Publications
The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.
Publications by the Reinert Lab
Preprints
If preprints are available, they will be listed here.
2025
DREAM-Stellar: Parallel and space efficient exact local alignment. bioRxiv: the preprint server for biology (2025)
Published
2025
Engineering rank queries on bit vectors and strings. Algorithms for Molecular Biology 20, 21 (2025)
DREAM-Stellar: Parallel and space efficient exact local alignment. bioRxiv: the preprint server for biology (2025)
TetRex: a novel algorithm for index-accelerated search of highly conserved motifs. NAR: genomics and bioinformatics 7 (2), Article lqaf039 (2025)
SeArcH schemes for Approximate stRing mAtching. NAR: genomics and bioinformatics 7 (1), Article lqaf025 (2025)
FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events. Nature Communications 16 (1), Article 2298 (2025)
2024
Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Research 34 (9), pp. 1355 - 1364 (2024)
Leaf: an ultrafast filter for population-scale long-read SV detection. Genome Biology: Biology for the Post-Genomic Era 25 (1), Article 155 (2024)
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics 40 (3), Article btae097 (2024)
Utilizing alignment-free methods to enable quantitative gene expression analysis of large collections of sequencing data. Dissertation, 143 Seiten pp. (2024)
A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics 40 (2), Article btae045 (2024)
2023
Algorithms for finding RNA sequence-structure motifs. Dissertation, XIII, 137 pp. (2023)
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology: Biology for the Post-Genomic Era 24 (1), 131 (2023)
Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models. Briefings in Bioinformatics 24 (2), bbad071 (2023)
2022
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics 28 (17), pp. 4100 - 4108 (2022)
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods 19 (4), pp. 429 - 440 (2022)
Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. In: FPGA '22, pp. 180 - 189. FPGA '22: Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, Virtual Event, February 27, 2022 - March 01, 2022. Association for Computing Machinery, New York, NY (2022)
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics 23, 18 (2022)
2021
RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data. Bioinformatics 37 (21), pp. 3934 - 3935 (2021)
Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience 24 (7), 102782 (2021)
2020
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics 36 (suppl.1), pp. i12 - i20 (2020)
Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology 16 (5), e1007843 (2020)
Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping. Frontiers in Microbiology 11, 11:636 (2020)
GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics 36 (12), pp. 3687 - 3692 (2020)
2019
Whole Genome Shotgun Sequencing Based Taxonomic Profiling Methods for Comparative Study of Microbial Communities. Dissertation, viii, 145 pp. (2019)
Approximate String Matching: Improving Data Structures and Algorithms. Dissertation, 175 pp. (2019)
2018
DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics 34 (17), pp. i766 - 1772 (2018)
Analysis of Antigen Receptor Repertoires Captured by High Throughput Sequencing. Dissertation, vii, 164 pp. (2018)
2017
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology 261, pp. 157 - 168 (2017)
2015
Tailored Analysis in Studying Transcriptome Landscape. Dissertation, 127 Seiten pp. (2015)
Approximate string matching for high-throughput sequencing. Dissertation, XI, 127 pp. (2015)
Linear Programming and Integer Linear Programming in Bioinformatics. Dissertation, XIV, 168 pp. (2015)
2014
Contributions to computing and modeling multiple whole-genome alignments. Dissertation, XVII, 161 pp. (2014)
2013
Next-generation sequencing algorithms: from read mapping to variant detection. Dissertation, 148 pp., Berlin, Freie Universität (2013)
2012
Quantification and simulation of liquid chromatography-mass spectrometry data. Dissertation, 147 pp. (2012)
2010
Dissecting multiple sequence alignment methods: the analysis, design and development of generic multiple sequence alignment components in SeqAn. Dissertation, IX, 175 pp., Freie Universität, Berlin (2010)
2009
Computational methods for Quantitative Peptide Mass Spectrometry. Dissertation, 124, [10] pp. (2009)
2008
A combinatorial approach to RNA sequence-structure alignments. Dissertation, 117 pp. (2008)
2007
Algorithm to identify protein complexes from high-throughput data. Dissertation, 118 pp., Freie Universität Berlin, Berlin (2007)