedman N, Regev A (2007). "Natural history and evolutionary principles of gene duplication in fungi". Nature 449 (7158): 54-61. doi:10.1038/nature06107. (pozrite aj Online supplement)

4. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF et al. (2007). "Distinguishing protein-coding and noncoding genes in the human genome.". Proc Natl Acad Sci U S A 104 (49): 19428-33.

5. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW et al. (2004). "Transcriptional regulatory code of a eukaryotic genome.". Nature 431 (7004): 99-104. doi:10.1038/nature02800.

6. Heger, Andreas, and Liisa Holm (2003). "Exhaustive enumeration of protein domain families". Journal of molecular biology 328 (3): 749-67.

7. Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A (2004). "A new algorithm for RNA secondary structure design.". J Mol Biol 336 (3): 607-24. doi:10.1016/j.jmb.2003.12.041.

8. 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. (2010). "A global protein kinase and phosphatase interaction network in yeast". Science 328 (5981): 1043-6. doi:10.1126/science.1176495. (pozrite aj Online supplement)