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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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/ }}  
 
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/ }}  
  
6. {{cite journal| author=Enright AJ, Van Dongen S, Ouzounis CA |title=An efficient algorithm for large-scale detection of protein families. | journal = Nucleic acids research | year = 2002 | volume = 30 | issue = 7 | pages = 1575-84 | url=http://nar.oxfordjournals.org/content/30/7/1575.full}}
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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 |url= https://www.researchgate.net/profile/Liisa_Holm/publication/10794155_Exhaustive_Enumeration_of_Protein_Domain_Families/links/55d35f0608ae0b8f3ef92c1b.pdf }}
  
 
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 }}  
 
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 }}  
  
 
8. {{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 | url=http://www.sciencemag.org/cgi/content/full/316/5822/240 |  doi=10.1126/science.1140462 }}
 
8. {{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 | url=http://www.sciencemag.org/cgi/content/full/316/5822/240 |  doi=10.1126/science.1140462 }}

Verzia zo dňa a času 20:26, 5. október 2016

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.

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. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J et al. (2007). "Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.". Science 316 (5822): 240-3. doi:10.1126/science.1140462.