Jens Zentgraf

Office

Campus E2.1,
room 1.13

Mails

Jens Zentgraf
Algorithmische Bioinformatik
Zentrum für Bioinformatik, Campus E2.1
Universität des Saarlandes
66123 Saarbrücken, Germany

Phone

+49 (681) 302-70848

I am a computer scientist with a focus on algorithm engineering and data analysis in bioinformatics. Right now I am working in the Algorithmic Bioinformatics group, led by Sven Rahmann at Saarland University. My current topics are:

Hashing
- Multi-Way Bucketed Cuckoo Hashing
- Comparison with other Hashing methods
- Parallelization using subtables
Alignment free approaches using k-mers
- xengsort2
- hackgap

Talks

2025	Blocked Bloom Filters with Choices	DSB	Pisa
2024	Efficient computing of strongly unique k-mers	GCB	Bielefeld
2024	Swiftly identifying strongly unique k-mers	WABI	London
2023	Xengsort2: Ultrafast accurate xenograft sorting	GCB	Hamburg
2022	Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tables	WABI	Potsdam
2022	Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tables	DSB	Düsseldorf
2020	On an assignment problem for multi-way bucketed Cuckoo Hash tables on genomescale data	SIGOPT	Dortmund
2020	Cost-Optimal Assignment of Elements in Genome-Scale Multi-Way Bucketed Cuckoo Hash Tables	DSB	Rennes
2020	Cost-Optimal Assignment of Elements in Genome-Scale Multi-Way Bucketed Cuckoo Hash Tables	ALENEX	Salt Lake City

Posters

2024	Xengsort2: Ultrafast accurate xenograft sorting	ISMB	Montreal
2024	Xengsort2: Ultrafast accurate xenograft sorting	HIPS Symposium	Saarbrücken
2023	k-mer counting combining super-k-mers and multi-way bucketed parallel Cuckoo hashing	CPM Summer school	Paris
2022	An efficient alignment-free method for finding genetic differences between pig races from individual whole genome sequencing data	Genome Informatics	Wellcome Genome Campus
2020	xengsort: Fast lightweight accurate xenograft sorting	HiTSeq	online
2019	Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables	GCB	Heidelberg
2017	PanGeA: Pan-Genome Annotation Indexing Annotated Human Genome Collections	GCB	Tübingen

Tutorials

2024	Just-in-Time Compiled Python for Bioinformatics Research	GCB	Bielefeld
2024	Just-in-time compiled Python for bioinformatics research	ISMB	Montréal
2021	Modern hashing for alignment-free sequence analysis	GCB	online
2020	Fundamentals of alignment free sequence analysis: k-mer hashing	ACM-BCB	online
2019	Fundamentals of alignment free sequence analysis: k-mer hashing	GCB	Heidelberg

Participations

2025	Snakemake Hackathon	CERN
2024	DSB	Montpellier
2023	DSB	Delft

Teaching

Courses

SS	25	Algorithms for Sequence Analysis	Tutorial	Saarland University
SS	25	Reproducible methods in metagenomics	(Pro-)Seminar	Saarland University
WS	24/25	Bioinformatik 1	Tutorial	Saarland University
SS	24	Algorithms for Sequence Analysis	Tutorial	Saarland University
WS	23/24	Modern Hashing and Filtering Algorithms	(Pro-)Seminar	Saarland University
SS	23	Algorithms for Sequence Analysis	Tutorials	Saarland University
WS	22/23	Programming with Python	Tutorial	Saarland University
SS	22	Algorithms for Sequence Analysis	Tutorials	Saarland University
WS	21/22	Statistics, Probability and Applications in Bioinformatics	Tutorials	Saarland University
SS	21	Effiziente Algorithmen	Tutorials	TU Dortmund
WS	20/21	PG: GeCoCoo		TU Dortmund
SS	20	PG: GeCoCoo		TU Dortmund
WS	19/20	Einführung in die Programmierung	Tutorials	TU Dortmund

Bachelor Theses

2021	Tom Voellmer	Entdeckung bipartiter Motive in DNA-Sequenzen
2021	Alexander Korn	Effiziente Implementierung und Vergleich exotischer Pattern Matching Algorithmen

Master Theses

2023	Jens Petermann	Copy number variation detection using strongly unique k-mers and subdivided multi-way bucketed Cuckoo hash tables
2020	Marvin Böcker	Assembly of molecular graphs from induced subgraphs

Please visit my Google Scholar page.