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teaching:2025summer:cg [2025/06/12 20:07] jstoye [Schedule] |
teaching:2025summer:cg [2025/06/28 08:26] (current) jstoye [Schedule] |
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| | 25.04.2025 (M) | Genomes, rearrangements, relational graph,\\ breakpoint distance,\\ SCJ distance | {{:teaching:2025summer:cg:relationalGraph.pdf|Basics}},\\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-120|Tannier et al. (BP distance)]],\\ [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis (SCJ)]] | {{:teaching:2025summer:cg:CG_Exercises-01.pdf|Exercises 1}} | | | 25.04.2025 (M) | Genomes, rearrangements, relational graph,\\ breakpoint distance,\\ SCJ distance | {{:teaching:2025summer:cg:relationalGraph.pdf|Basics}},\\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-120|Tannier et al. (BP distance)]],\\ [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis (SCJ)]] | {{:teaching:2025summer:cg:CG_Exercises-01.pdf|Exercises 1}} | | ||
| | 02.05.2025 (M) | Double cut and join (DCJ) model | {{:teaching:2025summer:cg:relationalGraph.pdf|Description}}, [[https://link.springer.com/chapter/10.1007/11851561_16|Bergeron et al.]] | {{:teaching:2025summer:cg:CG_Exercises-02.pdf|Exercises 2}} | | | 02.05.2025 (M) | Double cut and join (DCJ) model | {{:teaching:2025summer:cg:relationalGraph.pdf|Description}}, [[https://link.springer.com/chapter/10.1007/11851561_16|Bergeron et al.]] | {{:teaching:2025summer:cg:CG_Exercises-02.pdf|Exercises 2}} | | ||
| - | | 09.05.2025 (M) | Restricted DCJ Model,\\ DCJ genome 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:2025summer:cg:CG_Exercises-03.pdf|Exercises 3}} | | + | | 09.05.2025 (M) | Restricted DCJ Model,\\ DCJ genome 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:2025summer:cg:CG_Exercises-03.pdf|Exercises 3}} | |
| | 16.05.2025 (J) | Reversal distance | [[https://doi.org/10.1093/oso/9780198566106.003.0010|Bergeron et al.]] | {{:teaching:2025summer:cg:cg_exercises-4.pdf|Exercises 4}} | | | 16.05.2025 (J) | Reversal distance | [[https://doi.org/10.1093/oso/9780198566106.003.0010|Bergeron et al.]] | {{:teaching:2025summer:cg:cg_exercises-4.pdf|Exercises 4}} | | ||
| | 23.05.2025 (M) | SCJ halving and median, \\ Breakpoint median | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis (SCJ)]],\\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-120|Tannier et al. (BP median)]] | {{:teaching:2025summer:cg:cg_exercises-05.pdf|Exercises 5}} | | | 23.05.2025 (M) | SCJ halving and median, \\ Breakpoint median | [[https://ieeexplore.ieee.org/document/5719602|Feijão & Meidanis (SCJ)]],\\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-120|Tannier et al. (BP median)]] | {{:teaching:2025summer:cg:cg_exercises-05.pdf|Exercises 5}} | | ||
| | 30.05.2025 (J) | DCJ with insertions and deletions, \\ Metric version of the DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Willing et al.]], [[https://doi.org/10.1186/s13015-024-00253-7|Bohnenkämper]], \\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-S9-S13|Braga et al.]] | {{:teaching:2025summer:cg:cg_exercises-06.pdf|Exercises 6}} | | | 30.05.2025 (J) | DCJ with insertions and deletions, \\ Metric version of the DCJ-indel distance | [[https://doi.org/10.1089/cmb.2011.0118|Willing et al.]], [[https://doi.org/10.1186/s13015-024-00253-7|Bohnenkämper]], \\ [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-S9-S13|Braga et al.]] | {{:teaching:2025summer:cg:cg_exercises-06.pdf|Exercises 6}} | | ||
| | 06.06.2025 (M) | Safe inversions, capping | {{:teaching:2025summer:cg:DCJmodelWithCapping.pdf|DCJ model with capping}} | {{:teaching:2025summer:cg:cg_exercises-07.pdf|Exercises 7}} | | | 06.06.2025 (M) | Safe inversions, capping | {{:teaching:2025summer:cg:DCJmodelWithCapping.pdf|DCJ model with capping}} | {{:teaching:2025summer:cg:cg_exercises-07.pdf|Exercises 7}} | | ||
| - | | 13.06.2025 | ILP for DCJ of balanced genomes | [[https://doi.org/10.1089/cmb.2014.0096|Shao et al.]] | {{:teaching:2025summer:cg:cg_exercises-08.pdf|Exercises 8}} | | + | | 13.06.2025 (J) | ILP for DCJ of balanced genomes | [[https://doi.org/10.1089/cmb.2014.0096|Shao et al.]] | {{:teaching:2025summer:cg:cg_exercises-08.pdf|Exercises 8}} | |
| - | | 20.06.2025 | | | | | + | | 20.06.2025 (J) | DCJ-Indel of Natural Genomes | [[https://doi.org/10.1089/cmb.2020.0434|Bohnenkämper et al.]] | {{:teaching:2025summer:cg:cg_exercises-09.pdf|Exercises 9}} | |
| - | | 27.06.2025 (M) | | | | | + | | 27.06.2025 (M) | Family-free DCJ-indel distance | [[https://almob.biomedcentral.com/articles/10.1186/s13015-021-00183-8|Rubert et al.]], {{:teaching:2025summer:cg:balancednaturalfamilyfree.pdf|FF-DCJ-indel}} | {{:teaching:2025summer:cg:cg_exercises-10.pdf|Exercises 10}} | |
| - | | 04.07.2025 | | | | | + | | 04.07.2025 (J) | Gene Clusters I: Common intervals of permutations and strings | [[https://doi.org/10.1007/s004539910014|Uno & Yagiura]], [[https://doi.org/10.1007/s00453-009-9332-1|Heber et al.]], [[https://doi.org/10.1016/j.jda.2006.03.021|Didier et al.]] | | |
| - | | 11.07.2025 | | | | | + | | 11.07.2025 (J) | Gene Clusters II: Approximate common intervals | [[https://doi.org/10.1089/cmb.2009.0098|Böcker et al.]], [[https://doi.org/10.1089/cmb.2011.0132|Jahn]] | |
| - | | 18.07.2025 | | | | | + | | 18.07.2025 (J) | Gene Clusters III: Common intervals of indeterminate strings | [[https://doi.org/10.1186/1471-2164-15-S6-S2|Doerr et al.]] | | |
teaching/2025summer/cg.1749751643.txt.gz · Last modified: 2025/06/12 20:07 by jstoye
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