====== Classic Papers in Comparative Genomics (2S) ======


|  [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=340054133|392131]] | Bohnenkämper | Summer 2022 | Thursday, 14-16 in U10-146 |

===== Important Notice for New Students =====
If you are interested in the seminar (for example, because you need a seminar to complement the [[teaching:2022summer:phylogenetik| Phylogenetics ]]  course) but missed our first session, please send me an e-mail detailing which topic you would like to cover with your presentation and summary.


===== Contents =====

The students will read influential research papers on Comparative Genomics from earlier periods. Each student will select one such paper and give a preferably concise oral presentation (~ 25 min). They will subsequently write a summary of their chosen paper.
Whether the summary passes or not is decided primarily on its clarity and completeness, not its length.

Both the presentation and the summary are requested to be in English as it is the dominant language of the research in this area.

In the initial sessions after the assignment of topics, we will discuss the papers as a group and resolve any questions or difficulties together. Optionally (depending on the experience of the students), we will also cover an aspect of scientific reading and writing in each of these sessions.


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The class will be held in person in U10-146 as long as the current situation is favorable enough. On student request or resulting from a change in the situation, the class may be transferred to a hybrid or Zoom class.

===== Deadlines =====

  * The written summary is to be handed in **at most two weeks** after the presentation.
  * If you are unsure whether your presentation fits the format, you should make an appointment with me //approximately one week// before the presentation.

===== Schedule =====

^ **Date** ^ **Topic** ^ **Name** ^**Reading Homework**^
| 07.04.2022 | Topic Selection / Organizational Matters  | Leonard |  Sankoff 1992| 
| <del>14.04.2022</del> | Christian Holiday |  | Sankoff 1992, Hannenhalli & Pevzner 1999 (if you want) |
| 21.04.2022 | Discussion Sankoff 1992 / Introduction to Reversal Distance | Leonard | Caprara 1999 |
| 28.04.2022 | Discussion Caprara 1999 |  |  |
| 05.05.2022 | | |
| 12.05.2022 | Presentation Caprara 1999  | Luca  | TBA  | 
| 19.05.2022 | TBA (Discussion) |  | TBA |
| <del>26.05.2022</del> | Christian holiday, reading week  |  | |
| 02.06.2022 | TBA (Discussion)  |  | TBA |
| 09.06.2022 |  |  | |
| <del>16.06.2022</del> | Christian holiday, reading week |  | |
| 23.06.2022 |  |  | |
| 30.06.2022 |  |  | |
| <del>07.07.2022</del> | Leonard away, reading week |  | |
| 14.07.2022 |  |  | |

=====Suggested Literature=====

===Reversal Model===

  * Sankoff 1992: [[https://link.springer.com/chapter/10.1007/3-540-56024-6_10 | Edit distance for genome comparison based on non-local operations ]]
  * Hannenhalli & Pevzner 1999: [[ https://dl.acm.org/doi/abs/10.1145/300515.300516 |  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals ]]
  * (Hannenhalli & Pevzner 1995: [[ https://ieeexplore.ieee.org/abstract/document/492588 | Transforming men into mice (polynomial algorithm for genomic distance problem) ]])
  * Caprara 1999: [[ https://epubs.siam.org/doi/abs/10.1137/S089548019731994X  | Sorting Permutations by Reversals and Eulerian Cycle Decompositions ]]
  *  Bergeron 2001 : [[ https://link.springer.com/chapter/10.1007/3-540-48194-X_9 |  A Very Elementary Presentation of the Hannenhalli-Pevzner Theory ]] **and** Bergeron & Strasbourg 2001: [[ https://link.springer.com/chapter/10.1007/3-540-44696-6_13 | Experiments in Computing Sequences of Reversals ]]
  * Bader, Moret & Yan 2001 : [[ https://link.springer.com/chapter/10.1007/3-540-44634-6_34 | A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study]]

===DCJ Model===
  * (Yancopoulos, Attie & Friedberg 2005 : [[ https://doi.org/10.1093/bioinformatics/bti535 | Efficient sorting of genomic permutations by translocation, inversion and block interchange ]])
  * Braga, Willing & Stoye 2011 : [[ https://www.liebertpub.com/doi/10.1089/cmb.2011.0118 |  Double Cut and Join with Insertions and Deletions ]]
  * Compeau 2013 : [[ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655023/ | DCJ-Indel sorting revisited ]]

===Your own ideas?===
You might be inspired by
  * [[teaching:alggrliterature | the Algorithms in Genome Research Literature ]]
  * [[teaching:2021winter:cg |  the Algorithms in Comparative Genomics Literature ]]
  * reading the references of the papers listed here
  * ...