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

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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. Bánovský, Batmendijn, Bažík, Jura, Korman, Urbanová, Uhrová

2. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.". Bioinformatics 23 (13): i289-96. Balažovičová, Dej, Fedáková, Kantor, Klinovská, Šuba, Trizna

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) Eliaš, Fedák, Gažiová, Mihálová, Molčan, Pavlove, Šoltes

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. Čárska, Kovalčinová, Pašen, Šemelák, Sládeček, Sládek, Števaňák

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) Behinská, Beňo, Kokavcová, Kubík, Kyselica, Porubský, Suja

Nepoužité články

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. Čítajú Foltýn, Geisseová, Molčan, Sucháňová, Vargovčík, Váryová