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teaching:2026winter:seqalgbioinf [2026/04/16 11:30]
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-| [[https://​ekvv.uni-bielefeld.de/​kvv_publ/​publ/​vd?​id=659868809]] | Parmigiani | Summer 2026 | Wednesday 10:15-11:45 | U10-146 | 
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-This course is held in English.\\ 
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-Based on selected **book chapters** from *Genome-Scale Algorithm Design* (Veli Mäkinen, Djamal Belazzougui,​ Fabio Cunial, Alexandru I. Tomescu), ​ 
-the participants will give oral presentations (20-45 min) and write a  
-short summary (5-10 pages) about the an algorithmic problem in bioinformatics and their solutions. Talks and essays must be done in English. ​ 
-The first day covers an overview of possible topics, which will then be distributed to the students. 
-Aspects of scientific writing and presenting will be covered as well.\\ \\ 
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-The overarching topic of this semester are **string algorithms for genome-scale data**, with a focus on fundamental algorithmic techniques underlying modern bioinformatics tools, including indexing, pattern matching, compressed data structures, and graph-based genome representations.\\ 
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-To practice algorithm design and presentation,​ each participant will present one core algorithmic idea from the assigned book chapter using pseudocode (in LaTeX). ​ 
-Afterwards, they will implement the algorihtm as a basic prototype in a programming language of their choice (esoteric programming languages are accepted, as long as accompanied by a proper explanation ;)). 
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-Possible concrete chapters/​topics to be presented and discussed in the seminar include: 
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-==== Indexing and Pattern Matching ==== 
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-  * Exact pattern matching algorithms 
-  * Suffix arrays and suffix trees 
-  * Burrows-Wheeler Transform (BWT) 
-  * FM-index and backward search 
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-==== Compressed Data Structures ==== 
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-  * Rank and select data structures 
-  * Wavelet trees 
-  * Compressed suffix arrays 
-  * Succinct text indexes 
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-==== k-mer and q-gram based methods ==== 
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-  * q-gram indexes 
-  * Minimizers and sketches 
-  * Applications of k-mer spectra 
-  * String similarity and filtering techniques 
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-==== Graph-based genome representations ==== 
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-  * De Bruijn graphs 
-  * Compacted and colored de Bruijn graphs 
-  * Variation graphs and pan-genome models 
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-==== Approximate Matching ==== 
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-  * Edit distance algorithms 
-  * Seed-and-extend paradigm 
-  * Filtering techniques for approximate string matching 
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-==== Timetable ==== 
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-| 15.04. | --                                                | 
-| 22.04. | Organization,​ topic selection, Scientific reading | 
-| 29.04. |                                                   | 
-| 06.05. |                                                   | 
-| 13.05. |                                                   | 
-| 20.05. |                                                   | 
-| 27.05. | luca at conference ​                               | 
-| 03.06. |                                                   | 
-| 10.06. |                                                   | 
-| 17.06. |                                                   | 
-| 24.06. |                                                   | 
-| 01.07. |                                                   | 
-| 08.07. |                                                   | 
-| 15.07. |                                                   | 
-| 22.07. |                                                   | 
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