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teaching:2026summer:cg [2026/05/28 14:36] mbraga [Schedule] |
teaching:2026summer:cg [2026/07/24 12:27] (current) rwittler [Schedule] |
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| | 01.05. | -- (national holiday) |||| | | 01.05. | -- (national holiday) |||| | ||
| | 08.05. | Roland | Small Parsimony under SCJ | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]],\\ {{teaching:2026summer:cg:fitch.pdf | fitch.pdf}} | {{teaching:2026summer:cg:sheet03.pdf | Sheet 03}} | | | 08.05. | Roland | Small Parsimony under SCJ | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]],\\ {{teaching:2026summer:cg:fitch.pdf | fitch.pdf}} | {{teaching:2026summer:cg:sheet03.pdf | Sheet 03}} | | ||
| - | | 15.05. | Roland | Small Parsimony under SCJ | [[https://doi.org/10.1186/1471-2105-13-S19-S11|Manuch et al. 2012]],\\ [[https://doi.org/10.1109/TCBB.2018.2816034| Luhmann et al. 2014/2018]],\\ {{teaching:2023summer:cg:max-row_c1p.pdf|MAX-ROW_C1P.pdf}}| {{teaching:2026summer:cg:sheet04.pdf | Sheet 04}} | | + | | 15.05. | Roland | Small Parsimony under SCJ | [[https://doi.org/10.1186/1471-2105-13-S19-S11|Manuch et al. 2012]],\\ [[https://doi.org/10.1109/TCBB.2018.2816034| Luhmann et al. 2014/2018]],\\ {{teaching:2023summer:cg:max-row_c1p.pdf|MAX-ROW_C1P.pdf}}| {{teaching:2026summer:cg:sheet04.pdf | Sheet 04}} | |
| | 22.05. | Marilia | Double-Cut-and-Join (DCJ) model | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]] | {{teaching:2026summer:cg:sheet05.pdf | Sheet 05}} | | | 22.05. | Marilia | Double-Cut-and-Join (DCJ) model | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]] | {{teaching:2026summer:cg:sheet05.pdf | Sheet 05}} | | ||
| - | | 29.05. | Marilia | DCJ halving, Restricted DCJ sorting | [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]] | | | + | | 29.05. | Marilia | Restricted DCJ sorting,\\ DCJ halving | {{:teaching:2025summer:cg:restrictedDCJmodel.pdf|Restricted DCJ}}, [[https://www.liebertpub.com/doi/10.1089/cmb.2011.0116|Kovac et al.]],\\ [[https://link.springer.com/chapter/10.1007/978-3-540-69733-6_28|Mixtacki]] | {{teaching:2026summer:cg:sheet06.pdf | Sheet 06}} | |
| - | | 05.06. | Marilia | Inversion distance | [[https://doi.org/10.1145/300515.300516|Hannenhalli and Pevzner 1999]],\\ [[https://link.springer.com/chapter/10.1007/978-3-540-27801-6_29|Bergeron et al. 2004]] | | | + | | 05.06. | Marilia | Inversion distance of circular chromosomes | [[https://doi.org/10.1145/300515.300516|Hannenhalli and Pevzner 1999]],\\ [[https://academic.oup.com/book/52874/chapter-abstract/421908746|Bergeron et al. 2005]] | {{teaching:2026summer:cg:sheet07.pdf | Sheet 07}} | |
| - | | 12.06. | Marilia | DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | | | + | | 12.06. | Marilia | Inversion distance (cont.),\\ Inversion sorting | [[https://doi.org/10.1145/300515.300516|Hannenhalli and Pevzner 1999]],\\ [[https://academic.oup.com/book/52874/chapter-abstract/421908746|Bergeron et al. 2005]] | {{teaching:2026summer:cg:sheet08.pdf | Sheet 08}} | |
| - | | 19.06. | Marilia | Distances of non-singular genomes with DCJ | | | | + | | 19.06. | Marilia | DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | {{teaching:2026summer:cg:sheet09.pdf | Sheet 09}} | |
| - | | 26.06. | Roland | Consistency of gene clusters | {{teaching:2023summer:cg:consistent_gene_clusters_slides.pdf | Slides}},\\ [[https://doi.org/10.1109/TCBB.2008.135|Stoye et al. 2009]],\\ [[https://doi.org/10.1089/cmb.2011.0083|Wittler et al. 2011]],\\ {{https://n-coder.github.io/pqtree.js|PQ- & PC-Trees applet, D. Peters and S. D. Fink}}| | | + | | 26.06. | Roland | Consistency of gene clusters | {{teaching:2023summer:cg:consistent_gene_clusters_slides.pdf | Slides}},\\ [[https://doi.org/10.1109/TCBB.2008.135|Stoye et al. 2009]],\\ [[https://doi.org/10.1089/cmb.2011.0083|Wittler et al. 2011]],\\ {{https://n-coder.github.io/pqtree.js|PQ- & PC-Trees applet, D. Peters and S. D. Fink}}| {{teaching:2026summer:cg:sheet10.pdf | Sheet 10}} | |
| - | | 03.07. | Roland | Generators for common intervals | [[https://doi.org/10.1137/060651331|Bergeron et al. 2008]], Sections 1 and 2 | | | + | | 03.07. | Roland | Generators for common intervals | [[https://doi.org/10.1137/060651331|Bergeron et al. 2008]], Sections 1 and 2 | {{teaching:2026summer:cg:sheet11.pdf | Sheet 11}} | |
| - | | 10.07. | Roland | Generators, strong common intervals and PQ-trees | see above, Sections 3, 4, 5.1, and 5.3 | | | + | | 10.07. | Roland | Generators, strong common intervals and PQ-trees | see above, Sections 3, 4, 5.1, and 5.3 | {{teaching:2026summer:cg:sheet12.pdf | Sheet 12}} | |
| - | | 07.07. | Roland | Common intervals of strings | [[https://doi.org/10.1016/j.jda.2006.03.021|Didier at al., 2006]],\\ {{teaching:2023summer:cg:didier.pdf | Dany Doerr's notes}} | | | + | | 17.07. | Roland | Common intervals of strings | [[https://doi.org/10.1016/j.jda.2006.03.021|Didier at al., 2006]],\\ {{teaching:2023summer:cg:didier.pdf | Dany Doerr's notes}} | {{teaching:2026summer:cg:sheet13.pdf | Sheet 13}} | |
| - | | 17.07. | Roland | Common intervals of indeterminate strings | [[https://pub.uni-bielefeld.de/download/2902049/2902050/PhDThesis.pdf|Doerr, PhD thesis 2016]] | | | + | | 24.07. | Roland | Common intervals of indeterminate strings | [[https://pub.uni-bielefeld.de/download/2902049/2902050/PhDThesis.pdf|Doerr, PhD thesis 2016]],\\ {{teaching:2026summer:cg:ff.pdf | slides}} | | |
teaching/2026summer/cg.1779971773.txt.gz · Last modified: 2026/05/28 14:36 by mbraga
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