Algorithmic Bioinformatics · Saarland University
Jens Zentgraf
Algorithm engineering and data analysis for large-scale sequence data.
- Bluesky
- Google Scholar
- Campus E2.1, room 1.13
About
I am a computer scientist working on algorithm engineering and data analysis in bioinformatics, currently in the Algorithmic Bioinformatics group led by Sven Rahmann at Saarland University. Sequencing machines produce data faster than we can afford to align it, so I build methods that answer questions about sequences without always computing a full alignment by hashing, indexing, and filtering k-mers instead.
Office: Campus E2.1, room 1.13 · Center for Bioinformatics, Universität des Saarlandes, 66123 Saarbrücken, Germany · +49 (681) 302-70848
Stations
- since 2021 Researcher — Algorithmic Bioinformatics Center for Bioinformatics, Saarland Informatics Campus, Saarland University
- 2019 – 2021 Researcher — Genome Informatics TU Dortmund University
- until 2019 Master in computer science Focus on algorithm engineering
Current topics
- Modern hashing: multi-way bucketed Cuckoo hash tables, cost-optimal assignment of elements, parallelisation via subtables, and comparison against alternative schemes.
- Filters: blocked Bloom filters with choices; windows cuckoo filter; trading a little space for much better cache behaviour.
- Alignment-free analysis with k-mers: gapped and spaced k-mers, worst-case-optimal spaced seed design, strongly and weakly unique k-mers.
- Applications — xenograft sorting, decontamination of sequencing data, gene quantification in single-cell transcriptomics.
- Engineering — just-in-time compiled Python (Numba), cache-aware data structures, reproducible workflows.
Software
Talks
- 2026Error Correction Algorithms for Efficient Gene Quantification in Single Cell TranscriptomicsRECOMBThessaloniki
- 2025Cleanifier: Removing human DNA contamination with a pangenomic gapped k-mer indexGCBDüsseldorf
- 2025Design of Worst-Case-Optimal Spaced SeedsWABIonline
- 2025Blocked Bloom Filters with ChoicesSEAVenice
- 2025Blocked Bloom Filters with ChoicesDSBPisa
- 2024Efficient computing of strongly unique k-mersGCBBielefeld
- 2024Swiftly identifying strongly unique k-mersWABILondon
- 2023Xengsort2: Ultrafast accurate xenograft sortingGCBHamburg
- 2022Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tablesWABIPotsdam
- 2022Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tablesDSBDüsseldorf
- 2020On an assignment problem for multi-way bucketed Cuckoo hash tables on genome-scale dataSIGOPTDortmund
- 2020Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tablesDSBRennes
- 2020Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tablesALENEXSalt Lake City
Posters
- 2024Xengsort2: Ultrafast accurate xenograft sortingISMBMontreal
- 2024Xengsort2: Ultrafast accurate xenograft sortingHIPS Symp.Saarbrücken
- 2023k-mer counting combining super-k-mers and multi-way bucketed parallel Cuckoo hashingCPM SchoolParis
- 2022An efficient alignment-free method for finding genetic differences between pig races from individual whole genome sequencing dataGenome Inf.Wellcome Genome Campus
- 2020xengsort: Fast lightweight accurate xenograft sortingHiTSeqonline
- 2019Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tablesGCBHeidelberg
- 2017PanGeA: Pan-Genome Annotation — indexing annotated human genome collectionsGCBTübingen
Tutorials & participations
Tutorials
- 2024Just-in-time compiled Python for bioinformatics researchGCBBielefeld
- 2024Just-in-time compiled Python for bioinformatics researchISMBMontréal
- 2021Modern hashing for alignment-free sequence analysisGCBonline
- 2020Fundamentals of alignment-free sequence analysis: k-mer hashingACM-BCBonline
- 2019Fundamentals of alignment-free sequence analysis: k-mer hashingGCBHeidelberg
Participations
- 2025Snakemake HackathonCERNGeneva
- 2024Data Structures in BioinformaticsDSBMontpellier
- 2023Data Structures in BioinformaticsDSBDelft
Teaching
Courses
- SS 25Algorithms for Sequence AnalysisTutorialSaarland Univ.
- SS 25Reproducible methods in metagenomicsSeminarSaarland Univ.
- WS 24/25Bioinformatik 1TutorialSaarland Univ.
- SS 24Algorithms for Sequence AnalysisTutorialSaarland Univ.
- WS 23/24Modern Hashing and Filtering AlgorithmsSeminarSaarland Univ.
- SS 23Algorithms for Sequence AnalysisTutorialsSaarland Univ.
- WS 22/23Programming with PythonTutorialSaarland Univ.
- SS 22Algorithms for Sequence AnalysisTutorialsSaarland Univ.
- WS 21/22Statistics, Probability and Applications in BioinformaticsTutorialsSaarland Univ.
- SS 21Effiziente AlgorithmenTutorialsTU Dortmund
- WS 20/21Projektgruppe GeCoCooSupervisionTU Dortmund
- SS 20Projektgruppe GeCoCooSupervisionTU Dortmund
- WS 19/20Einführung in die ProgrammierungTutorialsTU Dortmund
Master theses
- 2023Jens PetermannCopy number variation detection using strongly unique k-mers and subdivided multi-way bucketed Cuckoo hash tables
- 2020Marvin BöckerAssembly of molecular graphs from induced subgraphs
Bachelor theses
- 2021Tom VoellmerEntdeckung bipartiter Motive in DNA-Sequenzen
- 2021Alexander KornEffiziente Implementierung und Vergleich exotischer Pattern-Matching-Algorithmen
Publications
A complete and current list is on my Google Scholar page.