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--- teaching:2026summer:cg [2026/04/17 12:16]
mbraga [Algorithms in Comparative Genomics (2V + 2Ü)]
+++ teaching:2026summer:cg [2026/04/17 12:50] (current)
mbraga [Schedule]
@@ Line 64: / Line 64: @@
 ^ Date ^ Teacher ^ Topic  ^ Literature ^ Exercises ^
 | 17.04. | Marilia | Introduction, Breakpoint (BP) and SCJ distances | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]],\\ [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]] | {{teaching:2026summer:cg:sheet01.pdf | Sheet 01}} |
-| 24.04. | Marilia | BP and SCJ 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:2026summer:cg:sheet02.pdf | Sheet 02}} |
+| 24.04. | Marilia | BP and SCJ 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]] | |
 | 01.05. | -- (national holiday) ||||
-| 08.05. | Roland | Small Parsimony under SCJ | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis 2011]],\\ {{teaching:2023summer:cg:spp-algo.pdf | SPP-algorithm.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:2023summer:cg:spp-algo.pdf | SPP-algorithm.pdf}}   |  |
-| 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}}| |
-| 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]] | |
-| 29.05. | Marilia | 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]] |  {{teaching:2026summer:cg:sheet06.pdf | Sheet 06}} |
+| 29.05. | Marilia | 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]] | |
-| 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]] | {{teaching:2026summer:cg:sheet07.pdf | Sheet 07}} |
+| 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]] | |
-| 12.06. | Marilia | 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]] | {{teaching:2026summer:cg:sheet08.pdf | Sheet 08}} |
+| 12.06. | Marilia | 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]] | |
-| 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}} |
+| 19.06. | Marilia | DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] | |
-| 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}}  |
+| 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}}|  |
-| 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}}  |
+| 03.07. | Roland | Generators for common intervals | [[https://doi.org/10.1137/060651331|Bergeron et al. 2008]], Sections 1 and 2 | |
-| 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}} |
+| 10.07. | Roland | Generators, strong common intervals and PQ-trees | see above, Sections 3, 4, 5.1, and 5.3 |  |
-| 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}} | {{teaching:2026summer:cg:sheet13.pdf | Sheet 13}} |
+| 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 indeterminate strings | [[https://pub.uni-bielefeld.de/download/2902049/2902050/PhDThesis.pdf|Doerr, PhD thesis 2016]] | |

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