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

Talks

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

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 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

2024 DSB Montpellier
2023 DSB Delft

Teaching

Courses

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

Publications

Please visit my Google Scholar page.

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