1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2023/24
Journal club papers: Rozdiel medzi revíziami
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| − | + | Zadelenie študentov do skupín: | |
| − | + | 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 Herencsár, B.Ivan, Šuníková, F.Marek, Gergeľ, Gibaštíková''' | |
| − | + | 4. {{cite journal| author=Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al.| title=Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | journal=Genome Res | year= 2005 | volume= 15 | issue= 8 | pages= 1034-50 | pmid=16024819 | doi=10.1101/gr.3715005}} '''Čítajú ''' | |
| − | + | 7. {{cite journal| author=Eisen MB, Spellman PT, Brown PO, Botstein D| title=Cluster analysis and display of genome-wide expression | |
| + | patterns. | journal=Proc Natl Acad Sci U S A | year= 1998 | volume= 95 | issue= 25 | pages= 14863-8 | pmid=9843981 }} '''Čítajú ''' | ||
| − | + | 10. {{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 }} '''Čítajú ''' | |
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| + | 11. {{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 ''' | ||
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| + | ==Nevybrané články== | ||
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| + | 1. {{cite journal| author=Zerbino DR, Birney E| title=Velvet: algorithms for de novo short read assembly using de Bruijn graphs. | journal=Genome Res | year= 2008 | volume= 18 | issue= 5 | pages= 821-0 | pmid=18349386 | doi=10.1101/gr.074492.107 }} | ||
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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 }} | ||
5. {{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}} | 5. {{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}} | ||
6. {{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}} | 6. {{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}} | ||
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8. {{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 }} | 8. {{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 }} | ||
9. {{cite journal |author=Bystroff C, Thorsson V, Baker D |title=HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins |journal=J. Mol. Biol. |volume=301 |issue=1 |pages=173–90 |year=2000 |month=August |pmid=10926500 |doi=10.1006/jmbi.2000.3837 |url=http://www.bioinfo.rpi.edu/bystrc/pdf/JMB301p173_2000.pdf}} | 9. {{cite journal |author=Bystroff C, Thorsson V, Baker D |title=HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins |journal=J. Mol. Biol. |volume=301 |issue=1 |pages=173–90 |year=2000 |month=August |pmid=10926500 |doi=10.1006/jmbi.2000.3837 |url=http://www.bioinfo.rpi.edu/bystrc/pdf/JMB301p173_2000.pdf}} | ||
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12. {{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 }} | 12. {{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 }} | ||
Verzia zo dňa a času 12:18, 25. október 2012
Zadelenie študentov do skupín:
3. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003). "Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.". Proc Natl Acad Sci U S A 100 (20): 11484-9. doi:10.1073/pnas.1932072100. PMID 14500911. Čítajú Herencsár, B.Ivan, Šuníková, F.Marek, Gergeľ, Gibaštíková
4. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al. (2005). "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes". Genome Res 15 (8): 1034-50. doi:10.1101/gr.3715005. PMID 16024819. Čítajú
7. Eisen MB, Spellman PT, Brown PO, Botstein D (1998). "Cluster analysis and display of genome-wide expression patterns.". Proc Natl Acad Sci U S A 95 (25): 14863-8. PMID 9843981. Čítajú
10. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P et al. (2005). "Conserved patterns of protein interaction in multiple species.". Proc Natl Acad Sci U S A 102 (6): 1974-9. doi:10.1073/pnas.0409522102. PMID 15687504. Čítajú
11. 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. PMID 15095976. Čítajú
Nevybrané články
1. Zerbino DR, Birney E (2008). "Velvet: algorithms for de novo short read assembly using de Bruijn graphs.". Genome Res 18 (5): 821-0. doi:10.1101/gr.074492.107. PMID 18349386.
2. Lunter G (2007). "Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.". Bioinformatics 23 (13): i289-96. doi:10.1093/bioinformatics/btm185. PMID 17646308.
5. 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. PMID 17805289.
6. 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. doi:10.1073/pnas.0709013104. PMID 18040051.
8. 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. PMID 15343339.
9. Bystroff C, Thorsson V, Baker D (August 2000). "HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins". J. Mol. Biol. 301 (1): 173–90. doi:10.1006/jmbi.2000.3837. PMID 10926500.
12. 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. PMID 17431170.
