Jens-Uwe Ulrich

Research Assistant & PhD Student

	Phone:	+49 (0)331 5509 - 4965
	Email:	jens-uwe.ulrich(at)hpi.de
	Address:	Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany
	Room:	HPI Campus I, K-E.08
	Profiles:	Linkedin

Research Interests

DNA Sequencing
Metagenomics Data Analysis
Pathogen Detection
Bayesian Statistics

Research

Precise and Scalable Adaptive Sampling for Nanopore Sequencing

Nanopore DNA sequencing has shown to be an excellent tool for the identification of pathogens in clinical metagenomics samples. However, most of the sequenced DNA in such samples originates from the human host, which makes the detection of pathogens difficult or even impossible. With adaptive sampling there exists a method that can reject uninteresting or overrepresented sequences during the sequencing run, which results in an enrichment of the underrepresented DNA without applying time-consuming and expensive laboratory protocols. We developed a new tool for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters and k-mer matching statistics. ReadBouncer shows a higher read classification sensitivity than other state-of-the-art classification tools for adaptive sampling while retaining a high specificity. Our tool also improves classification performance and memory usage compared to the other tools.

Teaching

Winter Term 2022

Applied Probabilistic Machine Learning (Tutorial)

Winter Term 2020

Applied Bayesian Statistics (Lecture/Project)

Summer Term 2020

Computational Statistics (Exercise)

Publications

Ulrich, J.-U., Epping, L., Pilz, T., Walther, B., Stingl, K., Semmler, T., Renard, B.Y.: In-silico enrichment of bacterial plasmids by chromosomal depletion using nanopore adaptive sampling. bioRxiv. (2022).

[ BibTeX ] [ URL ]

Ulrich, J.-U., Lutfi, A., Rutzen, K., Renard, B.Y.: ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing. Bioinformatics. 38, i153-i160 (2022).