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teaching:2020winter:cg [2021/01/07 09:43] mbraga [Schedule] |
teaching:2020winter:cg [2021/02/11 12:16] (current) mbraga [Schedule] |
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| ^ Date ^ Topic ^ Slides (S) ^ S + notes ^ Literature ^ Exercises ^ | ^ Date ^ Topic ^ Slides (S) ^ S + notes ^ Literature ^ Exercises ^ | ||
| - | | 29.10. | Introduction, Genomes, Breakpoint distance | {{teaching:2020winter:cg:cg01.pdf | S 1}} | {{teaching:2020winter:cg:cg01-notes.pdf | SN 1}} | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | {{teaching:2020winter:cg:sheet01.pdf | Ex 1}}| | + | | 29.10. | Introduction, Genomes, Breakpoint distance | {{teaching:2020winter:cg:cg01.pdf | S01}} | {{teaching:2020winter:cg:cg01-notes.pdf | SN01}} | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | {{teaching:2020winter:cg:sheet01.pdf | Ex01}}| |
| - | | 05.11. | Breakpoint and Single-Cut-or-Join (SCJ) distances | {{teaching:2020winter:cg:cg02.pdf | S 2}} | {{teaching:2020winter:cg:cg02-notes.pdf | SN 2}} | [[https://doi.org/10.1109/TCBB.2011.34|Feijão & Meidanis 2011]] | {{teaching:2020winter:cg:sheet02.pdf | Ex 2}} | | + | | 05.11. | Breakpoint and Single-Cut-or-Join (SCJ) distances | {{teaching:2020winter:cg:cg02.pdf | S02}} | {{teaching:2020winter:cg:cg02-notes.pdf | SN02}} | [[https://doi.org/10.1109/TCBB.2011.34|Feijão & Meidanis 2011]] | {{teaching:2020winter:cg:sheet02.pdf | Ex02}} | |
| - | | 12.11. | Breakpoint and SCJ median and halving | {{teaching:2020winter:cg:cg03.pdf | S 3}} | {{teaching:2020winter:cg:cg03-notes.pdf | SN 3}} | | {{teaching:2020winter:cg:sheet03.pdf | Ex 3}} | | + | | 12.11. | Breakpoint and SCJ median and halving | {{teaching:2020winter:cg:cg03.pdf | S03}} | {{teaching:2020winter:cg:cg03-notes.pdf | SN03}} | | {{teaching:2020winter:cg:sheet03.pdf | Ex03}} | |
| - | | 19.11. | Breakpoint median/ Double-Cut-and-Join (DCJ) halving | {{teaching:2020winter:cg:cg04.pdf | S 4}} | {{teaching:2020winter:cg:cg04-notes.pdf | SN 4}} | {{teaching:2020winter:cg:b1998.pdf | Bryant 1998}}, [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]] | {{teaching:2020winter:cg:sheet04.pdf | Ex 4}} | | + | | 19.11. | Breakpoint median/ Double-Cut-and-Join (DCJ) halving | {{teaching:2020winter:cg:cg04.pdf | S04}} | {{teaching:2020winter:cg:cg04-notes.pdf | SN04}} | {{teaching:2020winter:cg:b1998.pdf | Bryant 1998}}, [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]] | {{teaching:2020winter:cg:sheet04.pdf | Ex04}} | |
| - | | 26.11. | DCJ distance and relational graph | {{teaching:2020winter:cg:cg05.pdf | S 5}} | {{teaching:2020winter:cg:cg05-notes.pdf | SN 5}} | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]],\\ [[https://doi.org/10.1089/cmb.2011.0116|Kováč et al. 2011]] |{{teaching:2020winter:cg:sheet05.pdf | Ex 5}} | | + | | 26.11. | DCJ distance and relational graph | {{teaching:2020winter:cg:cg05.pdf | S05}} | {{teaching:2020winter:cg:cg05-notes.pdf | SN05}} | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]],\\ [[https://doi.org/10.1089/cmb.2011.0116|Kováč et al. 2011]] |{{teaching:2020winter:cg:sheet05.pdf | Ex05}} | |
| - | | 03.12. | Inversion distance and relational diagram | {{teaching:2020winter:cg:cg06.pdf | S 6}} | {{teaching:2020winter:cg:cg06-notes.pdf | SN 6}} | {{teaching:2020winter:cg:sorting-by-reversals.pdf | Sorting by Reversals}},\\ [[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:2020winter:cg:sheet06.pdf | Ex 6}} | | + | | 03.12. | Inversion distance and relational diagram | {{teaching:2020winter:cg:cg06.pdf | S06}} | {{teaching:2020winter:cg:cg06-notes.pdf | SN06}} | {{teaching:2020winter:cg:sorting-by-reversals.pdf | Sorting by Reversals}},\\ [[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:2020winter:cg:sheet06.pdf | Ex06}} | |
| - | | 10.12. | Inversion distance / DCJ-indel distance | {{teaching:2020winter:cg:cg07.pdf | S 7}} | {{teaching:2020winter:cg:cg07-notes.pdf | SN 7}} | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]]| {{teaching:2020winter:cg:sheet07.pdf | Ex 7}} | | + | | 10.12. | Inversion distance / DCJ-indel distance | {{teaching:2020winter:cg:cg07.pdf | S07}} | {{teaching:2020winter:cg:cg07-notes.pdf | SN07}} | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]]| {{teaching:2020winter:cg:sheet07.pdf | Ex07}} | |
| - | | 17.12. | DCJ-indel distance / Restricted DCJ-indel distance| {{teaching:2020winter:cg:cg08.pdf | S 8}} | {{teaching:2020winter:cg:cg08-notes.pdf | SN 8}}| [[https://doi.org/10.1109/TCBB.2014.2329297|Braga and Stoye, 2015]],\\ [[https://doi.org/10.1186/1471-2105-12-S9-S13|Braga et al. 2011b]] | {{teaching:2020winter:cg:sheet08-christmas.pdf | Ex 8 - Christmas}} | | + | | 17.12. | DCJ-indel distance / Restricted DCJ-indel distance| {{teaching:2020winter:cg:cg08.pdf | S08}} | {{teaching:2020winter:cg:cg08-notes.pdf | SN08}}| [[https://doi.org/10.1109/TCBB.2014.2329297|Braga and Stoye, 2015]],\\ [[https://doi.org/10.1186/1471-2105-12-S9-S13|Braga et al. 2011b]] | {{teaching:2020winter:cg:sheet08-christmas.pdf | Ex08 - Christmas}} | |
| - | | 07.01. | Capped relational graph | {{teaching:2020winter:cg:cg09.pdf | S 9}} | | [[https://doi.org/10.1007/978-3-030-45257-5_1|Bohnenkämper et al. 2011]] | | | + | | 07.01. | Capped relational graph | {{teaching:2020winter:cg:cg09.pdf | S09}} | {{teaching:2020winter:cg:cg09-notes.pdf | SN09}} | [[https://doi.org/10.1089/cmb.2020.0434|Bohnenkämper et al. 2020]] | {{teaching:2020winter:cg:sheet09.pdf | Ex09}} | |
| - | | 14.01. | DCJ with duplicated genes (double-distance / balanced genomes) | | | | | | + | | 14.01. | DCJ with duplicated genes (double-distance / balanced genomes) | {{teaching:2020winter:cg:cg10.pdf | S10}} | {{teaching:2020winter:cg:cg10-notes.pdf | SN10}} | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] | {{teaching:2020winter:cg:sheet10.pdf | Ex10}} | |
| - | | 21.01. | ILP / DCJ distance of balanced genomes | | | | | | + | | 21.01. | ILP / DCJ distance of balanced genomes | {{teaching:2020winter:cg:cg11.pdf | S11}} | {{teaching:2020winter:cg:cg11-notes.pdf | SN11}} | [[https://doi.org/10.1089/cmb.2014.0096|Shao et al. 2015]] | {{teaching:2020winter:cg:sheet11.pdf | Ex11}} | |
| - | | 28.01. | DCJ-indel distance of natural genomes | | | | | | + | | 28.01. | DCJ-indel distance of natural genomes\\ (guest lecture by L. Bohnenkämper) | {{teaching:2020winter:cg:cg12.pdf | S12}} | --- | [[https://doi.org/10.1089/cmb.2020.0434|Bohnenkämper et al. 2020]] | {{teaching:2020winter:cg:sheet12.pdf | Ex12}} | |
| - | | 04.02. | DCJ-indel distance of family-free genomes | | | | | | + | | 04.02. | DCJ distance and DCJ-indel distance\\ of family-free genomes | {{teaching:2020winter:cg:cg13.pdf | S13}} | {{teaching:2020winter:cg:cg13-notes.pdf | SN13}} | [[https://doi.org/10.4230/LIPIcs.WABI.2020.3|Rubert et al. 2020]] | {{teaching:2020winter:cg:sheet13.pdf | Ex13}} | |
| - | | 11.02. | t.b.a. | | | | | | + | | 11.02. | Small parsimony under SCJ / review | {{teaching:2020winter:cg:cg14.pdf | S14}} | {{teaching:2020winter:cg:cg14-notes.pdf | SN14}} | [[https://doi.org/10.1109/TCBB.2011.34|Feijão & Meidanis 2011]] | --- | |
teaching/2020winter/cg.1610009028.txt.gz · Last modified: 2021/01/07 09:43 by mbraga
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