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teaching:2024summer:cg [2024/04/12 09:33] leonard [Schedule] |
teaching:2024summer:cg [2024/05/06 15:13] leonard |
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| ^ Date ^ Teacher ^ Topic ^ Literature ^ Exercises ^ | ^ Date ^ Teacher ^ Topic ^ Literature ^ Exercises ^ | ||
| - | | 12.04. | Leonard | Introduction, Genes, Genomes, Breakpoint (BP) distance | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | {{teaching:2024summer:cg:cg_exercises.pdf | Exercises 1}} | | + | | 12.04. | Leonard | Introduction, Genes, Genomes, Breakpoint (BP) distance | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | {{teaching:2024summer:cg:cg_exercises-1.pdf | Exercises 1}} | |
| - | | 19.04. | Leonard | BP and SCJ distance, median and halving | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]],\\ [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]] | | | + | | 19.04. | Leonard | BP and SCJ distance, median (and halving) | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]],\\ [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]] | {{teaching:2024summer:cg:cg_exercises-2.pdf | Exercises 2}} | |
| - | | 26.04. | Roland | Small Parsimony under SCJ | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]],\\ {{teaching:2023summer:cg:spp-algo.pdf | SPP-algorithm.pdf}} | | | + | | 26.04. | Roland | Small Parsimony under SCJ | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]],\\ {{teaching:2023summer:cg:spp-algo.pdf | SPP-algorithm.pdf}} | {{teaching:2024summer:cg:cg_exercises-3.pdf | Exercises 3}} | |
| - | | 03.05. | 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}}| | | + | | 03.05. | 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:2024summer:cg:cg_exercises-4.pdf | Exercises 4}} | |
| | 10.05. | Leonard | Double-Cut-and-Join (DCJ) model | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]] | | | | 10.05. | Leonard | Double-Cut-and-Join (DCJ) model | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]] | | | ||
| | 17.05. | Leonard | DCJ halving, double distance and median | [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]],\\ [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | | | | 17.05. | Leonard | DCJ halving, double distance and median | [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]],\\ [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | | | ||
| | 24.05. | Leonard | 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]] | | | | 24.05. | Leonard | 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]] | | | ||
| | 31.05. | Leonard | Inversion distance/DCJ-indel distance | [[https://link.springer.com/chapter/10.1007/978-3-540-27801-6_29|Bergeron et al. 2004]],\\ [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | | | | 31.05. | Leonard | Inversion distance/DCJ-indel distance | [[https://link.springer.com/chapter/10.1007/978-3-540-27801-6_29|Bergeron et al. 2004]],\\ [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | | | ||
| - | | 07.06. | Leonard | DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | | | + | | 07.06. | Leonard | DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]],\\ [[https://doi.org/10.1186/1748-7188-8-6|Compeau 2013]],\\ [[https://doi.org/10.1186/s13015-024-00253-7|Bohnenkämper 2024]]\\ (ignore ILP section)| | |
| | 14.06. | 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]] | | | | 14.06. | 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]] | | | ||
| - | | 21.06. | Leonard | Rearrangement problems on natural genomes | | | + | | 21.06. | Leonard | Rearrangement problems on natural genomes | [[https://doi.org/10.1089/cmb.2014.0096|Shao, Lin & Moret 2015]],\\ [[https://doi.org/10.1186/s13015-024-00253-7|Bohnenkämper 2024]]| | |
| | 28.06. | Roland | Generators for common intervals | [[https://doi.org/10.1137/060651331|Bergeron et al. 2008]], Sections 1 and 2 | | | | 28.06. | Roland | Generators for common intervals | [[https://doi.org/10.1137/060651331|Bergeron et al. 2008]], Sections 1 and 2 | | | ||
| | 05.07. | Roland | Generators, strong common intervals and PQ-trees | see above, Sections 3, 4, 5.1, and 5.3 | | | | 05.07. | Roland | Generators, strong common intervals and PQ-trees | see above, Sections 3, 4, 5.1, and 5.3 | | | ||
| | 12.07. | 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}} | | | | 12.07. | 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}} | | | ||
| | 19.07. | Roland | Common intervals of indeterminate strings | [[https://pub.uni-bielefeld.de/download/2902049/2902050/PhDThesis.pdf|Doerr, PhD thesis 2016]] | | | | 19.07. | Roland | Common intervals of indeterminate strings | [[https://pub.uni-bielefeld.de/download/2902049/2902050/PhDThesis.pdf|Doerr, PhD thesis 2016]] | | | ||
teaching/2024summer/cg.txt · Last modified: 2024/05/18 15:14 by leonard
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