392107 Data Structures in Pangenomics

Schönhuth / Ghaffaari

Summer 2026

Thu 12-14 in S1-147 (S)

Individual presentations (S): 22 minutes, followed by 5 minutes of discussion
Report (S): 10-12 pages long, excluding references (but title, table of content, figures, and tables included)
Blog (S): ca. 30 minutes of reading time
Coding project (Ü): implement and reproduce the results of the paper you selected for your presentation, using the datasets provided in the paper where possible.

Please see on Google Drive. The link is password protected.
If there is any problem with accessing a paper, write an email to Jasper Matzat.

Date	Topic
16.04.2026	Introduction to seminar, Course organisation, How to present
23.04.2026	(no session)
30.04.2026	(no session)
07.05.2026	(no session)
14.05.2026	(no session)
21.05.2026	(no session)
28.05.2026	INTRODUCTORY SESSION, Report Writing Guidelines
04.06.2026	(holiday)
11.06.2026	Block presentations (3)
18.06.2026	Elastic-Degenerate String Matching via Fast Matrix Multiplication	Matthis
	Nucleotide Transformer: building and evaluating robust foundation models for human genomics	Eylül
	Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks	Lena
25.06.2026	ODGI: understanding pangenome graphs	Lukas
	Wheeler graphs: A framework for BWT-based data structures	Malte
	Efficient and accurate search in petabase-scale sequence repositories	Breia
02.07.2026	Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA	Lea
	Movi: A fast and cache-efficient full-text pangenome index	Özay
	Geometric deep learning framework for de novo genome assembly	Tim
09.07.2026	Efficient dynamic variation graphs	Nityakrushna
09.07.2026	Block presentations (2)
16.07.2026	CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS	Timo
	Mem-based pangenome indexing for k-mer queries	Nils
	Pangenome Graph Indexing via the Multidollar-BWT	Alexander
23.07.2026	Block presentations (3)

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